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Sample records for bronsted acid site

  1. Computational studies of Bronsted acid sites in zeolites

    SciTech Connect

    Curtiss, L.A.; Iton, L.E.; Zygmunt, S.A.

    1995-01-01

    The authors have performed high-level ab initio calculations using both Hartree-Fock (HF) and Moller-Plesset perturbation theory (MP2) to study the geometry and energetics of the adsorption complex involving H{sub 2}O and the Bronsted acid site in the zeolite H-ZSM-5. In these calculations, which use aluminosilicate cluster models for the zeolite framework with as many a 28 T atoms (T = Si, Al), we included geometry optimization in the local vicinity of the acid site at the HF/6-31G(d) level of theory, and have calculated corrections for zero-point energies, extensions for zero-point energies, extensions to higher basis sets, and the influence of electron correlation. Results for the adsorption energy and geometry of this complex are reported and compared with previous theoretical and experimental values.

  2. Support Effects on Bronsted acid site densities and alcohol dehydration turnover rates on tungsten oxide domains

    SciTech Connect

    Macht, Josef; Baertsch, Chelsey D.; May-Lozano, Marcos; Soled, Stuart L.; Wang, Yong; Iglesia, Enrique

    2005-03-01

    Initial activity and acid site density of several WAl, WSi (MCM41) and one WSn sample were determined. Trans/cis 2-butene selectivity is dependent on the support. Presumably, these differences are due to subtle differences in base strengths. 2-Butanol dehydration rates (per W-atom) reached maximum values at intermediate WOx surface densities on WAl, as reported for 2-butanol dehydration reactions on WZr. Titration results indicate that Bronsted acid sites are required for 2-butanol dehydration on WAl, WSi and WSn. UV-visible studies suggest that WAl is much more difficult to reduce than WZr. The detection of reduced centers on WAl, the number of which correlates to Bronsted acid site density and catalyst activity, as well as the temperature dependence of Bronsted acid site density indicate the in-situ formation of these active sites. We infer that this mechanism is common among all supported WOx samples described in this study. Turnover rates are a function of Bronsted acid site density only. High acid site densities lead to high turnover rates. Higher active site densities may cause stronger conjugate bases, as a higher electron density has to be stabilized, and thus weaker acidity, enabling a faster rate of product desorption. The maximum achievable active site density is dependent on the support. WZr reaches a higher active site density than WAl.

  3. The Bronsted-Lowery Acid-Base Concept.

    ERIC Educational Resources Information Center

    Kauffman, George B.

    1988-01-01

    Gives the background history of the simultaneous discovery of acid-base relationships by Johannes Bronsted and Thomas Lowry. Provides a brief biographical sketch of each. Discusses their concept of acids and bases in some detail. (CW)

  4. Modification of the surface pathways in alkane oxidation by selective doping of Bronsted acid sites of vanadyl pyrophosphate

    SciTech Connect

    Centi, G.; Golinelli, G.; Busca, G. )

    1990-08-23

    The modification of Bronsted POH groups of (VO){sub 2}P{sub 2}O{sub 7} by selective doping with K in an anhydrous medium causes a considerable modification of the surface oxidation pathways in C{sub 4}- and C{sub 5}-alkane oxidative transformation, with (i) a considerable decrease in the selective formation of maleic anhydride from n-butane and of maleic and phthalic anhydrides from n-pentane, (ii) an increase in the relative formation of C-containing surface residues. It is suggested that these effects are due to an inhibition of the catalyzed transformation of furan-like intermediates to corresponding lactones and then to anhydrides in the presence of gaseous O{sub 2} and to a change in the relative rates of O-insertion and H-abstraction on these surface intermediates. The role of the dynamics of competitive surface transformations of adsorbed intermediates on the overall behavior of vanadyl pyrophosphate in C{sub 4}- and C{sub 5}-alkane selective oxidation is also discussed.

  5. Evidence of Bronsted acidity on sulfided promoted and unpromoted Mo/Al sub 2 O sub 3 catalysts

    SciTech Connect

    Topsoe, N.Y.; Topsoe, H. ); Massoth, F.E. )

    1989-09-01

    It is uncertain what effect acidity, especially protonic (Bronsted) acidity, has on typical hydrotreating reactions over molybdenum-containing, sulfided catalysts. In a study of the hydrogenation of 1-hexene, small amounts of propylene were found together with the major product, hexane. The amount of the former increased with increase in the H{sub 2}S partial pressure, leading to the supposition that H{sub 2}S increased the Bronsted acidity of the sulfided catalyst. The hydrodenitrogenation of quinoline was also found to be promoted by H{sub 2}S, which was attributed to an increase in the number of Bronsted acid sites. However, no direct evidence for the presence of Bronsted acid sites was obtained. One of the advantages of using pyridine as the probe molecule for monitoring acidity is that it can adsorb both as coordinated and protonated pyridine on Lewis and Bronsted acid sites, respectively. These adsorbed pyridine species can be easily distinguished by infrared spectroscopy. Bronsted and Lewis acid sites have been detected for oxidic promoted and unpromoted Mo/Al{sub 2}/O{sub 3} catalysts but only Lewis acidity has been found on the corresponding sulfided catalysts. It should be pointed out that most of the previous IR studies have been carried out with pyridine adsorption at relatively low temperatures (below 423 K). It occurred to the authors that since the Bronsted acidity, if it exists, must be weak, higher temperatures may be required to produce the pyridinium ion. The present not reports IR evidence of Bronsted acidity at elevated temperatures corresponding to those typically employed under hydroprocessing reactions.

  6. Effects of Zeolite Structure and Si/Al Ratio on Adsorption Thermodynamics and Intrinsic Kinetics of Monomolecular Cracking and Dehydrogenation of Alkanes over Bronsted Acid Sites

    NASA Astrophysics Data System (ADS)

    Janda, Amber Leigh

    It is well known that the efficacy of acidic zeolite catalysts for the cracking of hydrocarbons originates from the shape and size of the zeolite pores. However, the mechanisms by which changes in pore structure influence cracking kinetics are not well understood or exploited. The aim of this dissertation is to use experiments and simulations to shed light on the ways by which zeolite structure and acid site location affect the apparent and intrinsic kinetics of n-alkane monomolecular cracking and dehydrogenation. In the rate-determining step of these processes, C-C or C-H bonds are cleaved catalytically by Bronsted protons. Thus, the kinetics of monomolecular activation reactions are useful for characterizing the influence of active site structural environment on catalysis. In Chapter 2, the effects of active site distribution on n-butane monomolecular activation kinetics are investigated for commercial samples of MFI having a range of the Si/Al ratio. Based on UV-visible spectroscopic analyses of (Co,Na)-MFI, it is inferred that, with increasing Al concentration, the fraction of Co---and, by extension, Bronsted protons in H-MFI---located at channel intersections increases relative to the fraction located at channels. Concurrently, the first-order rate coefficients (kapp) for cracking and dehydrogenation, the selectivity to terminal cracking versus central cracking, and the selectivity to dehydrogenation versus cracking increase. The stronger dependence of the selectivity to dehydrogenation on Al content is attributed to a product-like transition state, the stability of which is more sensitive to confinement than the stabilities of cracking transition states, which occur earlier along the reaction coordinate. For terminal cracking and dehydrogenation, the intrinsic activation entropy (DeltaS‡int ) increases with Al content, consistent with the larger dimensions of intersections relative to channels. Surprisingly, the rate of dehydrogenation is inhibited by

  7. Cyclopropane reactions over Bronsted, cation, and metal sites in Ni/NaX zeolites

    SciTech Connect

    Simon, M.W.; Suib, S.L.; Bennett, C.O. )

    1994-07-01

    The reactions of cyclopropane in helium and hydrogen were investigated over two different loadings (10.7 and 6.0 wt%) of ion-exchanged Ni/NaX zeolites. The effects of reduction temperatures and hydrogen treatment times on catalytic activity and acidity were studied. Apparent activation energies ranged from 35.5 to 95.4 kJ/mol for isomerization reactions over two loadings of Ni/NaX zeolite reduced under different conditions. Rates of isomerization, hydrogenation, and hydrogenolysis are also reported. Deactivation and regeneration of catalysts are discussed. Particle sizes of 8.9 and 17.3 nm were observed in highly reduced Ni zeolites. Sintering of Ni was observed on the surfaces of the zeolite crystallites. Temperature programmed reduction studies show that stoichiometric amounts of H[sub 2] were used to completely reduce reduce all Ni in the samples. Infrared analysis of chemisorbed pyridine on these materials show that higher loadings of Ni result in higher initial acidities. Increased amounts of reduced Ni significantly increase the number of Bronsted sites on the surface of the catalyst. Electron paramagnetic resonance revealed that Ni[sup +] was present in low loaded Ni/NaX samples upon reduction at low temperatures (350[degrees]C), while higher reduction temperatures (450[degrees]C) resulted in a broad EPR signal corresponding to Ni[sup 0] only. Na vapor deposition experiments, designed to selectively poison Bronsted sites on the catalyst, reveal that Ni[sup +] ions are active in cyclopropane isomerization reactions at high temperatures. 59 refs., 11 figs., 5 tabs.

  8. A {sup 13}C NMR study of the condensation chemistry of acetone and acetaldehyde adsorbed at the Bronsted acid sites in H-ZSM-5

    SciTech Connect

    Biaglow, A.I.; Sepa, J.; Gorte, R.J.

    1995-02-01

    Several bimolecular, acid-catalyzed condensation reactions of acetone and acetaldehyde have been examined in H-ZSM-5, along with the adsorption complexes formed by the products, using {sup 13}C NMR. For acetone, the hydrogen-bonded adsorption complex is stable at room temperature and coverages below one molecule per Broensted acid site. Reaction to mesityl oxide occurs only at higher coverages or temperatures, which are necessary to induce site exchange. The adsorption complex exhibits reaction chemistry analogous to that observed in solution phase, forming adsorption complexes of chloroacetone upon exposure to Cl{sub 2} and of imines upon exposure to NH{sub 3} or dimethylamine. The reactions of acetaldehyde to crotonaldehyde and imines are similar, although they occur at a faster rate due to the higher mobility of this molecule. The adsorption complexes formed by acetone, acetaldehyde, and their condensation products can all be described as rigid, hydrogen-bonded complexes at low coverages. Complexes formed from imines and enamines exhibit isotropic chemical shifts nearly identical to those observed in magic acids, indicating that proton transfer is nearly complete for these molecules. The extent of proton transfer for the remaining molecules varies with the proton affinity of the molecule, ranging from close to complete proton transfer for mesityl oxide and crotonaldehyde to almost complete absence of proton transfer for the chloroacetones. The differences and similarities between these reactions in the zeolite and in solution phase are discussed, along with the implications for understanding the primary processes responsible for these reactions in zeolites. 34 refs., 16 figs., 1 tab.

  9. Tailoring the Synergistic Bronsted-Lewis acidic effects in Heteropolyacid catalysts: Applied in Esterification and Transesterification Reactions.

    PubMed

    Tao, Meilin; Xue, Lifang; Sun, Zhong; Wang, Shengtian; Wang, Xiaohong; Shi, Junyou

    2015-01-01

    In order to investigate the influences of Lewis metals on acidic properties and catalytic activities, a series of Keggin heteropolyacid (HPA) catalysts, HnPW11MO39 (M = Ti(IV), Cu(II), Al(III), Sn(IV), Fe(III), Cr(III), Zr(IV) and Zn(II); for Ti and Zr, the number of oxygen is 40), were prepared and applied in the esterification and transesterification reactions. Only those cations with moderate Lewis acidity had a higher impact. Ti Substituted HPA, H5PW11TiO40, posse lower acid content compared with Ti(x)H(3-4x)PW12O40 (Ti partial exchanged protons in saturated H3PW12O40), which demonstrated that the Lewis metal as an addenda atom (H5PW11TiO40) was less efficient than those as counter cations (Ti(x)H(3-4x)PW12O40). On the other hand, the highest conversion reached 92.2% in transesterification and 97.4% in esterification. Meanwhile, a good result was achieved by H5PW11TiO40 in which the total selectivity of DAG and TGA was 96.7%. In addition, calcination treatment to H5PW11TiO40 make it insoluble in water which resulted in a heterogeneous catalyst feasible for reuse. PMID:26374393

  10. Tailoring the Synergistic Bronsted-Lewis acidic effects in Heteropolyacid catalysts: Applied in Esterification and Transesterification Reactions

    PubMed Central

    Tao, Meilin; Xue, Lifang; Sun, Zhong; Wang, Shengtian; Wang, Xiaohong; Shi, Junyou

    2015-01-01

    In order to investigate the influences of Lewis metals on acidic properties and catalytic activities, a series of Keggin heteropolyacid (HPA) catalysts, HnPW11MO39 (M = TiIV, CuII, AlIII, SnIV, FeIII, CrIII, ZrIV and ZnII; for Ti and Zr, the number of oxygen is 40), were prepared and applied in the esterification and transesterification reactions. Only those cations with moderate Lewis acidity had a higher impact. Ti Substituted HPA, H5PW11TiO40, posse lower acid content compared with TixH3−4xPW12O40 (Ti partial exchanged protons in saturated H3PW12O40), which demonstrated that the Lewis metal as an addenda atom (H5PW11TiO40) was less efficient than those as counter cations (TixH3−4xPW12O40). On the other hand, the highest conversion reached 92.2% in transesterification and 97.4% in esterification. Meanwhile, a good result was achieved by H5PW11TiO40 in which the total selectivity of DAG and TGA was 96.7%. In addition, calcination treatment to H5PW11TiO40 make it insoluble in water which resulted in a heterogeneous catalyst feasible for reuse. PMID:26374393

  11. Tailoring the Synergistic Bronsted-Lewis acidic effects in Heteropolyacid catalysts: Applied in Esterification and Transesterification Reactions

    NASA Astrophysics Data System (ADS)

    Tao, Meilin; Xue, Lifang; Sun, Zhong; Wang, Shengtian; Wang, Xiaohong; Shi, Junyou

    2015-09-01

    In order to investigate the influences of Lewis metals on acidic properties and catalytic activities, a series of Keggin heteropolyacid (HPA) catalysts, HnPW11MO39 (M = TiIV, CuII, AlIII, SnIV, FeIII, CrIII, ZrIV and ZnII; for Ti and Zr, the number of oxygen is 40), were prepared and applied in the esterification and transesterification reactions. Only those cations with moderate Lewis acidity had a higher impact. Ti Substituted HPA, H5PW11TiO40, posse lower acid content compared with TixH3-4xPW12O40 (Ti partial exchanged protons in saturated H3PW12O40), which demonstrated that the Lewis metal as an addenda atom (H5PW11TiO40) was less efficient than those as counter cations (TixH3-4xPW12O40). On the other hand, the highest conversion reached 92.2% in transesterification and 97.4% in esterification. Meanwhile, a good result was achieved by H5PW11TiO40 in which the total selectivity of DAG and TGA was 96.7%. In addition, calcination treatment to H5PW11TiO40 make it insoluble in water which resulted in a heterogeneous catalyst feasible for reuse.

  12. Luminescence and IR characterization of acid sites on alumina

    SciTech Connect

    Shen, Yan-Fei; Suib, S.L. ); Deeba, M.; Koermer, G.S. )

    1994-04-01

    Luminescence and infrared (IR) spectroscopies of pyridine and ammonia adsorption have been used to measure acidities of [gamma]-alumina. Neither luminescence nor IR spectra of pyridine adsorption show an Bronsted acidity on [gamma]-alumina pretreated to 400[degrees]C. However, luminescence emission data reveal four weak OH bands even when pretreatment is done at 600[degrees]C. Pyridine and subsequent water adsorption yield six luminescence emission bands. A red shift of the pyridine emission band is found when pretreatment or desorption temperature is increased. IR spectra of ammonia on alumina pretreated at 400[degrees]C show three deformation bands at 1452, 1465, and 1485 cm[sup [minus]1]. The first band is also observed together with a band at 1554 cm[sup [minus]1] even for pretreatment at 950[degrees]C, and it corresponds to NH[sup +][sub 4] formed from dissociative adsorption of ammonia, while the other two bands are assigned to ammonia adsorbed on Bronsted acid sites. These two bands disappear along with the appearance of a new band at 1429 cm[sup [minus]1], when deuterated alumina is pretreated at 400[degrees]C and subsequently subjected to ammonia. This new band at 1429 cm[sup [minus]1] is due to NH[sub 3]D[sup +] formed from ammonia adsorbed on acidic OD sites. Consequently, ammonia IR results demonstrate the existence of Bronsted acid sites on alumina pretreated at 400[degrees]C. 38 refs., 9 figs., 2 tabs.

  13. Brønsted acid sites in gmelinite

    NASA Astrophysics Data System (ADS)

    Benco, Łubomír; Demuth, Thomas; Hafner, Jürgen; Hutschka, François

    1999-10-01

    The structural properties of purely siliceous and Al-substituted protonated gmelinite, a zeolite with a medium-sized unit cell, are investigated by means of first-principles local-density functional calculations. For acid sites introduced into an Al-free structure, optimized geometries are compared with experimental data. The substitution of a Si-O fragment by Al-O-H induces a pronounced local deformation of the structure. Four symmetrically distinct O sites (O1-O4) are classified, according to the pattern of the deformation, into two categories showing rather localized (sites 2 and 3), and mostly delocalized (sites 1 and 4) distortions. Relative stabilities of protonated structures are shown to depend on the initial geometry of the site. Larger Si-O-Si angles lead to a higher stability of the acid site. Two approaches, a static and a dynamical one, are used to derive OH stretching frequencies. Both of them prove a rather complex relation between the infrared (IR) frequency, the acidity, and the local environment of the Bro/nsted acid site. The lowest OH stretching frequency is assigned to the O2 site as distinguished in the dynamical calculations. The shift occurs due to attractive interactions of H to the framework oxygen atoms.

  14. The influence of chemisorbed molecules on mass transfer in H-ZSM-5-type zeolites and the location of Broensted acid sites

    SciTech Connect

    Caro, J.; Buelow, M. ); Kaerger, J.; Pfeifer, H. )

    1988-11-01

    Heterogeneous catalysis is one of the most important applications of zeolites. Therefore, various methods have been developed to determine the strength and concentration of Bronsted acid sites in zeolites. Among them, in the last few years, {sup 1}H MAS NMR has become a powerful tool. In addition to the accessibility of the acid sites probed by chemisorption of N-bases, the steric environment of these catalytically active sites is of importance since it imposes constraints on the geometry of the transition state. However, only a few studies have been reported on this topic. Information was obtained from quantum chemical calculations, catalytic experiments, I.R. spectroscopy, and the arrangement of guest molecules. From these investigations it has been concluded that in H-ZSM-5 the channel intersections should be preferential location centers for the Bronsted acid sites. In adsorption technology, in the use of zeolites as shape-selective adsorbents, modification of the molecular sieve properties by chemisorption of nitrogen-containing bases (N-compounds) has become a common technique. The authors have applied the NMR pulsed field gradient technique to study the influence of chemisorbed N-compounds on transport properties of molecular sieves, considering the chemisorbed compounds as transport obstacles.

  15. Mechanism of hydrodenitrogenation (Part 4) infrared spectroscopy of acidic molybdena catalysts

    SciTech Connect

    Miranda, R.

    1990-01-01

    Mo oxide catalysts supported over a complete series of silica-aluminas have been characterized in the oxidic and reduced states, by means of total acidity measurements and by infrared spectroscopy. Ammonia chemisorption was used to titrate the total acidity of the catalysts, and IR absorption of adsorbed pyridine to distinguish Bronsted from Lewis acid sites. The formation of new acidity upon deposition of molybdena on silica-alumina supports was then explained on the basis of a simple surface model. The new acidity is of both Lewis and Bronsted type, the preponderance of one over the other depending on support composition, as well as loading and state of oxidation of Mo. High-alumina supports and low Mo loading favor dispersed Mo species, in particular bidentate and monodentate di-oxo Mo species. The latter is responsible for the new Bronsted acidity. Coordinative unsaturation of polymolybdates is responsible for the new Lewis acidity, which is increased upon reduction of Mo. High-silica supports favor monodentate species (high Bronsted acidity) up to 4 wt % MoO{sub 3}. Beyond that, polymolybdates species and Lewis acidity predominate. 7 refs., 4 figs.

  16. Solid-state NMR investigation of acid sites in dealuminated HZSM-5 zeolite.

    PubMed

    Deng, F; Du, Y; Ye, C H

    1996-01-01

    The acid sites and the hydration behaviors of dealuminated HZSM-5 zeolites (calcined at 550, 600, 650, and 700 degrees C) were characterized by high-resolution 1H MAS, 1H{27A1} spin-echo double resonance in combination with 27A1 MAS NMR. Apart from the usually observed peaks for dealuminated zeolite HZSM-5, a narrow plus a broad peak simultaneously appears at ca. 6.9 ppm in the 1H spectra and they exhibit different decay behavior in the 1H [27A1] double-resonance experiments. The existence of the former signal indicates that Lewis acid sites may'be formed in the zeolites after calcination. By means of the spin echo double resonance technique, we observed for the first time a previously unexpected narrow signal at 5.2 ppm, which resonates on the downfield side of Bronsted acid signal (4.3 ppm) and cannot be resolved in the 1H MAS spectra. This new signal is probably due to another kind of Bronsted acid site, locating in the small cages bounded by four- and five-membered rings. Three narrow peaks at 50 ppm, 30 ppm, and 0 ppm are superimposed on a very broad signal in the 27A1 MAS NMR spectra of dried HZSM-5. The intensity of the line at 50 ppm is significantly reduced compared with that of the rehydrated sample. 27A1 MAS NMR suggests that most part of the four-coordinated framework A1 turns into a intermediate case between four- and three-coordinated A1 after the dehydration and this process is reversible upon dehydration/rehydration. While some framework A1 atoms are transformed into three-coordinated A1 species and Lewis acid sites are, thus, generated in the dealuminated zeolites. For the signal at 30 ppm, the hydration leads to a dispersion in the chemical shift or the quadrupole interaction, which broadens its linewidth in hydrated samples. PMID:8970117

  17. Bronsted-Evans-Polany relationships for C-C bond forming and C-C bond breaking reactions in thiamine-catalyzed decarboxylation of 2-keto acids using density functional theory.

    SciTech Connect

    Assary, R. S.; Broadbelt, L. J.; Curtiss, L. A.

    2012-01-01

    The concept of generalized enzyme reactions suggests that a wide variety of substrates can undergo enzymatic transformations, including those whose biotransformation has not yet been realized. The use of quantum chemistry to evaluate kinetic feasibility is an attractive approach to identify enzymes for the proposed transformation. However, the sheer number of novel transformations that can be generated makes this impractical as a screening approach. Therefore, it is essential to develop structure/activity relationships based on quantities that are more efficient to calculate. In this work, we propose a structure/activity relationship based on the free energy of binding or reaction of non-native substrates to evaluate the catalysis relative to that of native substrates. While Broensted-Evans-Polanyi (BEP) relationships such as that proposed here have found broad application in heterogeneous catalysis, their extension to enzymatic catalysis is limited. We report here on density functional theory (DFT) studies for C-C bond formation and C-C bond cleavage associated with the decarboxylation of six 2-keto acids by a thiamine-containing enzyme (EC 1.2.7.1) and demonstrate a linear relationship between the free energy of reaction and the activation barrier. We then applied this relationship to predict the activation barriers of 17 chemically similar novel reactions. These calculations reveal that there is a clear correlation between the free energy of formation of the transition state and the free energy of the reaction, suggesting that this method can be further extended to predict the kinetics of novel reactions through our computational framework for discovery of novel biochemical transformations.

  18. [Experimental and kinetic modeling of acid/base and redox reactions over oxide catalysts

    SciTech Connect

    Not Available

    1993-01-01

    The research has involved the characterization of catalyst acidity, [sup 2]D NMR studies of Bronsted acid sites, and kinetic, calorimetric, and spectroscopic studies of methylamine synthesis and related reactions over acid catalysts. Approach of this work was to explore quantitative correlations between factors that control the generation, type, strength, and catalytic properties of acid sites on zeolite catalysts. Microcalorimetry, thermogravimetric analysis, IR spectroscopy, and NMR spectroscopy have provided information about the nature and strength of acid sites in zeolites. This was vital in understanding the catalytic cycles involved in methylamine synthesis and related reactions over zeolite catalysts.

  19. [Experimental and kinetic modeling of acid/base and redox reactions over oxide catalysts]. Technical progress report

    SciTech Connect

    Not Available

    1993-07-01

    The research has involved the characterization of catalyst acidity, {sup 2}D NMR studies of Bronsted acid sites, and kinetic, calorimetric, and spectroscopic studies of methylamine synthesis and related reactions over acid catalysts. Approach of this work was to explore quantitative correlations between factors that control the generation, type, strength, and catalytic properties of acid sites on zeolite catalysts. Microcalorimetry, thermogravimetric analysis, IR spectroscopy, and NMR spectroscopy have provided information about the nature and strength of acid sites in zeolites. This was vital in understanding the catalytic cycles involved in methylamine synthesis and related reactions over zeolite catalysts.

  20. Hydrocracking with new solid acid catalysts: Model compounds studies

    SciTech Connect

    Sharma, R.K.; Diehl, J.W.; Olson, E.S. )

    1990-01-01

    Two new solid acid catalysts have been prepared by supporting zinc chloride on silica gel and acid-exchanged montmorillonite. The acid properties of these catalysts were determined by Hammett indicator method which showed that highly Bronsted acidic sites were present. SEM/EDS studies indicated a uniform distribution of silicon, zinc, and chlorine in the silica gel-zinc chloride catalyst. The activities of these catalysts in the hydrocracking of bibenzyl, polybenzyl, alkylbenzenes, and other heteroatom substituted aromatics were investigated. Their results with model compounds account for the effectiveness of these solid acid catalysts for conversion of coals to lower molecular weight materials.

  1. Study of the acidic properties of ZrO2-pillared bentonite

    NASA Astrophysics Data System (ADS)

    Suseno, Ahmad; Priyono; Wijaya, Karna; Trisunaryanti, Wega

    2016-02-01

    Research on pillared clays prepared from purified bentonite of Boyolali Central Jawa, Indonesia, and polycation Zr at various concentration and calcination temperature had been done. Effect of acidity characteristic and structure of resulting materials were studied. The nature of acidic site of the material was identified on the basis of FTIRspectra of pyridine adsorbed on ZrO2- pillared bentonite catalysts. Analysis showed that increasing calcination temperature was followed by decreasing acidity and increasing ZrO2 content in the pillared bentonite accompanied by the increase of its acidity. FTIR spectra showed there was an intensity increase of the characteristic band of 1635 cm-1that indicates a Bronsted acid.

  2. Surface Acidity by Positronium Spectroscopy

    NASA Astrophysics Data System (ADS)

    Huang, Weifeng; Huang, Dinah C.

    2001-03-01

    The application of the technique of angular correlation of the annihilation radiation (ACAR) from positron-electron pairs for investigating Bronsted acid sites in zeolytic catalysts was initially introduced by the authors with remarkable success. As incident positrons enter polycrystalline zeolites, a portion of the incident positrons would diffuse through the bulk and emerge on the internal surfaces and form with electrons there hydrogen-like positronium atoms (Ps). The Ps atoms will eventually annihilate also and generate an ACAR spectrum that is distinctively narrower than the one from the bulk. In the presence of Bronsted acid sites, the Ps atom population would be reduced through oxidation by protons, resulting in alteration of the ACAR spectrum which is gauged by using a lineshape parameter S. In this report, results from ACAR measurements for based-adsorbed NaHY zeolites will be presented and discussed in light of acidic stregth and effect of molecular size. Acknowledgement: This project was partially supported by grants from NSF and Taiwan National Science Council.

  3. An Acid Hydrocarbon: A Chemical Paradox

    ERIC Educational Resources Information Center

    Burke, Jeffrey T.

    2004-01-01

    The chemical paradox of cyclopentadiene, a hydrocarbon, producing bubbles like a Bronsted acid is observed. The explanation that it is the comparative thermodynamic constancy of the fragrant cyclopentadienyl anion, which produces the powerful effect, resolves the paradox.

  4. Thermodynamic and kinetic aspects of surface acidity

    SciTech Connect

    Dumesic, J.A.

    1992-01-01

    Our research in the general area of acid catalysis involves the characterization of solid acidity and the corresponding assessment of catalytic performance of acidic materials. Acid characterization studies are required to provide essential information about the type of acid site (i.e., Lewis versus Bronsted), the strength of the sites, and the mobility of molecules adsorbed on the acid sites. An accurate measure of acid strength is given by the heat of adsorption of a basic probe molecule on the acid site. A thermodynamic representation of the mobility of adsorbed species on these sites is given by the entropy of adsorption. Important techniques used in these acid site characterization studies include microcalorimetry, thermogravimetric measurements, temperature programmed desorption, infrared spectroscopy and solid state nuclear magnetic resonance. The combination of these acid site characterization studies with reaction kinetics measurements of selected catalytic processes allows the elucidation of possible relationships between surface thermodynamic and kinetic properties of acidic sites. Such relationships are important milestones in formulating effective strategies for the effective utilization of solid acid catalysts. Current work in this direction involves methylamine syntheses over various zeolites, and the basic probe molecules employed include ammonia, methanol, water and mono-, di- and tri-methylamines. 31 refs., 18 figs., 1 tab.

  5. Thermodynamic and kinetic aspects of surface acidity. Progress report

    SciTech Connect

    Dumesic, J.A.

    1992-04-01

    Our research in the general area of acid catalysis involves the characterization of solid acidity and the corresponding assessment of catalytic performance of acidic materials. Acid characterization studies are required to provide essential information about the type of acid site (i.e., Lewis versus Bronsted), the strength of the sites, and the mobility of molecules adsorbed on the acid sites. An accurate measure of acid strength is given by the heat of adsorption of a basic probe molecule on the acid site. A thermodynamic representation of the mobility of adsorbed species on these sites is given by the entropy of adsorption. Important techniques used in these acid site characterization studies include microcalorimetry, thermogravimetric measurements, temperature programmed desorption, infrared spectroscopy and solid state nuclear magnetic resonance. The combination of these acid site characterization studies with reaction kinetics measurements of selected catalytic processes allows the elucidation of possible relationships between surface thermodynamic and kinetic properties of acidic sites. Such relationships are important milestones in formulating effective strategies for the effective utilization of solid acid catalysts. Current work in this direction involves methylamine syntheses over various zeolites, and the basic probe molecules employed include ammonia, methanol, water and mono-, di- and tri-methylamines. 31 refs., 18 figs., 1 tab.

  6. Acidic and catalytic properties of SiO{sub 2}-Ta{sub 2}O{sub 5} mixed oxides prepared by the sol-gel method

    SciTech Connect

    Guiu, G.; Grange, P.

    1995-09-15

    The acidic and catalytic properties of a series of silicon-tantalum mixed oxides containing between 0 and 30 at% tantalum were characterized by temperature-programmed desorption of ammonia, by FTIR spectra of adsorbed pyridine, and by the test reaction of 1-butanol dehydration at 250-300{degrees}C. Probe molecule adsorption and catalytic testing show an acid site generation in silicon-tantalum mixed oxides compared to pure tantalum oxide. Both Bronsted and Lewis acid sites are present on the mixed oxide surface. Bronsted and Lewis acid sites seem to be weaker in SiO{sub 2}-Ta{sub 2}O{sub 5} mixed oxide than in analogous SiO{sub 2}-Al{sub 2}O{sub 3}, since a greater reaction temperature is required to achieve the same conversion in the above test reaction. However, a great advantage of this new solid acid is the production of butenes with 100% selectivity. 30 refs., 5 figs., 3 tabs.

  7. Adverse experiences with nitric acid at the Savannah River Site

    SciTech Connect

    Durant, W.S.; Craig, D.K.; Vitacco, M.J.; McCormick, J.A.

    1991-06-01

    Nitric acid is used routinely at the Savannah River Site (SRS) in many processes. However, the site has experienced a number of adverse situations in handling nitric acid. These have ranged from minor injuries to personnel to significant explosions. This document compiles many of these events and includes discussions of process upsets, fires, injuries, and toxic effects of nitric acid and its decomposition products. The purpose of the publication is to apprise those using the acid that it is a potentially dangerous material and can react in many ways as demonstrated by SRS experience. 10 refs.

  8. Determination of the acidic sites of purified single-walled carbon nanotubes by acid base titration

    NASA Astrophysics Data System (ADS)

    Hu, H.; Bhowmik, P.; Zhao, B.; Hamon, M. A.; Itkis, M. E.; Haddon, R. C.

    2001-09-01

    We report the measurement of the acidic sites in three different samples of commercially available full-length purified single-walled carbon nanotubes (SWNTs) - as obtained from CarboLex (CLI), Carbon Solutions (CSI) and Tubes@Rice (TAR) - by simple acid-base titration methods. Titration of the purified SWNTs with NaOH and NaHCO 3 solutions was used to determine the total percentage of acidic sites and carboxylic acid groups, respectively. The total percentage of acidic sites in full length purified SWNTs from TAR, CLI and CSI are about 1-3%.

  9. FTIR studies on the acidity of sulfated zirconia prepared by thermolysis of zirconium sulfate

    SciTech Connect

    Platero, E.E.; Mentruit, M.P.; Arean, C.O.; Zecchina, A.

    1996-09-01

    Sulfated zirconia having a BET surface area of 90 m{sup 2}g{sup -1} and a temperature-resistant mesoporous texture was prepared by thermolysis (at 1000 K) of zirconium sulfate. Infrared studies of surface sulfates, CO adsorption at 77 K, and room temperature adsorption of pyridine showed close similarity to sulfated zirconias prepared by impregnation of doping from the gas phase. Four main families of Lewis acid centers were found, which gave CO adducts characterized by stretching frequencies of 2212, 2202, 2196, and 2188 cm{sup -1}. Interaction of CO (at liquid nitrogen temperature) with surface hydroxyls (in partially hydroxylated samples) was found to shift the O-H stretching frequency from 3650 to 3510 cm{sup -1}, due to formation of hydrogen-bonded OH{center_dot}{center_dot}CO complexes. This downward shift, {Delta}{nu}{sub OH} = 140 cm{sup -1}, is significantly larger than the corresponding value for pure zirconia ({Delta}{nu}{sub OH} = 90 cm{sup -1}), which strongly suggests enhancement of the Bronsted acidity. Samples showing the acidic OH group at 3650 cm{sup -1} were found to contain also disulfate groups and traces of molecular water. Surface hydroxyls is sulfated zirconia still appear, however, to be weaker Bronsted acid sites than are bridging OH groups in zeolites. 49 refs., 7 figs., 2 tabs.

  10. SITE PROGRAM EVALUATION OF INNOVATIVE ACID MINE DRAINAGE TREATMENT TECHNOLOGIES AT THE LEVIATHAN MINE SITE, CA

    EPA Science Inventory

    The EPA SITE Program is conducting a detailed sampling and evaluation of several innovative acid mine drainage treatment technologies at the Leviathan Mine Superfund site in California. Technologies include BiPhasic Lime Treatment Plant, an alkaline lagoon, and an innovative bio...

  11. Dehydration of lactic acid to acrylic acid over lanthanum phosphate catalysts: the role of Lewis acid sites.

    PubMed

    Guo, Zhen; Theng, De Sheng; Tang, Karen Yuanting; Zhang, Lili; Huang, Lin; Borgna, Armando; Wang, Chuan

    2016-09-14

    Lanthanum phosphate (LaP) nano-rods were synthesized using n-butylamine as a shape-directing agent (SDA). The resulting catalysts were applied in the dehydration of lactic acid to acrylic acid. Aiming to understand the nature of the active sites, the chemical and physical properties of LaP materials were studied using a variety of characterization techniques. This study showed that the SDA not only affected the porosity of the LaP materials but also modified the acid-base properties. Clearly, the modification of the acid-base properties played a more critical role in determining the catalytic performance than porosity. An optimized catalytic performance was obtained on the LaP catalyst with a higher concentration of Lewis acid sites. Basic sites showed negative effects on the stability of the catalysts. Good stability was achieved when the catalyst was prepared using the appropriate SDA/La ratio. PMID:27514871

  12. Electrophysiological evidence for acidic, basic, and neutral amino acid olfactory receptor sites in the catfish.

    PubMed

    Caprio, J; Byrd, R P

    1984-09-01

    Electrophysiological experiments indicate that olfactory receptors of the channel catfish, Ictalurus punctatus, contain different receptor sites for the acidic (A), basic (B), and neutral amino acids; further, at least two partially interacting neutral sites exist, one for the hydrophilic neutral amino acids containing short side chains (SCN), and the second for the hydrophobic amino acids containing long side chains (LCN). The extent of cross-adaptation was determined by comparing the electro-olfactogram (EOG) responses to 20 "test" amino acids during continuous bathing of the olfactory mucosa with water only (control) to those during each of the eight "adapting" amino acid regimes. Both the adapting and test amino acids were adjusted in concentrations to provide approximately equal response magnitudes in the unadapted state. Under all eight adapting regimes, the test EOG responses were reduced from those obtained in the unadapted state, but substantial quantitative differences resulted, depending upon the molecular structure of the adapting stimulus. Analyses of the patterns of EOG responses to the test stimuli identified and characterized the respective "transduction processes," a term used to describe membrane events initiated by a particular subset of amino acid stimuli that are intricately linked to the origin of the olfactory receptor potential. Only when the stimulus compounds interact with different transduction processes are the stimuli assumed to bind to different membrane "sites." Four relatively independent L-alpha-amino acid transduction processes (and thus at least four binding sites) identified in this report include: (a) the A process for aspartic and glutamic acids; (b) the B process for arginine and lysine; (c) the SCN process for glycine, alanine, serine, glutamine, and possibly cysteine; (d) the LCN process for methionine, ethionine, valine, norvaline, leucine, norleucine, glutamic acid-gamma-methyl ester, histidine, phenylalanine, and also

  13. Inorganic Nitrogen Cycling in an Extreme Acid Mine Drainage Site

    NASA Astrophysics Data System (ADS)

    Kalnejais, L. H.; Smith, R. L.; Nordstrom, D. K.; Banfield, J. F.

    2006-12-01

    Weathering of the massive sulfide ore body at Iron Mountain, northern California has generated sulfuric acid solutions with pH values ranging from 0.5 to 1, temperatures up to 50°C and high concentrations of toxic metals. Communities of microorganisms catalyze the oxidation of iron and sulfur that generates this extreme environment. The nitrogen requirements of these organisms and the nitrogen cycling within these waters are not understood. By adapting the chemiluminescence detection method of Baeseman (2004) we have constrained the stability of nitrate and nitrite species in acidic, high ferrous iron solutions and have measured a time series of the nitrate concentrations at sites within Iron Mountain. The half-life of nitrite is less than an hour due to reactions with ferrous ions, while nitrate is found at concentrations of up to 10 μM within the mine. By coupling this information with geochemical and microbial community information at each site together with culture enrichment studies using various nitrogen sources we hope to gain insight into the pathways of nitrogen utilization in this extreme environment. References Baeseman, J.L. (2004) Denitrification in acid-impacted mountain stream sediments. Ph.D. Dissertation, University of Colorado, Department of Civil, Environmental, and Architectural Engineering.

  14. On the behavior of Bronsted-Evans-Polanyi Relations for Transition Metal Oxides

    SciTech Connect

    Vojvodic, Aleksandra

    2011-08-22

    Versatile Broensted-Evans-Polanyi (BEP) relations are found from density functional theory for a wide range of transition metal oxides including rutiles and perovskites. For oxides, the relation depends on the type of oxide, the active site and the dissociating molecule. The slope of the BEP relation is strongly coupled to the adsorbate geometry in the transition state. If it is final state-like the dissociative chemisorption energy can be considered as a descriptor for the dissociation. If it is initial state-like, on the other hand, the dissociative chemisorption energy is not suitable as descriptor for the dissociation. Dissociation of molecules with strong intramolecular bonds belong to the former and molecules with weak intramolecular bonds to the latter group. We show, for the prototype system La-perovskites, that there is a 'cyclic' behavior in the transition state characteristics upon change of the active transition metal of the oxide.

