The nature of the active site in heterogeneous metal catalysis

DEFF Research Database (Denmark)

Nørskov, Jens Kehlet; Bligaard, Thomas; Larsen, Britt Hvolbæk

2008-01-01

This tutorial review, of relevance for the surface science and heterogeneous catalysis communities, provides a molecular-level discussion of the nature of the active sites in metal catalysis. Fundamental concepts such as "Bronsted-Evans-Polanyi relations'' and "volcano curves'' are introduced...

Students' Understanding of Acids/Bases in Organic Chemistry Contexts

Science.gov (United States)

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…

Modeling Ethanol Decomposition on Transition Metals: A Combined Application of Scaling and Bronsted-Evans-Polanyi Relations

DEFF Research Database (Denmark)

Ferrin, P.; Simonetti, D.; Kandoi, S.

2009-01-01

calculations necessary to describe trends in activity and selectivity across metal and alloy surfaces, thus extending the reach of DFT to more complex systems. In-this work, the well-known family of Bronsted-Evans-Polanyi (BEP) correlations, connecting minima with maxima in the potential energy surface...... on a subset of these surfaces are calculated. Experiments on supported catalysts verify that this simple model is reasonably accurate in describing reactivity trends across metals