  15. Carboxylic acid accelerated formation of diesters

    DOEpatents

    Tustin, G.C.; Dickson, T.J.

    1998-04-28

    This invention pertains to accelerating the rate of formation of 1,1-dicarboxylic esters from the reaction of an aldehyde with a carboxylic acid anhydride or a ketene in the presence of a non-iodide containing a strong Bronsted acid catalyst by the addition of a carboxylic acid at about one bar pressure and between about 0 and 80 C in the substantial absence of a hydrogenation or carbonylation catalyst.

  16. Carboxylic acid accelerated formation of diesters

    DOEpatents

    Tustin, Gerald Charles; Dickson, Todd Jay

    1998-01-01

    This invention pertains to accelerating the rate of formation of 1,1-dicarboxylic esters from the reaction of an aldehyde with a carboxylic acid anhydride or a ketene in the presence of a non-iodide containing a strong Bronsted acid catalyst by the addition of a carboxylic acid at about one bar pressure and between about 0.degree. and 80.degree. C. in the substantial absence of a hydrogenation or carbonylation catalyst.

  17. Specific Initiation Site for Simian Virus 40 Deoxyribonucleic Acid Replication

    PubMed Central

    Thoren, Marilyn M.; Sebring, Edwin D.; Salzman, Norman P.

    1972-01-01

    Replicating simian virus 40 (SV40) deoxyribonucleic acid (DNA) molecules have been isolated under conditions in which the newly synthesized DNA is uniformly labeled with 3H-thymidine. These newly synthesized strands are released from the replicative intermediate molecules by alkaline treatment, and it has been possible to isolate single-stranded SV40 DNA which varies in size from 157,000 daltons (from molecules that are 10% replicated) to 1,360,000 daltons (85% replicated). The rates of duplex formation of newly synthesized DNA have been used to relate their genetic complexity to the extent of DNA replication. As DNA replication proceeds, the time required to effect 50% renaturation of the newly synthesized DNA increases at a proportional rate. The data establish that DNA replication is not initiated at random, but rather that there is a single specific initiation site for DNA replication. PMID:4342054

  18. Students' Understanding of Acids/Bases in Organic Chemistry Contexts

    ERIC Educational Resources Information Center

    Cartrette, David P.; Mayo, Provi M.

    2011-01-01

    Understanding key foundational principles is vital to learning chemistry across different contexts. One such foundational principle is the acid/base behavior of molecules. In the general chemistry sequence, the Bronsted-Lowry theory is stressed, because it lends itself well to studying equilibrium and kinetics. However, the Lewis theory of…

  19. Possible intermolecular interaction between quinolones and biphenylacetic acid inhibits gamma-aminobutyric acid receptor sites.

    PubMed

    Akahane, K; Kimura, Y; Tsutomi, Y; Hayakawa, I

    1994-10-01

    The combination of some new quinolone antibacterial agents with 4-biphenylacetic acid (BPAA), a metabolite of fenbufen, is known to specifically induce functional blockade of the gamma-aminobutyric acid (GABA) receptors. The mechanisms of these drug interactions were further examined. Scatchard analysis of [3H]muscimol binding to rat brain plasma membranes in the presence of enoxacin and BPAA revealed that a significant decrease in the number of muscimol binding sites was produced without affecting the affinity of binding to the receptors. In the presence of norfloxacin, BPAA inhibited muscimol binding the most potently of the six BPAA-related compounds tested. Fenbufen and 9,10-dihydro-gamma-oxo-2-phenanthrenebutyric acid also inhibited the binding, and 4-biphenylcarboxylic acid and methyl 4-biphenylacetate inhibited it slightly, but 3-benzoylpropionic acid exhibited no competitive inhibition. Accordingly, hybrid molecules of norfloxacin and BPAA were synthesized for stereochemical analysis of these drug interactions. A hybrid with a -CONH(CH2)3- chain between norfloxacin and BPAA (flexible structure) inhibited muscimol binding, and intracisternal injection of this hybrid caused clonic convulsions in mice more potently than the combination of norfloxacin and BPAA did. In contrast, a hybrid linked by -CONH- (stretched structure) showed almost no such inhibitory effect. 1H NMR analysis indicated the presence of intramolecular attraction at the quinoline ring of the hybrid exhibiting the antagonistic activity. These results suggest the possibility that quinolones and BPAA interact with the GABA receptor at nearby sites and that the binding affinity of quinolones to the GABA receptors is largely enhanced by the intermolecular interaction with BPAA. PMID:7840564

  20. Possible intermolecular interaction between quinolones and biphenylacetic acid inhibits gamma-aminobutyric acid receptor sites.

    PubMed Central

    Akahane, K; Kimura, Y; Tsutomi, Y; Hayakawa, I

    1994-01-01

    The combination of some new quinolone antibacterial agents with 4-biphenylacetic acid (BPAA), a metabolite of fenbufen, is known to specifically induce functional blockade of the gamma-aminobutyric acid (GABA) receptors. The mechanisms of these drug interactions were further examined. Scatchard analysis of [3H]muscimol binding to rat brain plasma membranes in the presence of enoxacin and BPAA revealed that a significant decrease in the number of muscimol binding sites was produced without affecting the affinity of binding to the receptors. In the presence of norfloxacin, BPAA inhibited muscimol binding the most potently of the six BPAA-related compounds tested. Fenbufen and 9,10-dihydro-gamma-oxo-2-phenanthrenebutyric acid also inhibited the binding, and 4-biphenylcarboxylic acid and methyl 4-biphenylacetate inhibited it slightly, but 3-benzoylpropionic acid exhibited no competitive inhibition. Accordingly, hybrid molecules of norfloxacin and BPAA were synthesized for stereochemical analysis of these drug interactions. A hybrid with a -CONH(CH2)3- chain between norfloxacin and BPAA (flexible structure) inhibited muscimol binding, and intracisternal injection of this hybrid caused clonic convulsions in mice more potently than the combination of norfloxacin and BPAA did. In contrast, a hybrid linked by -CONH- (stretched structure) showed almost no such inhibitory effect. 1H NMR analysis indicated the presence of intramolecular attraction at the quinoline ring of the hybrid exhibiting the antagonistic activity. These results suggest the possibility that quinolones and BPAA interact with the GABA receptor at nearby sites and that the binding affinity of quinolones to the GABA receptors is largely enhanced by the intermolecular interaction with BPAA. PMID:7840564

  1. General Acid Catalysis: A Flexible Experiment, Adaptable to Student Ability and Various Teaching Approaches.

    ERIC Educational Resources Information Center

    Bulmer, R. S.; And Others

    1981-01-01

    The acid-catalyzed hydrolysis of N-vinyl pyrrolidone provides a simple spectrophotometric kinetic experiment to introduce general acid catalysis, solvent isotope effects, and other aspects of ionic reactions in solution in advanced courses. The Bronsted equation and concept of linear free-energy changes is also covered. (SK)

  2. A Sialic Acid Binding Site in a Human Picornavirus

    PubMed Central

    Frank, Martin; Hähnlein-Schick, Irmgard; Ekström, Jens-Ola; Arnberg, Niklas; Stehle, Thilo

    2014-01-01

    The picornaviruses coxsackievirus A24 variant (CVA24v) and enterovirus 70 (EV70) cause continued outbreaks and pandemics of acute hemorrhagic conjunctivitis (AHC), a highly contagious eye disease against which neither vaccines nor antiviral drugs are currently available. Moreover, these viruses can cause symptoms in the cornea, upper respiratory tract, and neurological impairments such as acute flaccid paralysis. EV70 and CVA24v are both known to use 5-N-acetylneuraminic acid (Neu5Ac) for cell attachment, thus providing a putative link between the glycan receptor specificity and cell tropism and disease. We report the structures of an intact human picornavirus in complex with a range of glycans terminating in Neu5Ac. We determined the structure of the CVA24v to 1.40 Å resolution, screened different glycans bearing Neu5Ac for CVA24v binding, and structurally characterized interactions with candidate glycan receptors. Biochemical studies verified the relevance of the binding site and demonstrated a preference of CVA24v for α2,6-linked glycans. This preference can be rationalized by molecular dynamics simulations that show that α2,6-linked glycans can establish more contacts with the viral capsid. Our results form an excellent platform for the design of antiviral compounds to prevent AHC. PMID:25329320

  3. Design of a Brønsted acid with two different acidic sites: synthesis and application of aryl phosphinic acid-phosphoric acid as a Brønsted acid catalyst.

    PubMed

    Momiyama, N; Narumi, T; Terada, M

    2015-12-11

    A Brønsted acid with two different acidic sites, aryl phosphinic acid-phosphoric acid, has been synthesized. Its catalytic performance was assessed in the hetero-Diels-Alder reaction of aldehyde hydrates with Danishefsky's diene, achieving high reaction efficiency. PMID:26445921

  4. Highly selective Lewis acid sites in desilicated MFI zeolites for dihydroxyacetone isomerization to lactic acid.

    PubMed

    Dapsens, Pierre Y; Mondelli, Cecilia; Pérez-Ramírez, Javier

    2013-05-01

    Desilication of commercial MFI-type (ZSM-5) zeolites in solutions of alkali metal hydroxides is demonstrated to generate highly selective heterogeneous catalysts for the aqueous-phase isomerization of biobased dihydroxyacetone (DHA) to lactic acid (LA). The best hierarchical ZSM-5 sample attains a LA selectivity exceeding 90 %, which is comparable to that of the state-of-the-art catalyst (i.e., the Sn-beta zeolite); this optimized hierarchical catalyst is recyclable over three runs. The Lewis acid sites, which are created through desilication along with the introduction of mesoporosity, are shown to play a crucial role in the formation of the desired product; these cannot be achieved by using other post-synthetic methods, such as steaming or impregnation of aluminum species. Desilication of other metallosilicates, such as Ga-MFI, also leads to high LA selectivity. In the presence of a soluble aluminum source, such as aluminum nitrate, alkaline-assisted alumination can introduce these unique Lewis acid centers in all-silica MFI zeolites. These findings highlight the potential of zeolites in the field of biomass-to-chemical conversion, and expand the applicability of desilication for the generation of selective catalytic centers. PMID:23554234

  5. Mesoporous Nb and Ta Oxides: Synthesis, Characterization and Applications in Heterogeneous Acid Catalysis

    NASA Astrophysics Data System (ADS)

    Rao, Yuxiang Tony

    In this work, a series of mesoporous Niobium and Tantalum oxides with different pore sizes (C6, C12, C18 , ranging from 12A to 30 A) were synthesized using the ligand-assisted templating approach and investigated for their activities in a wide range of catalytic applications including benzylation, alkylation and isomerization. The as-synthesized mesoporous materials were characterized by nitrogen adsorption, powder X-ray diffraction, transmission electron microscopy (TEM), scanning electron microscopy (SEM), thermo gravimetric analysis (TGA), differential scanning calorimetry (DSC), and solid-state Nuclear magnetic resonance (NMR) techniques. In order to probe into the structural and coordination geometry of mesoporous Nb oxide and in efforts to make meaningful comparisons of mesoporous niobia prepared by the amine-templating method with the corresponding bulk sol-gel prepared Nb2O5 phase, 17O magic-angle-spinning solid-state NMR studies were conducted. The results showed a very high local order in the mesoporous sample. The oxygen atoms are coordinated only as ONb 2 in contrast with bulk phases in which the oxygen atoms are always present in a mixture of ONb2 and ONb3 coordination environments. To enhance their surface acidities and thus improve their performance as solid acid catalysts in the acid-catalyzed reactions mentioned above, pure mesoporous Nb and Ta oxides were further treated with 1M sulfuric acid or phosphoric acid. Their surface acidities before and after acid treatment were measured by Fourier transform infraRed (FT IR), amine titration and temperature programmed desorption of ammonia (NH3-TPD). Results obtained in this study showed that sulfated mesoporous Nb and Ta oxides materials possess relative high surface areas (up to 612 m 2/g) and amorphous wormhole structure. These mesoporous structures are thus quite stable to acid treatment. It was also found that Bronsted (1540 cm-1) and Lewis (1450 cm-1) acid sites coexist in a roughly 50:50 mixture

  6. Preparation of solid acid catalyst from glucose-starch mixture for biodiesel production.

    PubMed

    Chen, Guo; Fang, Baishan

    2011-02-01

    The aim of this work is to study the catalyst prepared by glucose-starch mixture. Assessment experiments showed that solid acid behaved the highest esterification activity when glucose and corn powder were mixed at ratio of 1:1, carbonized at 400°C for 75 min and sulfonated with concentrated H(2)SO(4) (98%) at 150°C for 5 h. The catalyst was characterized by acid activity measurement, XPS, TEM and FT-IR. The results indicated that solid acid composed of CS(0.073)O(0.541) has both Lewis acid sites and Bronsted acid sites caused by SO(3)H and COOH. The conversions of oleic acid esterification and triolein transesterification are 96% and 60%, respectively. Catalyst for biodiesel production from waste cottonseed oil containing high free fatty acid (FFA 55.2 wt.%) afforded the methyl ester yield of about 90% after 12h. The catalyst deactivated gradually after recycles usage, but it could be regenerated by H(2)SO(4) treatment. PMID:21067915

  7. Nitrous Acid at Concordia (Inland Site) and Dumont d'Urville (Costal Site), East Antarctica

    NASA Astrophysics Data System (ADS)

    Kerbrat, M.; Legrand, M.; Preunkert, S.; Gallée, H.; Kleffman, J.

    2012-04-01

    One of the most recent important finding made in Antarctica after the discovery of the appearance of the Antarctic ozone hole in the early 80's was the discovery of a very oxidizing canopy over the South Pole region in relation with unexpected high levels of NO. There is a strong need however to extend investigations of the oxidation capacity of the lower atmosphere at the scale of the whole Antarctic continent, and in particular, over East Antarctica. That motivated the OPALE (Oxidant Production over Antarctic Land and its Export) project. Indeed the limited data gained by using aircraft sampling during ANTCI 2003 suggest that over the East Antarctic plateau even higher NO emissions persist. Among several not yet resolved questions related to the high level of oxidants over Antarctica is the role of nitrous acid (HONO). During the austral summer 2010/2011 the levels of nitrous acid (HONO) were for the first time investigated at Concordia (75°06'S, 123°33'E) and Dumont D'Urville (66°40'S, 140°01'E), two stations located in East Antarctica. Also for the first time in Antarctica, HONO was measured by deploying a long path absorption photometer (LOPAP). At Concordia, from the end of December 2010 to mid January 2011 HONO mixing ratios at 1 m above the snow surface ranged between 5 and 60 pptv. Diurnal cycles were observed with levels peaking in the morning (06:30 to 07:30) and the evening (19:00 to 20:00). At Dumont d'Urville, background mixing ratios close to 2 pptv were observed in February 2011. No clear diurnal cycles were observed at that site but several events of air masses export from inland Antarctica were encountered with enhanced HONO levels reaching 10 pptv at night. These first HONO data gained in East Antarctica are discussed in terms of sources and sinks along with synoptic weather conditions.

  8. Teachers' Perceptions of the Teaching of Acids and Bases in Swedish Upper Secondary Schools

    ERIC Educational Resources Information Center

    Drechsler, Michal; Van Driel, Jan

    2009-01-01

    We report in this paper on a study of chemistry teachers' perceptions of their teaching in upper secondary schools in Sweden, regarding models of acids and bases, especially the Bronsted and the Arrhenius model. A questionnaire consisting of a Likert-type scale was developed, which focused on teachers' knowledge of different models, knowledge of…

  9. Site specific incorporation of keto amino acids into proteins

    DOEpatents

    Schultz, Peter G.; Wang, Lei

    2011-12-06

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  10. Site specific incorporation of keto amino acids into proteins

    DOEpatents

    Schultz, Peter G.; Wang, Lei

    2011-03-22

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  11. Site specific incorporation of keto amino acids into proteins

    DOEpatents

    Schultz, Peter G.; Wang, Lei

    2008-10-07

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  12. Site specific incorporation of keto amino acids into proteins

    DOEpatents

    Schultz, Peter G.; Wang, Lei

    2012-02-14

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  13. Site specific incorporation of keto amino acids into proteins

    DOEpatents

    Schultz, Peter G.; Wang, Lei

    2009-04-28

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate keto amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with keto amino acids using these orthogonal pairs.

  14. Mechanism of hydrodenitrogenation low temperature oxygen chemisorption over acidic molybdenum catalysts: Part 7

    SciTech Connect

    Miranda, R.

    1991-01-01

    The low temperature oxygen chemisorption over acidic molybdena catalysts has evidenced the strong reducibility of near-surface Mo, and the effect of catalyst loading and support composition on such reducibility. It was determined that for supports with compositions under 50% silica, the optimum loading producing maximum surface reducibility is 8 wt% MoO{sub 3}, while for supports with more than 50% silica, the optimum loading is 4 wt% MoO{sub 3}. At this loading, a substantial portion of the support (containing acidic sites) is also exposed. The role of Lewis sites produced on the molybdena surface by coordinative unsaturation is the strong adsorption of aromatic or unsaturated amines, and the destabilization of C-C and C-N bonds. Hydrogenation and hydrogenolysis can then occur by H addition. The highly acidic Bronsted sites, present on the support as well as on the molybdena, strongly chemisorb the hydrogenated amines. The acidic sites contribute to denitrogenation by Hofmann elimination mechanism, as shown by the the abundance of unsaturated hydrocarbons produced, and are also active for cracking and cyclization, as shown by the selectivity towards methane and cyclopentene. 13 refs., 3 figs., 1 tab.

  15. Interaction of metal ions with acid sites of biosorbents peat moss and Vaucheria and model substances alginic and humic acids

    SciTech Connect

    Crist, R.H.; Martin, J.R.; Crist, D.R.

    1999-07-01

    The interaction between added metal ions and acid sites of two biosorbents, peat moss and the alga Vaucheria, was studied. Results were interpreted in terms of two model substances, alginic acid, a copolymer of guluronic and mannuronic acids present in marine algae, and humic acid in peat moss. For peat moss and Vaucheria at pH 4--6, two protons were displaced per Cd sorbed, after correction for sorbed metals also displaced by the heavy metal. The frequent neglect of exchange of heavy metals for metals either sorbed on the native material or added for pH adjustment leads to erroneous conclusions about proton displacement stoichiometry. Proton displacement constants K{sub ex}{sup H} decreased logarithmically with pH and had similar slopes for alginic acid and biosorbents. This pH effect was interpreted as an electrostatic effect of increasing anionic charge making proton removal less favorable. The maximum number of exchangeable acid sites (capacity C{sub H}) decreased with pH for alginic acid but increased with pH for biosorbents. Consistent with titration behavior, this difference was explained in terms of more weak acid sites in the biosorbents.

  16. Instructional Misconceptions in Acid-Base Equilibria: An Analysis from a History and Philosophy of Science Perspective

    ERIC Educational Resources Information Center

    Kousathana, Margarita; Demerouti, Margarita; Tsaparlis, Georgios

    2005-01-01

    The implications of history and philosophy of chemistry are explored in the context of chemical models. Models and modeling provide the context through which epistemological aspects of chemistry can be promoted. In this work, the development of ideas and models about acids and bases (with emphasis on the Arrhenius, the Bronsted-Lowry, and the…

  17. Structural and electronic features of a Broensted acid site in H-ZSM-5

    SciTech Connect

    Cook, S.J.; Chakraborty, A.K.; Bell, A.T.; Theodorou, D.N. Univ. of California, Berkeley )

    1993-06-24

    The authors report the results of local density functional theory calculations on a Broensted acid site of the zeolite H-ZSM-5. They have investigated the structural and electronic properties of the site. Comparison is made between their results and existing experimental data. It is shown that structural relaxation around an acid site must be performed to obtain accurate energetics for substitution of aluminum into the zeolite framework. The effects of cluster termination are studied by comparing results obtained for both isolated clusters and clusters embedded in a Madelung field generated by the zeolite framework. The properties of the electron density distribution in the region around an acidic proton indicate that the acidic moiety may be characterized as a rather soft acid. 47 refs., 5 figs., 4 tabs.

  18. Evidence that Chemical Chaperone 4-Phenylbutyric Acid Binds to Human Serum Albumin at Fatty Acid Binding Sites

    PubMed Central

    James, Joel; Shihabudeen, Mohamed Sham; Kulshrestha, Shweta; Goel, Varun; Thirumurugan, Kavitha

    2015-01-01

    Endoplasmic reticulum stress elicits unfolded protein response to counteract the accumulating unfolded protein load inside a cell. The chemical chaperone, 4-Phenylbutyric acid (4-PBA) is a FDA approved drug that alleviates endoplasmic reticulum stress by assisting protein folding. It is found efficacious to augment pathological conditions like type 2 diabetes, obesity and neurodegeneration. This study explores the binding nature of 4-PBA with human serum albumin (HSA) through spectroscopic and molecular dynamics approaches, and the results show that 4-PBA has high binding specificity to Sudlow Site II (Fatty acid binding site 3, subdomain IIIA). Ligand displacement studies, RMSD stabilization profiles and MM-PBSA binding free energy calculation confirm the same. The binding constant as calculated from fluorescence spectroscopic studies was found to be kPBA = 2.69 x 105 M-1. Like long chain fatty acids, 4-PBA induces conformational changes on HSA as shown by circular dichroism, and it elicits stable binding at Sudlow Site II (fatty acid binding site 3) by forming strong hydrogen bonding and a salt bridge between domain II and III of HSA. This minimizes the fluctuation of HSA backbone as shown by limited conformational space occupancy in the principal component analysis. The overall hydrophobicity of W214 pocket (located at subdomain IIA), increases upon occupancy of 4-PBA at any FA site. Descriptors of this pocket formed by residues from other subdomains largely play a role in compensating the dynamic movement of W214. PMID:26181488

  19. Organic acids in cloud water and rainwater at a mountain site in acid rain areas of South China.

    PubMed

    Sun, Xiao; Wang, Yan; Li, Haiyan; Yang, Xueqiao; Sun, Lei; Wang, Xinfeng; Wang, Tao; Wang, Wenxing

    2016-05-01

    To investigate the chemical characteristics of organic acids and to identify their source, cloud water and rainwater samples were collected at Mount Lu, a mountain site located in the acid rain-affected area of south China, from August to September of 2011 and March to May of 2012. The volume-weighted mean (VWM) concentration of organic acids in cloud water was 38.42 μeq/L, ranging from 7.45 to 111.46 μeq/L, contributing to 2.50 % of acidity. In rainwater samples, organic acid concentrations varied from 12.39 to 68.97 μeq/L (VWM of 33.39 μeq/L). Organic acids contributed significant acidity to rainwater, with a value of 17.66 %. Formic acid, acetic acid, and oxalic acid were the most common organic acids in both cloud water and rainwater. Organic acids had an obviously higher concentration in summer than in spring in cloud water, whereas there was much less discrimination in rainwater between the two seasons. The contribution of organic acids to acidity was lower during summer than during spring in both cloud water (2.20 % in summer vs 2.83 % in spring) and rainwater (12.24 % in summer vs 19.89 % in spring). The formic-to-acetic acid ratio (F/A) showed that organic acids were dominated by primary emissions in 71.31 % of the cloud water samples and whole rainwater samples. Positive matrix factorization (PMF) analysis determined four factors as the sources of organic acids in cloud water, including biogenic emissions (61.8 %), anthropogenic emissions (15.28 %), marine emissions (15.07 %) and soil emissions (7.85 %). The findings from this study imply an indispensable role of organic acids in wet deposition, but organic acids may have a limited capacity to increase ecological risks in local environments. PMID:26841776

  20. Probing the Binding Site of Bile Acids in TGR5.

    PubMed

    Macchiarulo, Antonio; Gioiello, Antimo; Thomas, Charles; Pols, Thijs W H; Nuti, Roberto; Ferrari, Cristina; Giacchè, Nicola; De Franco, Francesca; Pruzanski, Mark; Auwerx, Johan; Schoonjans, Kristina; Pellicciari, Roberto

    2013-12-12

    TGR5 is a G-protein-coupled receptor (GPCR) mediating cellular responses to bile acids (BAs). Although some efforts have been devoted to generate homology models of TGR5 and draw structure-activity relationships of BAs, none of these studies has hitherto described how BAs bind to TGR5. Here, we present an integrated computational, chemical, and biological approach that has been instrumental to determine the binding mode of BAs to TGR5. As a result, key residues have been identified that are involved in mediating the binding of BAs to the receptor. Collectively, these results provide new hints to design potent and selective TGR5 agonists. PMID:24900622

  1. Improving Evolutionary Models for Mitochondrial Protein Data with Site-Class Specific Amino Acid Exchangeability Matrices

    PubMed Central

    Dunn, Katherine A.; Jiang, Wenyi; Field, Christopher; Bielawski, Joseph P.

    2013-01-01

    Adequate modeling of mitochondrial sequence evolution is an essential component of mitochondrial phylogenomics (comparative mitogenomics). There is wide recognition within the field that lineage-specific aspects of mitochondrial evolution should be accommodated through lineage-specific amino-acid exchangeability matrices (e.g., mtMam for mammalian data). However, such a matrix must be applied to all sites and this implies that all sites are subject to the same, or largely similar, evolutionary constraints. This assumption is unjustified. Indeed, substantial differences are expected to arise from three-dimensional structures that impose different physiochemical environments on individual amino acid residues. The objectives of this paper are (1) to investigate the extent to which amino acid evolution varies among sites of mitochondrial proteins, and (2) to assess the potential benefits of explicitly modeling such variability. To achieve this, we developed a novel method for partitioning sites based on amino acid physiochemical properties. We apply this method to two datasets derived from complete mitochondrial genomes of mammals and fish, and use maximum likelihood to estimate amino acid exchangeabilities for the different groups of sites. Using this approach we identified large groups of sites evolving under unique physiochemical constraints. Estimates of amino acid exchangeabilities differed significantly among such groups. Moreover, we found that joint estimates of amino acid exchangeabilities do not adequately represent the natural variability in evolutionary processes among sites of mitochondrial proteins. Significant improvements in likelihood are obtained when the new matrices are employed. We also find that maximum likelihood estimates of branch lengths can be strongly impacted. We provide sets of matrices suitable for groups of sites subject to similar physiochemical constraints, and discuss how they might be used to analyze real data. We also discuss how

  2. Transport and signaling via the amino acid binding site of the yeast Gap1 amino acid transceptor.

    PubMed

    Van Zeebroeck, Griet; Bonini, Beatriz Monge; Versele, Matthias; Thevelein, Johan M

    2009-01-01

    Transporter-related nutrient sensors, called transceptors, mediate nutrient activation of signaling pathways through the plasma membrane. The mechanism of action of transporting and nontransporting transceptors is unknown. We have screened 319 amino acid analogs to identify compounds that act on Gap1, a transporting amino acid transceptor in yeast that triggers activation of the protein kinase A pathway. We identified competitive and noncompetitive inhibitors of transport, either with or without agonist action for signaling, including nontransported agonists. Using substituted cysteine accessibility method (SCAM) analysis, we identified Ser388 and Val389 as being exposed into the amino acid binding site, and we show that agonist action for signaling uses the same binding site as used for transport. Our results provide the first insight, to our knowledge, into the mechanism of action of transceptors. They indicate that signaling requires a ligand-induced specific conformational change that may be part of but does not require the complete transport cycle. PMID:19060912

  3. Na+ Inhibits the Epithelial Na+ Channel by Binding to a Site in an Extracellular Acidic Cleft*

    PubMed Central

    Kashlan, Ossama B.; Blobner, Brandon M.; Zuzek, Zachary; Tolino, Michael; Kleyman, Thomas R.

    2015-01-01

    The epithelial Na+ channel (ENaC) has a key role in the regulation of extracellular fluid volume and blood pressure. ENaC belongs to a family of ion channels that sense the external environment. These channels have large extracellular regions that are thought to interact with environmental cues, such as Na+, Cl−, protons, proteases, and shear stress, which modulate gating behavior. We sought to determine the molecular mechanism by which ENaC senses high external Na+ concentrations, resulting in an inhibition of channel activity. Both our structural model of an ENaC α subunit and the resolved structure of an acid-sensing ion channel (ASIC1) have conserved acidic pockets in the periphery of the extracellular region of the channel. We hypothesized that these acidic pockets host inhibitory allosteric Na+ binding sites. Through site-directed mutagenesis targeting the acidic pocket, we modified the inhibitory response to external Na+. Mutations at selected sites altered the cation inhibitory preference to favor Li+ or K+ rather than Na+. Channel activity was reduced in response to restraining movement within this region by cross-linking structures across the acidic pocket. Our results suggest that residues within the acidic pocket form an allosteric effector binding site for Na+. Our study supports the hypothesis that an acidic cleft is a key ligand binding locus for ENaC and perhaps other members of the ENaC/degenerin family. PMID:25389295

  4. Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination

    DOEpatents

    Xie, Jianming; Wang, Lei; Wu, Ning; Schultz, Peter G.

    2008-07-15

    Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

  5. Evolution of HLA class II molecules: Allelic and amino acid site variability across populations.

    PubMed Central

    Salamon, H; Klitz, W; Easteal, S; Gao, X; Erlich, H A; Fernandez-Viña, M; Trachtenberg, E A; McWeeney, S K; Nelson, M P; Thomson, G

    1999-01-01

    Analysis of the highly polymorphic beta1 domains of the HLA class II molecules encoded by the DRB1, DQB1, and DPB1 loci reveals contrasting levels of diversity at the allele and amino acid site levels. Statistics of allele frequency distributions, based on Watterson's homozygosity statistic F, reveal distinct evolutionary patterns for these loci in ethnically diverse samples (26 populations for DQB1 and DRB1 and 14 for DPB1). When examined over all populations, the DQB1 locus allelic variation exhibits striking balanced polymorphism (P < 10(-4)), DRB1 shows some evidence of balancing selection (P < 0.06), and while there is overall very little evidence for selection of DPB1 allele frequencies, there is a trend in the direction of balancing selection (P < 0.08). In contrast, at the amino acid level all three loci show strong evidence of balancing selection at some sites. Averaged over polymorphic amino acid sites, DQB1 and DPB1 show similar deviation from neutrality expectations, and both exhibit more balanced polymorphic amino acid sites than DRB1. Across ethnic groups, polymorphisms at many codons show evidence for balancing selection, yet data consistent with directional selection were observed at other codons. Both antigen-binding pocket- and non-pocket-forming amino acid sites show overall deviation from neutrality for all three loci. Only in the case of DRB1 was there a significant difference between pocket- and non-pocket-forming amino acid sites. Our findings indicate that balancing selection at the MHC occurs at the level of polymorphic amino acid residues, and that in many cases this selection is consistent across populations. PMID:10224269

  6. Atmospheric geochemistry of formic and acetic acids at a mid-latitude temperate site

    NASA Technical Reports Server (NTRS)

    Talbot, R. W.; Beecher, K. M.; Harriss, R. C.; Cofer, R. W., III

    1988-01-01

    Tropospheric concentrations of formic and acetic acids in the gas, the aerosol, and the rainwater phases were determined in samples collected 1-2 m above ground level at an open field site in eastern Virginia. These acids were found to occur principally (98 percent or above) in the gas phase, with a marked annual seasonality, averaging 1890 ppt for formate and 1310 ppt for acetate during the growing season, as compared to 695 ppt and 700 ppt, respectively, over the nongrowing season. The data support the hypothesis that biogenic emissions from vegatation are important sources of atmospheric formic and acetic acid during the local growing season. The same time trends were observed for precipitation, although with less defined seasonality. The relative increase of the acetic acid/formic acid ratio during the nongrowing season points to the dominance of anthropogenic inputs of acetic acid from motor vehicles and biomass combustion in the wintertime.

  7. Dissolution of Simulated and Radioactive Savannah River Site High-Level Waste Sludges with Oxalic Acid & Citric Acid Solutions

    SciTech Connect

    STALLINGS, MARY

    2004-07-08

    This report presents findings from tests investigating the dissolution of simulated and radioactive Savannah River Site sludges with 4 per cent oxalic acid and mixtures of oxalic and citric acid previously recommended by a Russian team from the Khlopin Radium Institute and the Mining and Chemical Combine (MCC). Testing also included characterization of the simulated and radioactive waste sludges. Testing results showed the following: Dissolution of simulated HM and PUREX sludges with oxalic and citric acid mixtures at SRTC confirmed general trends reported previously by Russian testing. Unlike the previous Russian testing six sequential contacts of a mixture of oxalic acid citric acids at a 2:1 ratio (v/w) of acid to sludge did not produce complete dissolution of simulated HM and PUREX sludges. We observed that increased sludge dissolution occurred at a higher acid to sludge ratio, 50:1 (v/w), compared to the recommended ratio of 2:1 (v/w). We observed much lower dissolution of aluminum in a simulated HM sludge by sodium hydroxide leaching. We attribute the low aluminum dissolution in caustic to the high fraction of boehmite present in the simulated sludge. Dissolution of HLW sludges with 4 per cent oxalic acid and oxalic/citric acid followed general trends observed with simulated sludges. The limited testing suggests that a mixture of oxalic and citric acids is more efficient for dissolving HM and PUREX sludges and provides a more homogeneous dissolution of HM sludge than oxalic acid alone. Dissolution of HLW sludges in oxalic and oxalic/citric acid mixtures produced residual sludge solids that measured at higher neutron poison to equivalent 235U weight ratios than that in the untreated sludge solids. This finding suggests that residual solids do not present an increased nuclear criticality safety risk. Generally the neutron poison to equivalent 235U weight ratios of the acid solutions containing dissolved sludge components are lower than those in the untreated

  8. Gas phase acidity measurement of local acidic groups in multifunctional species: controlling the binding sites in hydroxycinnamic acids.

    PubMed

    Guerrero, Andres; Baer, Tomas; Chana, Antonio; González, Javier; Dávalos, Juan Z

    2013-07-01

    The applicability of the extended kinetic method (EKM) to determine the gas phase acidities (GA) of different deprotonable groups within the same molecule was tested by measuring the acidities of cinnamic, coumaric, and caffeic acids. These molecules differ not only in the number of acidic groups but in their nature, intramolecular distances, and calculated GAs. In order to determine independently the GA of groups within the same molecule using the EKM, it is necessary to selectively prepare pure forms of the hydrogen-bound heterodimer. In this work, the selectivity was achieved by the use of solvents of different vapor pressure (water and acetonitrile), as well as by variation of the drying temperature in the ESI source, which affected the production of heterodimers with different solvation energies and gas-phase dissociation energies. A particularly surprising finding is that the calculated solvation enthalpies of water and the aprotic acetonitrile are essentially identical, and that the different gas-phase products generated are apparently the result of their different vapor pressures, which affects the drying mechanism. This approach for the selective preparation of heterodimers, which is based on the energetics, appears to be quite general and should prove useful for other studies that require the selective production of heterodimers in ESI sources. The experimental results were supported by density functional theory (DFT) calculations of both gas-phase and solvated species. The experimental thermochemical parameters (deprotonation ΔG, ΔH, and ΔS) are in good agreement with the calculated values for the monofunctional cinnamic acid, as well as the multifunctional coumaric and caffeic acids. The measured GA for cinnamic acid is 334.5 ± 2.0 kcal/mol. The measured acidities for the COOH and OH groups of coumaric and caffeic acids are 332.7 ± 2.0, 318.7 ± 2.1, 332.2 ± 2.0, and 317.3 ± 2.2 kcal/mol, respectively. PMID:23799241

  9. Efficient solid acid catalyst containing Lewis and Brønsted Acid sites for the production of furfurals.

    PubMed

    Mazzotta, Michael G; Gupta, Dinesh; Saha, Basudeb; Patra, Astam K; Bhaumik, Asim; Abu-Omar, Mahdi M

    2014-08-01

    Self-assembled nanoparticulates of porous sulfonated carbonaceous TiO2 material that contain Brønsted and Lewis acidic sites were prepared by a one-pot synthesis method. The material was characterized by XRD, FTIR spectroscopy, NH3 temperature-programmed desorption, pyridine FTIR spectroscopy, field-emission scanning electron microscopy, high-resolution transmission electron microscopy, N2 -sorption, atomic absorbance spectroscopy, and inductively coupled plasma optical emission spectroscopy. The carbonaceous heterogeneous catalyst (Glu-TsOH-Ti) with a Brønsted-to-Lewis acid density ratio of 1.2 and more accessible acid sites was effective to produce 5-hydroxymethylfurfural and furfural from biomass-derived mono- and disaccharides and xylose in a biphasic solvent that comprised water and biorenewable methyltetrahydrofuran. The catalyst was recycled in four consecutive cycles with a total loss of only 3 % activity. Thus, Glu-TsOH-Ti, which contains isomerization and dehydration catalytic sites and is based on a cheap and biorenewable carbon support, is a sustainable catalyst for the production of furfurals, platform chemicals for biofuels and chemicals. PMID:24807741

  10. Effect of sun elevation upon remote sensing of ocean color over an acid waste dump site

    NASA Technical Reports Server (NTRS)

    Bressette, W. E.

    1978-01-01

    Photographic flights were made over an ocean acid waste dump site while dumping was in progress. The flights resulted in wide angle, broadband, spectral radiance film exposure data between the wavelengths of 500 to 900 nanometers for sun elevation angles ranging from 26 to 42 degrees. It is shown from densitometer data that the spectral signature of acid waste discharged into ocean water can be observed photographically, the influence of sun elevation upon remotely sensed apparent color can be normalized by using a single spectral band ratioing technique, and photographic quantification and mapping of acid waste through its suspended iron precipitate appears possible.

  11. Acidic properties of sulfated zirconia: An infrared spectroscopic study

    SciTech Connect

    Babou, F.; Coudurier, G.; Vedrine, J.C.

    1995-04-01

    Sulfated zirconia with S content of 2 wt.% equivalent to complete coverage of its surface was studied by infrared spectroscopy. At least four sulfated species were identified and exhibited an important and reversible sensitivity to water. These equilibria were demonstrated to exist by the study of adsorption of incremental amounts of water. D{sub 2}O and H{sub 2}{sup 18}O isotopically enriched water molecules were used to assist interpretation of IR spectra. To characterize acidity features, the probe molecules butane, CO, and H{sub 2}O (as weak bases) or pyridine (as a strong base) were adsorbed. Two Lewis acid sites (L{sub 1} and L{sub 2}) were observed and one Bronsted site (B) related to the zirconia support (L{sub 1}) and the sulfated species (L{sub 2}, B). They were evidenced by pyridine adsorption which was shown to partly displace adsorbed sulfate species. With the help of previous theoretical calculations using an ab initio method and representing the zirconia surface by a mononuclear zirconium complex, it is emphasized that the sulfated zirconia can be visualized as a H{sub 2}SO{sub 4} compound grafted onto the surface of zirconia in a way which makes it very sensitive to water but in a reversible way. Its acidity is similar to that of sulfuric acid but it is not really superacidic. Comparison with other oxides leads us to suggest that the cationic charge borne by the metallic cation is of prime importance for the acidity strength. The role of water on the acidic and catalytic properties for n-butane isomerization reaction is emphasized. 33 refs., 11 figs., 2 tabs.

  12. Identification and Pharmacological Characterization of Multiple Allosteric Binding Sites on the Free Fatty Acid 1 Receptor

    PubMed Central

    Lin, Daniel C.-H.; Guo, Qi; Luo, Jian; Zhang, Jane; Nguyen, Kathy; Chen, Michael; Tran, Thanh; Dransfield, Paul J.; Brown, Sean P.; Houze, Jonathan; Vimolratana, Marc; Jiao, Xian Yun; Wang, Yingcai; Birdsall, Nigel J. M.

    2012-01-01

    Activation of FFA1 (GPR40), a member of G protein-coupling receptor family A, is mediated by medium- and long-chain fatty acids and leads to amplification of glucose-stimulated insulin secretion, suggesting a potential role for free fatty acid 1 (FFA1) as a target for type 2 diabetes. It was assumed previously that there is a single binding site for fatty acids and synthetic FFA1 agonists. However, using members of two chemical series of partial and full agonists that have been identified, radioligand binding interaction studies revealed that the full agonists do not bind to the same site as the partial agonists but exhibit positive heterotropic cooperativity. Analysis of functional data reveals positive functional cooperativity between the full agonists and partial agonists in various functional assays (in vitro and ex vivo) and also in vivo. Furthermore, the endogenous fatty acid docosahexaenoic acid (DHA) shows negative or neutral cooperativity with members of both series of agonists in binding assays but displays positive cooperativity in functional assays. Another synthetic agonist is allosteric with members of both agonist series, but apparently competitive with DHA. Therefore, there appear to be three allosterically linked binding sites on FFA1 with agonists specific for each of these sites. Activation of free fatty acid 1 receptor (FFAR1) by each of these agonists is differentially affected by mutations of two arginine residues, previously found to be important for FFAR1 binding and activation. These ligands with their high potencies and strong positive functional cooperativity with endogenous fatty acids, demonstrated in vitro and in vivo, have the potential to deliver therapeutic benefits. PMID:22859723

  13. Identification and pharmacological characterization of multiple allosteric binding sites on the free fatty acid 1 receptor.

    PubMed

    Lin, Daniel C-H; Guo, Qi; Luo, Jian; Zhang, Jane; Nguyen, Kathy; Chen, Michael; Tran, Thanh; Dransfield, Paul J; Brown, Sean P; Houze, Jonathan; Vimolratana, Marc; Jiao, Xian Yun; Wang, Yingcai; Birdsall, Nigel J M; Swaminath, Gayathri

    2012-11-01

    Activation of FFA1 (GPR40), a member of G protein-coupling receptor family A, is mediated by medium- and long-chain fatty acids and leads to amplification of glucose-stimulated insulin secretion, suggesting a potential role for free fatty acid 1 (FFA1) as a target for type 2 diabetes. It was assumed previously that there is a single binding site for fatty acids and synthetic FFA1 agonists. However, using members of two chemical series of partial and full agonists that have been identified, radioligand binding interaction studies revealed that the full agonists do not bind to the same site as the partial agonists but exhibit positive heterotropic cooperativity. Analysis of functional data reveals positive functional cooperativity between the full agonists and partial agonists in various functional assays (in vitro and ex vivo) and also in vivo. Furthermore, the endogenous fatty acid docosahexaenoic acid (DHA) shows negative or neutral cooperativity with members of both series of agonists in binding assays but displays positive cooperativity in functional assays. Another synthetic agonist is allosteric with members of both agonist series, but apparently competitive with DHA. Therefore, there appear to be three allosterically linked binding sites on FFA1 with agonists specific for each of these sites. Activation of free fatty acid 1 receptor (FFAR1) by each of these agonists is differentially affected by mutations of two arginine residues, previously found to be important for FFAR1 binding and activation. These ligands with their high potencies and strong positive functional cooperativity with endogenous fatty acids, demonstrated in vitro and in vivo, have the potential to deliver therapeutic benefits. PMID:22859723

  14. In Situ Oxalic Acid Injection to Accelerate Arsenic Remediation at a Superfund Site in New Jersey

    PubMed Central

    Wovkulich, Karen; Stute, Martin; Mailloux, Brian J.; Keimowitz, Alison R.; Ross, James; Bostick, Benjamin; Sun, Jing; Chillrud, Steven N.

    2015-01-01

    Arsenic is a prevalent contaminant at a large number of US Superfund sites; establishing techniques that accelerate As remediation could benefit many sites. Hundreds of tons of As were released into the environment by the Vineland Chemical Co. in southern New Jersey during its manufacturing lifetime (1949–1994), resulting in extensive contamination of surface and subsurface soils and sediments, groundwater, and the downstream watershed. Despite substantial intervention at this Superfund site, sufficient aquifer cleanup could require many decades if based on traditional pump and treat technologies only. Laboratory column experiments have suggested that oxalic acid addition to contaminated aquifer solids could promote significant As release from the solid phase. To evaluate the potential of chemical additions to increase As release in situ and boost treatment efficiency, a forced gradient pilot scale study was conducted on the Vineland site. During spring/summer 2009, oxalic acid and bromide tracer were injected into a small portion (~50 m2) of the site for 3 months. Groundwater samples indicate that introduction of oxalic acid led to increased As release. Between 2.9 and 3.6 kg of As were removed from the sampled wells as a result of the oxalic acid treatment during the 3-month injection. A comparison of As concentrations on sediment cores collected before and after treatment and analyzed using X-ray fluorescence spectroscopy suggested reduction in As concentrations of ~36% (median difference) to 48% (mean difference). While further study is necessary, the addition of oxalic acid shows potential for accelerating treatment of a highly contaminated site and decreasing the As remediation time-scale. PMID:25598701

  15. LIME TREATMENT LAGOONS TECHNOLOGY FOR TREATING ACID MINE DRAINAGE FROM TWO MINING SITES

    EPA Science Inventory

    Runoff and drainage from active and inactive mines are someof the most environmentally damaging land uses i the US. Acid Mine drainage (AMD) from mining sites across the country requires treatment because of high metal concentrations that exceed regulatory standards for safe disc...

  16. PHYSICAL SOLUTIONS FOR ACID ROCK DRAINAGE AT REMOTE SITES DEMONSTRATION PROJECT

    EPA Science Inventory

    This report summarizes the results of Mine Waste Technology Program, Activity III, Project 42, Physical Solutions for Acid Rock Drainage at Remote Sites, funded by the U.S. Environmental Protection Agency (EPA) and jointly administered by EPA and the U.S. Department of Energy. A...

  17. Proton-Binding Sites of Acid-Sensing Ion Channel 1

    PubMed Central

    Ishikita, Hiroshi

    2011-01-01

    Acid-sensing ion channels (ASICs) are proton-gated cation channels that exist throughout the mammalian central and peripheral nervous systems. ASIC1 is the most abundant of all the ASICs and is likely to modulate synaptic transmission. Identifying the proton-binding sites of ASCI1 is required to elucidate its pH-sensing mechanism. By using the crystal structure of ASIC1, the protonation states of each titratable site of ASIC1 were calculated by solving the Poisson-Boltzmann equation under conditions wherein the protonation states of all these sites are simultaneously in equilibrium. Four acidic-acidic residue pairs—Asp238-Asp350, Glu220-Asp408, Glu239-Asp346, and Glu80-Glu417—were found to be highly protonated. In particular, the Glu80-Glu417 pair in the inner pore was completely protonated and possessed 2 H+, implying its possible importance as a proton-binding site. The pKa of Glu239, which forms a pair with a possible pH-sensing site Asp346, differs among each homo-trimer subunit due to the different H-bond pattern of Thr237 in the different protein conformations of the subunits. His74 possessed a pKa of ≈6–7. Conservation of His74 in the proton-sensitive ASIC3 that lacks a residue corresponding to Asp346 may suggest its possible pH-sensing role in proton-sensitive ASICs. PMID:21340031

  18. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

    SciTech Connect

    Gangi Setty, Thanuja; Cho, Christine; Govindappa, Sowmya; Apicella, Michael A.; Ramaswamy, S.

    2014-07-01

    Structure–function studies of sialic acid-binding proteins from F. nucleatum, P. multocida, V. cholerae and H. influenzae reveal a conserved network of hydrogen bonds involved in conformational change on ligand binding. Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.

  19. Characterization and acidic properties of Al-SBA-15 materials prepared by post-synthesis alumination of a low-cost ordered mesoporous silica

    SciTech Connect

    Gomez-Cazalilla, M.; Merida-Robles, J.M.; Gurbani, A.; Rodriguez-Castellon, E.; Jimenez-Lopez, A.

    2007-03-15

    A series of Al-containing SBA-15 type materials with different Si/Al ratio, were prepared by post-synthesis modification of a pure highly ordered mesoporous silica SBA-15 obtained by using sodium silicate as silica source, and amphiphilic block copolymer as structure-directing agent. A high level of aluminum incorporation was achieved, reaching an Si/Al ratio of up to 5.5, without any significant loss in the textural properties of SBA-15. These materials were fully characterized by powder X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), {sup 27}Al NMR spectroscopy, and N{sub 2} adsorption at 77 K. The acid properties of these materials have been evaluated by NH{sub 3}-TPD, adsorption of pyridine and deuterated acetonitrile coupled to FTIR spectroscopy. The effective acidity of these materials was evaluated using two catalytic reactions: 2-propanol dehydrogenation and 1-butene isomerization. The adsorption of basic probe molecules and the catalytic behavior revealed an evolution of the acid properties with the Al content. These studies have shown that the Al-SBA-15 materials contain Bronsted and Lewis acid sites with medium acidity which makes them appropriate to be used as acid catalysts in heterogeneous catalysis, catalytic supports, and adsorbents. - Graphical abstract: Al KLL spectra of Al-SBA-15 materials with different Si/Al ratios.

  20. Site-Specific Radiofluorination of Biomolecules with 8-[(18)F]-Fluorooctanoic Acid Catalyzed by Lipoic Acid Ligase.

    PubMed

    Drake, Christopher R; Sevillano, Natalia; Truillet, Charles; Craik, Charles S; VanBrocklin, Henry F; Evans, Michael J

    2016-06-17

    New methodologies for site-specifically radiolabeling proteins with (18)F are required to generate high quality radiotracers for preclinical and clinical applications with positron emission tomography. Herein, we report an approach by which we use lipoic acid ligase (LplA) to conjugate [(18)F]-fluorooctanoic acid to an antibody fragment bearing the peptide substrate of LplA. The mild conditions of the reaction preserve antibody immunoreactivity, and the efficiency of LplA allows for >90% yield even with very small amounts of peptidic precursor (1-10 nmol). These features are advantageous compared to the current gold standard in the field. Moreover, the methodology introduces a new application for an important tool in chemical biology. PMID:27008570

  1. Lipid Classes and Fatty Acids in Ophryotrocha cyclops, a Dorvilleid from Newfoundland Aquaculture Sites

    PubMed Central

    Salvo, Flora; Dufour, Suzanne C.; Hamoutene, Dounia; Parrish, Christopher C.

    2015-01-01

    A new opportunistic annelid (Ophryotrocha cyclops) discovered on benthic substrates underneath finfish aquaculture sites in Newfoundland (NL) may be involved in the remediation of organic wastes. At those aquaculture sites, bacterial mats and O. cyclops often coexist and are used as indicators of organic enrichment. Little is known on the trophic strategies used by these annelids, including whether they might consume bacteria or other aquaculture-derived wastes. We studied the lipid and fatty acid composition of the annelids and their potential food sources (degraded flocculent organic matter, fresh fish pellets and bacterial mats) to investigate feeding relationships in these habitats and compared the lipid and fatty acid composition of annelids before and after starvation. Fish pellets were rich in lipids, mainly terrestrially derived C18 fatty acids (18:1ω9, 18:2ω6, 18:3ω3), while bacterial samples were mainly composed of ω7 fatty acids, and flocculent matter appeared to be a mixture of fresh and degrading fish pellets, feces and bacteria. Ophryotrocha cyclops did not appear to store excessive amounts of lipids (13%) but showed a high concentration of ω3 and ω6 fatty acids, as well as a high proportion of the main fatty acids contained in fresh fish pellets and bacterial mats. The dorvilleids and all potential food sources differed significantly in their lipid and fatty acid composition. Interestingly, while all food sources contained low proportions of 20:5ω3 and 20:2ω6, the annelids showed high concentrations of these two fatty acids, along with 20:4ω6. A starvation period of 13 days did not result in a major decrease in total lipid content; however, microscopic observations revealed that very few visible lipid droplets remained in the gut epithelium after three months of starvation. Ophryotrocha cyclops appears well adapted to extreme environments and may rely on lipid-rich organic matter for survival and dispersal in cold environments. PMID:26308719

  2. Zinc-induced oligomerization of zinc α2 glycoprotein reveals multiple fatty acid-binding sites.

    PubMed

    Zahid, Henna; Miah, Layeque; Lau, Andy M; Brochard, Lea; Hati, Debolina; Bui, Tam T T; Drake, Alex F; Gor, Jayesh; Perkins, Stephen J; McDermott, Lindsay C

    2016-01-01

    Zinc α2 glycoprotein (ZAG) is an adipokine with a class I MHC protein fold and is associated with obesity and diabetes. Although its intrinsic ligand remains unknown, ZAG binds the dansylated C11 fatty acid 11-(dansylamino)undecanoic acid (DAUDA) in the groove between the α1 and α2 domains. The surface of ZAG has approximately 15 weak zinc-binding sites deemed responsible for precipitation from human plasma. In the present study the functional significance of these metal sites was investigated. Analytical ultracentrifugation (AUC) and CD showed that zinc, but not other divalent metals, causes ZAG to oligomerize in solution. Thus ZAG dimers and trimers were observed in the presence of 1 and 2 mM zinc. Molecular modelling of X-ray scattering curves and sedimentation coefficients indicated a progressive stacking of ZAG monomers, suggesting that the ZAG groove may be occluded in these. Using fluorescence-detected sedimentation velocity, these ZAG-zinc oligomers were again observed in the presence of the fluorescent boron dipyrromethene fatty acid C16-BODIPY (4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-hexadecanoic acid). Fluorescence spectroscopy confirmed that ZAG binds C16-BODIPY. ZAG binding to C16-BODIPY, but not to DAUDA, was reduced by increased zinc concentrations. We conclude that the lipid-binding groove in ZAG contains at least two distinct fatty acid-binding sites for DAUDA and C16-BODIPY, similar to the multiple lipid binding seen in the structurally related immune protein CD1c. In addition, because high concentrations of zinc occur in the pancreas, the perturbation of these multiple lipid-binding sites by zinc may be significant in Type 2 diabetes where dysregulation of ZAG and zinc homoeostasis occurs. PMID:26487699

  3. Characterization of Naphthaleneacetic Acid Binding to Receptor Sites on Cellular Membranes of Maize Coleoptile Tissue 1

    PubMed Central

    Ray, Peter M.; Dohrmann, Ulrike; Hertel, Rainer

    1977-01-01

    Characteristics of and optimum conditions for saturable (“specific”) binding of [14C]naphthaleneacetic acid to sites located on membranous particles from maize (Zea mays L.) coleoptiles are described. Most, if not all, of the specific binding appears to be due to a single kinetic class of binding sites having a KD of 5 to 7 × 10−7m for naphthalene-1-acetic acid (NAA). Binding of NAA is insensitive to high monovalent salt concentrations, indicating that binding is not primarily ionic. However, specific binding is inhibited by Mg2+ or Ca2+ above 5 mm. Specific binding is improved by organic acids, especially citrate. Binding is heat-labile and is sensitive to agents that act either on proteins or on lipids. Specific binding is reversibly inactivated by reducing agents such as dithioerythritol; a reducible group, possibly a disulfide group, may be located at the binding site and required for its function. The affinity of the specific binding sites for auxins is modified by an unidentified dialyzable, heat-stable, apparently amphoteric, organic factor (“supernatant factor”) found in maize tissue. PMID:16659851

  4. Site-specific study on stabilization of acid-generating mine tailings using coal fly ash

    SciTech Connect

    Shang, J.Q.; Wang, H.L.; Kovac, V.; Fyfe, J.

    2006-03-15

    A site-specific study on stabilizing acid-generating mine tailings from Sudbury Mine using a coal fly ash from Nanticoke Generating Station is presented in this paper. The objective of the study is to evaluate the feasibility of codisposal of the fly ash and mine tailings to reduce environmental impacts of Sudbury tailings disposal sites. The study includes three phases, i.e., characterization of the mine tailings, and coal fly ash, oxidation tests on the mine tailings and kinetic column permeation tests. The results of the experiments indicate that when permeated with acid mine drainage, the hydraulic conductivity of Nanticoke coal fly ash decreased more than three orders of magnitude (from 1 x 10{sup -6} to 1 x 10{sup -9} cm/s), mainly due to chemical reactions between the ash solids and acid mine drainage. Furthermore, the hydraulic gradient required for acid mine drainage to break through the coal fly ash is increased up to ten times (from 17 to 150) as compared with that for water. The results also show that the leachate from coal fly ash neutralizes the acidic pore fluid of mine tailings. The concentrations of trace elements in effluents from all kinetic column permeation tests indicated that coplacement of coal fly ash with mine tailings has the benefit of immobilizing trace elements, especially heavy metals. All regulated element concentrations from effluent during testing are well below the leachate quality criteria set by the local regulatory authority.

  5. Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles.

    PubMed

    Rodrigue, Nicolas; Philippe, Hervé; Lartillot, Nicolas

    2010-03-01

    Modeling the interplay between mutation and selection at the molecular level is key to evolutionary studies. To this end, codon-based evolutionary models have been proposed as pertinent means of studying long-range evolutionary patterns and are widely used. However, these approaches have not yet consolidated results from amino acid level phylogenetic studies showing that selection acting on proteins displays strong site-specific effects, which translate into heterogeneous amino acid propensities across the columns of alignments; related codon-level studies have instead focused on either modeling a single selective context for all codon columns, or a separate selective context for each codon column, with the former strategy deemed too simplistic and the latter deemed overparameterized. Here, we integrate recent developments in nonparametric statistical approaches to propose a probabilistic model that accounts for the heterogeneity of amino acid fitness profiles across the coding positions of a gene. We apply the model to a dozen real protein-coding gene alignments and find it to produce biologically plausible inferences, for instance, as pertaining to site-specific amino acid constraints, as well as distributions of scaled selection coefficients. In their account of mutational features as well as the heterogeneous regimes of selection at the amino acid level, the modeling approaches studied here can form a backdrop for several extensions, accounting for other selective features, for variable population size, or for subtleties of mutational features, all with parameterizations couched within population-genetic theory. PMID:20176949

  6. Site-Specific Characterization of d-Amino Acid Containing Peptide Epimers by Ion Mobility Spectrometry

    PubMed Central

    2013-01-01

    Traditionally, the d-amino acid containing peptide (DAACP) candidate can be discovered by observing the differences of biological activity and chromatographic retention time between the synthetic peptides and naturally occurring peptides. However, it is difficult to determine the exact position of d-amino acid in the DAACP candidates. Herein, we developed a novel site-specific strategy to rapidly and precisely localize d-amino acids in peptides by ion mobility spectrometry (IMS) analysis of mass spectrometry (MS)-generated epimeric fragment ions. Briefly, the d/l-peptide epimers were separated by online reversed-phase liquid chromatography and fragmented by collision-induced dissociation (CID), followed by IMS analysis. The epimeric fragment ions resulting from d/l-peptide epimers exhibit conformational differences, thus showing different mobilities in IMS. The arrival time shift between the epimeric fragment ions was used as criteria to localize the d-amino acid substitution. The utility of this strategy was demonstrated by analysis of peptide epimers with different molecular sizes, [d-Trp]-melanocyte-stimulating hormone, [d-Ala]-deltorphin, [d-Phe]-achatin-I, and their counterparts that contain all-l amino acids. Furthermore, the crustacean hyperglycemia hormones (CHHs, 8.5 kDa) were isolated from the American lobster Homarus americanus and identified by integration of MS-based bottom-up and top-down sequencing approaches. The IMS data acquired using our novel site-specific strategy localized the site of isomerization of l- to d-Phe at the third residue of the CHHs from the N-terminus. Collectively, this study demonstrates a new method for discovery of DAACPs using IMS technique with the ability to localize d-amino acid residues. PMID:24328107

  7. FT-IR characterization of the acidic and basic sites on a nanostructured aluminum nitride surface

    SciTech Connect

    Baraton, M.I.; Chen, X.; Gonsalves, K.E.

    1997-12-31

    A nanostructured aluminum nitride powder prepared by sol-gel type chemical synthesis is analyzed by Fourier transform infrared spectrometry. The surface acidic and basic sites are probed out by adsorption of several organic molecules. Resulting from the unavoidable presence of oxygen, the aluminum nitride surface is an oxinitride layer in fact, and its surface chemistry should present some analogies with alumina. Therefore, a thorough comparison between the acido-basicity of aluminum nitride and aluminum oxide is discussed. The remaining nitrogen atoms in the first atomic layer modify the acidity-basicity relative balance and reveals the specificity of the aluminum nitride surface.

  8. The control of acid mine drainage at the Summitville Mine Superfund Site

    SciTech Connect

    Ketellapper, V.L.; Williams, L.O.

    1996-11-01

    The Summitville Mine Superfund Site is located about 25 miles south of Del Norte, Colorado, in Rio Grande County. Occurring at an average elevation of 11,500 feet in the San Juan Mountain Range, the mine site is located two miles east of the Continental Divide. Mining at Summitville has occurred since 1870. The mine was most recently operated by Summitville Consolidated Mining Company, Inc. (SCMCI) as an open pit gold mine with extraction by means of a cyanide leaching process. In December of 1992, SCMCI declared bankruptcy and vacated the mine site. At that time, the US Environmental Protection Agency (EPA) took over operations of the water treatment facilities to prevent a catastrophic release of cyanide and metal-laden water from the mine site. Due to high operational costs of water treatment (approximately $50,000 per day), EPA established a goal to minimize active water treatment by reducing or eliminating acid mine drainage (AMD). All of the sources of AMD generation on the mine site were evaluated and prioritized. Of the twelve areas identified as sources of AMD, the Cropsy Waste Pile, the Summitville Dam Impoundment, the Beaver Mud Dump, the Reynolds and Chandler adits, and the Mine Pits were consider to be the most significant contributors to the generation of metal-laden acidic (low pH) water. A two part plan was developed to control AMD from the most significant sources. The first part was initiated immediately to control AMD being released from the Site. This part focused on improving the efficiency of the water treatment facilities and controlling the AMD discharges from the mine drainage adits. The second part of the plan was aimed at reducing the AMD generated in groundwater and surface water runoff from the mine wastes. A lined and capped repository located in the mine pits for acid generating mining waste and water treatment plant sludge was found to be the most feasible alternative.

  9. Site-specific incorporation of keto amino acids into functional G protein-coupled receptors using unnatural amino acid mutagenesis.

    PubMed

    Ye, Shixin; Köhrer, Caroline; Huber, Thomas; Kazmi, Manija; Sachdev, Pallavi; Yan, Elsa C Y; Bhagat, Aditi; RajBhandary, Uttam L; Sakmar, Thomas P

    2008-01-18

    G protein-coupled receptors (GPCRs) are ubiquitous heptahelical transmembrane proteins involved in a wide variety of signaling pathways. The work described here on application of unnatural amino acid mutagenesis to two GPCRs, the chemokine receptor CCR5 (a major co-receptor for the human immunodeficiency virus) and rhodopsin (the visual photoreceptor), adds a new dimension to studies of GPCRs. We incorporated the unnatural amino acids p-acetyl-L-phenylalanine (Acp) and p-benzoyl-L-phenylalanine (Bzp) into CCR5 at high efficiency in mammalian cells to produce functional receptors harboring reactive keto groups at three specific positions. We obtained functional mutant CCR5, at levels up to approximately 50% of wild type as judged by immunoblotting, cell surface expression, and ligand-dependent calcium flux. Rhodopsin containing Acp at three different sites was also purified in high yield (0.5-2 microg/10(7) cells) and reacted with fluorescein hydrazide in vitro to produce fluorescently labeled rhodopsin. The incorporation of reactive keto groups such as Acp or Bzp into GPCRs allows their reaction with different reagents to introduce a variety of spectroscopic and other probes. Bzp also provides the possibility of photo-cross-linking to identify precise sites of protein-protein interactions, including GPCR binding to G proteins and arrestins, and for understanding the molecular basis of ligand recognition by chemokine receptors. PMID:17993461

  10. Generation of Food-Grade Recombinant Lactic Acid Bacterium Strains by Site-Specific Recombination

    PubMed Central

    Martín, M. Cruz; Alonso, Juan C.; Suárez, Juan E.; Alvarez, Miguel A.

    2000-01-01

    The construction of a delivery and clearing system for the generation of food-grade recombinant lactic acid bacterium strains, based on the use of an integrase (Int) and a resolvo-invertase (β-recombinase) and their respective target sites (attP-attB and six, respectively) is reported. The delivery system contains a heterologous replication origin and antibiotic resistance markers surrounded by two directly oriented six sites, a multiple cloning site where passenger DNA could be inserted (e.g., the cI gene of bacteriophage A2), the int gene, and the attP site of phage A2. The clearing system provides a plasmid-borne gene encoding β-recombinase. The nonreplicative vector-borne delivery system was transformed into Lactobacillus casei ATCC 393 and, by site-specific recombination, integrated as a single copy in an orientation- and Int-dependent manner into the attB site present in the genome of the host strain. The transfer of the clearing system into this strain, with the subsequent expression of the β-recombinase, led to site-specific DNA resolution of the non-food-grade DNA. These methods were validated by the construction of a stable food-grade L. casei ATCC 393-derived strain completely immune to phage A2 infection during milk fermentation. PMID:10831443

  11. Estimates of cloud water deposition at Mountain Acid Deposition Program sites in the Appalachian Mountains.

    PubMed

    Baumgardner, Ralph E; Isil, Selma S; Lavery, Thomas F; Rogers, Christopher M; Mohnen, Volker A

    2003-03-01

    Cloud water deposition was estimated at three high-elevation sites in the Appalachian Mountains of the eastern United States (Whiteface Mountain, NY; Whitetop Mountain, VA; and Clingman's Dome, TN) from 1994 through 1999 as part of the Mountain Acid Deposition Program (MADPro). This paper provides a summary of cloud water chemistry, cloud liquid water content, cloud frequency, estimates of cloud water deposition of sulfur and nitrogen species, and estimates of total deposition of sulfur and nitrogen at these sites. Other cloud studies in the Appalachians and their comparison to MADPro are also summarized. Whiteface Mountain exhibited the lowest mean and median concentrations of sulfur and nitrogen ions in cloud water, while Clingman's Dome exhibited the highest mean and median concentrations. This geographic gradient is partly an effect of the different meteorological conditions experienced at northern versus southern sites in addition to the difference in pollution content of air masses reaching the sites. All sites measured seasonal cloud water deposition rates of SO4(2-) greater than 50 kg/ha and NO3(-) rates of greater than 25 kg/ha. These high-elevation sites experienced additional deposition loading of SO4(2-) and NO3(-) on the order of 6-20 times greater compared with lower elevation Clean Air Status and Trends Network (CASTNet) sites. Approximately 80-90% of this extra loading is from cloud deposition. PMID:12661689

  12. Disulfide bridge regulates ligand-binding site selectivity in liver bile acid-binding proteins.

    PubMed

    Cogliati, Clelia; Tomaselli, Simona; Assfalg, Michael; Pedò, Massimo; Ferranti, Pasquale; Zetta, Lucia; Molinari, Henriette; Ragona, Laura

    2009-10-01

    Bile acid-binding proteins (BABPs) are cytosolic lipid chaperones that play central roles in driving bile flow, as well as in the adaptation to various pathological conditions, contributing to the maintenance of bile acid homeostasis and functional distribution within the cell. Understanding the mode of binding of bile acids with their cytoplasmic transporters is a key issue in providing a model for the mechanism of their transfer from the cytoplasm to the nucleus, for delivery to nuclear receptors. A number of factors have been shown to modulate bile salt selectivity, stoichiometry, and affinity of binding to BABPs, e.g. chemistry of the ligand, protein plasticity and, possibly, the formation of disulfide bridges. Here, the effects of the presence of a naturally occurring disulfide bridge on liver BABP ligand-binding properties and backbone dynamics have been investigated by NMR. Interestingly, the disulfide bridge does not modify the protein-binding stoichiometry, but has a key role in modulating recognition at both sites, inducing site selectivity for glycocholic and glycochenodeoxycholic acid. Protein conformational changes following the introduction of a disulfide bridge are small and located around the inner binding site, whereas significant changes in backbone motions are observed for several residues distributed over the entire protein, both in the apo form and in the holo form. Site selectivity appears, therefore, to be dependent on protein mobility rather than being governed by steric factors. The detected properties further establish a parallelism with the behaviour of human ileal BABP, substantiating the proposal that BABPs have parallel functions in hepatocytes and enterocytes. PMID:19754879

  13. Site-specific analysis of protein hydration based on unnatural amino acid fluorescence.

    PubMed

    Amaro, Mariana; Brezovský, Jan; Kováčová, Silvia; Sýkora, Jan; Bednář, David; Němec, Václav; Lišková, Veronika; Kurumbang, Nagendra Prasad; Beerens, Koen; Chaloupková, Radka; Paruch, Kamil; Hof, Martin; Damborský, Jiří

    2015-04-22

    Hydration of proteins profoundly affects their functions. We describe a simple and general method for site-specific analysis of protein hydration based on the in vivo incorporation of fluorescent unnatural amino acids and their analysis by steady-state fluorescence spectroscopy. Using this method, we investigate the hydration of functionally important regions of dehalogenases. The experimental results are compared to findings from molecular dynamics simulations. PMID:25815779

  14. Ionization-site effects on the photofragmentation of chloro- and bromoacetic acid molecules

    NASA Astrophysics Data System (ADS)

    Levola, Helena; Itälä, Eero; Schlesier, Kim; Kooser, Kuno; Laine, Sanna; Laksman, Joakim; Ha, Dang Trinh; Rachlew, Elisabeth; Tarkanovskaja, Marta; Tanzer, Katrin; Kukk, Edwin

    2015-12-01

    Fragmentation of gas-phase chloro- and bromoacetic acid samples, particularly its dependency on the atomic site of the initial core ionization, was studied in photoelectron-photoion-photoion coincidence (PEPIPICO) measurements. The fragmentation was investigated after ionizing carbon 1 s and bromine 3 d or chlorine 2 p core orbitals. It was observed that the samples had many similar fragmentation pathways and that their relative weights depended strongly on the initial ionization site. Additional Auger PEPIPICO measurements revealed a clear dependence of fragment pair intensities on the kinetic energy of the emitted Auger electrons. The modeled and measured Auger electron spectra indicated that the average internal energy of the molecule was larger following the carbon 1 s core-hole decay than after the decay of the halogen core hole. This difference in the internal energies was found to be the source of the site-dependent photofragmentation behavior.

  15. Remaining Sites Verification Package for the 120-B-1, 105-B Battery Acid Sump, Waste Site Reclassification Form 2006-057

    SciTech Connect

    L. M. Dittmer

    2006-09-25

    The 120-B-1 waste site, located in the 100-BC-1 Operable Unit of the Hanford Site, consisted of a concrete battery acid sump that was used from 1944 to 1969 to neutralize the spent sulfuric acid from lead cell batteries of emergency power packs and the emergency lighting system. The battery acid sump was associated with the 105-B Reactor Building and was located adjacent to the building's northwest corner. The results of verification sampling demonstrated that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also showed that residual contaminant concentrations are protective of groundwater and the Columbia River.

  16. Microbial Communities in Biofilms of an Acid Mine Drainage Site Determined by Phospholipid Analysis

    NASA Astrophysics Data System (ADS)

    Das Gupta, S.; Fang, J.

    2008-12-01

    Phospholipids were extracted to determine the microbial biomass and community structure of biofims from an acid mine drainage (AMD) at the Green Valley coal mine site (GVS) in western Indiana. The distribution of specific biomarkers indicated the presence of a variety of microorganisms. Phototrophic microeukaryotes, which include Euglena mutabilis, algae, and cyanobacteria were the most dominant organisms, as indicated by the presence of polyunsaturated fatty acids. The presence of terminally methyl branched fatty acids suggests the presence of Gram-positive bacteria, and the mid-methyl branched fatty acids indicates the presence of sulfate-reducing bacteria. Fungi appear to also be an important part of the AMD microbial communities as suggested by the presence of 18:2 fatty acid. The acidophilic microeukaryotes Euglena dominated the biofilm microbial communities. These microorganisms appear to play a prominent role in the formation and preservation of stromatolites and in releasing oxygen to the atmosphere by oxygenic photosynthesis. Thus, the AMD environment comprises a host of microorganisms spreading out within the phylogenetic tree of life. Novel insights on the roles of microbial consortia in the formation and preservation of stromatolites and the production of oxygen through photosynthesis in AMD systems may have significance in the understanding of the interaction of Precambrian microbial communities in environments that produced microbially-mediated sedimentary structures and that caused oxygenation of Earth's atmosphere.

  17. Characterizing Surface Acidic Sites in Mesoporous-Silica-Supported Tungsten Oxide Catalysts Using Solid State NMR and Quantum Chemistry Calculations

    SciTech Connect

    Hu, Jian Z.; Kwak, Ja Hun; Wang, Yong; Hu, Mary Y.; Turcu, Romulus VF; Peden, Charles HF

    2011-10-18

    The acidic sites in dispersed tungsten oxide supported on SBA-15 mesoporous silica were investigated using a combination of pyridine titration, both fast-, and slow-MAS {sup 15}N NMR, static {sup 2}H NMR, and quantum chemistry calculations. It is found that the bridged acidic -OH groups in surface adsorbed tungsten dimers (i.e., W-OH-W) are the Broensted acid sites. The unusually strong acidity of these Broensted acid sites is confirmed by quantum chemistry calculations. In contrast, terminal W-OH sites are very stable and only weakly acidic as are terminal Si-OH sites. Furthermore, molecular interactions between pyridine molecules and the dimer Broensted and terminal W-OH sites for dispersed tungsten oxide species is strong. This results in restricted molecular motion for the interacting pyridine molecules even at room temperature, i.e., a reorientation mainly about the molecular 2-fold axis. This restricted reorientation makes it possible to estimate the relative ratio of the Broensted (tungsten dimer) to the weakly acidic terminal W-OH sites in the catalyst using the slow-MAS {sup 1}H-{sup 15}N CP PASS method.

  18. Computational study on the roles of amino acid residues in the active site formation mechanism of blue-light photoreceptors

    NASA Astrophysics Data System (ADS)

    Sato, Ryuma; Kitoh-Nishioka, Hirotaka; Ando, Koji; Yamato, Takahisa

    2015-07-01

    To examine the functional roles of the active site methionine (M-site) and glutamic acid (E-site) residues of blue-light photoreceptors, we performed in silico mutation at the M-site in a systematic manner and focused on the hydrogen bonding between the E-site and the substrate: the cyclobutane-pyrimidine dimer (CPD). Fragment molecular orbital calculations with electron correlations demonstrated that substitution of the M-site methionine with either alanine or glutamine always destabilizes the interaction energy between the E-site and the CPD by more than 12.0 kcal/mol, indicating that the methionine and glutamic acid residues cooperatively facilitate the enzymatic reaction in the active site.

  19. Mechanism of dehydroxylation of naturally occurring high-silica zeolites involving the formation of Lewis acid sites

    SciTech Connect

    Kazanskii, V.B.

    1987-11-01

    Using low-temperature adsorbed dihydrogen and carbon monoxide as molecular probes, the dehydroxylation of the hydrogen forms of the zeolites Y, and ZSM-5 has been studied. The high stability of the high-silica zeolites to dealumination and their difference from faujasites has been established as being due not only to the strength of their Broensted acid sites but also to the nature of their Lewis acid sites. The chemical properties of the Lewis acid sites and their possible role in catalytic reactions are discussed.

  20. Site characterization and containment/remediation of acid mine drainage at an abandoned mine waste dump

    SciTech Connect

    Djahanguiri, F.; Snodgrass, J.; Koerth, J.

    1996-12-31

    This paper focuses on the preliminary results of laboratory tests to evaluate a new suspension grout consisting of a mixture of a naturally occurring lignite coal based wax {open_quotes}montan wax{close_quotes}, sodium bentonite {open_quotes}pure gold grout{close_quotes}, and water. The test program assesses the suitability of the grout for creating subsurface containment barriers in coal waste dump sites for acid mine seepage control to surface and ground waters. The laboratory activities evaluated the reduction in permeability that could be achieved in a coal waste dump site under optimum conditions and the compatibility of the grout with representative waste from the test site. Information on geological, geochemical and geophysical about the test site is presented. Laboratory formulation of the grout is complete and simulation of field condition is in progress. Pregrout geophysical surveys for determination of hydrogeologic conditions at the site are also completed. Based on geophysical surveys, a grout curtain is proposed which will consist of two rows of grout placement holes in an array across the seepage area toward Belt Creek in Montana, Post-grout geophysical survey will be carried out immediately after grouting work. Performance of the grout curtain will be monitored by collection of water samples from monitoring wells in the Belt Creek and seepage area.

  1. A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs.

    PubMed

    Miao, Zhichao; Westhof, Eric

    2015-12-01

    Computational prediction of nucleic acid binding sites in proteins are necessary to disentangle functional mechanisms in most biological processes and to explore the binding mechanisms. Several strategies have been proposed, but the state-of-the-art approaches display a great diversity in i) the definition of nucleic acid binding sites; ii) the training and test datasets; iii) the algorithmic methods for the prediction strategies; iv) the performance measures and v) the distribution and availability of the prediction programs. Here we report a large-scale assessment of 19 web servers and 3 stand-alone programs on 41 datasets including more than 5000 proteins derived from 3D structures of protein-nucleic acid complexes. Well-defined binary assessment criteria (specificity, sensitivity, precision, accuracy…) are applied. We found that i) the tools have been greatly improved over the years; ii) some of the approaches suffer from theoretical defects and there is still room for sorting out the essential mechanisms of binding; iii) RNA binding and DNA binding appear to follow similar driving forces and iv) dataset bias may exist in some methods. PMID:26681179

  2. A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs

    PubMed Central

    Miao, Zhichao; Westhof, Eric

    2015-01-01

    Computational prediction of nucleic acid binding sites in proteins are necessary to disentangle functional mechanisms in most biological processes and to explore the binding mechanisms. Several strategies have been proposed, but the state-of-the-art approaches display a great diversity in i) the definition of nucleic acid binding sites; ii) the training and test datasets; iii) the algorithmic methods for the prediction strategies; iv) the performance measures and v) the distribution and availability of the prediction programs. Here we report a large-scale assessment of 19 web servers and 3 stand-alone programs on 41 datasets including more than 5000 proteins derived from 3D structures of protein-nucleic acid complexes. Well-defined binary assessment criteria (specificity, sensitivity, precision, accuracy…) are applied. We found that i) the tools have been greatly improved over the years; ii) some of the approaches suffer from theoretical defects and there is still room for sorting out the essential mechanisms of binding; iii) RNA binding and DNA binding appear to follow similar driving forces and iv) dataset bias may exist in some methods. PMID:26681179

  3. Density functional theoretical and NMR study of Hammett bases in acidic zeolites

    SciTech Connect

    Nicholas, J.B.; Haw, J.F.; Beck, L.W.; Krawietz, T.R.; Ferguson, D.B.

    1995-12-13

    We demonstrate here that theoretical calculations using density functional theory (DFT) accurately model proton transfer reactions between Bronsted sites in zeolites (the archetypal solid acids) and Hammett bases. The validity of the theoretical results is verified by NMR measurements of key nuclei of the same Hammett bases in zeolites HZSM-5 (MFI) and HY (FAU), the first such experiments. The accuracy of the predictions of the DFT calculations for the HZSM-5 zeolite model suggests that they may be extended to other zeolite cluster models, including those which have not yet been realized experimentally and hence are not available for NMR study. We optimized the adsorbate zeolite complexes with this angle constrained to larger values; to our surprise, the SVWN/DNP calculations resulted in the proton being transferred from p-fluoronitrobenzene back to the zeolite, even if the Si-O-Al angle was held fixed at 180{degree}. Further tests at higher levels of theory are in progress. This investigation used a choice of indicators that necessarily resulted in wide limits on zeolite acid strength, but the theoretical and experimental methodologies have been established. 21 refs., 3 figs.

  4. Modelling metal centres, acid sites and reaction mechanisms in microporous catalysts.

    PubMed

    O'Malley, Alexander J; Logsdail, A J; Sokol, A A; Catlow, C R A

    2016-07-01

    We discuss the role of QM/MM (embedded cluster) computational techniques in catalytic science, in particular their application to microporous catalysis. We describe the methodologies employed and illustrate their utility by briefly summarising work on metal centres in zeolites. We then report a detailed investigation into the behaviour of methanol at acidic sites in zeolites H-ZSM-5 and H-Y in the context of the methanol-to-hydrocarbons/olefins process. Studying key initial steps of the reaction (the adsorption and subsequent methoxylation), we probe the effect of framework topology and Brønsted acid site location on the energetics of these initial processes. We find that although methoxylation is endothermic with respect to the adsorbed system (by 17-56 kJ mol(-1) depending on the location), there are intriguing correlations between the adsorption/reaction energies and the geometries of the adsorbed species, of particular significance being the coordination of methyl hydrogens. These observations emphasise the importance of adsorbate coordination with the framework in zeolite catalysed conversions, and how this may vary with framework topology and site location, particularly suited to investigation by QM/MM techniques. PMID:27136967

  5. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history.

    PubMed

    Risso, Valeria A; Manssour-Triedo, Fadia; Delgado-Delgado, Asunción; Arco, Rocio; Barroso-delJesus, Alicia; Ingles-Prieto, Alvaro; Godoy-Ruiz, Raquel; Gavira, Jose A; Gaucher, Eric A; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

    2015-02-01

    Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations. PMID:25392342

  6. Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History

    PubMed Central

    Risso, Valeria A.; Manssour-Triedo, Fadia; Delgado-Delgado, Asunción; Arco, Rocio; Barroso-delJesus, Alicia; Ingles-Prieto, Alvaro; Godoy-Ruiz, Raquel; Gavira, Jose A.; Gaucher, Eric A.; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M.

    2015-01-01

    Local protein interactions (“molecular context” effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations. PMID:25392342

  7. REMOVING SLUDGE HEELS FROM SAVANNAH RIVER SITE WASTE TANKS BY OXALIC ACID DISSOLUTION

    SciTech Connect

    Poirier, M; David Herman, D; Fernando Fondeur, F; John Pareizs, J; Michael Hay, M; Bruce Wiersma, B; Kim Crapse, K; Thomas Peters, T; Samuel Fink, S; Donald Thaxton, D

    2009-03-01

    The Savannah River Site (SRS) will remove sludge as part of waste tank closure operations. Typically the bulk sludge is removed by mixing it with supernate to produce a slurry, and transporting the slurry to a downstream tank for processing. Experience shows that a residual heel may remain in the tank that cannot be removed by this conventional technique. In the past, SRS used oxalic acid solutions to disperse or dissolve the sludge heel to complete the waste removal. To better understand the actual conditions of oxalic acid cleaning of waste from carbon steel tanks, the authors developed and conducted an experimental program to determine its effectiveness in dissolving sludge, the hydrogen generation rate, the generation rate of other gases, the carbon steel corrosion rate, the impact of mixing on chemical cleaning, the impact of temperature, and the types of precipitates formed during the neutralization process. The test samples included actual SRS sludge and simulated SRS sludge. The authors performed the simulated waste tests at 25, 50, and 75 C by adding 8 wt % oxalic acid to the sludge over seven days. They conducted the actual waste tests at 50 and 75 C by adding 8 wt % oxalic acid to the sludge as a single batch. Following the testing, SRS conducted chemical cleaning with oxalic acid in two waste tanks. In Tank 5F, the oxalic acid (8 wt %) addition occurred over seven days, followed by inhibited water to ensure the tank contained enough liquid to operate the mixer pumps. The tank temperature during oxalic acid addition and dissolution was approximately 45 C. The authors analyzed samples from the chemical cleaning process and compared it with test data. The conclusions from the work are: (1) Oxalic acid addition proved effective in dissolving sludge heels in the simulant demonstration, the actual waste demonstration, and in SRS Tank 5F. (2) The oxalic acid dissolved {approx} 100% of the uranium, {approx} 100% of the iron, and {approx} 40% of the manganese

  8. Studies on the acidity of mordenite and ZSM-5. 1. Determination of Broensted acid site concentrations in mordenite and ZSM-5 by conductometric titration

    SciTech Connect

    Crocker, M.; Herold, R.H.M.; Sonnemans, M.H.W.; Emeis, C.A.; Wilson, A.E.; Moolen, J.N. van der )

    1993-01-14

    The Broensted acidity of H-mordenite and H-ZSM-5 samples of varying proton concentration has been studied using aqueous conductometric titration, IR spectroscopy, and aqueous potentiometric titration. Good agreement is observed between Broensted acid site concentrations determined by conductometric titration and IR measurements, while indirect potentiometric titration affords acid site concentrations consistently lower than those measured using the conductometric technique. This finding is rationalized on the basis that, in a conductometric titration, all the accessible Broensted acid sites are direct;y titrated, whereas in the potentiometric procedure utilized, only those protons which can be ion-exchanged out of the zeolite are titrated. After allowing for the presence of extraframework aluminum in the zeolites (determined by [sup 27]Al NMR), the measured acidity for H-mordenite is found to increase linearly with increasing Al content within the range 0-1.5 mmol Al/g but appears to reach a limiting value at higher Al concentrations. For H-ZSM-5, the experimentally determined number of Broensted acid sites is also found to be linearly dependent on the Al molar fraction within the range measured (0-1.20 mmol Al/g). For both series of zeolite samples, the measured acidity is generally found to be less than the theoretical maximum calculated on the basis of an H[sup +]/Al ratio of 1. 43 refs., 10 figs., 4 tabs.

  9. In situ detection of salicylic acid binding sites in plant tissues.

    PubMed

    Liu, Jing-Wen; Deng, Da-Yi; Yu, Ying; Liu, Fang-Fei; Lin, Bi-Xia; Cao, Yu-Juan; Hu, Xiao-Gang; Wu, Jian-Zhong

    2015-02-01

    The determination of hormone-binding sites in plants is essential in understanding the mechanisms behind hormone function. Salicylic acid (SA) is an important plant hormone that regulates responses to biotic and abiotic stresses. In order to label SA-binding sites in plant tissues, a quantum dots (QDs) probe functionalized with a SA moiety was successfully synthesized by coupling CdSe QDs capped with 3-mercaptopropionic acid (MPA) to 4-amino-2-hydroxybenzoic acid (PAS), using 1-ethyl-3-(3-dimethyllaminopropyl) carbodiimide (EDC) as the coupling agent. The probe was then characterized by dynamic light scattering and transmission electron microscopy, as well as UV/vis and fluorescence spectrophotometry. The results confirmed the successful conjugation of PAS to CdSe QDs and revealed that the conjugates maintained the properties of the original QDs, with small core diameters and adequate dispersal in solution. The PAS-CdSe QDs were used to detect SA-binding sites in mung bean and Arabidopsis thaliana seedlings in vitro and in vivo. The PAS-CdSe QDs were effectively transported into plant tissues and specifically bound to SA receptors in vivo. In addition, the effects of the PAS-CdSe QDs on cytosolic Ca(2+) levels in the tips of A. thaliana seedlings were investigated. Both SA and PAS-CdSe QDs had similar effects on the trend in cytosolic-free Ca(2+) concentrations, suggesting that the PAS-CdSe QDs maintained the bioactivity of SA. To summarize, PAS-CdSe QDs have high potential as a fluorescent probe for the in vitro/in vivo labeling and imaging of SA receptors in plants. PMID:24833131

  10. Enhanced concentrations of citric acid in spring aerosols collected at the Gosan background site in East Asia

    NASA Astrophysics Data System (ADS)

    Jung, Jinsang; Kawamura, Kimitaka

    2011-09-01

    In order to investigate water-soluble dicarboxylic acids and related compounds in the aerosol samples under the Asian continent outflow, total suspended particle (TSP) samples ( n = 32) were collected at the Gosan site in Jeju Island over 2-5 days integration during 23 March-1 June 2007 and 16-24 April 2008. The samples were analyzed for water-soluble dicarboxylic acids, ketocarboxylic acids, and α-dicarbonyls using a capillary gas chromatography technique. We found elevated concentrations of atmospheric citric acid (range: 20-320 ng m -3) in the TSP samples during mid- to late April of 2007 and 2008. To specify the sources of citric acid, dicarboxylic acids and related compounds were measured in the pollen sample collected at the Gosan site (Pollen_Gosan), authentic pollen samples from Japanese cedar ( Cryptomeria) (Pollen_cedar) and Japanese cypress ( Chamaecyparis obtusa) (Pollen_cypress), and tangerine fruit produced from Jeju Island. Citric acid (2790 ng in unit mg of pollen mass) was found as most abundant species in the Pollen_Gosan, followed by oxalic acid (2390 ng mg -1). Although citric acid was not detected in the Pollen_cedar and Pollen_cypress as major species, it was found as a dominant species in the tangerine juice while malic acid was detected as major species in the tangerine peel, followed by oxalic and citric acids. Since Japanese cedar trees are planted around tangerine farms to prevent strong winds from the Pacific Ocean, citric acid that may be directly emitted from tangerine is likely adsorbed on pollens emitted from Japanese cedar and then transported to the Gosan site. Much lower malic/citric acid ratios obtained under cloudy condition than clear condition suggest that malic acid may rapidly decompose to lower molecular weight compounds such as oxalic and malonic acids (

  11. The species- and site-specific acid-base properties of penicillamine and its homodisulfide

    NASA Astrophysics Data System (ADS)

    Mirzahosseini, Arash; Szilvay, András; Noszál, Béla

    2014-08-01

    Penicillamine, penicillamine disulfide and 4 related compounds were studied by 1H NMR-pH titrations and case-tailored evaluation methods. The resulting acid-base properties are quantified in terms of 14 macroscopic and 28 microscopic protonation constants and the concomitant 7 interactivity parameters. The species- and site-specific basicities are interpreted by means of inductive and shielding effects through various intra- and intermolecular comparisons. The thiolate basicities determined this way are key parameters and exclusive means for the prediction of thiolate oxidizabilities and chelate forming properties in order to understand and influence chelation therapy and oxidative stress at the molecular level.

  12. Locations of the three primary binding sites for long-chain fatty acids on bovine serum albumin

    SciTech Connect

    Hamilton, J.A.; Era, S.; Bhamidipati, S.P. ); Reed, R.G. )

    1991-03-15

    Binding of {sup 13}C-enriched oleic acid to bovine serum albumin and to three large proteolytic fragments of albumin - two complementary fragments corresponding to the two halved of albumin and one fragment corresponding to the carboxyl-terminal domain - yielded unique patterns of NMR resonances (chemical shifts and relative intensities) that were used to identify the locations of binding of the first 5 mol of oleic acid to the multidomain albumin molecule. The first 3 mol of oleic acid added to intact albumin generated three distinct NMR resonances as a result of simultaneous binding of oleic acid to three heterogeneous sites (primary sites). This distribution suggests albumin to be a less symmetrical binding molecule than theoretical models predict. This work also demonstrates the power of NMR for the study of microenvironments of individual fatty acid binding sites in specific domain.

  13. Chronic caffeine or theophylline exposure reduces gamma-aminobutyric acid/benzodiazepine receptor site interactions.

    PubMed

    Roca, D J; Schiller, G D; Farb, D H

    1988-05-01

    Methylxanthines, such as caffeine and theophylline, are adenosine receptor antagonists that exert dramatic effects upon the behavior of vertebrate animals by increasing attentiveness, anxiety, and convulsive activity. Benzodiazepines, such as flunitrazepam, generally exert behavioral effects that are opposite to those of methylxanthines. We report the finding that chronic exposure of embryonic brain neurons to caffeine or theophylline reduces the ability of gamma-aminobutyric acid (GABA) to potentiate the binding of [3H]flunitrazepam to the GABA/benzodiazepine receptor. This theophylline-induced "uncoupling" of GABA- and benzodiazepine-binding site allosteric interactions is blocked by chloroadenosine, an adenosine receptor agonist, indicating that the chronic effects of theophylline are mediated by a site that resembles an adenosine receptor. We speculate that adverse central nervous system effects of long-term exposure to methylxanthines such as in caffeine-containing beverages or theophylline-containing medications may be exerted by a cell-mediated modification of the GABAA receptor. PMID:2835648

  14. Site-Specific Mapping of Sialic Acid Linkage Isomers by Ion Mobility Spectrometry.

    PubMed

    Guttman, Miklos; Lee, Kelly K

    2016-05-17

    Detailed structural elucidation of protein glycosylation is a tedious process often involving several techniques. Glycomics and glycoproteomics approaches with mass spectrometry offer a rapid platform for glycan profiling but are limited by the inability to resolve isobaric species such as linkage and positional isomers. Recently, ion mobility spectrometry (IMS) has been shown to effectively resolve isobaric oligosaccharides, but the utility of IMS to obtain glycan structural information on a site-specific level with proteomic analyses has yet to be investigated. Here, we report that the addition of IMS to conventional glycoproteomics platforms adds additional information regarding glycan structure and is particularly useful for differentiation of sialic acid linkage isomers on both N- and O-linked glycopeptides. With further development IMS may hold the potential for rapid and complete structural elucidation of glycan chains at a site-specific level. PMID:27089023

  15. SAVANNAH RIVER SITE TANK CLEANING: CORROSION RATE FOR ONE VERSUS EIGHT PERCENT OXALIC ACID SOLUTION

    SciTech Connect

    Ketusky, E.; Subramanian, K.

    2011-01-20

    Until recently, the use of oxalic acid for chemically cleaning the Savannah River Site (SRS) radioactive waste tanks focused on using concentrated 4 and 8-wt% solutions. Recent testing and research on applicable dissolution mechanisms have concluded that under appropriate conditions, dilute solutions of oxalic acid (i.e., 1-wt%) may be more effective. Based on the need to maximize cleaning effectiveness, coupled with the need to minimize downstream impacts, SRS is now developing plans for using a 1-wt% oxalic acid solution. A technology gap associated with using a 1-wt% oxalic acid solution was a dearth of suitable corrosion data. Assuming oxalic acid's passivation of carbon steel was proportional to the free oxalate concentration, the general corrosion rate (CR) from a 1-wt% solution may not be bound by those from 8-wt%. Therefore, after developing the test strategy and plan, the corrosion testing was performed. Starting with the envisioned process specific baseline solvent, a 1-wt% oxalic acid solution, with sludge (limited to Purex type sludge-simulant for this initial effort) at 75 C and agitated, the corrosion rate (CR) was determined from the measured weight loss of the exposed coupon. Environmental variations tested were: (a) Inclusion of sludge in the test vessel or assuming a pure oxalic acid solution; (b) acid solution temperature maintained at 75 or 45 C; and (c) agitation of the acid solution or stagnant. Application of select electrochemical testing (EC) explored the impact of each variation on the passivation mechanisms and confirmed the CR. The 1-wt% results were then compared to those from the 8-wt%. The immersion coupons showed that the maximum time averaged CR for a 1-wt% solution with sludge was less than 25-mils/yr for all conditions. For an agitated 8-wt% solution with sludge, the maximum time averaged CR was about 30-mils/yr at 50 C, and 86-mils/yr at 75 C. Both the 1-wt% and the 8-wt% testing demonstrated that if the sludge was removed from

  16. Heavy metal binding to heparin disaccharides. I. Iduronic acid is the main binding site.

    PubMed

    Whitfield, D M; Choay, J; Sarkar, B

    1992-06-01

    As model compounds for Ni(II)-binding heparin-like compounds isolated from human kidneys (Templeton, D.M. & Sarkar, B. (1985) Biochem. J. 230 35-42.), we investigated two disaccharides--4-O-(2-O-sulfo-alpha-L-idopyranosyluronic acid)-2,5-anhydro- D-mannitol, disodium salt (1a), and 4-O-(2-O-sulfo-alpha-L-idopyranosyluronic acid)-6-O- sulfo-2,5-anhydro-D-mannitol, trisodium salt (1b)--that were isolated from heparin after nitrous acid hydrolysis and reduction. The monosulfate (1a) was active whereas the disulfate (1b) was inactive in a high-performance liquid chromatography (HPLC) binding assay with the tracer ions 63Ni(II) 54Mn(II), 65Zn(II), and 109Cd(II). This result is in accord with the isolation of two 67Cu(II) and 63Ni(II) binding fractions from a complete pool of nitrous-acid-derived heparin disaccharides using sulfate gradients and a MonoQ anion exchange column on an FPLC system. One was identified as compound (1a) and the other as a tetrasulfated trisaccharide by high resolution FAB-MS, NMR and HPLC-PAD. Similarly, two synthetic disaccharides-methyl, 2-O-sulfo-4-O-(alpha-L-idopyranosyluronic acid)-2-deoxy-2-sulfamide-alpha-D-glucosamine, trisodium salt [IdopA2S(alpha 1,4)GlcNS alpha Me, 2a], and 2-O-sulfo-4-O-(alpha-L-idopyranosyluronic acid)-2-deoxy-2-sulfamide-6-O-sulfo- alpha-D-glucosamine, tetrasodium salt [IdopA2S (alpha 1,4)GlcNS6S alpha Me, 2b]--were shown to bind tracer amounts of 63Ni and 67Cu using chromatographic assays. Subsequently, 1H NMR titrations of 1a, 1b, 2a, and 2b with Zn (OAc)2 were analyzed to yield 1:1 Zn(II)-binding constants of 472 +/- 59, 698 +/- 120, 8,758 +/- 2,237 and 20,100 +/- 5,598 M-1, respectively. The values for 2a and 2b suggest chelation. It is suggested that the idopyranosiduronic acid residue is the major metal binding site. NMR evidence for this hypothesis comes from marked 1H and 13C chemical shift changes to the iduronic acid resonances after addition of diamagnetic Zn(II) ions. PMID:1643264

  17. SuccinSite: a computational tool for the prediction of protein succinylation sites by exploiting the amino acid patterns and properties.

    PubMed

    Hasan, Md Mehedi; Yang, Shiping; Zhou, Yuan; Mollah, Md Nurul Haque

    2016-03-01

    Lysine succinylation is an emerging protein post-translational modification, which plays an important role in regulating the cellular processes in both eukaryotic and prokaryotic cells. However, the succinylation modification site is particularly difficult to detect because the experimental technologies used are often time-consuming and costly. Thus, an accurate computational method for predicting succinylation sites may help researchers towards designing their experiments and to understand the molecular mechanism of succinylation. In this study, a novel computational tool termed SuccinSite has been developed to predict protein succinylation sites by incorporating three sequence encodings, i.e., k-spaced amino acid pairs, binary and amino acid index properties. Then, the random forest classifier was trained with these encodings to build the predictor. The SuccinSite predictor achieves an AUC score of 0.802 in the 5-fold cross-validation set and performs significantly better than existing predictors on a comprehensive independent test set. Furthermore, informative features and predominant rules (i.e. feature combinations) were extracted from the trained random forest model for an improved interpretation of the predictor. Finally, we also compiled a database covering 4411 experimentally verified succinylation proteins with 12 456 lysine succinylation sites. Taken together, these results suggest that SuccinSite would be a helpful computational resource for succinylation sites prediction. The web-server, datasets, source code and database are freely available at http://systbio.cau.edu.cn/SuccinSite/. PMID:26739209

  18. The effect of the distance between acidic site and basic site immobilized on mesoporous solid on the activity in catalyzing aldol condensation

    NASA Astrophysics Data System (ADS)

    Yu, Xiaofang; Yu, Xiaobo; Wu, Shujie; Liu, Bo; Liu, Heng; Guan, Jingqi; Kan, Qiubin

    2011-02-01

    Acid-base bifunctional heterogeneous catalysts containing carboxylic and amine groups, which were immobilized at defined distance from one another on the mesoporous solid were synthesized by immobilizing lysine onto carboxyl-SBA-15. The obtained materials were characterized by X-ray diffraction (XRD), N 2 adsorption, Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), scanning electron micrographs (SEM), transmission electron micrographs (TEM), elemental analysis, and back titration. Proximal-C-A-SBA-15 with a proximal acid-base distance was more active than maximum-C-A-SBA-15 with a maximum acid-base distance in aldol condensation reaction between acetone and various aldehydes. It appears that the distance between acidic site and basic site immobilized on mesoporous solid should be an essential factor for catalysis optimization.

  19. Hatching success in salamanders and chorus frogs at two sites in Colorado, USA: Effects of acidic deposition and climate

    USGS Publications Warehouse

    Muths, E.; Campbell, D.H.; Corn, P.S.

    2003-01-01

    The snowpack in the vicinity of the Mount Zirkel Wilderness Area is among the most acidic in the western United States. We analyzed water chemistry and examined hatching success in tiger salamanders and chorus frogs at ponds there and at nearby Rabbit Ears Pass (Dumont) to determine whether acid deposition affects amphibians or their breeding habitats at these potentially sensitive locations. We found a wide range of acid neutralizing capacity among ponds within sites; the minimum pH recorded during the experiment was 5.4 at one of 12 ponds with all others at pH ??? 5.7. At Dumont, hatching success for chorus frogs was greater in ponds with low acid neutralizing capacity; however, lowest pHs were >5.8. At current levels of acid deposition, weather and pond characteristics are likely more important than acidity in influencing hatching success in amphibian larvae at these sites.

  20. Evaluation Of Sludge Heel Dissolution Efficiency With Oxalic Acid Cleaning At Savannah River Site

    SciTech Connect

    Sudduth, Christie; Vitali, Jason; Keefer, Mark

    2014-01-08

    The chemical cleaning process baseline strategy at the Savannah River Site was revised to improve efficiency during future execution of the process based on lessons learned during previous bulk oxalic acid cleaning activities and to account for operational constraints imposed by safety basis requirements. These improvements were also intended to transcend the difficulties that arise from waste removal in higher rheological yield stress sludge tanks. Tank 12 implemented this improved strategy and the bulk oxalic acid cleaning efforts concluded in July 2013. The Tank 12 radiological removal results were similar to previous bulk oxalic acid cleaning campaigns despite the fact that Tank 12 contained higher rheological yield stress sludge that would make removal more difficult than the sludge treated in previous cleaning campaigns. No appreciable oxalate precipitation occurred during the cleaning process in Tank 12 compared to previous campaigns, which aided in the net volume reduction of 75-80%. Overall, the controls established for Tank 12 provide a template for an improved cleaning process.

  1. Composite active site of chondroitin lyase ABC accepting both epimers of uronic acid

    SciTech Connect

    Shaya, D.; Hahn, Bum-Soo; Bjerkan, Tonje Marita; Kim, Wan Seok; Park, Nam Young; Sim, Joon-Soo; Kim, Yeong-Shik; Cygler, M.

    2008-03-19

    Enzymes have evolved as catalysts with high degrees of stereospecificity. When both enantiomers are biologically important, enzymes with two different folds usually catalyze reactions with the individual enantiomers. In rare cases a single enzyme can process both enantiomers efficiently, but no molecular basis for such catalysis has been established. The family of bacterial chondroitin lyases ABC comprises such enzymes. They can degrade both chondroitin sulfate (CS) and dermatan sulfate (DS) glycosaminoglycans at the nonreducing end of either glucuronic acid (CS) or its epimer iduronic acid (DS) by a {beta}-elimination mechanism, which commences with the removal of the C-5 proton from the uronic acid. Two other structural folds evolved to perform these reactions in an epimer-specific fashion: ({alpha}/{alpha}){sub 5} for CS (chondroitin lyases AC) and {beta}-helix for DS (chondroitin lyases B); their catalytic mechanisms have been established at the molecular level. The structure of chondroitinase ABC from Proteus vulgaris showed surprising similarity to chondroitinase AC, including the presence of a Tyr-His-Glu-Arg catalytic tetrad, which provided a possible mechanism for CS degradation but not for DS degradation. We determined the structure of a distantly related Bacteroides thetaiotaomicron chondroitinase ABC to identify additional structurally conserved residues potentially involved in catalysis. We found a conserved cluster located {approx}12 {angstrom} from the catalytic tetrad. We demonstrate that a histidine in this cluster is essential for catalysis of DS but not CS. The enzyme utilizes a single substrate-binding site while having two partially overlapping active sites catalyzing the respective reactions. The spatial separation of the two sets of residues suggests a substrate-induced conformational change that brings all catalytically essential residues close together.

  2. SITE EVALUATION OF INNOVATIVE SEMI-PASSIVE ACID MINE DRAINAGE TREATMENT TECHNOLOGIES AT THE SUMMITVILLE SUPERFUND SITE, COLORADO

    EPA Science Inventory

    The EPA SITE Program is conducting a detailed sampling and evaluation of two innovative passive mine drainage treatment technologies at the Summitville Superfund Mining site in Southern Colorado. The technologies evaluated include the Aquafix automatic hydraulic lime dispensing s...

  3. Characteristics of fluoride in pore-water at accidental hydrofluoric acid spillage site, Gumi, Korea

    NASA Astrophysics Data System (ADS)

    Kwon, E. H.; Lee, H. A.; Lee, J.; Kim, D.; Lee, S.; Yoon, H. O.

    2015-12-01

    A leakage accident of hydrofluoric acid (HF) occurred in Gumi, South Korea at Sep. 2012. The study site is located in the borderline between a large-scale industrial complex and a rural area. The HF plume was made immediately, and moved toward the rural area through air. After the accident, 212 ha of farm land were influenced and most of crops were withered. To recover the soil, CaO was applied after six months. Although several studies have done to estimate the extension and movement of HF plume in the air and to assess the impact on human health or plant after the incident, the long-term fate of fluoride (F) in the affected soils is not identified clearly. Thus, this study aimed to understand the behavior of F in the soil after HF releasing from accident site through chemical analysis and geochemical modeling. Within the radius of 1 km of accident site, 16 pore-water and soil samples were collected. The semi-quantitative soil composition (i.e., Al, Ca, Fe, K, Mg, Mn, Na, P, Si, Ti), total F, total P, OM contents in soil, and soil pH have already been measured, and pore-water compositions are also identified. From these experimental and modeling data, we could be evaluate if impact of accident exists until now, and also could be select and identify existing form of fluoride in soil and pore-water.

  4. Generation of Broensted and Lewis acid sites on the surface of silica by addition of dopant cations

    SciTech Connect

    Connell, G.; Dumesic, J.A.

    1987-06-01

    Pyridine adsorption was used to study the acidic properties of silica doped with the following cations: Sc/sup 3 +/, Mg/sup 2 +/, Fe/sup 2 +/, Fe/sup 3 +/, Zn/sup 2 +/, Al/sup 3 +/, and Ga/sup 3 +/. All samples were exposed to pyridine at 423 K and subsequently evacuated at successively higher temperatures to 723 K. Infrared spectra of the adsorbed pyridine indicated that all of these cations generated Lewis acid sites. This can be explained by the presence of coordinatively unsaturated dopant cations on the surface of silica, in accord with a model based on Pauling's electrostatic bond strength rules. The infrared frequency of the 19b band of pyridine adsorbed on these Lewis acid sites was found to increase with increasing electronegativity of the dopant cation. It is suggested that both of these quantities are related to the strength of the Lewis acid sites. Broensted acid sites were also observed by infrared spectroscopy for Sc/sup 3 +/, Al/sup 3 +/, and Ga/sup 3 +/ on silica. These dopant cations are believed to be bonded tetrahedrally on the surface of silica, generating bridging hydroxyl groups between the dopant cation and Si/sup 4 +/. As for zeolite catalysts, the proton associated with these groups and required for charge neutrality is the Broensted acid site. Finally, Broensted acid sites can also be generated on silica by highly electronegative anions, such as HPO/sub 4//sup 2 -/, which generate Broensted acidity in a different manner. 55 references.

  5. Fabrication of hydrophobic polymer foams with double acid sites on surface of macropore for conversion of carbohydrate.

    PubMed

    Pan, Jianming; Mao, Yanli; Gao, Heping; Xiong, Qingang; Qiu, Fengxian; Zhang, Tao; Niu, Xiangheng

    2016-06-01

    Herein we reported a simple and novel synthetic strategy for the fabrication of two kinds of hydrophobic polymer foam catalysts (i.e. Cr(3+)-HPFs-1-H(+) and HPFs-1-H(+)) with hierarchical porous structure, inhomogeneous acidic composition and Lewis-Brønsted double acid sites distributed on the surface, which was used to one-pot conversion of carbohydrate (such as cellulose, glucose and fructose) to a key chemical platform (i.e. 5-hydroxymethylfurfural, HMF). The water-in-oil (W/O) high internal phase emulsions (HIPEs), stabilized by both Span 80 and acidic prepolymers as analogous particles offered the acidic actives, were used as the template for simultaneous polymerization of oil phase in the presence of divinylbenzene (DVB) and styrene (St). After subsequent ion-exchange process, Lewis and Brønsted acid sites derived from exchanged Cr(3+) and H(+) ion were both fixed on the surface of cell of the catalysts. The HPFs-1-H(+) and Cr(3+)-HPFs-1-H(+) had similar hierarchical porous, hydrophobic surface and acid sites (HPFs-1-H(+) with macropores ranging from 0.1 μm to 20 μm, uniform mesopores in 14.4 nm, water contact angle of 122° and 0.614 mmolg(-1) of Brønsted acid sites, as well as Cr(3+)-HPFs-1-H(+) with macropores ranging from 0.1 μm to 20 μm, uniform mesopores in 13.3 nm, water contact angle of 136° and 0.638 mmolg(-1) of Lewis-Brønsted acid sites). It was confirmed that Lewis acid sites of catalyst had a slight influence on the HMF yield of fructose came from the function of Brønsted acid sites, and Lewis acid sites were in favor of improving the HMF yield from cellulose and glucose. This work opens up a simple and novel route to synthesize multifunctional polymeric catalysts for efficient one-pot conversion of carbohydrate to HMF. PMID:27083362

  6. Dansyl labeling to modulate the relative affinity of bile acids for the binding sites of human serum albumin.

    PubMed

    Rohacova, Jana; Sastre, German; Marin, M Luisa; Miranda, Miguel A

    2011-09-01

    Binding of natural bile acids to human serum albumin (HSA) is an important step in enterohepatic circulation and provides a measure of liver function. In this article, we report on the use of four dansyl (Dns) derivatives of cholic acid (ChA) to demonstrate a regiodifferentiation in their relative affinity for the two binding sites of HSA. Using both steady-state and time-resolved fluorescence, formation of Dns-ChA@HSA complexes was confirmed; the corresponding binding constants were determined, and their distribution between bulk solution and HSA microenvironment was estimated. By means of energy transfer from Trp to the Dns moiety, donor-acceptor distances were estimated (21-25 Å) and found to be compatible with both site 1 and site 2 occupancies. Nevertheless, titration using warfarin and ibuprofen as specific displacement probes clearly indicated that 3α- and 3β-Dns-ChA bind to HSA at site 2, whereas their C-7 regioisomers bind to HSA at site 1. Furthermore, the C-3-labeled compounds are displaced by lithocholic acid, whereas they are insensitive to ChA, confirming the assumption that the former binds to HSA at site 2. Thus, Dns labeling provides a useful tool to modulate the relative affinity of ChA to the major binding sites of HSA and, in combination with other fluorescent ChA analogs, to mimic the binding behavior of natural bile acids. PMID:21797258

  7. Role of Criegee Intermediates in Formation of Sulfuric Acid at BVOCs-rich Cape Corsica Site

    NASA Astrophysics Data System (ADS)

    Kukui, A.; Dusanter, S.; Sauvage, S.; Gros, V.; Bourrianne, T.; Sellegri, K.; Wang, J.; Colomb, A.; Pichon, J. M.; Chen, H.; Kalogridis, C.; Zannoni, N.; Bonsang, B.; Michoud, V.; Locoge, N.; Leonardis, T.

    2015-12-01

    Oxidation of SO2 in reactions with stabilised Criegee Intermediates (sCI) was suggested as an additional source of gaseous sulfuric acid (H2SO4) in the atmosphere, complementary to the conventional H2SO4 formation in reaction of SO2 with OH radicals. Evaluation of the importance of this additional source is complicated due to large uncertainty in the mechanism and rate constants for the reactions of different sCI with SO2, water vapor and other atmospheric species. Here we present an evaluation of the role of sCI in H2SO4 production at remote site on Cape Corsica near the North tip of Corsica Island (Ersa station, Western Mediterranean). In July 2013 comprehensive field observations including gas phase (OH and RO2 radicals, H2SO4, VOCs, NOx, SO2, others) and aerosol measurements were conducted at this site in the frame of ChArMEx project. During the field campaign the site was strongly influenced by local emissions of biogenic volatile compounds (BVOCs), including isoprene and terpenes, forming different sCI in reactions with ozone and, hence, presenting additional source of H2SO4 via sCI+SO2. However, this additional source of H2SO4 at the Ersa site was found to be insignificant. The observed concentrations of H2SO4 were found to be in good agreement with those estimated from the H2SO4 condensation sink and the production of H2SO4 only in the reaction of OH with SO2, without accounting for any additional H2SO4 source. Using the BVOCs observations we present estimation of the upper limit for the rate constants of H2SO4 production via reactions of different sCI with SO2.

  8. Methane to acetic acid over Cu-exchanged zeolites: mechanistic insights from a site-specific carbonylation reaction.

    PubMed

    Narsimhan, Karthik; Michaelis, Vladimir K; Mathies, Guinevere; Gunther, William R; Griffin, Robert G; Román-Leshkov, Yuriy

    2015-02-11

    The selective low temperature oxidation of methane is an attractive yet challenging pathway to convert abundant natural gas into value added chemicals. Copper-exchanged ZSM-5 and mordenite (MOR) zeolites have received attention due to their ability to oxidize methane into methanol using molecular oxygen. In this work, the conversion of methane into acetic acid is demonstrated using Cu-MOR by coupling oxidation with carbonylation reactions. The carbonylation reaction, known to occur predominantly in the 8-membered ring (8MR) pockets of MOR, is used as a site-specific probe to gain insight into important mechanistic differences existing between Cu-MOR and Cu-ZSM-5 during methane oxidation. For the tandem reaction sequence, Cu-MOR generated drastically higher amounts of acetic acid when compared to Cu-ZSM-5 (22 vs 4 μmol/g). Preferential titration with sodium showed a direct correlation between the number of acid sites in the 8MR pockets in MOR and acetic acid yield, indicating that methoxy species present in the MOR side pockets undergo carbonylation. Coupled spectroscopic and reactivity measurements were used to identify the genesis of the oxidation sites and to validate the migration of methoxy species from the oxidation site to the carbonylation site. Our results indicate that the Cu(II)-O-Cu(II) sites previously associated with methane oxidation in both Cu-MOR and Cu-ZSM-5 are oxidation active but carbonylation inactive. In turn, combined UV-vis and EPR spectroscopic studies showed that a novel Cu(2+) site is formed at Cu/Al <0.2 in MOR. These sites oxidize methane and promote the migration of the product to a Brønsted acid site in the 8MR to undergo carbonylation. PMID:25562431

  9. 36C1 measurements and the hydrology of an acid injection site

    USGS Publications Warehouse

    Vourvopoulos, G.; Brahana, J.V.; Nolte, E.; Korschinek, G.; Priller, A.; Dockhorn, B.

    1990-01-01

    In an area in western Tennessee (United States), an industrial firm is injecting acidic (pH = 0.1) iron chloride into permeable zones of carbonate rocks at depths ranging from 1000 to 2200 m below land surface. Overlying the injection zone at a depth of approximately 500 m below land surface is a regional fresh-water aquifer, the Knox aquifer. A study is currently underway to investigate whether the injection wells are hydraulically isolated from the fresh-water aquifer. Drilling of a test well that will reach a total depth of 2700 m has been initiated. The 36Cl content of 15 samples from the Knox aquifer, from monitor wells in the vicinity of the injection site, and from the test well have been analyzed. ?? 1990.

  10. Comparison of the autoradiographic binding distribution of [3H]-gabapentin with excitatory amino acid receptor and amino acid uptake site distributions in rat brain.

    PubMed Central

    Thurlow, R. J.; Hill, D. R.; Woodruff, G. N.

    1996-01-01

    1. Gabapentin is a novel anticonvulsant with an unknown mechanism of action. Recent homogenate binding studies with [3H]-gabapentin have suggested a structure-activity relationship similar to that shown for the amino acid transport system responsible for the uptake of large neutral amino acids (LNAA). 2. The autoradiographic binding distribution of [3H]-gabapentin in rat brain was compared with the distributions for excitatory amino acid receptor subtypes and the uptake sites for excitatory and large neutral amino acids in consecutive rat brain sections. 3. Densitometric measurement of the autoradiographic images followed by normalisation with respect to the hippocampus CA1 stratum radiatum, was carried out before comparison of each binding distribution with that of [3H]-gabapentin by linear regression analysis. The correlation coefficients observed showed no absolute correlation was observed between the binding distributions of [3H]-gabapentin and those of the excitatory amino acid receptor subtypes. The acidic and large neutral amino acid uptake site distributions demonstrated a much closer correlation to the [3H]-gabapentin binding site distribution. The correlation coefficients for D-[3H]-aspartate, L-[3H]-leucine and L-[3H]-isoleucine binding site distributions were 0.76, 0.90 and 0.88 respectively. 4. Concentration-dependent inhibition by unlabelled gabapentin of autoradiographic binding of L-[3H]-leucine and L-[3H]-isoleucine was observed, with non-specific binding levels being reached at concentrations between 10 and 100 microM. 5. Excitotoxic quinolinic acid lesion studies in rat brain caudate putamen and autoradiography were carried out for the amino acid uptake sites mentioned above. The resulting glial infiltration of the lesioned areas was visualized by autoradiography using the peripheral benzodiazepine receptor specific ligand [3H]-PK11195. A significant decrease in binding density in the lesioned area compared with sham-operated animals was observed

  11. Volatile aromatic hydrocarbons and dicarboxylic acid concentrations in air at an urban site in the Southwestern US

    NASA Astrophysics Data System (ADS)

    Tran, Ngoc K.; Steinberg, Spencer M.; Johnson, Brian J.

    Concentrations of benzene, toluene, ethylbenzene, o-xylene, and m- and p-xylene were measured at an urban sampling site in Las Vegas, NV by sorbent sampling followed by thermal desorption and determination by GC-PID. Simultaneously, measurements of oxalic, malonic, succinic, and adipic acids were made at the same site by collection on quartz filters, extraction, esterification, and determination by GC-FID. For the period from April 7, 1997 to June 11, 1997, 201 sets of hydrocarbon measurements and 99 sets of acid measurements were made. Additional measurements of dicarboxylic acids were made on samples that represented potential direct sources, e.g. green plants and road dust. Correlations between the hydrocarbon and CO concentrations (measured by the Clark County Health District at a nearby site) were highly significant and a strong negative correlation of hydrocarbon concentration with ozone concentration (also from the county site) was observed under quiescent atmospheric conditions. In general, dicarboxylic acid concentrations were well correlated with one another (with the exception of adipic acid) but not well correlated with hydrocarbon, CO, and ozone concentrations. Multiple sources and complex formation processes are indicated for the dicarboxylic acids.

  12. Site-specific acid-base properties of pholcodine and related compounds.

    PubMed

    Kovács, Z; Hosztafi, S; Noszál, B

    2006-11-01

    The acid-base properties of pholcodine, a cough-depressant agent, and related compounds including metabolites were studied by 1H NMR-pH titrations, and are characterised in terms of macroscopic and microscopic protonation constants. New N-methylated derivatives were also synthesized in order to quantitate site- and nucleus-specific protonation shifts and to unravel microscopic acid-base equilibria. The piperidine nitrogen was found to be 38 and 400 times more basic than its morpholine counterpart in pholcodine and norpholcodine, respectively. The protonation data show that the molecule of pholcodine bears an average of positive charge of 1.07 at physiological pH, preventing it from entering the central nervous system, a plausible reason for its lack of analgesic or addictive properties. The protonation constants of pholcodine and its derivatives are interpreted by comparing with related molecules of pharmaceutical interest. The pH-dependent relative concentrations of the variously protonated forms of pholcodine and morphine are depicted in distribution diagrams. PMID:17004059

  13. Hybridoma antibodies to the lipid-binding site(s) in the amino-terminal region of fibronectin inhibits binding of streptococcal lipoteichoic acid.

    PubMed

    Stanislawski, L; Courtney, H S; Simpson, W A; Hasty, D L; Beachey, E H; Robert, L; Ofek, I

    1987-08-01

    In this report, we present evidence to suggest that streptococci and lipoteichoic acid (LTA) interact with a fatty acid binding site located near the NH2-terminus of fibronectin. The evidence is based on the following observations. Antibodies directed against a synthetic peptide (residues 1-30 of the amino-terminus of fibronectin) reacted with the two thermolysin-generated peptides (24 and 28 kilodaltons [kDa]) that were adsorbed by and eluted from streptococci. The adsorption of the 24- and 28-kDa peptides to streptococci was inhibited by LTA. The two monoclonal antibodies that inhibited the binding of LTA to fibronectin reacted only with the 24- and 28-kDa fragments of fibronectin. Conversely, LTA, as well as lauric acid and oleic acid, blocked the binding of the same monoclonal antibodies to fibronectin. LTA had no effect on the binding of hybridoma antibodies directed against the collagen or cell-binding domain. PMID:3298457

  14. The Protonation Site of para-Dimethylaminobenzoic Acid Using Atmospheric Pressure Ionization Methods

    NASA Astrophysics Data System (ADS)

    Chai, Yunfeng; Weng, Guofeng; Shen, Shanshan; Sun, Cuirong; Pan, Yuanjiang

    2015-04-01

    The protonation site of para-dimethylaminobenzoic acid ( p-DMABA) was investigated using atmospheric pressure ionization methods (ESI and APCI) coupled with collision-induced dissociation (CID), nuclear magnetic resonance (NMR), and computational chemistry. Theoretical calculations and NMR experiments indicate that the dimethyl amino group is the preferred site of protonation both in the gas phase and aqueous solution. Protonation of p-DMABA occurs at the nitrogen atom by ESI independent of the solvents and other operation conditions under typical thermodynamic control. However, APCI produces a mixture of the nitrogen- and carbonyl oxygen-protonated p-DMABA when aprotic organic solvents (acetonitrile, acetone, and tetrahydrofuran) are used, exhibiting evident kinetic characteristics of protonation. But using protic organic solvents (methanol, ethanol, and isopropanol) in APCI still leads to the formation of thermodynamically stable N-protonated p-DMABA. These structural assignments were based on the different CID behavior of the N- and O-protonated p-DMABA. The losses of methyl radical and water are the diagnostic fragmentations of the N- and O-protonated p-DMABA, respectively. In addition, the N-protonated p-DMABA is more stable than the O-protonated p-DMABA in CID revealed by energy resolved experiments and theoretical calculations.

  15. Diversity of acidophilic prokaryotes at two acid mine drainage sites in Turkey.

    PubMed

    Aytar, Pınar; Kay, Catherine Melanie; Mutlu, Mehmet Burçin; Çabuk, Ahmet; Johnson, David Barrie

    2015-04-01

    The biodiversity of acidophilic prokaryotes in two acidic (pH 2.8-3.05) mine drainage (AMD) sites (Balya and Çan) in Turkey was examined using a combined cultivation-based and cultivation-independent approach. The latter included analyzing microbial diversity using fluorescent in situ hybridization (FISH), terminal restriction enzyme fragment length polymorphism (`T-RFLP), and quantitative PCR (qPCR). Numbers of cultivatable heterotrophic acidophilic bacteria were over an order of magnitude greater than those of chemolithotrophic acidophiles in both AMD ponds examined. Isolates identified as strains of Acidithiobacillus ferrivorans, Acidiphilium organovorum, and Ferrimicrobium acidiphilum were isolated from the Balya AMD pond, and others identified as strains of Leptospirillum ferriphilum, Acidicapsa ligni, and Acidiphilium rubrum from Çan AMD. Other isolates were too distantly related (from analysis of their 16S rRNA genes) to be identified at the species level. Archaeal diversity in the two ponds appeared to be far more limited. T-RFLP and qPCR confirmed the presence of Ferroplasma-like prokaryotes, but no archaea were isolated from the two sites. qPCR generated semiquantitative data for genera of some of the iron-oxidizing acidophiles isolated and/or detected, suggesting the order of abundance was Leptospirillum > Ferroplasma > Acidithiobacillus (Balya AMD) and Ferroplasma > Leptospirillum > Acidithiobacillus (Çan AMD). PMID:25380633

  16. Chemical characteristics and sources of organic acids in precipitation at a semi-urban site in Southwest China

    NASA Astrophysics Data System (ADS)

    Zhang, Y. L.; Lee, X. Q.; Cao, F.

    2011-01-01

    In order to investigate the chemical characteristics and sources of organic acids in precipitation in Southwest China, 105 rainwater samples were collected at a semi-urban site in Anshun from June 2007 to June 2008. Organic acids and major anions were analyzed along with pH and electrical conductivity. The pH values varied from 3.57 to 7.09 for all the rainfall events sampled, with an average of 4.67 which was typical acidic value. Formic, acetic and oxalic acids were found to be the predominant carboxylic acids and their volume weighted average (VWA) concentrations were 8.77, 6.93 and 2.84 μmol l -1, respectively. These organic acids were estimated to account for 8.1% to the total free acidity (TFA) in precipitation. The concentrations of the majority organic acids at studied site had a clear seasonal pattern, reaching higher levels during the non-growing season than those in growing season, which was attributed to dilution effect of heavy rainfall during the growing season. The seasonal variation of wet deposition flux of these organic acids confirmed higher source strength of biogenic emissions from vegetation during the growing season. Formic-to-acetic acids ratio (F/A), an indicator of primary versus secondary sources of these organic acids, suggested that primary sources from vehicular emission, biomass burning, soil and vegetation emissions were dominant sources. In addition, the lowest concentrations of organic acids were found under type S, when air masses originated from the marine (South China Sea) during Southern Asian Monsoon period. And the highest concentrations were observed in precipitation events from Northeast China (type NE), prevailing mostly during winter with the lowest rainfall.

  17. Site-specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and Staudinger-Bertozzi ligation

    PubMed Central

    Chakraborty, Anirban; Mazumder, Abhishek; Lin, Miaoxin; Hasemeyer, Adam; Xu, Qumiao; Wang, Dongye; Ebright, Yon W.; Ebright, Richard H.

    2015-01-01

    Summary A three-step procedure comprising (i) unnatural-amino-acid mutagenesis with 4-azido-phenylalanine, (ii) Staudinger-Bertozzi ligation with a probe-phosphine derivative, and (iii) in vitro reconstitution of RNA polymerase (RNAP) enables the efficient site-specific incorporation of a fluorescent probe, a spin label, a crosslinking agent, a cleaving agent, an affinity tag, or any other biochemical or biophysical probe, at any site of interest in RNAP. Straightforward extensions of the procedure enable the efficient site-specific incorporation of two or more different probes in two or more different subunits of RNAP. We present protocols for synthesis of probe-phosphine derivatives, preparation of RNAP subunits and the transcription initiation factor σ, unnatural amino acid mutagenesis of RNAP subunits and σ, Staudinger ligation with unnatural-amino-acid-containing RNAP subunits and σ, quantitation of labelling efficiency and labelling specificity, and reconstitution of RNAP. PMID:25665560

  18. Investigation of prototypal MOFs consisting of polyhedral cages with accessible Lewis-acid sites for quinoline synthesis.

    PubMed

    Gao, Wen-Yang; Leng, Kunyue; Cash, Lindsay; Chrzanowski, Matthew; Stackhouse, Chavis A; Sun, Yinyong; Ma, Shengqian

    2015-03-21

    A series of prototypal metal-organic frameworks (MOFs) consisting of polyhedral cages with accessible Lewis-acid sites, have been systematically investigated for Friedländer annulation reaction, a straightforward approach to synthesizing quinoline and its derivatives. Amongst them MMCF-2 demonstrates significantly enhanced catalytic activity compared with the benchmark MOFs, HKUST-1 and MOF-505, as a result of a high-density of accessible Cu(II) Lewis acid sites and large window size in the cuboctahedral cage-based nanoreactor of MMCF-2. PMID:25693429

  19. Direct photoaffinity labeling of cellular retinoic acid-binding protein I (CRABP-I) with all-trans-retinoic acid: identification of amino acids in the ligand binding site.

    PubMed

    Chen, G; Radominska-Pandya, A

    2000-10-17

    Cellular retinoic acid-binding proteins I and II (CRABP-I and -II, respectively) are transport proteins for all-trans-retinoic acid (RA), an active metabolite of vitamin A (retinol), and have been reported to be directly involved in the metabolism of RA. In this study, direct photoaffinity labeling with [11,12-(3)H]RA was used to identify amino acids comprising the ligand binding site of CRABP-I. Photoaffinity labeling of CRABP-I with [(3)H]RA was light- and concentration-dependent and was protected by unlabeled RA and various retinoids, indicating that the labeling was directed to the RA-binding site. Photolabeled CRABP-I was hydrolyzed with endoproteinase Lys-C to yield radioactive peptides, which were separated by reversed-phase HPLC for analysis by Edman degradation peptide sequencing. This method identified five modified amino acids from five separate HPLC fractions: Trp7, Lys20, Arg29, Lys38, and Trp109. All five amino acids are located within one side of the "barrel" structure in the area indicated by the reported crystal structure as the ligand binding site. This is the first direct identification of specific amino acids in the RA-binding site of CRABPs by photoaffinity labeling. These results provide significant information about the ligand binding site of the CRABP-I molecule in solution. PMID:11027136

  20. Locating high-affinity fatty acid-binding sites on albumin by x-ray crystallography and NMR spectroscopy

    PubMed Central

    Simard, J. R.; Zunszain, P. A.; Ha, C.-E.; Yang, J. S.; Bhagavan, N. V.; Petitpas, I.; Curry, S.; Hamilton, J. A.

    2005-01-01

    Human serum albumin (HSA) is a versatile transport protein for endogenous compounds and drugs. To evaluate physiologically relevant interactions between ligands for the protein, it is necessary to determine the locations and relative affinities of different ligands for their binding site(s). We present a site-specific investigation of the relative affinities of binding sites on HSA for fatty acids (FA), the primary physiological ligand for the protein. Titration of HSA with [13C]carboxyl-labeled FA was used initially to identify three NMR chemical shifts that are associated with high-affinity binding pockets on the protein. To correlate these peaks with FA-binding sites identified from the crystal structures of FA–HSA complexes, HSA mutants were engineered with substitutions of amino acids involved in coordination of the bound FA carboxyl. Titration of [13C]palmitate into solutions of HSA mutants for either FA site four (R410A/Y411A) or site five (K525A) within domain III of HSA each revealed loss of a specific NMR peak that was present in spectra of wild-type protein. Because these peaks are among the first three to be observed on titration of HSA with palmitate, sites four and five represent two of the three high-affinity long-chain FA-binding sites on HSA. These assignments were confirmed by titration of [13C]palmitate into recombinant domain III of HSA, which contains only sites four and five. These results establish a protocol for direct probing of the relative affinities of FA-binding sites, one that may be extended to examine competition between FA and other ligands for specific binding sites. PMID:16330771

  1. Locating high-affinity fatty acid-binding sites on albumin by x-ray crystallography and NMR spectroscopy.

    PubMed

    Simard, J R; Zunszain, P A; Ha, C-E; Yang, J S; Bhagavan, N V; Petitpas, I; Curry, S; Hamilton, J A

    2005-12-13

    Human serum albumin (HSA) is a versatile transport protein for endogenous compounds and drugs. To evaluate physiologically relevant interactions between ligands for the protein, it is necessary to determine the locations and relative affinities of different ligands for their binding site(s). We present a site-specific investigation of the relative affinities of binding sites on HSA for fatty acids (FA), the primary physiological ligand for the protein. Titration of HSA with [(13)C]carboxyl-labeled FA was used initially to identify three NMR chemical shifts that are associated with high-affinity binding pockets on the protein. To correlate these peaks with FA-binding sites identified from the crystal structures of FA-HSA complexes, HSA mutants were engineered with substitutions of amino acids involved in coordination of the bound FA carboxyl. Titration of [(13)C]palmitate into solutions of HSA mutants for either FA site four (R410A/Y411A) or site five (K525A) within domain III of HSA each revealed loss of a specific NMR peak that was present in spectra of wild-type protein. Because these peaks are among the first three to be observed on titration of HSA with palmitate, sites four and five represent two of the three high-affinity long-chain FA-binding sites on HSA. These assignments were confirmed by titration of [(13)C]palmitate into recombinant domain III of HSA, which contains only sites four and five. These results establish a protocol for direct probing of the relative affinities of FA-binding sites, one that may be extended to examine competition between FA and other ligands for specific binding sites. PMID:16330771

  2. CHARACTERIZATION OF INDIVIDUAL CHEMICAL REACTIONS CONSUMING ACID DURING NUCLEAR WASTE PROCESSING AT THE SAVANNAH RIVER SITE - 136B

    SciTech Connect

    Koopman, D.; Pickenheim, B.; Lambert, D.; Newell, J.; Stone, M.

    2009-09-02

    Conversion of legacy radioactive high-level waste at the Savannah River Site into a stable glass waste form involves a chemical pretreatment process to prepare the waste for vitrification. Waste slurry is treated with nitric and formic acids to achieve certain goals. The total quantity of acid added to a batch of waste slurry is constrained by the catalytic activity of trace noble metal fission products in the waste that can convert formic acid into hydrogen gas at many hundreds of times the radiolytic hydrogen generation rate. A large block of experimental process simulations were performed to characterize the chemical reactions that consume acid prior to hydrogen generation. The analysis led to a new equation for predicting the quantity of acid required to process a given volume of waste slurry.

  3. Early smelter sites: A neglected chapter in the history and geography of acid rain in the United States

    NASA Astrophysics Data System (ADS)

    Quinn, M.-L.

    Dominant spatial and temporal theories of acid rain in the U.S. are identified, followed by brief comments on how historical data have generally been used in modern acid rain research. A frequently-cited 1982 article by E.B. Cowling is examined, one that has influenced much thinking on the history of acid rain. The article overlooks early American smelters, however, and the role they played in the true history and geography of acid rain in the United States. Continuing with this theme, a connection is established between acid rain and turn-of-the-century smelter smoke problems. Literature on the latter subject is discussed, and American and German examples are given. A beginning is then made on writing acid rain's neglected chapter, focusing on Tennessee's Copper Basin (Ducktown District) where copper smelting dates back to the 1850s. A short historical overview of this area's smelting operations is given, with particular attention to the air pollution and other environmental problems resulting from large emissions of sulfur dioxide. Five additional early smelter sites for potential study are mentioned as well. The paper concludes with some observations regarding the way in which expanded research of early smelter sites could affect the general perception of acid rain in the U.S. It is also suggested that such research might contribute to a better atmosphere for making decisions and policies pertaining to the phenomenon as it exists today.

  4. Isotope geochemistry of waters affected by acid mine drainage in old labour sites (SE, Spain).

    NASA Astrophysics Data System (ADS)

    Pérez-Sirvent, Carmen; Martinez-Sanchez, Maria Jose; Garcia-Lorenzo, Maria Luz; Agudo, Ines; Hernandez-Cordoba, Manuel; Recio, Clemente

    2015-04-01

    The ore deposits of this zone have iron, lead and zinc as the main metal components. Iron is present in oxides, hydroxides, sulfides, sulfates, carbonates, and silicates; lead and zinc occur in sulfides (galena and sphalerite, respectively), carbonates, sulfates, and lead or zinc-bearing (manganese, iron) oxides. Mining started with the Romans and activity peaked in the second half of the 19th century and throughout the 20th century until the 1980's. From 1940 to 1957, mineral concentration was made by froth flotation and, prior to this, by gravimetric techniques. The mining wastes, or tailings, with a very fine particle size were deposited inland (tailings dams) and, since 1957, huge releases were made in directly the sea coast. The objective of this work was to evaluate processes affecting waters from abandoned mine sites by way of stable isotopic analysis, particularly H and O stable isotopes from water and S and O from dissolved sulfates. Several common chemical and physical processes, such as evaporation, water-rock interaction and mixing could alter water isotopic composition. Evaporation, which causes an enrichment in δD and δ18O in the residual water, is an important process in semiarid areas. The results obtained indicate that, for sites near the coast, waters are meteoric, and marine infiltration only takes place in the deepest layers near the shore or if water remains stagnated in sediments with low permeability. The main source of sulfate was the oxidation of sulfides, resulting in the liberation of acid, sulfate and metals. In order to assess the mechanism responsible for sulfide oxidation, the stoichiometric isotope balance model and the general isotope balance model were tested, suggesting that the oxidation via Fe3+ was predominant in the surface, and controlled by A. ferrooxidans, while at depth, sulfate reduction occurred.

  5. Iodine 125-lysergic acid diethylamide binds to a novel serotonergic site on rat choroid plexus epithelial cells

    SciTech Connect

    Yagaloff, K.A.; Hartig, P.R.

    1985-12-01

    /sup 125/I-Lysergic acid diethylamide (/sup 125/I-LSD) binds with high affinity to serotonergic sites on rat choroid plexus. These sites were localized to choroid plexus epithelial cells by use of a novel high resolution stripping film technique for light microscopic autoradiography. In membrane preparations from rat choroid plexus, the serotonergic site density was 3100 fmol/mg of protein, which is 10-fold higher than the density of any other serotonergic site in brain homogenates. The choroid plexus site exhibits a novel pharmacology that does not match the properties of 5-hydroxytryptamine-1a (5-HT1a), 5-HT1b, or 5-HT2 serotonergic sites. /sup 125/I-LSD binding to the choroid plexus site is potently inhibited by mianserin, serotonin, and (+)-LSD. Other serotonergic, dopaminergic, and adrenergic agonists and antagonists exhibit moderate to weak affinities for this site. The rat choroid plexus /sup 125/I-LSD binding site appears to represent a new type of serotonergic site which is located on non-neuronal cells in this tissue.

  6. Hydrolysis of phosphodiesters by diiron complexes: design of nonequivalent iron sites in purple acid phosphatase models.

    PubMed

    Verge, François; Lebrun, Colette; Fontecave, Marc; Ménage, Stéphane

    2003-01-27

    New mu-oxo-diferric complexes have been designed for hydrolysis of phosphodiesters. To mimic the diiron active site of purple acid phosphatase, a combinatorial method has been used to select complexes containing two distinct iron coordination spheres. The introduction of a bidentate ligand, a substituted phenanthroline (L) into complex 1, [Fe2O(bipy)4(OH2)2](NO3)4, generates in solution the complex [Fe2O(bipy)3(L)(OH2)2](NO3)4 as shown by ESI/MS and 1H NMR studies. The latter complex was found to be 20-fold more active than complex 1. On the basis of kinetic studies, we demonstrated that the complex [Fe2O(bipy)3(L)(OH)(OH2)](NO3)3 was the active species and the reaction proceeded through the formation of a ternary complex in which one iron binds a hydroxide and the second, the substrate. At nonsaturating concentrations of the substrate, the increased activity with increased methyl substituents in L was due to an increased affinity of the complex for the substrate. The activity of [Fe2O(bipy)3(33'44'Me2-Phen)(OH2)2](NO3)4 [33'44'Me2Phen = 3,3',4,4'-dimethyl-1,10-phenanthroline] was found to be comparable to that reported for Co(III) or Ce(IV) complexes. PMID:12693232

  7. High-Temperature Decomposition of Brønsted Acid Sites in Gallium-Substituted Zeolites

    SciTech Connect

    K Al-majnouni; N Hould; W Lonergan; D Vlachos; R Lobo

    2011-12-31

    The dehydroxylation of Broensted acid sites (BAS) in Ga-substituted zeolites was investigated at temperatures up to 850 C using X-ray absorption spectroscopy (XAS), Fourier transform infrared spectroscopy (FTIR), and mass spectrometry-temperature programmed desorption (MS-TPD). X-ray absorption near-edge spectroscopy (XANES) revealed that the majority of gallium has tetrahedral coordination even after complete dehydroxylation. The interatomic gallium-oxygen distance and gallium coordination number determined by extended X-ray absorption fine structure (EXAFS) are consistent with gallium in tetrahedral coordination at low T (< 550 C). Upon heating Ga-Beta and Ga-ZSM5 to 850 C, analysis of the EXAFS showed that 70 and 80% of the gallium was still in tetrahedral coordination. The remainder of the gallium was found to be in octahedral coordination. No trigonal Ga atoms were observed. FTIR measurements carried out at similar temperatures show that the intensity of the OH vibration due to BAS has been eliminated. MS-TPD revealed that hydrogen in addition to water evolved from the samples during dehydroxylation. This shows that dehydrogenation in addition to dehydration is a mechanism that contributes to BAS decomposition. Dehydrogenation was further confirmed by exposing the sample to hydrogen to regenerate some of the BAS as monitored by FTIR and MS-TPD.

  8. Identification of gamma-aminobutyric acid and its binding sites in Caenorhabditis elegans

    SciTech Connect

    Schaeffer, J.M.; Bergstrom, A.R.

    1988-01-01

    Gamma-aminobutyric acid (GABA), glutamate decarboxylase and GABA-transaminase were identified in the nematode Caenorhabditis elegans. The concentration of GABA in C. elegans is approximately 10-fold lower than the concentration of GABA in rat brain. Glutamate decarboxylase and GABA-transaminase, the GABA anabolic and catabolic enzymes, are also present in C. elegans. Crude membrane fractions were prepared from C. elegans and used to study specific (/sup 3/H) GABA binding sites. GABA binds to C. elegans membranes with high affinity and low capacity. Muscimol is a competitive inhibitor of specific GABA binding with a K/sub I/ value of 120 nM. None of the other GABA agonists or antagonists inhibited greater than 40% of the specific GABA binding at concentrations up to 10/sup -4/M. Thirteen spider venoms were examined as possible GABA agonists or antagonists, the venom from Calilena agelenidae inhibits specific GABA binding with a K/sub I/ value of 6 nl/ml. These results suggest that GABA has a physiological role as a neurotransmitter in C. elegans.

  9. Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models

    PubMed Central

    Maaskola, Jonas; Rajewsky, Nikolaus

    2014-01-01

    We present a discriminative learning method for pattern discovery of binding sites in nucleic acid sequences based on hidden Markov models. Sets of positive and negative example sequences are mined for sequence motifs whose occurrence frequency varies between the sets. The method offers several objective functions, but we concentrate on mutual information of condition and motif occurrence. We perform a systematic comparison of our method and numerous published motif-finding tools. Our method achieves the highest motif discovery performance, while being faster than most published methods. We present case studies of data from various technologies, including ChIP-Seq, RIP-Chip and PAR-CLIP, of embryonic stem cell transcription factors and of RNA-binding proteins, demonstrating practicality and utility of the method. For the alternative splicing factor RBM10, our analysis finds motifs known to be splicing-relevant. The motif discovery method is implemented in the free software package Discrover. It is applicable to genome- and transcriptome-scale data, makes use of available repeat experiments and aside from binary contrasts also more complex data configurations can be utilized. PMID:25389269

  10. ESTIMATES OF CLOUD WATER DEPOSITION AT MOUNTAIN DEPOSITION AT MOUNTAIN ACID DEPOSITION PROGRAM SITES IN THE APPALACHIAN MOUNTAINS

    EPA Science Inventory

    Cloud water deposition was estimated at three high elevation sites in the Appalachian Mountains of the eastern United States (Whiteface Mountain, NY, Whitetop Mountain, VA, and Clingrnan's Dome, TN) from 1994 through 1999 as part of the Mountain Acid Deposition Program (MADPro). ...

  11. Non-thermal plasma-assisted NOx reduction over Na-Y zeolites: The promotional effect of acid sites

    SciTech Connect

    Kwak, Ja Hun; Peden, Charles HF; Szanyi, Janos

    2006-06-01

    The effect of acid sites on the catalytic activities of a series of H+-modified Na-Y zeolites was investigated in the non-thermal plasma assisted NOx reduction reaction using a simulated diesel engine exhaust gas mixture. The acid sites were formed by NH4+ ion exchange and subsequent heat treatment of a NaY zeolite. The catalytic activities of these H+-modified NaY zeolites significantly increased with the number of acid sites. This NOx conversion increase was correlated with the decrease in the amount of unreacted NO2. The increase in the number of acid sites did not change the NO level, it stayed constant. Temperature programmed desorption following NO2 adsorption showed the appearance of a high temperature desorption peak at 453 K in addition to the main desorption feature of 343 K observed for the base Na-Y. The results of both the IR and TPD experiments revealed the formation of crotonaldehyde, resulting from condensation reaction of adsorbed acetaldehyde. Strong adsorptions of both NOx and hydrocarbon species are proposed to be responsible for the higher catalytic activity of H+-modified Na-Y zeolites in comparison to the base NaY material

  12. The two active sites in human branched-chain alpha-keto acid dehydrogenase operate independently without an obligatory alternating-site mechanism.

    PubMed

    Li, Jun; Machius, Mischa; Chuang, Jacinta L; Wynn, R Max; Chuang, David T

    2007-04-20

    A long standing controversy is whether an alternating activesite mechanism occurs during catalysis in thiamine diphosphate (ThDP)-dependent enzymes. We address this question by investigating the ThDP-dependent decarboxylase/dehydrogenase (E1b) component of the mitochondrial branched-chain alpha-keto acid dehydrogenase complex (BCKDC). Our crystal structure reveals that conformations of the two active sites in the human E1b heterotetramer harboring the reaction intermediate are identical. Acidic residues in the core of the E1b heterotetramer, which align with the proton-wire residues proposed to participate in active-site communication in the related pyruvate dehydrogenase from Bacillus stearothermophilus, are mutated. Enzyme kinetic data show that, except in a few cases because of protein misfolding, these alterations are largely without effect on overall activity of BCKDC, ruling out the requirement of a proton-relay mechanism in E1b. BCKDC overall activity is nullified at 50% phosphorylation of E1b, but it is restored to nearly half of the pre-phosphorylation level after dissociation and reconstitution of BCKDC with the same phosphorylated E1b. The results suggest that the abolition of overall activity likely results from the specific geometry of the half-phosphorylated E1b in the BCKDC assembly and not due to a disruption of the alternating active-site mechanism. Finally, we show that a mutant E1b containing only one functional active site exhibits half of the wild-type BCKDC activity, which directly argues against the obligatory communication between active sites. The above results provide evidence that the two active sites in the E1b heterotetramer operate independently during the ThDP-dependent decarboxylation reaction. PMID:17329260

  13. Forced Ambiguity of the Leucine Codons for Multiple-Site-Specific Incorporation of a Noncanonical Amino Acid

    PubMed Central

    Kwon, Inchan; Choi, Eun Sil

    2016-01-01

    Multiple-site-specific incorporation of a noncanonical amino acid into a recombinant protein would be a very useful technique to generate multiple chemical handles for bioconjugation and multivalent binding sites for the enhanced interaction. Previously combination of a mutant yeast phenylalanyl-tRNA synthetase variant and the yeast phenylalanyl-tRNA containing the AAA anticodon was used to incorporate a noncanonical amino acid into multiple UUU phenylalanine (Phe) codons in a site-specific manner. However, due to the less selective codon recognition of the AAA anticodon, there was significant misincorporation of a noncanonical amino acid into unwanted UUC Phe codons. To enhance codon selectivity, we explored degenerate leucine (Leu) codons instead of Phe degenerate codons. Combined use of the mutant yeast phenylalanyl-tRNA containing the CAA anticodon and the yPheRS_naph variant allowed incorporation of a phenylalanine analog, 2-naphthylalanine, into murine dihydrofolate reductase in response to multiple UUG Leu codons, but not to other Leu codon sites. Despite the moderate UUG codon occupancy by 2-naphthylalaine, these results successfully demonstrated that the concept of forced ambiguity of the genetic code can be achieved for the Leu codons, available for multiple-site-specific incorporation. PMID:27028506

  14. Effects of sex and site on amino acid metabolism enzyme gene expression and activity in rat white adipose tissue

    PubMed Central

    Arriarán, Sofía; Agnelli, Silvia; Remesar, Xavier; Fernández-López, José Antonio

    2015-01-01

    Background and Objectives. White adipose tissue (WAT) shows marked sex- and diet-dependent differences. However, our metabolic knowledge of WAT, especially on amino acid metabolism, is considerably limited. In the present study, we compared the influence of sex on the amino acid metabolism profile of the four main WAT sites, focused on the paths related to ammonium handling and the urea cycle, as a way to estimate the extent of WAT implication on body amino-nitrogen metabolism. Experimental Design. Adult female and male rats were maintained, undisturbed, under standard conditions for one month. After killing them under isoflurane anesthesia. WAT sites were dissected and weighed. Subcutaneous, perigonadal, retroperitoneal and mesenteric WAT were analyzed for amino acid metabolism gene expression and enzyme activities. Results. There was a considerable stability of the urea cycle activities and expressions, irrespective of sex, and with only limited influence of site. Urea cycle was more resilient to change than other site-specialized metabolic pathways. The control of WAT urea cycle was probably related to the provision of arginine/citrulline, as deduced from the enzyme activity profiles. These data support a generalized role of WAT in overall amino-N handling. In contrast, sex markedly affected WAT ammonium-centered amino acid metabolism in a site-related way, with relatively higher emphasis in males’ subcutaneous WAT. Conclusions. We found that WAT has an active amino acid metabolism. Its gene expressions were lower than those of glucose-lipid interactions, but the differences were quantitatively less important than usually reported. The effects of sex on urea cycle enzymes expression and activity were limited, in contrast with the wider variations observed in other metabolic pathways. The results agree with a centralized control of urea cycle operation affecting the adipose organ as a whole. PMID:26587356

  15. Effects of sex and site on amino acid metabolism enzyme gene expression and activity in rat white adipose tissue.

    PubMed

    Arriarán, Sofía; Agnelli, Silvia; Remesar, Xavier; Fernández-López, José Antonio; Alemany, Marià

    2015-01-01

    Background and Objectives. White adipose tissue (WAT) shows marked sex- and diet-dependent differences. However, our metabolic knowledge of WAT, especially on amino acid metabolism, is considerably limited. In the present study, we compared the influence of sex on the amino acid metabolism profile of the four main WAT sites, focused on the paths related to ammonium handling and the urea cycle, as a way to estimate the extent of WAT implication on body amino-nitrogen metabolism. Experimental Design. Adult female and male rats were maintained, undisturbed, under standard conditions for one month. After killing them under isoflurane anesthesia. WAT sites were dissected and weighed. Subcutaneous, perigonadal, retroperitoneal and mesenteric WAT were analyzed for amino acid metabolism gene expression and enzyme activities. Results. There was a considerable stability of the urea cycle activities and expressions, irrespective of sex, and with only limited influence of site. Urea cycle was more resilient to change than other site-specialized metabolic pathways. The control of WAT urea cycle was probably related to the provision of arginine/citrulline, as deduced from the enzyme activity profiles. These data support a generalized role of WAT in overall amino-N handling. In contrast, sex markedly affected WAT ammonium-centered amino acid metabolism in a site-related way, with relatively higher emphasis in males' subcutaneous WAT. Conclusions. We found that WAT has an active amino acid metabolism. Its gene expressions were lower than those of glucose-lipid interactions, but the differences were quantitatively less important than usually reported. The effects of sex on urea cycle enzymes expression and activity were limited, in contrast with the wider variations observed in other metabolic pathways. The results agree with a centralized control of urea cycle operation affecting the adipose organ as a whole. PMID:26587356

  16. A nuclear magnetic resonance-based structural rationale for contrasting stoichiometry and ligand binding site(s) in fatty acid-binding proteins.

    PubMed

    He, Yan; Estephan, Rima; Yang, Xiaomin; Vela, Adriana; Wang, Hsin; Bernard, Cédric; Stark, Ruth E

    2011-03-01

    Liver fatty acid-binding protein (LFABP) is a 14 kDa cytosolic polypeptide, differing from other family members in the number of ligand binding sites, the diversity of bound ligands, and the transfer of fatty acid(s) to membranes primarily via aqueous diffusion rather than direct collisional interactions. Distinct two-dimensional (1)H-(15)N nuclear magnetic resonance (NMR) signals indicative of slowly exchanging LFABP assemblies formed during stepwise ligand titration were exploited, without determining the protein-ligand complex structures, to yield the stoichiometries for the bound ligands, their locations within the protein binding cavity, the sequence of ligand occupation, and the corresponding protein structural accommodations. Chemical shifts were monitored for wild-type LFABP and an R122L/S124A mutant in which electrostatic interactions viewed as being essential to fatty acid binding were removed. For wild-type LFABP, the results compared favorably with the data for previous tertiary structures of oleate-bound wild-type LFABP in crystals and in solution: there are two oleates, one U-shaped ligand that positions the long hydrophobic chain deep within the cavity and another extended structure with the hydrophobic chain facing the cavity and the carboxylate group lying close to the protein surface. The NMR titration validated a prior hypothesis that the first oleate to enter the cavity occupies the internal protein site. In contrast, (1)H and (15)N chemical shift changes supported only one liganded oleate for R122L/S124A LFABP, at an intermediate location within the protein cavity. A rationale based on protein sequence and electrostatics was developed to explain the stoichiometry and binding site trends for LFABPs and to put these findings into context within the larger protein family. PMID:21226535

  17. Protons and Psalmotoxin-1 reveal nonproton ligand stimulatory sites in chicken acid-sensing ion channel

    PubMed Central

    Smith, Rachel N; Gonzales, Eric B

    2014-01-01

    Acid-sensing ion channels (ASICs) are proton-sensitive, sodium-selective channels expressed in the nervous system that sense changes in extracellular pH. These ion channels are sensitive to an increasing number of nonproton ligands that include natural venom peptides and guanidine compounds. In the case of chicken ASIC1, the spider toxin Psalmotoxin-1 (PcTx1) activates the channel, resulting in an inward current. Furthermore, a growing class of ligands containing a guanidine group has been identified that stimulate peripheral ASICs (ASIC3), but exert subtle influence on other ASIC subtypes. The effects of the guanidine compounds on cASIC1 have not been the focus of previous study. Here, we investigated the interaction of the guanidine compound 2-guanidine-4-methylquinazoline (GMQ) on cASIC1 proton activation and PcTx1 stimulation. Exposure of expressed cASIC1 to PcTx1 resulted in biphasic currents consisting of a transient peak followed by an irreversible cASIC1 PcTx1 persistent current. This cASIC1 PcTx1 persistent current may be the result of locking the cASIC1 protein into a desensitized transition state. The guanidine compound GMQ increased the apparent affinity of protons on cASIC1 and decreased the half-maximal constant of the cASIC1 steady-state desensitization profile. Furthermore, GMQ stimulated the cASIC1 PcTx1 persistent current in a concentration-dependent manner, which resulted in a non-desensitizing inward current. Our data suggests that GMQ may have multiple sites within cASIC1 and may act as a “molecular wedge” that forces the PcTx1-desensitized ASIC into an open state. Our findings indicate that guanidine compounds, such as GMQ, may alter acid-sensing ion channel activity in combination with other stimuli, and that additional ASIC subtypes (along with ASIC3) may serve to sense and mediate signals from multiple stimuli. PMID:24262969

  18. Contrasting microbial functional genes in two distinct saline-alkali and slightly acidic oil-contaminated sites.

    PubMed

    Liang, Yuting; Zhao, Huihui; Zhang, Xu; Zhou, Jizhong; Li, Guanghe

    2014-07-15

    To compare the functional gene structure and diversity of microbial communities in saline-alkali and slightly acidic oil-contaminated sites, 40 soil samples were collected from two typical oil exploration sites in North and South China and analyzed with a comprehensive functional gene array (GeoChip 3.0). The overall microbial pattern was significantly different between the two sites, and a more divergent pattern was observed in slightly acidic soils. Response ratio was calculated to compare the microbial functional genes involved in organic contaminant degradation and carbon, nitrogen, phosphorus, and sulfur cycling. The results indicated a significantly low abundance of most genes involved in organic contaminant degradation and in the cycling of nitrogen and phosphorus in saline-alkali soils. By contrast, most carbon degradation genes and all carbon fixation genes had similar abundance at both sites. Based on the relationship between the environmental variables and microbial functional structure, pH was the major factor influencing the microbial distribution pattern in the two sites. This study demonstrated that microbial functional diversity and heterogeneity in oil-contaminated environments can vary significantly in relation to local environmental conditions. The limitation of nitrogen and phosphorus and the low degradation capacity of organic contaminant should be carefully considered, particularly in most oil-exploration sites with saline-alkali soils. PMID:24784752

  19. Gamma-aminobutyric acid-modulated benzodiazepine binding sites in bacteria

    SciTech Connect

    Lummis, S.C.R.; Johnston, G.A.R. ); Nicoletti, G. ); Holan, G. )

    1991-01-01

    Benzodiazepine binding sites, which were once considered to exist only in higher vertebrates, are here demonstrated in the bacteria E. coli. The bacterial ({sup 3}H)diazepam binding sites are modulated by GABA; the modulation is dose dependent and is reduced at high concentrations. The most potent competitors of E.Coli ({sup 3}H)diazepam binding are those that are active in displacing ({sup 3}H)benzodiazepines from vertebrate peripheral benzodiazepine binding sites. These vertebrate sites are not modulated by GABA, in contrast to vertebrate neuronal benzodiazepine binding sites. The E.coli benzodiazepine binding sites therefore differ from both classes of vertebrate benzodiazepine binding sites; however the ligand spectrum and GABA-modulatory properties of the E.coli sites are similar to those found in insects. This intermediate type of receptor in lower species suggests a precursor for at least one class of vertebrate benzodiazepine binding sites may have existed.

  20. Effects of acidic recharge on groundwater at the St. Kevin Gulch site, Leadville, Colorado

    USGS Publications Warehouse

    Paschke, S.S.; Harrison, W.J.; Walton-Day, K.

    2001-01-01

    The acid rock drainage-affected stream of St. Kevin Gulch recharges the Quaternary sand and gravel aquifer of Tennessee Park, near Leadville, Colorado, lowering pH and contributing iron, cadmium, copper, zinc and sulphate to the ground-water system. Dissolved metal mobility is controlled by the seasonal spring runoff as well as oxidation/reduction (redox) reactions in the aquifer. Oxidizing conditions occur in the unconfined portions of the aquifer whilst sulphate-reducing conditions are found down gradient where semi-confined groundwater flow occurs beneath a natural wetland. Iron-reducing conditions occur in the transition from unconfined to semi-confined groundwater flow. Dissolved iron concentrations are low to not detectable in the alluvial fan recharge zone and increase in a down gradient direction. The effects of low-pH, metal-rich recharge are pronounced during low-flow in the fall when there is a defined area of low pH groundwater with elevated concentrations of dissolved zinc, cadmium, copper and sulphate adjacent to St. Kevin Gulch. Dissolved metal and sulphate concentrations in the recharge zone are diluted during spring runoff, although the maximum concentrations of dissolved zinc, cadmium, copper and sulphate occur at selected down gradient locations during high flow. Dissolved zinc, cadmium and copper concentrations are low to not detectable, whereas dissolved iron concentrations are greatest, in groundwater samples from the sulphate-reducing zone. Attenuation of zinc, cadmium and copper beneath the wetland suggests sulphide mineral precipitation is occurring in the semi-confined aquifer, in agreement with previous site investigations and saturation index calculations. Adsorption of dissolved zinc, cadmium and copper onto iron hydroxides is a minor attenuation process due to the low pH of the groundwater system.

  1. Acid-Sulfate-Weathering Activity in Shergottite Sites on Mars Recorded in Grim Glasses

    NASA Technical Reports Server (NTRS)

    Rao, M. N.; Nyquist, L. E.; Ross, K.; Sutton, S. R.; Schwandt, C. S.

    2011-01-01

    Based on mass spectrometric studies of sulfur species in Shergotty and EET79001, [1] and [2] showed that sulfates and sulfides occur in different proportions in shergottites. Sulfur speciation studies in gas-rich impact-melt (GRIM) glasses in EET79001 by the XANES method [3] showed that S K-XANES spectra in GRIM glasses from Lith A indicate that S is associated with Ca and Al presumably as sulfides/sulfates whereas the XANES spectra of amorphous sulfide globules in GRIM glasses from Lith B indicate that S is associated with Fe as FeS. In these amorphous iron sulfide globules, [4] found no Ni using FE-SEM and suggested that the globules resulting from immiscible sulfide melt may not be related to the igneous iron sulfides having approximately 1-3% Ni. Furthermore, in the amorphous iron sulfides from 507 GRIM glass, [5] determined delta(sup 34)S values ranging from +3.5%o to -3.1%o using Nano-SIMS. These values plot between the delta(sup 34)S value of +5.25%o determined in the sulfate fraction in Shergotty [6] at one extreme and the value of -1.7%o obtained for igneous sulfides in EET79001 and Shergotty [7] at the other. These results suggest that the amorphous Fe-S globules likely originated by shock reduction of secondary iron sulfate phases occurring in the regolith precursor materials during impact [7]. Sulfates in the regolith materials near the basaltic shergottite sites on Mars owe their origin to surficial acid-sulfate interactions. We examine the nature of these reactions by studying the composition of the end products in altered regolith materials. For the parent material composition, we use that of the host shergottite material in which the impact glasses are situated.

  2. Site-specific regulation of adult neurogenesis by dietary fatty acid content, vitamin E and flight exercise in European starlings.

    PubMed

    Hall, Zachary J; Bauchinger, Ulf; Gerson, Alexander R; Price, Edwin R; Langlois, Lillie A; Boyles, Michelle; Pierce, Barbara; McWilliams, Scott R; Sherry, David F; Macdougall-Shackleton, Scott A

    2014-03-01

    Exercise is known to have a strong effect on neuroproliferation in mammals ranging from rodents to humans. Recent studies have also shown that fatty acids and other dietary supplements can cause an upregulation of neurogenesis. It is not known, however, how exercise and diet interact in their effects on adult neurogenesis. We examined neuronal recruitment in multiple telencephalic sites in adult male European starlings (Sturnus vulgaris) exposed to a factorial combination of flight exercise, dietary fatty acids and antioxidants. Experimental birds were flown in a wind tunnel following a training regime that mimicked the bird's natural flight behaviour. In addition to flight exercise, we manipulated the composition of dietary fatty acids and the level of enrichment with vitamin E, an antioxidant reported to enhance neuronal recruitment. We found that all three factors - flight exercise, fatty acid composition and vitamin E enrichment - regulate neuronal recruitment in a site-specific manner. We also found a robust interaction between flight training and vitamin E enrichment at multiple sites of neuronal recruitment. Specifically, flight training was found to enhance neuronal recruitment across the telencephalon, but only in birds fed a diet with a low level of vitamin E. Conversely, dietary enrichment with vitamin E upregulated neuronal recruitment, but only in birds not flown in the wind tunnel. These findings indicate conserved modulation of adult neurogenesis by exercise and diet across vertebrate taxa and indicate possible therapeutic interventions in disorders characterized by reduced adult neurogenesis. PMID:24372878

  3. Screening and assessment of solidification/stabilization amendments suitable for soils of lead-acid battery contaminated site.

    PubMed

    Zhang, Zhuo; Guo, Guanlin; Teng, Yanguo; Wang, Jinsheng; Rhee, Jae Seong; Wang, Sen; Li, Fasheng

    2015-05-15

    Lead exposure via ingestion of soil and dust generally occurs at lead-acid battery manufacturing and recycling sites. Screening solidification/stabilization (S/S) amendments suitable for lead contaminated soil in an abandoned lead-acid battery factory site was conducted based on its chemical forms and environmental risks. Twelve amendments were used to immobilize the Pb in soil and assess the solidification/stabilization efficiency by toxicity leaching tests. The results indicated that three amendments, KH₂PO₄ (KP), KH₂PO₄:oyster shell power=1:1 (by mass ratio; SPP), and KH₂PO₄:sintered magnesia=1:1 (by mass ratio; KPM) had higher remediation efficiencies that led to a 92% reduction in leachable Pb with the addition of 5% amendments, while the acid soluble fraction of Pb (AS-Pb) decreased by 41-46% and the residual fraction (RS-Pb) increased by 16-25%. The S/S costs of the three selected amendments KP, SPP, and KPM could be controlled to $22.3 per ton of soil when the Pb concentration in soil ranged from 2000 to 3000 mg/kg. The results of this study demonstrated that KP, SPP, and KPM can effectively decrease bioavailability of Pb. These findings could provide basis for decision-making of S/S remediation of lead-acid battery contaminated sites. PMID:25699676

  4. Distribution and integrated assessment of lead in an abandoned lead-acid battery site in Southwest China before redevelopment.

    PubMed

    Wang, Mei; Zhang, Chao; Zhang, Zhuo; Li, Fasheng; Guo, Guanlin

    2016-06-01

    Lead-acid battery sites have contributed enormous amounts of lead to the environment, significantly affecting its global biogeochemical cycle and leaving the potential risks to human health. An abandoned lead-acid battery site prepared for redevelopment was selected in order to study the distribution of lead in soils, plants, rhizosphere soils and soil solutions. In total, 197 samples from 77 boreholes were collected and analyzed. Single extractions by acetic acid (HOAc) were conducted to assess the bioavailability and speciation of lead in soils for comparison with the parts of the plants that are aboveground. Health risks for future residential development were evaluated by the integrated exposure uptake biokinetic (IEUBK) model. The results indicated that lead concentrations in 83% of the soil samples exceeded the Chinese Environmental Quality Standard for soil (350 mg/kg for Pb) and mainly occurred at depths between 0 and 1.5 m while accumulating at the surface of demolished construction waste and miscellaneous fill. Lead concentrations in soil solutions and HOAc extraction leachates were linked closely to the contents of aboveground Broussonetia papyrifera and Artemisia annua, two main types of local plants that were found at the site. The probability density of lead in blood (PbB) in excess of 10 µg/dL could overtake the 99% mark in the residential scenario. The findings provided a relatively integrated method to illustrate the onsite investigations and assessment for similar sites before remediation and future development from more comprehensive aspects. PMID:26921546

  5. Site-directed mutagenesis of dicarboxylic acids near the active site of Bacillus cereus 5/B/6 beta-lactamase II.

    PubMed Central

    Lim, H M; Iyer, R K; Pène, J J

    1991-01-01

    An amino acid residue functioning as a general base has been proposed to assist in the hydrolysis of beta-lactam antibiotics by the zinc-containing Bacillus cereus beta-lactamase II [Bicknell & Waley (1985) Biochemistry 24, 6876-6887]. Oligonucleotide-directed mutagenesis of cloned Bacillus cereus 5/B/6 beta-lactamase II was used in an 'in vivo' study to investigate the role of carboxy-group-containing amino acids near the active site of the enzyme. Substitution of asparagine for the wild-type aspartic acid residue at position 81 resulted in fully functional enzyme. An aspartic acid residue at position 90 is essential for beta-lactamase II to confer any detectable ampicillin and cephalosporin C resistance to Escherichia coli. Conversion of Asp90 into Asn90 or Glu90 lead to the synthesis of inactive enzyme, suggesting that the spatial position of the beta-carboxy group of Asp90 is critical for enzyme function. Images Fig. 2. Fig. 3. PMID:1904717

  6. On the nature and formation of the active sites in Re[sub 2]O[sub 7] metathesis catalysts supported on borated alumina

    SciTech Connect

    Sibeijn, M.; Bliek, A. ); Veen, J.A.R. van ); Moulijn, J.A. )

    1994-02-01

    Re[sub 2]O[sub 7] catalysts on borated aluminas have been investigated with a view to correlating the structure of the active site and its activity in the metathesis of methyl oleate. Modification of alumina with boria results in much more active metathesis catalysts. Infrared spectroscopy was used for the characterization, pyridine adsorption measurements for determining the Lewis acid and Bronsted acid sites, and temperature-programmed IR measurements to follow the reactions occurring during calcination of the supports and catalysts. Boria binds to the surface via the alumina hydroxyls. Upon Re[sub 2]O[sub 7] loading of nonborated alumina, the ReO[sub 4] groups react first with Lewis acid sites, onto which they are strongly bonded. Above a Re[sub 2]O[sub 7] loading of 3 wt% surface hydroxyls are also substituted by Re[sub 2]O[sub 7] groups, resulting in an increase in catalytic activity. When the borated supports are loaded with Re[sub 2]O[sub 7], the ReO[sub 4] groups are also first bonded to the Lewis acid sites. During calcination these ReO[sub 4] groups substitute surface hydroxyls preferably on alumina hydroxyls. The substitution of the boron hydroxyls only takes place at a calcination time of at least 2 h at 823 K. At high borate loadings (>10 wt%) the reaction of ReO[sub 4] groups with boron hydroxyls competes with the condensation reaction of two neighbouring boron hydroxyls. Taking into account that a ReO[sub 4] group which has substituted in acidic OH group on the support is the precursor of an active site, the increase in activity of Re[sub 2]O[sub 7] catalysts by modification of the alumina support with boria can be ascribed to two effects, namely, the reduction of the bonding strength of Lewis acid sites with ReO[sub 4], making the ReO[sub 4]-OH substitution reaction possible during calcination even at low rhenium loadings, and the formation of acidic surface hydroxyls. 16 refs., 11 figs., 3 tabs.

  7. High desolvation temperature facilitates the ESI-source H/D exchange at non-labile sites of hydroxybenzoic acids and aromatic amino acids.

    PubMed

    Zherebker, Alexander; Kostyukevich, Yury; Kononikhin, Alexey; Roznyatovsky, Vitaliy A; Popov, Igor; Grishin, Yuri K; Perminova, Irina V; Nikolaev, Eugene

    2016-04-21

    Hydrogen/deuterium exchange coupled with high-resolution mass spectrometry has become a powerful analytical approach for structural investigations of complex organic matrices. Here we report the feasibility of the site-specific H/D exchange of non-labile hydrogens directly in the electrospray ionization (ESI) source, which was facilitated by an increase in the desolvation temperature from 200 °C up to 400 °C. We have found that the exchanges at non-labile sites were observed only for the model compounds capable of keto-enol tautomeric transformations (e.g., 2,3-, 2,4-dihydroxybenzoic acids, gallic acid, DOPA), and only when water was used as a solvent. We hypothesized that the detected additional exchanges were induced by the presence of hydroxyls in the sprayed water droplets generated in the negative ESI mode. It was indicative of the exchange reactions taking place in the sprayed droplets rather than in the gas phase. To support this hypothesis, the H/D exchange experiments were run in deuterated water under base-catalyzed conditions for three model compounds, which showed the most intensive exchanges in the MS experiments: DOPA, 2,4-DHB, and 5-acetylsalicylic acid. (2)H NMR spectroscopy has confirmed keto-enolic transformations of the model compounds leading to the specific labeling of the corresponding non-labile sites. We believe that the proposed technique will be useful for structural investigations of natural complex mixtures (e.g. proteins, humic substances) using site-specific H/D exchange. PMID:27002310

  8. ACIDIC EPISODES AND SURFACE WATER CHEMISTRY: A COMPARISON OF NORTHEAST AND SOUTHEAST STUDY SITES

    EPA Science Inventory

    Much of the emphasis in the National Acid Precipitation Assessment Program (NAPAP) has been on historical or longterm trends in surface water acidification. Short-term acidic episodes, however, also might have significant adverse effects on aquatic ecosystems. The U.S. EPA is pre...

  9. Site-specific incorporation of redox active amino acids into proteins

    DOEpatents

    Alfonta, Lital; Schultz, Peter G.; Zhang, Zhiwen

    2011-08-30

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate redox active amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with redox active amino acids using these orthogonal pairs.

  10. Site-specific incorporation of redox active amino acids into proteins

    DOEpatents

    Alfonta, Lital; Schultz, Peter G.; Zhang, Zhiwen

    2009-02-24

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate redox active amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with redox active amino acids using these orthogonal pairs.

  11. Site-specific incorporation of redox active amino acids into proteins

    DOEpatents

    Alfonta, Lital; Schultz, Peter G.; Zhang, Zhiwen

    2012-02-14

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate redox active amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with redox active amino acids using these orthogonal pairs.

  12. Site-specific incorporation of redox active amino acids into proteins

    DOEpatents

    Alfonta; Lital , Schultz; Peter G. , Zhang; Zhiwen

    2010-10-12

    Compositions and methods of producing components of protein biosynthetic machinery that include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, and orthogonal pairs of tRNAs/synthetases, which incorporate redox active amino acids into proteins are provided. Methods for identifying these orthogonal pairs are also provided along with methods of producing proteins with redox active amino acids using these orthogonal pairs.

  13. Probing the steric requirements of the γ-aminobutyric acid aminotransferase active site with fluorinated analogues of vigabatrin

    PubMed Central

    Juncosa, Jose I.; Groves, Andrew P.; Xia, Guoyao; Silverman, Richard B.

    2012-01-01

    We have synthesized three analogues of 4-amino-5-fluorohexanoic acids as potential inactivators of γ-aminobutyric acid aminotransferase (GABA-AT), which were designed to combine the potency of their shorter chain analogue, 4-amino-5-fluoropentanoic acid (AFPA), with the greater enzyme selectivity of the antiepileptic vigabatrin (Sabril®). Unexpectedly, these compounds failed to inactivate or inhibit the enzyme, even at high concentrations. On the basis of molecular modeling studies, we propose that the GABA-AT active site has an accessory binding pocket that accommodates the vinyl group of vigabatrin and the fluoromethyl group of AFPA, but is too narrow to support the extra width of one distal methyl group in the synthesized analogues. PMID:23306054

  14. Novel human D-amino acid oxidase inhibitors stabilize an active-site lid-open conformation

    PubMed Central

    Terry-Lorenzo, Ryan T.; Chun, Lawrence E.; Brown, Scott P.; Heffernan, Michele L. R.; Fang, Q. Kevin; Orsini, Michael A.; Pollegioni, Loredano; Hardy, Larry W.; Spear, Kerry L.; Large, Thomas H.

    2014-01-01

    The NMDAR (N-methyl-D-aspartate receptor) is a central regulator of synaptic plasticity and learning and memory. hDAAO (human D-amino acid oxidase) indirectly reduces NMDAR activity by degrading the NMDAR co-agonist D-serine. Since NMDAR hypofunction is thought to be a foundational defect in schizophrenia, hDAAO inhibitors have potential as treatments for schizophrenia and other nervous system disorders. Here, we sought to identify novel chemicals that inhibit hDAAO activity. We used computational tools to design a focused, purchasable library of compounds. After screening this library for hDAAO inhibition, we identified the structurally novel compound, ‘compound 2’ [3-(7-hydroxy-2-oxo-4-phenyl-2H-chromen-6-yl)propanoic acid], which displayed low nM hDAAO inhibitory potency (Ki=7 nM). Although the library was expected to enrich for compounds that were competitive for both D-serine and FAD, compound 2 actually was FAD uncompetitive, much like canonical hDAAO inhibitors such as benzoic acid. Compound 2 and an analog were independently co-crystalized with hDAAO. These compounds stabilized a novel conformation of hDAAO in which the active-site lid was in an open position. These results confirm previous hypotheses regarding active-site lid flexibility of mammalian D-amino acid oxidases and could assist in the design of the next generation of hDAAO inhibitors. PMID:25001371

  15. Selective synthesis and characterization of single-site HY zeolite-supported rhodium complexes and their use as catalysts for ethylene hydrogenation and dimerization

    NASA Astrophysics Data System (ADS)

    Khivantsev, Konstantin

    Single-site Rh(CO)2, Rh(C2H4)2 and Rh(NO)2 complexes anchored on various dealuminated HY zeolites can be used as precursors for the selective surface mediated synthesis of well-defined site-isolated Rh(CO)(H)x complexes. DFT calculations and D 2 isotope exchange experiments provide strong evidence for the formation of a family of site isolated mononuclear rhodium carbonyl hydride complexes (including the first examples of RhH complexes with undissociated H2 ligands): Rh(CO)(H2), Rh(CO)(H)2, and Rh(CO)(H). The fraction of each individual complex formed varies significantly with the Si/Al ratio of the zeolite and the nature of the precursor used. HY zeolite-supported mononuclear Rh(CO)2 complexes are very active in ethylene hydrogenation and ethylene dimerization under ambient conditions. There is strong evidence for the cooperation mechanism between mononuclear rhodium complexes and Bronsted acid sites of the zeolite support in C-C bond formation process, as well as ethane formation. Finally, it is shown that the dimerization pathway selectivity can be progressively tuned (and completely switched off) by modifying the number of Bronsted acid sites on the zeolite surface. HY zeolite-supported mononuclear Rh(NO)2 complexes can be selectively formed upon exposure of Rh(CO)2/HY to the gas phase NO/He. They are structurally similar to Rh(CO)2/HY with Rh(I) retaining square planar geometry and nitrosyl ligands adopting a linear configuration. Rh(NO)2/HY30 is active in ethylene hydrogenation and ethylene dimerization under ambient conditions. This is the first unprecedented example of a supported transition-metal nitrosyl complex capable of performing a catalytic reaction. Moreover, this is the first example of a site-isolated Rh complex with ligands other than ethylene or carbonyl, which can catalyze both ethylene hydrogenation and dimerization. Unlike its dicarbonyl counterpart, dinitrosyl rhodium complex has a uniquely different reactivity towards ethylene and hydrogen

  16. Conceptual Model of Uranium in the Vadose Zone for Acidic and Alkaline Wastes Discharged at the Hanford Site Central Plateau

    SciTech Connect

    Truex, Michael J.; Szecsody, James E.; Qafoku, Nikolla; Serne, R. Jeffrey

    2014-09-01

    Historically, uranium was disposed in waste solutions of varying waste chemistry at the Hanford Site Central Plateau. The character of how uranium was distributed in the vadose zone during disposal, how it has continued to migrate through the vadose zone, and the magnitude of potential impacts on groundwater are strongly influenced by geochemical reactions in the vadose zone. These geochemical reactions can be significantly influenced by the disposed-waste chemistry near the disposal location. This report provides conceptual models and supporting information to describe uranium fate and transport in the vadose zone for both acidic and alkaline wastes discharged at a substantial number of waste sites in the Hanford Site Central Plateau. The conceptual models include consideration of how co-disposed acidic or alkaline fluids influence uranium mobility in terms of induced dissolution/precipitation reactions and changes in uranium sorption with a focus on the conditions near the disposal site. This information, when combined with the extensive information describing uranium fate and transport at near background pH conditions, enables focused characterization to support effective fate and transport estimates for uranium in the subsurface.

  17. Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: a site-specific genetically encoded unnatural amino acid and an active site ligand.

    PubMed

    Thielges, Megan C; Axup, Jun Y; Wong, Daryl; Lee, Hyun Soo; Chung, Jean K; Schultz, Peter G; Fayer, Michael D

    2011-09-29

    Protein dynamics and interactions in myoglobin (Mb) were characterized via two vibrational dynamics labels (VDLs): a genetically incorporated site-specific azide (Az) bearing unnatural amino acid (AzPhe43) and an active site CO ligand. The Az-labeled protein was studied using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy. CO bound at the active site of the heme serves as a second VDL located nearby. Therefore, it was possible to use Fourier transform infrared (FT-IR) and 2D IR spectroscopic experiments on the Az in unligated Mb and in Mb bound to CO (MbAzCO) and on the CO in MbCO and MbAzCO to investigate the environment and motions of different states of one protein from the perspective of two spectrally resolved VDLs. A very broad bandwidth 2D IR spectrum, encompassing both the Az and CO spectral regions, found no evidence of direct coupling between the two VDLs. In MbAzCO, both VDLs reported similar time scale motions: very fast homogeneous dynamics, fast, ∼1 ps dynamics, and dynamics on a much slower time scale. Therefore, each VDL reports independently on the protein dynamics and interactions, and the measured dynamics are reflective of the protein motions rather than intrinsic to the chemical nature of the VDL. The AzPhe VDL also permitted study of oxidized Mb dynamics, which could not be accessed previously with 2D IR spectroscopy. The experiments demonstrate that the combined application of 2D IR spectroscopy and site-specific incorporation of VDLs can provide information on dynamics, structure, and interactions at virtually any site throughout any protein. PMID:21823631

  18. Two-Dimensional IR Spectroscopy of Protein Dynamics Using Two Vibrational Labels: A Site-Specific Genetically Encoded Unnatural Amino Acid and an Active Site Ligand

    PubMed Central

    Thielges, Megan C.; Axup, Jun Y.; Wong, Daryl; Lee, Hyun Soo; Chung, Jean K.; Schultz, Peter G.; Fayer, Michael D.

    2012-01-01

    Protein dynamics and interactions in myoglobin (Mb) were characterized via two vibrational dynamics labels (VDLs): a genetically incorporated site-specific azide (Az) bearing unnatural amino acid (AzPhe43) and an active site CO ligand. The Az-labeled protein was studied using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy. CO bound at the active site of the heme serves as a second VDL located nearby. Therefore, it was possible to use Fourier transform infrared (FT-IR) and 2D IR spectroscopic experiments on the Az in unligated Mb and in Mb bound to CO (MbAzCO) and on the CO in MbCO and MbAzCO to investigate the environment and motions of different states of one protein from the perspective of two spectrally resolved VDLs. A very broad bandwidth 2D IR spectrum, encompassing both the Az and CO spectral regions, found no evidence of direct coupling between the two VDLs. In MbAzCO, both VDLs reported similar time scale motions: very fast homogeneous dynamics, fast, ~1 ps dynamics, and dynamics on a much slower time scale. Therefore, each VDL reports independently on the protein dynamics and interactions, and the measured dynamics are reflective of the protein motions rather than intrinsic to the chemical nature of the VDL. The AzPhe VDL also permitted study of oxidized Mb dynamics, which could not be accessed previously with 2D IR spectroscopy. The experiments demonstrate that the combined application of 2D IR spectroscopy and site-specific incorporation of VDLs can provide information on dynamics, structure, and interactions at virtually any site throughout any protein. PMID:21823631

  19. Characterization of Fe(II) oxidizing bacterial activities and communities at two acidic Appalachian coalmine drainage-impacted sites

    SciTech Connect

    Senko, John M.; Wanjugi, Pauline; Lucas, Melanie; Bruns, Mary Ann; Burgos, William D.

    2008-06-12

    We characterized the microbiologically mediated oxidative precipitation of Fe(II) from coalminederived acidic mine drainage (AMD) along flow-paths at two sites in northern Pennsylvania. At the Gum Boot site, dissolved Fe(II) was efficiently removed from AMD whereas minimal Fe(II) removal occurred at the Fridays-2 site. Neither site received human intervention to treat the AMD. Culturable Fe(II) oxidizing bacteria were most abundant at sampling locations along the AMD flow path corresponding to greatest Fe(II) removal and where overlying water contained abundant dissolved O2. Rates of Fe(II) oxidation determined in laboratory-based sediment incubations were also greatest at these sampling locations. Ribosomal RNA intergenic spacer analysis and sequencing of partial 16S rRNA genes recovered from sediment bacterial communities revealed similarities among populations at points receiving regular inputs of Fe(II)-rich AMD and provided evidence for the presence of bacterial lineages capable of Fe(II) oxidation. A notable difference between bacterial communities at the two sites was the abundance of Chloroflexi-affiliated 16S rRNA gene sequences in clone libraries derived from the Gum Boot sediments. Our results suggest that inexpensive and reliable AMD treatment strategies can be implemented by mimicking the conditions present at the Gum Boot field site.

  20. Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids.

    PubMed

    Kim, Ki-Hyun; Nielsen, Peter E; Glazer, Peter M

    2007-01-01

    Sequence-specific DNA-binding molecules such as triple helix-forming oligonucleotides (TFOs) provide a means for inducing site-specific mutagenesis and recombination at chromosomal sites in mammalian cells. However, the utility of TFOs is limited by the requirement for homopurine stretches in the target duplex DNA. Here, we report the use of pseudo-complementary peptide nucleic acids (pcPNAs) for intracellular gene targeting at mixed sequence sites. Due to steric hindrance, pcPNAs are unable to form pcPNA-pcPNA duplexes but can bind to complementary DNA sequences by Watson-Crick pairing via double duplex-invasion complex formation. We show that psoralen-conjugated pcPNAs can deliver site-specific photoadducts and mediate targeted gene modification within both episomal and chromosomal DNA in mammalian cells without detectable off-target effects. Most of the induced psoralen-pcPNA mutations were single-base substitutions and deletions at the predicted pcPNA-binding sites. The pcPNA-directed mutagenesis was found to be dependent on PNA concentration and UVA dose and required matched pairs of pcPNAs. Neither of the individual pcPNAs alone had any effect nor did complementary PNA pairs of the same sequence. These results identify pcPNAs as new tools for site-specific gene modification in mammalian cells without purine sequence restriction, thereby providing a general strategy for designing gene targeting molecules. PMID:17977869

  1. A novel method to identify nucleic acid binding sites in proteins by scanning mutagenesis: application to iron regulatory protein.

    PubMed Central

    Neupert, B; Menotti, E; Kühn, L C

    1995-01-01

    We describe a new procedure to identify RNA or DNA binding sites in proteins, based on a combination of UV cross-linking and single-hit chemical peptide cleavage. Site-directed mutagenesis is used to create a series of mutants with single Asn-Gly sequences in the protein to be analysed. Recombinant mutant proteins are incubated with their radiolabelled target sequence and UV irradiated. Covalently linked RNA- or DNA-protein complexes are digested with hydroxylamine and labelled peptides identified by SDS-PAGE and autoradiography. The analysis requires only small amounts of protein and is achieved within a relatively short time. Using this method we mapped the site at which human iron regulatory protein (IRP) is UV cross-linked to iron responsive element RNA to amino acid residues 116-151. Images PMID:7544459

  2. Computational investigation of locked nucleic acid (LNA) nucleotides in the active sites of DNA polymerases by molecular docking simulations.

    PubMed

    Poongavanam, Vasanthanathan; Madala, Praveen K; Højland, Torben; Veedu, Rakesh N

    2014-01-01

    Aptamers constitute a potential class of therapeutic molecules typically selected from a large pool of oligonucleotides against a specific target. With a scope of developing unique shorter aptamers with very high biostability and affinity, locked nucleic acid (LNA) nucleotides have been investigated as a substrate for various polymerases. Various reports showed that some thermophilic B-family DNA polymerases, particularly KOD and Phusion DNA polymerases, accepted LNA-nucleoside 5'-triphosphates as substrates. In this study, we investigated the docking of LNA nucleotides in the active sites of RB69 and KOD DNA polymerases by molecular docking simulations. The study revealed that the incoming LNA-TTP is bound in the active site of the RB69 and KOD DNA polymerases in a manner similar to that seen in the case of dTTP, and with LNA structure, there is no other option than the locked C3'-endo conformation which in fact helps better orienting within the active site. PMID:25036012

  3. In situ fluorescence labelling of jasmonic acid binding sites in plant tissues with cadmium-free quantum dots.

    PubMed

    Liao, Qiumei; Yu, Ying; Cao, Yujuan; Lin, Bixia; Wei, Jingjing

    2015-02-01

    The fluorescence labelling of plant hormone binding sites is an important analytical technique in research on the molecular mechanisms of plant hormone activities. The authors synthesised a jasmonic acid (JA)-conjugated ZnS:Mn quantum dot (QD) probe, with a cubic structure and average hydrodynamic sizes of about 17.0 nm. The maximum fluorescence emission of the probe was recorded at about 585 nm. The probe was used for fluorescence labelling of JA binding sites in mung bean seedling tissues. Analysis revealed that the probe exhibited high selectivity to JA binding sites and good performance in eliminating interference from background fluorescence in plant tissues. In addition, the probe did not exhibit any apparent biotoxicity, and is much more suitable than probes constructed from CdTe QDs for the analysis of biological samples. PMID:25650324

  4. Low-cost silica, calcite and metal sulfide scale control through on-site production of sulfurous acid from H{sub 2}S or elemental sulfur

    SciTech Connect

    Gallup, D.L.; Kitz, K.

    1997-12-31

    UNOCAL Corporation currently utilizes brine pH modification technology to control scale deposition. Acids utilized in commercial operations include, sulfuric and hydrochloric. A new process reduces costs by producing acid on-site by burning hydrogen sulfide or elemental sulfur. Hydrogen sulfide in non-condensible gas emissions is reduced by oxidization to sulfurous acid. Brine or condensate is treated with sulfurous acid to control scale deposition, mitigate corrosion and improve gas partitioning in condensers.

  5. Extending the Diffuse Layer Model of Surface Acidity Behavior: III. Estimating Bound Site Activity Coefficients

    EPA Science Inventory

    Although detailed thermodynamic analyses of the 2-pK diffuse layer surface complexation model generally specify bound site activity coefficients for the purpose of accounting for those non-ideal excess free energies contributing to bound site electrochemical potentials, in applic...

  6. Seasonal and diurnal cycles of ammonia, nitrous acid and nitric acid at a forest site in Finland

    NASA Astrophysics Data System (ADS)

    Virkkula, A.; Makkonen, U.; Mäntykenttä, J.; Hakola, H.

    2012-04-01

    Background In July - August 2010 a large campaign "Hyytiälä United Measurements of Photochemistry and Particles in Air - Comprehensive Organic Precursor Emission Concentration 2010 (HUMPPA - COPEC-10)", was conducted in a boreal forest at the SMEAR II station in Hyytiälä, southwestern central Finland. The general goal was to study links between gas phase oxidation chemistry and particle properties and processes. The Finnish Meteorological Institute contributed to the campaign with an on-line analyzer MARGA 2S (Ten Brink et al., 2007) for semi-continuous (1-hr time resolution) measurement of water-soluble gases and ions. Concentrations of gases (HCl, HNO3, HNO2, NH3, SO2) and major ions in particles (Cl, NO3, SO4, NH4, Na, K, Mg, Ca) were measured in two size fractions: PM2.5 and PM10. The MARGA was kept running at SMEAR II also after the campaign. Here we discuss data collected until 30 April, 2011, and restrict the analysis to the nitrogen-containing gases. Ammonia plays a key role in neutralizing acidic atmospheric compounds and in aerosol formation. The concentration of semi-volatile aerosol species such as ammonium nitrate and ammonium chloride is strongly dependent on the gas phase precursors, NH3, HNO3 and HCl. HONO is of atmospheric importance due to its expected significant contribution to the production of OH radicals. Results and discussion The median concentrations of ammonia (NH3), nitrous acid (HONO) and nitric acid (HNO3) during whole period of 21 June 2010 - 30 April 2011 were 85, 54, and 57 ppt, respectively. The seasonal cycle was such that in summer the concentrations of all of these gases were the highest, the respective medians were 356, 70, and 81 ppt in June 21 - August 12, and lowest in winter (December - February), the respective medians were 38, 54, and 52 ppt. A very clear diurnal cycle of all these gases was observed, especially in July. In December there were no cyclic diurnal variation of these but in spring, especially in April the

  7. Formic acid requirement for the Savannah River Site Defense Waste Processing Facility melter feed preparation

    SciTech Connect

    Hsu, C.W.

    1991-01-01

    The Westinghouse Savannah River Company (WSRC) will vitrify the high-level radioactive waste into a borosilicate glass wasteform using a slurry-fed, joule-heated melter. Formic acid is used to treat the sludge slurry for melter feed preparation. Both a minimum formate requirement and a maximum allowable formate level need to be established to adequately prepare the sludge for melter feed. The data from the Savannah River Laboratory (SRL) Scale Glass Melter (SGM), Integrated DWPF Melter System (IDMS), and research mini-melter runs were used for this purpose. The stoichiometry for major reactions during formic acid treatment was revised to reflect the more predominant chemical reactions and their yields. A minimum formic acid requirement was established according to this revised stoichiometry. Methods for determining the minimum level of formic acid were specified. An operating envelope that includes the maximum total formate level and the minimum nitrate levels, was also proposed. 5 refs., 3 figs., 4 tabs.

  8. Specificity of the Antibody Receptor Site to D-Lysergamide: Model of a Physiological Receptor for Lysergic Acid Diethylamide

    PubMed Central

    Vunakis, Helen Van; Farrow, John T.; Gjika, Hilda B.; Levine, Lawrence

    1971-01-01

    Antibodies to D-lysergic acid have been produced in rabbits and guinea pigs and a radioimmunoassay for the hapten was developed. The specificity of this lysergamide-antilysergamide reaction was determined by competitive binding with unlabeled lysergic acid diethylamide (LSD), psychotomimetic drugs, neurotransmitters, and other compounds with diverse structures. LSD and several related ergot alkaloids were potent competitors, three to seven times more potent than lysergic acid itself. The N,N-dimethyl derivatives of several compounds, including tryptamine, 5-hydroxytryptamine, 4-hydroxytryptamine, 5-methoxytryptamine, tyramine, and mescaline, were only about ten times less effective than lysergic acid, even though these compounds lack some of the ring systems of lysergic acid. The pattern of inhibition by related compounds with various substituents suggests that the antibody receptor site recognizes structural features resembling the LSD molecule. In particular, the aromatic nucleus and the dimethylated ethylamine side chain in phenylethylamine and tryptamine derivatives may assume in solution a conformation resembling ring A and the methylated nitrogen in ring C of LSD. Among the tryptamine derivatives, a large percentage of the most potent competitors are also psychotomimetic compounds. PMID:5283939

  9. Envelope Membranes from Spinach Chloroplasts Are a Site of Metabolism of Fatty Acid Hydroperoxides.

    PubMed Central

    Blee, E.; Joyard, J.

    1996-01-01

    Enzymes in envelope membranes from spinach (Spinacia oleracea L.) chloroplasts were found to catalyze the rapid breakdown of fatty acid hydroperoxides. In contrast, no such activities were detected in the stroma or in thylakoids. In preparations of envelope membranes, 9S-hydroperoxy-10(E),12(Z)-octadecadienoic acid, 13S-hydroperoxy-9(Z),11(E)-octadecadienoic acid, or 13S-hydroperoxy-9(Z),11(E),15(Z)-octadecatrienoic acid were transformed at almost the same rates (1-2 [mu]mol min-1 mg-1 protein). The products formed were separated by reversed-phase high-pressure liquid chromatography and further characterized by gas chromatography-mass spectrometry. Fatty acid hydroperoxides were cleaved (a) into aldehydes and oxoacid fragments, corresponding to the functioning of a hydroperoxide lyase, (b) into ketols that were spontaneously formed from allene oxide synthesized by a hydroperoxide dehydratase, (c) into hydroxy compounds synthesized enzymatically by a system that has not yet been characterized, and (d) into oxoenes resulting from the hydroperoxidase activity of a lipoxygenase. Chloroplast envelope membranes therefore contain a whole set of enzymes that catalyze the synthesis of a variety of fatty acid derivatives, some of which may act as regulatory molecules. The results presented demonstrate a new role for the plastid envelope within the plant cell. PMID:12226196

  10. Self-catalyzed syntheses, structural characterization, DPPH radical scavenging-, cytotoxicity-, and DFT studies of phenoxyaliphatic acids of 1,8-dioxo-octahydroxanthene derivatives

    NASA Astrophysics Data System (ADS)

    Suresh Kumar, G. S.; Antony Muthu Prabhu, A.; Seethalashmi, P. G.; Bhuvanesh, N.; Kumaresan, S.

    2014-02-01

    One-pot, in-water syntheses of phenoxyaliphatic acids of 1,8-dioxo-octahydroxanthene derived from dimedone and formylphenoxyaliphatic acids are reported. Geometries of compounds 2b, 2c, and 5a have been examined crystallographically. The synthesized compounds showed better DPPH radical scavenging activity and cytotoxicity against A431 cancer cell line. The molecular properties of all synthesized xanthenes have been investigated using single crystal XRD and DFT method. Self-catalyzed Bronsted-Lowry acid catalytic behavior was also investigated by both experimental and theoretical methods.

  11. CD44 Binding to Hyaluronic Acid Is Redox Regulated by a Labile Disulfide Bond in the Hyaluronic Acid Binding Site

    PubMed Central

    Kellett-Clarke, Helena; Stegmann, Monika; Barclay, A. Neil; Metcalfe, Clive

    2015-01-01

    CD44 is the primary leukocyte cell surface receptor for hyaluronic acid (HA), a component of the extracellular matrix. Enzymatic post translational cleavage of labile disulfide bonds is a mechanism by which proteins are structurally regulated by imparting an allosteric change and altering activity. We have identified one such disulfide bond in CD44 formed by Cys77 and Cys97 that stabilises the HA binding groove. This bond is labile on the surface of leukocytes treated with chemical and enzymatic reducing agents. Analysis of CD44 crystal structures reveal the disulfide bond to be solvent accessible and in the–LH hook configuration characteristic of labile disulfide bonds. Kinetic trapping and binding experiments on CD44-Fc chimeric proteins show the bond is preferentially reduced over the other disulfide bonds in CD44 and reduction inhibits the CD44-HA interaction. Furthermore cells transfected with CD44 no longer adhere to HA coated surfaces after pre-treatment with reducing agents. The implications of CD44 redox regulation are discussed in the context of immune function, disease and therapeutic strategies. PMID:26379032

  12. Active-site amino acid residues in γ-glutamyltransferase and the nature of the γ-glutamyl-enzyme bond

    PubMed Central

    Elce, John S.

    1980-01-01

    Active-site residues in rat kidney γ-glutamyltransferase (EC 2.3.2.2) were investigated by means of chemical modification. 1. In the presence of maleate, the activity was inhibited by phenylmethanesulphonyl fluoride, and the inhibition was not reversed by β-mercaptoethanol, suggesting that a serine residue is close to the active site, but is shielded except in the presence of maleate. 2. Treatment of the enzyme with N-acetylimidazole modified an amino group, exposed a previously inaccessible cysteine residue and inhibited hydrolysis of the γ-glutamyl-enzyme intermediate, but not its formation. 3. After reaction of the enzyme successively with N-acetylimidazole and with non-radioactive iodoacetamide/serine/borate, two active-site residues reacted with iodo[14C]acetamide. One of these possessed a carboxy group, which formed a [14C]glycollamide ester, and the other was cysteine, shown by isolation of S-[14C]carboxymethylcysteine after acid hydrolysis. When N-acetylimidazole treatment was omitted, only the carboxy group reacted with iodo[14C]acetamide. 4. Isolation of the γ-[14C]glutamyl-enzyme intermediate was made easier by prior treatment of the enzyme with N-acetylimidazole. The γ-glutamyl-enzyme bond was stable to performic acid, and to hydroxylamine/urea at pH10, but was hydrolysed slowly at pH12, indicating attachment of the γ-[14C]glutamyl group in amide linkage to an amino group on the enzyme. Proteolysis of the γ-[14C]glutamyl-enzyme after performic acid oxidation gave rise to a small acidic radioactive peptide that was resistant to further proteolysis and was not identical with γ-glutamyl-ε-lysine. 5. A scheme for the catalytic mechanism is proposed. PMID:6104953

  13. Site and chirality selective chemical modifications of boron nitride nanotubes (BNNTs) via Lewis acid-base interactions.

    PubMed

    Sundaram, Rajashabala; Scheiner, Steve; Roy, Ajit K; Kar, Tapas

    2015-02-01

    The pristine BNNTs contain both Lewis acid (boron) and Lewis base (nitrogen) centers at their surface. Interactions of ammonia and borane molecules, representatives of Lewis base and acid as adsorbates respectively, with matching sites at the surface of BNNTs, have been explored in the present DFT study. Adsorption energies suggest stronger chemisorption (about 15-20 kcal mol(-1)) of borane than ammonia (about 5-10 kcal mol(-1)) in both armchair (4,4) and zigzag (8,0) variants of the tube. NH3 favors (8,0) over the (4,4) tube, whereas BH3 exhibits the opposite preference, indicating some chirality dependence on acid-base interactions. A new feature of bonding is found in BH3/AlH3-BNNTs (at the edge site) complexes, where one hydrogen of the guest molecule is involved in three-center two-electron bonding, in addition to dative covalent bond (N: → B). This interaction causes a reversal of electron flow from borane/alane to BNNT, making the tube an electron acceptor, suggesting tailoring of electronic properties could be possible by varying strength of incoming Lewis acids. On the contrary, BNNTs always behave as electron acceptor in ammonia complexes. IR, XPS and NMR spectra show some characteristic features of complexes and can help experimentalists to identify not only structures of such complexes but also the location of the guest molecules and design second functionalizations. Interaction with several other neutral BF3, BCl3, BH2CH3 and ionic CH3(+) acids as well as amino group (CH3NH2 and NH2COOH) were also studied. The strongest interaction (>100 kcal mol(-1)) is found in BNNT-CH3(+) complexes and H-bonds are the only source of stability of NH2COOH-BNNT complexes. PMID:25559141

  14. Chromatographic analysis of the effects of fatty acids and glycation on binding by probes for Sudlow sites I and II to human serum albumin.

    PubMed

    Anguizola, Jeanethe; Debolt, Erin; Suresh, D; Hage, David S

    2016-05-15

    The primary endogenous ligands of human serum albumin (HSA) are non-esterified fatty acids, with 0.1-2mol of fatty acids normally being bound to HSA. In type II diabetes, fatty acid levels in serum are often elevated, and the presence of high glucose results in an increase in the non-enzymatic glycation of HSA. High-performance affinity chromatography (HPAC) was used to examine the combined effects of glycation and the presence of long chain fatty acids on the binding of HSA with R-warfarin and l-tryptophan (i.e., probes for Sudlow sites I and II, the major sites for drugs on this protein). Zonal elution competition studies were used to examine the interactions of myristic acid, palmitic acid and stearic acid with these probes on HSA. It was found that all these fatty acids had direct competition with R-warfarin at Sudlow site I of normal HSA and glycated HSA, with the glycated HSA typically having stronger binding for the fatty acids at this site. At Sudlow site II, direct competition was observed for all the fatty acids with l-tryptophan when using normal HSA, while glycated HSA gave no competition or positive allosteric interactions between these fatty acids and l-tryptophan. These data indicated that glycation can alter the interactions of drugs and fatty acids at specific binding sites on HSA. The results of this study should lead to a better understanding of how these interactions may change during diabetes and demonstrate how HPAC can be used to examine drug/solute-protein interactions in complex systems. PMID:26468085

  15. Site-directed mutagenesis of conserved amino acids in the alpha subunit of toluene dioxygenase: potential mononuclear non-heme iron coordination sites.

    PubMed Central

    Jiang, H; Parales, R E; Lynch, N A; Gibson, D T

    1996-01-01

    The terminal oxygenase component of toluene dioxygenase from Pseudomonas putida F1 is an iron-sulfur protein (ISP(TOL)) that requires mononuclear iron for enzyme activity. Alignment of all available predicted amino acid sequences for the large (alpha) subunits of terminal oxygenases showed a conserved cluster of potential mononuclear iron-binding residues. These were between amino acids 210 and 230 in the alpha subunit (TodC1) of ISP(TOL). The conserved amino acids, Glu-214, Asp-219, Tyr-221, His-222, and His-228, were each independently replaced with an alanine residue by site-directed mutagenesis. Tyr-266 in TodC1, which has been suggested as an iron ligand, was treated in an identical manner. To assay toluene dioxygenase activity in the presence of TodC1 and its mutant forms, conditions for the reconstitution of wild-type ISP(TOL) activity from TodC1 and purified TodC2 (beta subunit) were developed and optimized. A mutation at Glu-214, Asp-219, His-222, or His-228 completely abolished toluene dioxygenase activity. TodC1 with an alanine substitution at either Tyr-221 or Tyr-266 retained partial enzyme activity (42 and 12%, respectively). In experiments with [14C]toluene, the two Tyr-->Ala mutations caused a reduction in the amount of Cis-[14C]-toluene dihydrodiol formed, whereas a mutation at Glu-214, Asp-219, His-222, or His-228 eliminated cis-toluene dihydrodiol formation. The expression level of all of the mutated TWO proteins was equivalent to that of wild-type TodC1 as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot (immunoblot) analyses. These results, in conjunction with the predicted amino acid sequences of 22 oxygenase components, suggest that the conserved motif Glu-X3-4,-Asp-X2-His-X4-5-His is critical for catalytic function and the glutamate, aspartate, and histidine residues may act as mononuclear iron ligands at the site of oxygen activation. PMID:8655491

  16. Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs.

    PubMed

    Hasan, Md Mehedi; Zhou, Yuan; Lu, Xiaotian; Li, Jinyan; Song, Jiangning; Zhang, Ziding

    2015-01-01

    Prokaryotic proteins are regulated by pupylation, a type of post-translational modification that contributes to cellular function in bacterial organisms. In pupylation process, the prokaryotic ubiquitin-like protein (Pup) tagging is functionally analogous to ubiquitination in order to tag target proteins for proteasomal degradation. To date, several experimental methods have been developed to identify pupylated proteins and their pupylation sites, but these experimental methods are generally laborious and costly. Therefore, computational methods that can accurately predict potential pupylation sites based on protein sequence information are highly desirable. In this paper, a novel predictor termed as pbPUP has been developed for accurate prediction of pupylation sites. In particular, a sophisticated sequence encoding scheme [i.e. the profile-based composition of k-spaced amino acid pairs (pbCKSAAP)] is used to represent the sequence patterns and evolutionary information of the sequence fragments surrounding pupylation sites. Then, a Support Vector Machine (SVM) classifier is trained using the pbCKSAAP encoding scheme. The final pbPUP predictor achieves an AUC value of 0.849 in 10-fold cross-validation tests and outperforms other existing predictors on a comprehensive independent test dataset. The proposed method is anticipated to be a helpful computational resource for the prediction of pupylation sites. The web server and curated datasets in this study are freely available at http://protein.cau.edu.cn/pbPUP/. PMID:26080082

  17. Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs

    PubMed Central

    Lu, Xiaotian; Li, Jinyan; Song, Jiangning; Zhang, Ziding

    2015-01-01

    Prokaryotic proteins are regulated by pupylation, a type of post-translational modification that contributes to cellular function in bacterial organisms. In pupylation process, the prokaryotic ubiquitin-like protein (Pup) tagging is functionally analogous to ubiquitination in order to tag target proteins for proteasomal degradation. To date, several experimental methods have been developed to identify pupylated proteins and their pupylation sites, but these experimental methods are generally laborious and costly. Therefore, computational methods that can accurately predict potential pupylation sites based on protein sequence information are highly desirable. In this paper, a novel predictor termed as pbPUP has been developed for accurate prediction of pupylation sites. In particular, a sophisticated sequence encoding scheme [i.e. the profile-based composition of k-spaced amino acid pairs (pbCKSAAP)] is used to represent the sequence patterns and evolutionary information of the sequence fragments surrounding pupylation sites. Then, a Support Vector Machine (SVM) classifier is trained using the pbCKSAAP encoding scheme. The final pbPUP predictor achieves an AUC value of 0.849 in10-fold cross-validation tests and outperforms other existing predictors on a comprehensive independent test dataset. The proposed method is anticipated to be a helpful computational resource for the prediction of pupylation sites. The web server and curated datasets in this study are freely available at http://protein.cau.edu.cn/pbPUP/. PMID:26080082

  18. Interaction of P-aminobenzoic acid with normal and sickel erythrocyte membrane: photoaffinity labelling of the binding sites

    SciTech Connect

    Premachandra, B.R.

    1986-03-05

    Electron microscopic studies revealed that P-Amino benzoic acid (PABA) could prevent eichinocytosis of red cells in vitro. Equilibrium binding studies with right side out membrane vesicles (ROV) revealed a similar number of binding sites (1.2-1.4 ..mu..mol/mg) and Kd (1.4-1.6 mM) values for both normal and sickle cell membranes. /sup 14/C-Azide analogue of PABA was synthesized as a photoaffinity label to probe its sites of interaction on the erythrocyte membranes. Competitive binding studies of PABA with its azide indicated that both the compounds share common binding sites on the membrane surface since a 20 fold excess of azide inhibited PABA binding in a linear fashion. The azide was covalently incorporated into the membrane components only upon irradiation (52-35% of the label found in the proteins and the rest in lipids). Electrophoretic analysis of photolabelled ROV revealed that the azide interacts chiefly with Band 3 protein. PABA inhibited both high and low affinity calcium (Ca) binding sites situated on either surface of the membrane in a non-competitive manner; however, Ca binding stimulated by Mg-ATP was not affected. Ca transport into inside out vesicles was inhibited by PABA; but it did not affect the calcium ATP-ase activity. The authors studies suggest that the mechanism of action of PABA is mediated by its interaction with Band 3 protein (anion channel), calcium channel and calcium binding sites of erythrocyte membrane.

  19. Counting Active Sites on Titanium Oxide-Silica Catalysts for Hydrogen Peroxide Activation through In Situ Poisoning with Phenylphosphonic Acid

    SciTech Connect

    Eaton, Todd R.; Boston, Andrew M.; Thompson, Anthony B.; Gray, Kimberly A.; Notestein, Justin M.

    2015-06-04

    Quantifying specific active sites in supported catalysts improves our understanding and assists in rational design. Supported oxides can undergo significant structural changes as surface densities increase from site-isolated cations to monolayers and crystallites, which changes the number of kinetically relevant sites. Herein, TiOx domains are titrated on TiOx–SiO2 selectively with phenylphosphonic acid (PPA). An ex situ method quantifies all fluid-accessible TiOx, whereas an in situ titration during cis-cyclooctene epoxidation provides previously unavailable values for the number of tetrahedral Ti sites on which H2O2 activation occurs. We use this method to determine the active site densities of 22 different catalysts with different synthesis methods, loadings, and characteristic spectra and find a single intrinsic turnover frequency for cis-cyclooctene epoxidation of (40±7) h-1. This simple method gives molecular-level insight into catalyst structure that is otherwise hidden when bulk techniques are used.

  20. Fluorescence properties and sequestration of peripheral anionic site specific ligands in bile acid hosts: Effect on acetylcholinesterase inhibition activity.

    PubMed

    Islam, Mullah Muhaiminul; Aguan, Kripamoy; Mitra, Sivaprasad

    2016-05-01

    The increase in fluorescence intensity of model acetyl cholinesterase (AChE) inhibitors like propidium iodide (PI) and ethidium bromide (EB) is due to sequestration of the probes in primary micellar aggregates of bile acid (BA) host medium with moderate binding affinity of ca. 10(2)-10(3)M(-1). Multiple regression analysis of solvent dependent fluorescence behavior of PI indicates the decrease in total nonradiative decay rate due to partial shielding of the probe from hydrogen bond donation ability of the aqueous medium in bile acid bound fraction. Both PI and EB affects AChE activity through mixed inhibition and consistent with one site binding model; however, PI (IC50=20±1μM) shows greater inhibition in comparison with EB (IC50=40±3μM) possibly due to stronger interaction with enzyme active site. The potency of AChE inhibition for both the compounds is drastically reduced in the presence of bile acid due to the formation of BA-inhibitor complex and subsequent reduction of active inhibitor fraction in the medium. Although the inhibition mechanism still remains the same, the course of catalytic reaction critically depends on equilibrium binding among several species present in the solution; particularly at low inhibitor concentration. All the kinetic parameters for enzyme inhibition reaction are nicely correlated with the association constant for BA-inhibitor complex formation. PMID:26974580

  1. Analysis of a nucleotide-binding site of 5-lipoxygenase by affinity labelling: binding characteristics and amino acid sequences.

    PubMed Central

    Zhang, Y Y; Hammarberg, T; Radmark, O; Samuelsson, B; Ng, C F; Funk, C D; Loscalzo, J

    2000-01-01

    5-Lipoxygenase (5LO) catalyses the first two steps in the biosynthesis of leukotrienes, which are inflammatory mediators derived from arachidonic acid. 5LO activity is stimulated by ATP; however, a consensus ATP-binding site or nucleotide-binding site has not been found in its protein sequence. In the present study, affinity and photoaffinity labelling of 5LO with 5'-p-fluorosulphonylbenzoyladenosine (FSBA) and 2-azido-ATP showed that 5LO bound to the ATP analogues quantitatively and specifically and that the incorporation of either analogue inhibited ATP stimulation of 5LO activity. The stoichiometry of the labelling was 1.4 mol of FSBA/mol of 5LO (of which ATP competed with 1 mol/mol) or 0.94 mol of 2-azido-ATP/mol of 5LO (of which ATP competed with 0.77 mol/mol). Labelling with FSBA prevented further labelling with 2-azido-ATP, indicating that the same binding site was occupied by both analogues. Other nucleotides (ADP, AMP, GTP, CTP and UTP) also competed with 2-azido-ATP labelling, suggesting that the site was a general nucleotide-binding site rather than a strict ATP-binding site. Ca(2+), which also stimulates 5LO activity, had no effect on the labelling of the nucleotide-binding site. Digestion with trypsin and peptide sequencing showed that two fragments of 5LO were labelled by 2-azido-ATP. These fragments correspond to residues 73-83 (KYWLNDDWYLK, in single-letter amino acid code) and 193-209 (FMHMFQSSWNDFADFEK) in the 5LO sequence. Trp-75 and Trp-201 in these peptides were modified by the labelling, suggesting that they were immediately adjacent to the C-2 position of the adenine ring of ATP. Given the stoichiometry of the labelling, the two peptide sequences of 5LO were probably near each other in the enzyme's tertiary structure, composing or surrounding the ATP-binding site of 5LO. PMID:11042125

  2. Identification of Rosmarinic Acid-Adducted Sites in Meat Proteins in a Gel Model under Oxidative Stress by Triple TOF MS/MS.

    PubMed

    Tang, Chang-Bo; Zhang, Wan-Gang; Wang, Yao-Song; Xing, Lu-Juan; Xu, Xing-Lian; Zhou, Guang-Hong

    2016-08-24

    Triple TOF MS/MS was used to identify adducts between rosmarinic acid (RosA)-derived quinones and meat proteins in a gel model under oxidative stress. Seventy-five RosA-modified peptides responded to 67 proteins with adduction of RosA. RosA conjugated with different amino acids in proteins, and His, Arg, and Lys adducts with RosA were identified for the first time in meat. A total of 8 peptides containing Cys, 14 peptides containing His, 48 peptides containing Arg, 64 peptides containing Lys, and 5 peptides containing N-termini that which participated in adduction reaction with RosA were identified, respectively. Seventy-seven adduction sites were subdivided into all adducted proteins including 2 N-terminal adduction sites, 3 Cys adduction sites, 4 His adduction sites, 29 Arg adduction sites, and 39 Lys adduction sites. Site occupancy analyses showed that approximately 80.597% of the proteins carried a single RosA-modified site, 14.925% retained two sites, 1.492% contained three sites, and the rest 2.985% had four or more sites. Large-scale triple TOF MS/MS mapping of RosA-adducted sites reveals the adduction regulations of quinone and different amino acids as well as the adduction ratios, which clarify phenol-protein adductions and pave the way for industrial meat processing and preservation. PMID:27486909

  3. Gas/particle partitioning of low-molecular-weight dicarboxylic acids at a suburban site in Saitama, Japan

    NASA Astrophysics Data System (ADS)

    Bao, Linfa; Matsumoto, Mariko; Kubota, Tsutomu; Sekiguchi, Kazuhiko; Wang, Qingyue; Sakamoto, Kazuhiko

    2012-02-01

    Low-molecular-weight dicarboxylic acids (diacids) exhibit semivolatile behavior in the atmosphere, but their partitioning between the gaseous and particulate phases is still unclear. An annular denuder-filter pack system with a cyclone PM 2.5 was employed to investigate the gaseous and particulate phase concentrations of diacids, with high collection efficiency of most target compounds. Saturated diacids, unsaturated diacids, ketocarboxylic acids, and dicarbonyls were determined in gaseous and particulate samples collected from a suburban site in Japan, during 2007 summer, 2008 late-winter and early-winter. The concentrations of gaseous and particulate diacids in early-winter were lower than those in summer, but higher than those in late-winter. Individual diacid in gaseous phase showed a relatively good correlation with ambient oxidants, but a low correlation with NO gas (a primary pollutant). Particulate fraction to the total amount ( FP) of individual acid was larger in winter than in summer, and also was larger at night than in the daytime. In the same sample, individual diacid and ketocarboxylic acid had higher particulate phase occurrence ( FP > 56% in summer), whereas unsaturated diacid had higher gaseous phase occurrence ( FP < 18% in summer). In summer, gas/particle partitioning of diacids varied diurnally; FP values of oxalic and glyoxylic acids increased from their lowest values in the morning to their highest values at night, exhibiting the similar diurnal variation of relative humidity in the atmosphere. The higher humidity at night may lead to the formation of droplets in which water-soluble gaseous phases can dissolve, thus promoting gas-to-particle conversion. These results suggest that gas/particle partitioning of diacids depends not only on the concentrations in the gaseous phase by photochemical oxidation, but also on the characteristics of the atmosphere (e.g., temperature, sunlight, and relative humidity) and the aerosols (e.g., acidity

  4. Investigation of metal binding sites on soil fulvic acid using Eu(III) luminescence spectroscopy

    SciTech Connect

    Yoon, T.H.; Moon, H. ); Park, Y.J.; Park, K.K. )

    1994-11-01

    The [sup 7]F[sub 0] [yields] [sup 5]D[sub 0] excitation spectra of Eu(III) complexed with soil fulvic acid (FA) were acquired over a range of solution pH (2.9-7.8) and FA concentrations (800-3200 mg L[sup [minus]1]) using a pulsed tunable dye laser system. The broad asymmetric excitation spectra were well-fitted to a sum of two conventional Lorentzian-shaped curves, revealing the existence of two types of carboxylate moieties for the binding of metal ions on FA which formed 1:1 (EuL[sup 2+]; L = carboxylate) and 1:2 complexes (EuL[sub 2][sup +]). The weaker binding species, EuL[sup 2+], seemed to be quite abundant and showed a rapid increase as the pH was raised from 2.9 to 6.3, but it was susceptible to hydrolysis at pH higher than 7 while the stronger binding species, EuL[sub 2][sup +], showed only a modest growth with an increase in pH. By contrast, on a more flexible synthetic linear polymer, poly(acrylic acid) (PAA) and poly(vinylbenzoic acid) (PVBA) as model polymers, EuL[sub 2][sup +] was seen as the dominant species except in acidic media. 28 refs., 10 figs., 3 tabs.

  5. Identification of a Binding Site for Unsaturated Fatty Acids in the Orphan Nuclear Receptor Nurr1.

    PubMed

    de Vera, Ian Mitchelle S; Giri, Pankaj K; Munoz-Tello, Paola; Brust, Richard; Fuhrmann, Jakob; Matta-Camacho, Edna; Shang, Jinsai; Campbell, Sean; Wilson, Henry D; Granados, Juan; Gardner, William J; Creamer, Trevor P; Solt, Laura A; Kojetin, Douglas J

    2016-07-15

    Nurr1/NR4A2 is an orphan nuclear receptor, and currently there are no known natural ligands that bind Nurr1. A recent metabolomics study identified unsaturated fatty acids, including arachidonic acid and docosahexaenoic acid (DHA), that interact with the ligand-binding domain (LBD) of a related orphan receptor, Nur77/NR4A1. However, the binding location and whether these ligands bind other NR4A receptors were not defined. Here, we show that unsaturated fatty acids also interact with the Nurr1 LBD, and solution NMR spectroscopy reveals the binding epitope of DHA at its putative ligand-binding pocket. Biochemical assays reveal that DHA-bound Nurr1 interacts with high affinity with a peptide derived from PIASγ, a protein that interacts with Nurr1 in cellular extracts, and DHA also affects cellular Nurr1 transactivation. This work is the first structural report of a natural ligand binding to a canonical NR4A ligand-binding pocket and indicates a natural ligand can bind and affect Nurr1 function. PMID:27128111

  6. [Studies of the fundamental nature of catalytic acidity, sites and intermediates]: Final performance (technical progress) report

    SciTech Connect

    Not Available

    1993-12-31

    This project was concerned with the fundamental nature of catalyst acidity in the H-zeolites and silica/alumina cracking catalysts. This report summarizes the progress on this project over the past five years. The titles of the twelve papers generated by this research are provided in the attached bibliography in chronological order.

  7. Chicoric acid binds to two sites and decreases the activity of the YopH bacterial virulence factor.

    PubMed

    Kuban-Jankowska, Alicja; Sahu, Kamlesh K; Gorska, Magdalena; Tuszynski, Jack A; Wozniak, Michal

    2016-01-19

    Chicoric acid (CA) is a phenolic compound present in dietary supplements with a large spectrum of biological properties reported ranging from antioxidant, to antiviral, to immunostimulatory properties. Due to the fact that chicoric acid promotes phagocytic activity and was reported as an allosteric inhibitor of the PTP1B phosphatase, we examined the effect of CA on YopH phosphatase from pathogenic bacteria, which block phagocytic processes of a host cell. We performed computational studies of chicoric acid binding to YopH as well as validation experiments with recombinant enzymes. In addition, we performed similar studies for caffeic and chlorogenic acids to compare the results. Docking experiments demonstrated that, from the tested compounds, only CA binds to both catalytic and secondary binding sites of YopH. Our experimental results showed that CA reduces activity of recombinant YopH phosphatase from Yersinia enterocolitica and human CD45 phosphatase. The inhibition caused by CA was irreversible and did not induce oxidation of catalytic cysteine. We proposed that inactivation of YopH induced by CA is involved with allosteric inhibition by interacting with essential regions responsible for ligand binding. PMID:26735581

  8. Chicoric acid binds to two sites and decreases the activity of the YopH bacterial virulence factor

    PubMed Central

    Kuban-Jankowska, Alicja; Sahu, Kamlesh K.; Gorska, Magdalena; Tuszynski, Jack A.; Wozniak, Michal

    2016-01-01

    Chicoric acid (CA) is a phenolic compound present in dietary supplements with a large spectrum of biological properties reported ranging from antioxidant, to antiviral, to immunostimulatory properties. Due to the fact that chicoric acid promotes phagocytic activity and was reported as an allosteric inhibitor of the PTP1B phosphatase, we examined the effect of CA on YopH phosphatase from pathogenic bacteria, which block phagocytic processes of a host cell. We performed computational studies of chicoric acid binding to YopH as well as validation experiments with recombinant enzymes. In addition, we performed similar studies for caffeic and chlorogenic acids to compare the results. Docking experiments demonstrated that, from the tested compounds, only CA binds to both catalytic and secondary binding sites of YopH. Our experimental results showed that CA reduces activity of recombinant YopH phosphatase from Yersinia enterocolitica and human CD45 phosphatase. The inhibition caused by CA was irreversible and did not induce oxidation of catalytic cysteine. We proposed that inactivation of YopH induced by CA is involved with allosteric inhibition by interacting with essential regions responsible for ligand binding. PMID:26735581

  9. Hydrogenation of biofuels with formic acid over a palladium-based ternary catalyst with two types of active sites.

    PubMed

    Wang, Liang; Zhang, Bingsen; Meng, Xiangju; Su, Dang Sheng; Xiao, Feng-Shou

    2014-06-01

    A composite catalyst including palladium nanoparticles on titania (TiO2) and on nitrogen-modified porous carbon (Pd/TiO2@N-C) is synthesized from palladium salts, tetrabutyl titanate, and chitosan. N2 sorption isotherms show that the catalyst has a high BET surface area (229 m(2)  g(-1)) and large porosity. XPS and TEM characterization of the catalyst shows that palladium species with different chemical states are well dispersed across the TiO2 and nitrogen-modified porous carbon, respectively. The Pd/TiO2@N-C catalyst is very active and shows excellent stability towards hydrogenation of vanillin to 2-methoxy-4-methylphenol using formic acid as hydrogen source. This activity can be attributed to a synergistic effect between the Pd/TiO2 (a catalyst for dehydrogenation of formic acid) and Pd/N-C (a catalyst for hydrogenation of vanillin) sites. PMID:24861954

  10. Subnucleosomes and their relationships to the arrangement of histone binding sites along nucleosome deoxyribonucleic acid

    SciTech Connect

    Nelson, D.A.; Mencke, A.J.; Chambers, S.A.; Oosterhof, D.K.; Rill, R.L.

    1982-01-01

    Micrococcal nuclease cleaves within nucleosomes at sites spaced about 10.4 base pairs (bp) apart. Cleavages at sites equivalent to 30-35 bp from the ends of 146-bp cores cause spontaneous loss of an H2a-H2b pair associated with 30-40 bp length DNA. Cleavages at certain other sites do not affect the nucleosome integrity unless a solvent perturbant such as urea is added. Chromatin moderately digested with micrococcal nuclease, when fractionated by sedimentation or electrophoresis in the presence of 3 M urea, yielded four previously unobserved subnucleosomes with the following histone/DNA compositions: (H3)/sub 2/(H4)/sub 2/(H2a)(H2b)/95-115 bp; (H3)(H4)/70-80 bp DNA; (H2a)(H2b)/50-60 bp DNA; and (H1)/60-70 bp DNA. All but the latter subnucleosome were also obtained upon DNase I digestion of purified nucleosome cores labeled on the 5' ends with /sup 32/P. Only subnucleosomes that retained H2a and H2b also retained labeled ends. These results show that H2a and H2b are paired on the terminal 30-40 bp of core DNA, as suggested from analyses of histone-DNA cross-link products by Mirzabekov and coworkers. Considerations of the orgins and compositions of subnucleosomes and of cross-linking data suggest an expanded model for the locations of histone binding sites along nucleosome core DNA. The principal features of this model are (i) strong electrostatic binding sites of H2a and H2b occur at positions approximately 20-30 bp from the core ends, (ii) strong electrostatic binding sites of H3 and H4 occur primarily on the central 40 bp of core DNA, (iii) strong nonelectrostatic, urea-sensitive binding sites of H3 and H4 occur at positions approximately 30-50 bp from the core ends, and (iv) urea-sensitive binding sites of H2a or H2b may occur on the terminal 10-20 bp of core DNA.

  11. Remediation of acid mine drainage at the friendship hill national historic site with a pulsed limestone bed process

    USGS Publications Warehouse

    Sibrell, P.L.; Watten, B.; Boone, T.

    2003-01-01

    A new process utilizing pulsed fluidized limestone beds was tested for the remediation of acid mine drainage at the Friendship Hill National Historic Site, in southwestern Pennsylvania. A 230 liter-per-minute treatment system was constructed and operated over a fourteen-month period from June 2000 through September 2001. Over this period of time, 50,000 metric tons of limestone were used to treat 50 million liters of water. The influent water pH was 2.5 and acidity was 1000 mg/L as CaCO3. Despite the high potential for armoring at the site, effluent pH during normal plant operation ranged from 5.7 to 7.8 and averaged 6.8. As a result of the high influent acidity, sufficient CO2 was generated and recycled to provide a net alkaline discharge with about 50 mg/L as CaCO3 alkalinity. Additions of commercial CO2 increased effluent alkalinity to as high as 300 mg/L, and could be a useful process management tool for transient high flows or acidities. Metal removal rates were 95% for aluminum (60 mg/L in influent), 50 to 90% for iron (Fe), depending on the ratio of ferrous to ferric iron, which varied seasonally (200 mg/L in influent), and <10% of manganese (Mn) (10 mg/L in influent). Ferrous iron and Mn removal was incomplete because of the high pH required for precipitation of these species. Iron removal could be improved by increased aeration following neutralization, and Mn removal could be effected by a post treatment passive settling/oxidation pond. Metal hydroxide sludges were settled in settling tanks, and then hauled from the site for aesthetic purposes. Over 450 metric tons of sludge were removed from the water over the life of the project. The dried sludge was tested by the Toxicity Characteristics Leaching Protocol (TCLP) and was found to be non-hazardous. Treatment costs were $43,000 per year and $1.08 per m 3, but could be decreased to $22,000 and $0.51 per m3 by decreasing labor use and by onsite sludge handling. These results confirm the utility of the new

  12. Site-Specifically Labeled Immunoconjugates for Molecular Imaging--Part 2: Peptide Tags and Unnatural Amino Acids.

    PubMed

    Adumeau, Pierre; Sharma, Sai Kiran; Brent, Colleen; Zeglis, Brian M

    2016-04-01

    Molecular imaging using radioisotope- or fluorophore-labeled antibodies is increasingly becoming a critical component of modern precision medicine. Yet despite this promise, the vast majority of these immunoconjugates are synthesized via the random coupling of amine-reactive bifunctional probes to lysines within the antibody, a process that can result in heterogeneous and poorly defined constructs with suboptimal pharmacological properties. In an effort to circumvent these issues, the last 5 years have played witness to a great deal of research focused on the creation of effective strategies for the site-specific attachment of payloads to antibodies. These chemoselective modification methods yield immunoconjugates that are more homogenous and better defined than constructs created using traditional synthetic approaches. Moreover, site-specifically labeled immunoconjugates have also been shown to exhibit superior in vivo behavior compared to their randomly modified cousins. The over-arching goal of this two-part review is to provide a broad yet detailed account of the various site-specific bioconjugation approaches that have been used to create immunoconjugates for positron emission tomography (PET), single photon emission computed tomography (SPECT), and fluorescence imaging. In Part 1, we covered site-specific bioconjugation techniques based on the modification of cysteine residues and the chemoenzymatic manipulation of glycans. In Part 2, we will detail two families of bioconjugation approaches that leverage biochemical tools to achieve site-specificity. First, we will discuss modification methods that employ peptide tags either as sites for enzyme-catalyzed ligations or as radiometal coordination architectures. And second, we will examine bioconjugation strategies predicated on the incorporation of unnatural or non-canonical amino acids into antibodies via genetic engineering. Finally, we will compare the advantages and disadvantages of the modification

  13. Site-Specifically Labeled Immunoconjugates for Molecular Imaging—Part 2: Peptide Tags and Unnatural Amino Acids

    PubMed Central

    Adumeau, Pierre; Sharma, Sai Kiran; Brent, Colleen; Zeglis, Brian M.

    2016-01-01

    Molecular imaging using radioisotope- or fluorophore-labeled antibodies is increasingly becoming a critical component of modern precision medicine. Yet despite this promise, the vast majority of these immunoconjugates are synthesized via the random coupling of amine-reactive bifunctional probes to lysines within the antibody, a process that can result in heterogeneous and poorly defined constructs with suboptimal pharmacological properties. In an effort to circumvent these issues, the last 5 years have played witness to a great deal of research focused on the creation of effective strategies for the site-specific attachment of payloads to antibodies. These chemoselective modification methods yield immunoconjugates that are more homogenous and better defined than constructs created using traditional synthetic approaches. Moreover, site-specifically labeled immunoconjugates have also been shown to exhibit superior in vivo behavior compared to their randomly modified cousins. The over-arching goal of this two-part review is to provide a broad yet detailed account of the various site-specific bioconjugation approaches that have been used to create immunoconjugates for positron emission tomography (PET), single photon emission computed tomography (SPECT), and fluorescence imaging. In Part 1, we covered site-specific bioconjugation techniques based on the modification of cysteine residues and the chemoenzymatic manipulation of glycans. In Part 2, we will detail two families of bioconjugation approaches that leverage biochemical tools to achieve site-specificity. First, we will discuss modification methods that employ peptide tags either as sites for enzyme-catalyzed ligations or as radiometal coordination architectures. And second, we will examine bioconjugation strategies predicated on the incorporation of unnatural or non-canonical amino acids into antibodies via genetic engineering. Finally, we will compare the advantages and disadvantages of the modification

  14. Technology development for phosphoric acid fuel cell powerplant (phase 2). [on site integrated energy systems

    NASA Technical Reports Server (NTRS)

    Christner, L.

    1980-01-01

    Progress is reported in the development of material, cell components, and reformers for on site integrated energy systems. Internal resistance and contact resistance were improved. Dissolved gases (O2, N2, and CO2) were found to have no effect on the electrochemical corrosion of phenolic composites. Stack performance was increased by 100 mV over the average 1979 level.

  15. Prediction of posttranslational modification sites from amino acid sequences with kernel methods.

    PubMed

    Xu, Yan; Wang, Xiaobo; Wang, Yongcui; Tian, Yingjie; Shao, Xiaojian; Wu, Ling-Yun; Deng, Naiyang

    2014-03-01

    Post-translational modification (PTM) is the chemical modification of a protein after its translation and one of the later steps in protein biosynthesis for many proteins. It plays an important role which modifies the end product of gene expression and contributes to biological processes and diseased conditions. However, the experimental methods for identifying PTM sites are both costly and time-consuming. Hence computational methods are highly desired. In this work, a novel encoding method PSPM (position-specific propensity matrices) is developed. Then a support vector machine (SVM) with the kernel matrix computed by PSPM is applied to predict the PTM sites. The experimental results indicate that the performance of new method is better or comparable with the existing methods. Therefore, the new method is a useful computational resource for the identification of PTM sites. A unified standalone software PTMPred is developed. It can be used to predict all types of PTM sites if the user provides the training datasets. The software can be freely downloaded from http://www.aporc.org/doc/wiki/PTMPred. PMID:24291233

  16. Structure and Mutagenesis of Neural Cell Adhesion Molecule Domains Evidence for Flexibility in the Placement of Polysialic Acid Attachment Sites

    SciTech Connect

    Foley, Deirdre A.; Swartzentruber, Kristin G.; Lavie, Arnon; Colley, Karen J.

    2010-11-09

    The addition of {alpha}2,8-polysialic acid to the N-glycans of the neural cell adhesion molecule, NCAM, is critical for brain development and plays roles in synaptic plasticity, learning and memory, neuronal regeneration, and the growth and invasiveness of cancer cells. Our previous work indicates that the polysialylation of two N-glycans located on the fifth immunoglobulin domain (Ig5) of NCAM requires the presence of specific sequences in the adjacent fibronectin type III repeat (FN1). To understand the relationship of these two domains, we have solved the crystal structure of the NCAM Ig5-FN1 tandem. Unexpectedly, the structure reveals that the sites of Ig5 polysialylation are on the opposite face from the FN1 residues previously found to be critical for N-glycan polysialylation, suggesting that the Ig5-FN1 domain relationship may be flexible and/or that there is flexibility in the placement of Ig5 glycosylation sites for polysialylation. To test the latter possibility, new Ig5 glycosylation sites were engineered and their polysialylation tested. We observed some flexibility in glycosylation site location for polysialylation and demonstrate that the lack of polysialylation of a glycan attached to Asn-423 may be in part related to a lack of terminal processing. The data also suggest that, although the polysialyltransferases do not require the Ig5 domain for NCAM recognition, their ability to engage with this domain is necessary for polysialylation to occur on Ig5 N-glycans.

  17. The Significance of Lewis Acid Sites for the Selective Catalytic Reduction of Nitric Oxide on Vanadium-Based Catalysts.

    PubMed

    Marberger, Adrian; Ferri, Davide; Elsener, Martin; Kröcher, Oliver

    2016-09-19

    The long debated reaction mechanisms of the selective catalytic reduction (SCR) of nitric oxide with ammonia (NH3 ) on vanadium-based catalysts rely on the involvement of Brønsted or Lewis acid sites. This issue has been clearly elucidated using a combination of transient perturbations of the catalyst environment with operando time-resolved spectroscopy to obtain unique molecular level insights. Nitric oxide reacts predominantly with NH3 coordinated to Lewis sites on vanadia on tungsta-titania (V2 O5 -WO3 -TiO2 ), while Brønsted sites are not involved in the catalytic cycle. The Lewis site is a mono-oxo vanadyl group that reduces only in the presence of both nitric oxide and NH3 . We were also able to verify the formation of the nitrosamide (NH2 NO) intermediate, which forms in tandem with vanadium reduction, and thus the entire mechanism of SCR. Our experimental approach, demonstrated in the specific case of SCR, promises to progress the understanding of chemical reactions of technological relevance. PMID:27553251

  18. Capture and Recycling of Sortase A through Site-Specific Labeling with Lithocholic Acid.

    PubMed

    Rosen, Christian B; Kwant, Richard L; MacDonald, James I; Rao, Meera; Francis, Matthew B

    2016-07-18

    Enzyme-mediated protein modification often requires large amounts of biocatalyst, adding significant costs to the process and limiting industrial applications. Herein, we demonstrate a scalable and straightforward strategy for the efficient capture and recycling of enzymes using a small-molecule affinity tag. A proline variant of an evolved sortase A (SrtA 7M) was N-terminally labeled with lithocholic acid (LA)-an inexpensive bile acid that exhibits strong binding to β-cyclodextrin (βCD). Capture and recycling of the LA-Pro-SrtA 7M conjugate was achieved using βCD-modified sepharose resin. The LA-Pro-SrtA 7M conjugate retained full enzymatic activity, even after multiple rounds of recycling. PMID:27239057

  19. One site is enough: a theoretical investigation of iron-catalyzed dehydrogenation of formic Acid.

    PubMed

    Sánchez-de-Armas, Rocío; Xue, Liqin; Ahlquist, Mårten S G

    2013-09-01

    Dehydrogenation of HCO2H: The reaction mechanism for the dehydrogenation of formic acid catalyzed by a highly active and selective iron complex has been studied by DFT. The most favorable pathway shows the hydride in Fe-H complexes acting as a spectator ligand throughout the catalytic cycle. This result opens up the Fe complex for modification in order to achieve more efficient and selective catalysts. PMID:23907850

  20. (3H) 5,7-dichlorokynurenic acid, a high affinity ligand for the NMDA receptor glycine regulatory site

    SciTech Connect

    Hurt, S.D.; Baron, B.M. )

    1991-01-01

    The NMDA subtype of glutamate receptors is allosterically linked to a strychnine-insensitive glycine regulatory site. Kynurenic acid and its halogenated derivatives are non-competitive NMDA antagonists acting at the glycine site. The authors have prepared (3H) 5,7-dichlorokyrurenic acid (DCKA) as an antagonist radioligand and have characterized its binding. 3-Bromo-5,7-DCKA was catalytically dehalogenated in the presence of tritium gas and HPLC purified to yield (3H) 5,7-DCKA with a specific activity of 17.6 Ci/mmol. (3H) 5,7-DCKA bound to rat brain synaptosomes with a Kd of 69 {plus minus} 23 nM and Bmax = 14.5 {plus minus} 3.2 pmoles/mg protein. Binding was 65-70% specific at 10 nM (3H) 5,7-DCKA. This ligand is thus more selective and has higher affinity than (3H) glycine, in addition to being an antagonist.

  1. Distinguishing two groups of flavin reductases by analyzing the protonation state of an active site carboxylic acid.

    PubMed

    Dumit, Verónica I; Cortez, Néstor; Matthias Ullmann, G

    2011-07-01

    Flavin-containing reductases are involved in a wide variety of physiological reactions such as photosynthesis, nitric oxide synthesis, and detoxification of foreign compounds, including therapeutic drugs. Ferredoxin-NADP(H)-reductase (FNR) is the prototypical enzyme of this family. The fold of this protein is highly conserved and occurs as one domain of several multidomain enzymes such as the members of the diflavin reductase family. The enzymes of this family have emerged as fusion of a FNR and a flavodoxin. Although the active sites of these enzymes are very similar, different enzymes function in opposite directions, that is, some reduce oxidized nicotinamide adenine dinucleotide phosphate (NADP(+)) and some oxidize reduced nicotinamide adenine dinucleotide phosphate (NADPH). In this work, we analyze the protonation behavior of titratable residues of these enzymes through electrostatic calculations. We find that a highly conserved carboxylic acid in the active site shows a different titration behavior in different flavin reductases. This residue is deprotonated in flavin reductases present in plastids, but protonated in bacterial counterparts and in diflavin reductases. The protonation state of the carboxylic acid may also influence substrate binding. The physiological substrate for plastidic enzymes is NADP(+), but it is NADPH for the other mentioned reductases. In this article, we discuss the relevance of the environment of this residue for its protonation and its importance in catalysis. Our results allow to reinterpret and explain experimental data. PMID:21538544

  2. Heterogeneous Chemistry of Lipopolysaccharides with Gas-Phase Nitric Acid: Reactive Sites and Reaction Pathways.

    PubMed

    Trueblood, Jonathan V; Estillore, Armando D; Lee, Christopher; Dowling, Jacqueline A; Prather, Kimberly A; Grassian, Vicki H

    2016-08-18

    Recent studies have shown that sea spray aerosol (SSA) has a size-dependent, complex composition consisting of biomolecules and biologically derived organic compounds in addition to salts. This additional chemical complexity most likely influences the heterogeneous reactivity of SSA, as these other components will have different reactive sites and reaction pathways. In this study, we focus on the reactivity of a class of particles derived from some of the biological components of sea spray aerosol including lipopolysaccharides (LPS) that undergo heterogeneous chemistry within the reactive sites of the biological molecule. Examples of these reactions and the relevant reactive sites are proposed as follows: R-COONa(s) + HNO3(g) → NaNO3 + R-COOH and R-HPO4Na(s) + HNO3(g) → NaNO3 + R-H2PO4. These reactions may be a heterogeneous pathway not only for sea spray aerosol but also for a variety of other types of atmospheric aerosol as well. PMID:27445084

  3. Impact of acid mine drainages on surficial waters of an abandoned mining site.

    PubMed

    García-Lorenzo, M L; Marimón, J; Navarro-Hervás, M C; Pérez-Sirvent, C; Martínez-Sánchez, M J; Molina-Ruiz, José

    2016-04-01

    Weathering of sulphide minerals produces a great variety of efflorescences of soluble sulphate salts. These minerals play an important role for environmental pollution, since they can be either a sink or a source for acidity and trace elements. This paper aims to characterise surface waters affected by mining activities in the Sierra Minera of Cartagena-La Union (SE, Spain). Water samples were analysed for trace metals (Zn, Cd, Pb, Cu, As and Fe), major ions (Na(+), K(+), Ca(2+) and Mg(2+)) and anions (F(-), Cl(-), NO3 (-), CO3 (2-), SO4 (2-)) concentrations and were submitted to an "evaporation-precipitation" experiment that consisted in identifying the salts resulting from the evaporation of the water aliquots sampled onsite. Mineralogy of the salts was studied using X-ray diffraction and compared with the results of calculations using VISUAL MINTEQ. The study area is heavily polluted as a result of historical mining and processing activities that has produced large amount of wastes characterised by a high trace elements content, acidic pH and containing minerals resulting from the supergene alteration of the raw materials. The mineralogical study of the efflorescences obtained from waters shows that magnesium, zinc, iron and aluminium sulphates predominate in the acid mine drainage precipitates. Minerals of the hexahydrite group have been quantified together with minerals of the rozenite group, alunogen and other phases such as coquimbite and copiapite. Calcium sulphates correspond exclusively to gypsum. In a semiarid climate, such as that of the study area, these minerals contribute to understand the response of the system to episodic rainfall events. MINTEQ model could be used for the analysis of waters affected by mining activities but simulation of evaporation gives more realistic results considering that MINTEQ does not consider soluble hydrated salts. PMID:26347422

  4. Genetic Incorporation of the Unnatural Amino Acid p-Acetyl Phenylalanine into Proteins for Site-Directed Spin Labeling

    PubMed Central

    Evans, Eric G.B.; Millhauser, Glenn L.

    2016-01-01

    Site-directed spin labeling (SDSL) is a powerful tool for the characterization of protein structure and dynamics; however, its application in many systems is hampered by the reliance on unique and benign cysteine substitutions for the site-specific attachment of the spin label. An elegant solution to this problem involves the use of genetically encoded unnatural amino acids (UAAs) containing reactive functional groups that are chemically orthogonal to those of the 20 amino acids found naturally in proteins. These unique functional groups can then be selectively reacted with an appropriately functionalized spin probe. In this chapter, we detail the genetic incorporation of the ketone-bearing amino acid p-acetyl phenylalanine (pAcPhe) into recombinant proteins expressed in E. coli. Incorporation of pAcPhe is followed by chemoselective reaction of the ketone side chain with a hydroxylamine-functionalized nitroxide to afford the spin-labeled side chain “K1,” and we present two protocols for successful K1 labeling of proteins bearing site-specific pAcPhe. We outline the basic requirements for pAcPhe incorporation and labeling, with an emphasis on practical aspects that must be considered by the researcher if high yields of UAA incorporation and efficient labeling reactions are to be achieved. To this end, we highlight recent advances that have led to increased yields of pAcPhe incorporation, and discuss the use of aniline-based catalysts allowing for facile conjugation of the hydroxylamine spin label under mild reaction conditions. To illustrate the utility of K1 labeling in proteins where traditional cysteine-based SDSL methods are problematic, we site-specifically K1 label the cellular prion protein at two positions in the C-terminal domain and determine the interspin distance using double electron–electron resonance EPR. Recent advances in UAA incorporation and ketone-based bioconjugation, in combination with the commercial availability of all requisite

  5. Element mobility during pyrite weathering: implications for acid and heavy metal pollution at mining-impacted sites

    NASA Astrophysics Data System (ADS)

    Lu, Long; Wang, Rucheng; Chen, Fanrong; Xue, Jiyue; Zhang, Peihua; Lu, Jianjun

    2005-11-01

    Based on back scattered electron images and electron micro-probe analysis results, four alteration layers, including a transition layer, a reticulated ferric oxide layer, a nubby ferric oxide layer and a cellular ferric oxide layer, were identified in the naturally weathering products of pyrite. These layers represent a progressive alteration sequence of pyrite under weathering conditions. The cellular ferric oxide layer correlates with the strongest weathering phase and results from the dissolution of nubby ferric oxide by acidic porewater. Leaching coefficient was introduced to better express the response of element mobility to the degree of pyrite weathering. Its variation shows that the mobility of S, Co and Bi is stronger than As, Cu and Zn. Sulfur in pyrite is oxidized to sulfuric acid and sulfate that are basically released into to porewater, and heavy metals Co and Bi are evidently released by acid dissolution. As, Cu and Zn are enriched in ferric oxide by adsorption and by co-precipitation, but they would re-release to the environment via desorption or dissolution when porewater pH becomes low enough. Consequently, Co, Bi, As, Cu and Zn may pose a substantial impact on water quality. Considering that metal mobility and its concentration in mine waste are two important factors influencing heavy metal pollution at mining-impacted sites, Bi and Co are more important pollutants in this case.

  6. Fatty Acids and Breast Cancer: Make Them on Site or Have Them Delivered.

    PubMed

    Kinlaw, William B; Baures, Paul W; Lupien, Leslie E; Davis, Wilson L; Kuemmerle, Nancy B

    2016-10-01

    Brisk fatty acid (FA) production by cancer cells is accommodated by the Warburg effect. Most breast and other cancer cell types are addicted to fatty acids (FA), which they require for membrane phospholipid synthesis, signaling purposes, and energy production. Expression of the enzymes required for FA synthesis is closely linked to each of the major classes of signaling molecules that stimulate BC cell proliferation. This review focuses on the regulation of FA synthesis in BC cells, and the impact of FA, or the lack thereof, on the tumor cell phenotype. Given growing awareness of the impact of dietary fat and obesity on BC biology, we will also examine the less-frequently considered notion that, in addition to de novo FA synthesis, the lipolytic uptake of preformed FA may also be an important mechanism of lipid acquisition. Indeed, it appears that cancer cells may exist at different points along a "lipogenic-lipolytic axis," and FA uptake could thwart attempts to exploit the strict requirement for FA focused solely on inhibition of de novo FA synthesis. Strategies for clinically targeting FA metabolism will be discussed, and the current status of the medicinal chemistry in this area will be assessed. J. Cell. Physiol. 231: 2128-2141, 2016. © 2016 Wiley Periodicals, Inc. PMID:26844415

  7. Acid-induced change in ozone-reactive site in indole ring of tryptophan

    SciTech Connect

    Matsumura, Sueo Yoshimura, Ayuko; Okazaki, Kazuyuki; Fijitani, Noboru; Hattori, Hideki

    2009-03-13

    It is well established that ozone as well as oxygen activated by tryptophan 2,3-dioxygenase or indoleamine 2,3-dioxygenase cleave the 2,3-C=C bond of the indole ring of tryptophan to produce N-formylkynurenine. In the present study, however, we found that exposure of tryptophan to aqueous ozone at and below pH 4.5 generated a different compound. The compound was identified as kynurenine by high performance liquid chromatography and mass spectrometry. Exposure of N-formylkynurenine to acidic ozone did not generate a significant amount of kynurenine, indicating that the kynurenine was not produced via N-formylkynurenine. Acidic ozone thus appears to cleave the 1, 2-N-C bond in place of the 2,3-C=C bond of the indole ring, followed by liberation of the 2-C atom. The 1,2-N-C bond and 2,3-C=C bond are likely to undergo changes in their nature of bonding on acidification, enabling ozone to react with the former bond but not with the latter bond.

  8. One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections.

    PubMed

    Mingo, Janire; Erramuzpe, Asier; Luna, Sandra; Aurtenetxe, Olaia; Amo, Laura; Diez, Ibai; Schepens, Jan T G; Hendriks, Wiljan J A J; Cortés, Jesús M; Pulido, Rafael

    2016-01-01

    Site-directed mutagenesis (SDM) is a powerful tool to create defined collections of protein variants for experimental and clinical purposes, but effectiveness is compromised when a large number of mutations is required. We present here a one-tube-only standardized SDM approach that generates comprehensive collections of amino acid substitution variants, including scanning- and single site-multiple mutations. The approach combines unified mutagenic primer design with the mixing of multiple distinct primer pairs and/or plasmid templates to increase the yield of a single inverse-PCR mutagenesis reaction. Also, a user-friendly program for automatic design of standardized primers for Ala-scanning mutagenesis is made available. Experimental results were compared with a modeling approach together with stochastic simulation data. For single site-multiple mutagenesis purposes and for simultaneous mutagenesis in different plasmid backgrounds, combination of primer sets and/or plasmid templates in a single reaction tube yielded the distinct mutations in a stochastic fashion. For scanning mutagenesis, we found that a combination of overlapping primer sets in a single PCR reaction allowed the yield of different individual mutations, although this yield did not necessarily follow a stochastic trend. Double mutants were generated when the overlap of primer pairs was below 60%. Our results illustrate that one-tube-only SDM effectively reduces the number of reactions required in large-scale mutagenesis strategies, facilitating the generation of comprehensive collections of protein variants suitable for functional analysis. PMID:27548698

  9. One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections

    PubMed Central

    Mingo, Janire; Erramuzpe, Asier; Luna, Sandra; Aurtenetxe, Olaia; Amo, Laura; Diez, Ibai; Schepens, Jan T. G.; Hendriks, Wiljan J. A. J.; Cortés, Jesús M.; Pulido, Rafael

    2016-01-01

    Site-directed mutagenesis (SDM) is a powerful tool to create defined collections of protein variants for experimental and clinical purposes, but effectiveness is compromised when a large number of mutations is required. We present here a one-tube-only standardized SDM approach that generates comprehensive collections of amino acid substitution variants, including scanning- and single site-multiple mutations. The approach combines unified mutagenic primer design with the mixing of multiple distinct primer pairs and/or plasmid templates to increase the yield of a single inverse-PCR mutagenesis reaction. Also, a user-friendly program for automatic design of standardized primers for Ala-scanning mutagenesis is made available. Experimental results were compared with a modeling approach together with stochastic simulation data. For single site-multiple mutagenesis purposes and for simultaneous mutagenesis in different plasmid backgrounds, combination of primer sets and/or plasmid templates in a single reaction tube yielded the distinct mutations in a stochastic fashion. For scanning mutagenesis, we found that a combination of overlapping primer sets in a single PCR reaction allowed the yield of different individual mutations, although this yield did not necessarily follow a stochastic trend. Double mutants were generated when the overlap of primer pairs was below 60%. Our results illustrate that one-tube-only SDM effectively reduces the number of reactions required in large-scale mutagenesis strategies, facilitating the generation of comprehensive collections of protein variants suitable for functional analysis. PMID:27548698

  10. Increase in the Bmax of gamma-aminobutyric acid-A recognition sites in brain regions of mice receiving diazepam.

    PubMed Central

    Ferrero, P; Guidotti, A; Costa, E

    1984-01-01

    gamma-Aminobutyric acid (GABA) receptors were characterized in vivo by studying ex vivo the binding of [3H]muscimol to cerebellum, cortex, hippocampus, and corpus striatum of mice receiving intravenous injections of tracer doses of high-specific-activity (approximately equal to 30 Ci/mmol) [3H]muscimol. This ligand binds with high affinity (apparent Kd, 2-3 X 10(-9) M) to a single population of binding sites (apparent Bmax, 250-180 fmol per 10 mg of protein). Pharmacological studies using drugs that selectively bind to GABAA or GABAB receptors suggest that [3H]muscimol specifically labels a GABAA recognition site. Moreover, diazepam (1.5 mumol/kg, i.p.) increases the Bmax but fails to change the affinity of [3H]muscimol binding to different brain areas. This diazepam-elicited increase in Bmax is blocked in mice receiving the diazepam antagonist Ro 15-1788 (ethyl-8-fluoro-5,6-dihydro-5-methyl-6-oxo-4H-imidazo[1,5a]-[1,4] benzodiazepine-3-carboxylate). Since the diazepam-induced increase of [3H]muscimol binding is paralleled by a significant potentiation of the inhibitory effect of muscimol on locomotor activity, it is proposed that the facilitatory action on GABAergic transmission elicited in vivo by diazepam is mediated by an increase in the Bmax of the binding sites of GABAA receptors. Images PMID:6326115

  11. Computational Investigation of Locked Nucleic Acid (LNA) Nucleotides in the Active Sites of DNA Polymerases by Molecular Docking Simulations

    PubMed Central

    Poongavanam, Vasanthanathan; Madala, Praveen K.; Højland, Torben; Veedu, Rakesh N.

    2014-01-01

    Aptamers constitute a potential class of therapeutic molecules typically selected from a large pool of oligonucleotides against a specific target. With a scope of developing unique shorter aptamers with very high biostability and affinity, locked nucleic acid (LNA) nucleotides have been investigated as a substrate for various polymerases. Various reports showed that some thermophilic B-family DNA polymerases, particularly KOD and Phusion DNA polymerases, accepted LNA-nucleoside 5′-triphosphates as substrates. In this study, we investigated the docking of LNA nucleotides in the active sites of RB69 and KOD DNA polymerases by molecular docking simulations. The study revealed that the incoming LNA-TTP is bound in the active site of the RB69 and KOD DNA polymerases in a manner similar to that seen in the case of dTTP, and with LNA structure, there is no other option than the locked C3′-endo conformation which in fact helps better orienting within the active site. PMID:25036012

  12. Isolation and properties of the acid site-specific endonuclease from mature eggs of the sea urchin Strongylocentrotus intermedius

    SciTech Connect

    Sibirtsev, Yu.T.; Konechnyi, A.A.; Rasskazov, V.A.

    1986-01-10

    An acid site-specific endonuclease has been detected in mature sea urchin eggs and cells of embryos at early stages of differentiation. Fractionation with ammonium sulfate, followed by chromatography on columns with DEAE, phosphocellulose, and hydroxyapatite resulted in an 18,000-fold purification. The molecular weight of the enzyme was determined at approx. 29,000, the optimum pH 5.5. The activity of the enzyme does not depend on divalent metal ions, EDTA, ATP, and tRNA, but it is modulated to a substantial degree by NaCl. The maximum rate of cleavage of the DNA supercoil (form I) is observed at 100 mM NaCl. Increasing the NaCl concentration to 350 mM only slightly lowers the rate of cleavage of form I, yielding form II, but entirely suppresses the accumulation of form III. Restriction analysis of the products of enzymatic hydrolysis of Co1E1 and pBR322 DNA showed that at the early stages of hydrolysis the enzyme exhibits pronounced specificity for definite sites, the number of which is 12 for Co1 E1 DNA and 8 sites for pBR322 DNA.

  13. Schiff base structured acid-base cooperative dual sites in an ionic solid catalyst lead to efficient heterogeneous knoevenagel condensations.

    PubMed

    Zhang, Mingjue; Zhao, Pingping; Leng, Yan; Chen, Guojian; Wang, Jun; Huang, Jun

    2012-10-01

    An acid-base bifunctional ionic solid catalyst [PySaIm](3)PW was synthesized by the anion exchange of the ionic-liquid (IL) precursor 1-(2-salicylaldimine)pyridinium bromide ([PySaIm]Br) with the Keggin-structured sodium phosphotungstate (Na(3) PW). The catalyst was characterized by FTIR, UV/Vis, XRD, SEM, Brunauer-Emmett-Teller (BET) theory, thermogravimetric analysis, (1)H NMR spectroscopy, ESI-MS, elemental analysis, and melting points. Together with various counterparts, [PySaIm](3)PW was evaluated in Knoevenagel condensation under solvent and solvent-free conditions. The Schiff base structure attached to the IL cation of [PySaIm](3)PW involves acidic salicyl hydroxyl and basic imine, and provides a controlled nearby position for the acid-base dual sites. The high melting and insoluble properties of [PySaIm](3)PW are relative to the large volume and high valence of PW anions, as well as the intermolecular hydrogen-bonding networks among inorganic anions and IL cations. The ionic solid catalyst [PySaIm](3)PW leads to heterogeneous Knoevenagel condensations. In solvent-free condensation of benzaldehyde with ethyl cyanoacetate, it exhibits a conversion of 95.8 % and a selectivity of 100 %; the conversion is even much higher than that (78.2 %) with ethanol as a solvent. The solid catalyst has a convenient recoverability with only a slight decrease in conversion following subsequent recyclings. Furthermore, the new catalyst is highly applicable to many substrates of aromatic aldehydes with activated methylene compounds. On the basis of the characterization and reaction results, a unique acid-base cooperative mechanism within a Schiff base structure is proposed and discussed, which thoroughly explains not only the highly efficient catalytic performance of [PySaIm](3)PW, but also the lower activities of various control catalysts. PMID:22907828

  14. Characterization of cyclo-Acetoacetyl-L-Tryptophan Dimethylallyltransferase in Cyclopiazonic Acid Biosynthesis: Substrate Promiscuity and Site Directed Mutagenesis Studies

    PubMed Central

    Liu, Xinyu; Walsh, Christopher T.

    2009-01-01

    The fungal neurotoxin α-cyclopiazonic acid (CPA), a nanomolar inhibitor of Ca2+-ATPase with a unique pentacyclic indole tetramic acid scaffold is assembled by a three enzyme pathway CpaS, CpaD and CpaO in Aspergillus sp. We recently characterized the first pathway-specific enzyme CpaS, a hybrid two module polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) that generates cyclo-acetoacetyl-L-tryptophan (cAATrp). Here we report the characterization of the second pathway-specific enzyme CpaD that regiospecifically dimethylallylates cAATrp to form β-cyclopiazonic acid. By exploring the tryptophan and tetramate moieties of cAATrp, we demonstrate that CpaD discriminates against free Trp but accepts tryptophan-containing thiohydantoins, diketopiperazines and linear peptides as substrates for C4-prenylation and also acts as regiospecific O-dimethylallyltransferase (DMAT) on a tyrosine-derived tetramic acid. Comparative evaluation of CpaDs from A. oryzae RIB40 and A. flavus NRRL3357 indicated the importance of the N-terminal region for its activity. Sequence alignment of CpaD with eleven homologous fungal Trp-DMATs revealed five regions of conservation suggesting the presense of critical motifs that could be diagonostic for discovering additional Trp-DMATs. Subsequent site-directed mutagenesis studies identified five polar/charged residues and five tyrosine residues within these motifs that are critical for CpaD activity. This motif characerization will enable a gene probe-based approach to discover additional biosynthetic Trp-DMATs. PMID:19877600

  15. Acid potentiation of the capsaicin receptor determined by a key extracellular site.

    PubMed

    Jordt, S E; Tominaga, M; Julius, D

    2000-07-01

    The capsaicin (vanilloid) receptor, VR1, is a sensory neuron-specific ion channel that serves as a polymodal detector of pain-producing chemical and physical stimuli. The response of VR1 to capsaicin or noxious heat is dynamically potentiated by extracellular protons within a pH range encountered during tissue acidosis, such as that associated with arthritis, infarction, tumor growth, and other forms of injury. A molecular determinant for this important physiological activity was localized to an extracellular Glu residue (E600) in the region linking the fifth transmembrane domain with the putative pore-forming region of the channel. We suggest that this residue serves as a key regulatory site of the receptor by setting sensitivity to other noxious stimuli in response to changes in extracellular proton concentration. We also demonstrate that protons, vanilloids, and heat promote channel opening through distinct pathways, because mutations at a second site (E648) selectively abrogate proton-evoked channel activation without diminishing responses to other noxious stimuli. Our findings provide molecular evidence for stimulus-specific steps in VR1 activation and offer strategies for the development of novel analgesic agents. PMID:10859346

  16. Synthesis and Site-Specific Incorporation of Red-Shifted Azobenzene Amino Acids into Proteins.

    PubMed

    John, Alford A; Ramil, Carlo P; Tian, Yulin; Cheng, Gang; Lin, Qing

    2015-12-18

    A series of red-shifted azobenzene amino acids were synthesized in moderate-to-excellent yields via a two-step procedure in which tyrosine derivatives were first oxidized to the corresponding quinonoidal spirolactones followed by ceric ammonium nitrate-catalyzed azo formation with the substituted phenylhydrazines. The resulting azobenzene-alanine derivatives exhibited efficient trans/cis photoswitching upon irradiation with a blue (448 nm) or green (530 nm) LED light. Moreover, nine superfolder green fluorescent protein (sfGFP) mutants carrying the azobenzene-alanine analogues were expressed in E. coli in good yields via amber codon suppression with an orthogonal tRNA/PylRS pair, and one of the mutants showed durable photoswitching with the LED light. PMID:26650435

  17. Tunable translational control using site-specific unnatural amino acid incorporation in Escherichia coli

    PubMed Central

    2015-01-01

    Translation of target gene transcripts in Escherichia coli harboring UAG amber stop codons can be switched on by the amber-codon-specific incorporation of an exogenously supplied unnatural amino acid, 3-iodo-L-tyrosine. Here, we report that this translational switch can control the translational efficiency at any intermediate magnitude by adjustment of the 3-iodo-L-tyrosine concentration in the medium, as a tunable translational controller. The translational efficiency of a target gene reached maximum levels with 10−5 M 3-iodo-L-tyrosine, and intermediate levels were observed with suboptimal concentrations (approximately spanning a 2-log10 concentration range, 10−7–10−5 M). Such intermediate-level expression was also confirmed in individual bacteria. PMID:25945307

  18. Site-Selective Binding of Nanoparticles to Double-Stranded DNA via Peptide Nucleic Acid "Invasion"

    SciTech Connect

    Stadler, A.L.; van der Lelie, D.; Sun, D.; Maye, M. M.; Gang, O.

    2011-04-01

    We demonstrate a novel method for by-design placement of nano-objects along double-stranded (ds) DNA. A molecular intercalator, designed as a peptide nucleic acid (PNA)-DNA chimera, is able to invade dsDNA at the PNA-side due to the hybridization specificity between PNA and one of the duplex strands. At the same time, the single-stranded (ss) DNA tail of the chimera, allows for anchoring of nano-objects that have been functionalized with complementary ssDNA. The developed method is applied for interparticle attachment and for the fabrication of particle clusters using a dsDNA template. This method significantly broadens the molecular toolbox for constructing nanoscale systems by including the most conventional not yet utilized DNA motif, double helix DNA.

  19. Neurologic syndrome associated with homozygous mutation at MAG sialic acid binding site.

    PubMed

    Roda, Ricardo H; FitzGibbon, Edmond J; Boucekkine, Houda; Schindler, Alice B; Blackstone, Craig

    2016-08-01

    The MAG gene encodes myelin-associated glycoprotein (MAG), an abundant protein involved in axon-glial interactions and myelination during nerve regeneration. Several members of a consanguineous family with a clinical syndrome reminiscent of Pelizaeus-Merzbacher disease and demyelinating leukodystrophy on brain MRI were recently found to harbor a homozygous missense p.Ser133Arg MAG mutation. Here, we report two brothers from a nonconsanguineous family afflicted with progressive cognitive impairment, neuropathy, ataxia, nystagmus, and gait disorder. Exome sequencing revealed the homozygous missense mutation p.Arg118His in MAG. This Arg118 residue in immunoglobulin domain 1 is critical for sialic acid binding, providing a compelling mechanistic basis for disease pathogenesis. PMID:27606346

  20. Magic-angle-spinning NMR studies of acid sites in zeolite H-ZSM-5

    SciTech Connect

    Brunner, E.; Ernst, H.; Freude, D.; Froehlich, T.; Hunger, M.; Pfeifer, H. )

    1991-01-01

    {sup 1}H, {sup 13}C, {sup 27}Al, and {sup 29}Si magic-angle-spinning (MAS) NMR was used to elucidate the nature of the catalytic activity of zeolite H-ZSM-5. {sup 1}H MAS NMR of sealed samples after mild hydrothermal dealumination shows that the enhanced activity for n-hexane cracking is not due to an enhanced Bronstead acidity. The concentrations of the various OH groups and aluminous species suggest that the reason for the enhanced catalytic activity is the interaction of the n-hexane molecule with a bridging hydroxyl group and with extra-framework aluminium species, which give rise to the enhanced activity, cannot be easily removed from their positions, and are therefore immobilized by the zeolitic framework.

  1. Direct conversion of bio-ethanol to isobutene on nanosized Zn(x)Zr(y)O(z) mixed oxides with balanced acid-base sites.

    PubMed

    Sun, Junming; Zhu, Kake; Gao, Feng; Wang, Chongmin; Liu, Jun; Peden, Charles H F; Wang, Yong

    2011-07-27

    We report the design and synthesis of nanosized Zn(x)Zr(y)O(z) mixed oxides for direct and high-yield conversion of bio-ethanol to isobutene (~83%). ZnO is addded to ZrO(2) to selectively passivate zirconia's strong Lewis acidic sites and weaken Brönsted acidic sites, while simultaneously introducing basicity. As a result, the undesired reactions of bio-ethanol dehydration and acetone polymerization/coking are suppressed. Instead, a surface basic site-catalyzed ethanol dehydrogenation to acetaldehyde, acetaldehyde to acetone conversion via a complex pathway including aldol-condensation/dehydrogenation, and a Brönsted acidic site-catalyzed acetone-to-isobutene reaction pathway dominates on the nanosized Zn(x)Zr(y)O(z) mixed oxide catalyst, leading to a highly selective process for direct conversion of bio-ethanol to isobutene. PMID:21682296

  2. Drug-nucleic acid interactions: conformational flexibility at the intercalation site.

    PubMed Central

    Berman, H M; Neidle, S; Stodola, R K

    1978-01-01

    The conformational features of the intercalation site in polynucleotides were examined. We found that, for all the crystal structures of drug-dinucleoside complexes studied thus far, two torsion angles differ from those found in A RNA (phi and chi) and that alternate sugar puckering is not a prerequisite for intercalation. This intercalation geometry, which is the basis of helix axis displacement in a polymer, would necessitate conformational changes in the adjacent nucleotides. The base-turn angle is less sensitive to the conformation of the backbone than it is to small alterations in the base-pairing geometry. We postulate that this angle is dependent on the nature of the intercalating drug. PMID:273246

  3. Characterization of an intracellular hyaluronic acid binding site in isolated rat hepatocytes

    SciTech Connect

    Frost, S.J.; Raja, R.H.; Weigel, P.H. )

    1990-11-13

    125I-HA, prepared by chemical modification at the reducing sugar, specifically binds to rat hepatocytes in suspension or culture. Intact hepatocytes have relatively few surface 125I-HA binding sites and show low specific binding. However, permeabilization of hepatocytes with the nonionic detergent digitonin results in increased specific 125I-HA binding (45-65%) and a very large increase in the number of specific 125I-HA binding sites. Scatchard analysis of equilibrium 125I-HA binding to permeabilized hepatocytes in suspension at 4 degrees C indicates a Kd = 1.8 x 10(-7) M and 1.3 x 10(6) molecules of HA (Mr approximately 30,000) bound per cell at saturation. Hepatocytes in primary culture for 24 h show the same affinity but the total number of HA molecules bound per cell at saturation decreases to approximately 6.2 x 10(5). Increasing the ionic strength above physiologic concentrations decreases 125I-HA binding to permeable cells, whereas decreasing the ionic strength above causes an approximately 4-fold increase. The divalent cation chelator EGTA does not prevent binding nor does it release 125I-HA bound in the presence of 2 mM CaCl2, although higher divalent cation concentrations stimulate 125I-HA binding. Ten millimolar CaCl2 or MnCl2 increases HA binding 3-6-fold compared to EGTA-treated cells. Ten millimolar MgCl2, SrCl2, or BaCl2 increased HA binding by 2-fold. The specific binding of 125I-HA to digitonin-treated hepatocytes at 4{degrees}C increased greater than 10-fold at pH 5.0 as compared to pH 7.

  4. A Mutational Analysis of Active Site Residues in trans-3-Chloroacrylic Acid Dehalogenase

    PubMed Central

    Poelarends, Gerrit J.; Serrano, Hector; Huddleston, Jamison P.; Johnson, William H.; Whitman, Christian P.

    2013-01-01

    trans -3-Chloroacrylic acid dehalogenase (CaaD) catalyzes the hydrolytic dehalogenation of trans-3-haloacrylates to yield malonate semialdehyde by a mechanism utilizing βPro-1, αArg-8, αArg-11, and αGlu-52. These residues are implicated in a promiscuous hydratase activity where 2-oxo-3-pentynoate is processed to acetopyruvate. The roles of three nearby residues (βAsn-39, αPhe-39, and αPhe-50) are unexplored. Mutants were constructed at these positions (βN39A, αF39A, αF39T, αF50A and αF50Y) and kinetic parameters determined along with those of the αR8K and αR11K mutants. Analysis indicates that αArg-8, αArg-11, and βAsn-39 are critical for dehalogenase activity whereas αArg-11 and αPhe-50 are critical for hydratase activity. Docking studies suggest structural bases for these observations. PMID:23851010

  5. Changes in polysialic acid expression on myeloid cells during differentiation and recruitment to sites of inflammation: Role in phagocytosis

    PubMed Central

    Stamatos, Nicholas M; Zhang, Lei; Jokilammi, Anne; Finne, Jukka; Chen, Wilbur H; El-Maarouf, Abderrahman; Cross, Alan S; Hankey, Kim G

    2014-01-01

    Polysialic acid (polySia) is a unique linear homopolymer of α2,8-linked sialic acid that has been studied extensively as a posttranslational modification of neural cell adhesion molecule in the central nervous system. Only two proteins are known to be polysialylated in cells of the immune system: CD56 on human natural killer cells and murine bone marrow (BM) leukocytes, and neuropilin-2 (NRP-2) on dendritic cells (DCs). We tested the hypothesis that polySia expression is regulated during maturation and migration of leukocytes and plays a role in functional activity. Using wild-type and NCAM−/− mice, we show that BM neutrophils express only polysialylated CD56, whereas a subset of BM monocytes expresses polysialylated CD56 and/or another polysialylated protein(s). We demonstrate that polysialylated CD56 expression is progressively down-regulated in wild-type monocytes and monocyte-derived cells during migration from BM through peripheral blood to pulmonary and peritoneal sites of inflammation. Freshly isolated monocyte-derived peritoneal macrophages are devoid of polySia yet re-express polySia on NRP-2 and an additional protein(s) after maintenance in culture. Removal of polySia from these cells enhances phagocytosis of Klebsiella pneumoniae, suggesting that down-regulation of polySia on macrophages facilitates bacterial clearance. Using wild-type and NRP-2−/− mice, we demonstrate that NRP-2 and an additional protein(s) are polysialylated by ST8 SiaIV in BM-derived DCs. We conclude that polySia expression in monocyte-derived cells is dynamically regulated by ST8 SiaIV activity and by expression of carrier proteins during recruitment to sites of inflammation and influences cellular interactions with microbes, contributing to innate and adaptive immune responses. PMID:24865221

  6. Site-directed mutagenesis of tobacco anionic peroxidase: Effect of additional aromatic amino acids on stability and activity.

    PubMed

    Poloznikov, A A; Zakharova, G S; Chubar, T A; Hushpulian, D M; Tishkov, V I; Gazaryan, I G

    2015-08-01

    Tobacco anionic peroxidase (TOP) is known to effectively catalyze luminol oxidation without enhancers, in contrast to horseradish peroxidase (HRP). To pursue structure-activity relationship studies for TOP, two amino acids have been chosen for mutation, namely Thr151, close to the heme plane, and Phe140 at the entrance to the active site pocket. Three mutant forms TOP F140Y, T151W and F140Y/T151W have been expressed in Escherichia coli, and reactivated to yield active enzymes. Single-point mutations introducing additional aromatic amino acid residues at the surface of TOP exhibit a significant effect on the enzyme catalytic activity and stability as judged by the results of steady-state and transient kinetics studies. TOP T151W is up to 4-fold more active towards a number of aromatic substrates including luminol, whereas TOP F140Y is 2-fold more stable against thermal inactivation and 8-fold more stable in the reaction course. These steady-state observations have been rationalized with the help of transient kinetic studies on the enzyme reaction with hydrogen peroxide in a single turnover regime. The stopped-flow data reveal (a) an increased stability of F140Y Compound I towards hydrogen peroxide, and thus, a higher operational stability as compared to the wild-type enzyme, and (b) a lesser leakage of oxidative equivalents from TOP T151W Compound I resulting in the increased catalytic activity. The results obtained show that TOP unique properties can be further improved for practical applications by site-directed mutagenesis. PMID:25957835

  7. Acid mine drainage risks - A modeling approach to siting mine facilities in Northern Minnesota USA

    NASA Astrophysics Data System (ADS)

    Myers, Tom

    2016-02-01

    Most watershed-scale planning for mine-caused contamination concerns remediation of past problems while future planning relies heavily on engineering controls. As an alternative, a watershed scale groundwater fate and transport model for the Rainy Headwaters, a northeastern Minnesota watershed, has been developed to examine the risks of leaks or spills to a pristine downstream watershed. The model shows that the risk depends on the location and whether the source of the leak is on the surface or from deeper underground facilities. Underground sources cause loads that last longer but arrive at rivers after a longer travel time and have lower concentrations due to dilution and attenuation. Surface contaminant sources could cause much more short-term damage to the resource. Because groundwater dominates baseflow, mine contaminant seepage would cause the most damage during low flow periods. Groundwater flow and transport modeling is a useful tool for decreasing the risk to downgradient sources by aiding in the placement of mine facilities. Although mines are located based on the minerals, advance planning and analysis could avoid siting mine facilities where failure or leaks would cause too much natural resource damage. Watershed scale transport modeling could help locate the facilities or decide in advance that the mine should not be constructed due to the risk to downstream resources.

  8. An arylaminopyridazine derivative of gamma-aminobutyric acid (GABA) is a selective and competitive antagonist at the GABAA receptor site.

    PubMed Central

    Chambon, J P; Feltz, P; Heaulme, M; Restle, S; Schlichter, R; Biziere, K; Wermuth, C G

    1985-01-01

    In view of finding a new gamma-aminobutyric acid (GABA) receptor ligand we synthesized an arylaminopyridazine derivative of GABA, SR 95103 [2-(carboxy-3'-propyl)-3-amino-4-methyl-6-phenylpyridazinium chloride]. SR 95103 displaced [3H]GABA from rat brain membranes with an apparent Ki of 2.2 microM and a Hill number near 1.0. SR 95103 (1-100 microM) antagonized the GABA-mediated enhancement of [3H]diazepam binding in a concentration-dependent manner without affecting [3H]diazepam binding per se. SR 95103 competitively antagonized GABA-induced membrane depolarization in rat spinal ganglia. In all these experiments, the potency of SR 95103 was close to that of bicuculline. SR 95103 (100 microM) did not interact with a variety of central receptors--in particular the GABAB, the strychnine, and the glutamate receptors--did not inhibit Na+-dependent synaptosomal GABA uptake, and did not affect GABA-transaminase and glutamic acid decarboxylase activities. Intraperitoneally administered SR 95103 elicited clonicotonic seizures in mice (ED50 = 180 mg/kg). On the basis of these results it is postulated that St 95103 is a competitive antagonist of GABA at the GABAA receptor site. In addition to being an interesting lead structure for the search of GABA ligands, SR 95103 could also be a useful tool to investigate GABA receptor subtypes because it is freely soluble in water and chemically stable. Images PMID:2984669

  9. Vesiculoviral matrix (M) protein occupies nucleic acid binding site at nucleoporin pair (Rae1∙Nup98)

    SciTech Connect

    Quan, Beili; Seo, Hyuk-Soo; Blobel, Günter; Ren, Yi

    2014-07-01

    mRNA export factor 1 (Rae1) and nucleoporin 98 (Nup98) are host cell targets for the matrix (M) protein of vesicular stomatitis virus (VSV). How Rae1 functions in mRNA export and how M protein targets both Rae1 and Nup98 are not understood at the molecular level. To obtain structural insights, we assembled a 1:1:1 complex of M•Rae1•Nup98 and established a crystal structure at 3.15-Å resolution. We found that the M protein contacts the Rae1•Nup98 heterodimer principally by two protrusions projecting from the globular domain of M like a finger and thumb. Both projections clamp to the side of the β-propeller of Rae1, with the finger also contacting Nup98. The most prominent feature of the finger is highly conserved Methionine 51 (Met51) with upstream and downstream acidic residues. The complementary surface on Rae1 displays a deep hydrophobic pocket, into which Met51 fastens like a bolt, and a groove of basic residues on either side, which bond to the acidic residues of the finger. Notably, the M protein competed for in vitro binding of various oligonucleotides to Rae1•Nup98. We localized this competing activity of M to its finger using a synthetic peptide. Collectively, our data suggest that Rae1 serves as a binding protein for the phosphate backbone of any nucleic acid and that the finger of M mimics this ligand. In the context of mRNA export, we propose that a given mRNA segment, after having been deproteinated by helicase, is transiently reproteinated by Nup98-tethered Rae1. We suggest that such repetitive cycles provide cytoplasmic stopover sites required for ratcheting mRNA across the nuclear pore.

  10. CS2 activation at uranium(III) siloxide ate complexes: the effect of a Lewis acidic site.

    PubMed

    Camp, Clément; Cooper, Oliver; Andrez, Julie; Pécaut, Jacques; Mazzanti, Marinella

    2015-02-14

    Multimetallic cooperative binding of heteroallenes provides an attractive route to their activation, but the reduction of CS(2) at heterobimetallic sites, associating an electron-rich metal with a main group Lewis acid has not been explored. Here we show that the presence of a heterometallic U, K site plays an important role in the CS(2) reduction by uranium(iii) complexes of the electron-rich and the sterically demanding tris(tert-butoxy)siloxide ligand. Specifically, the ion-pair complex [K(18c6)][U(OSi(O(t)Bu)(3))(4)], 1, leads preferentially to the reductive disproportionation of CS(2) to K(2)CS(3) and CS. The crystal structure of the thiocarbonate intermediate complex [U(OSi(O(t)Bu(3)(4) (μ(3)-κ(2):κ(2):κ(2-)CS(3))K(2)(18c6)(2)], 2, isolated from the toluene reaction mixture has been determined. In contrast, the heterobimetallic complex [U(OSi(O(t)Bu(3)(4)K], 3, promotes preferentially the reductive dimerization of CS(2) to K(2)C(2)S(4) and K(2)C(3)S(5). The [K(2)C(2)S(4)(DMSO)(3)](n), 5, and [U(OSi(O(t)Bu)(3))(4)K(2)(C(3)S(5))](n), 6, polymeric compounds were isolated from this reaction and structurally characterized. PMID:25436831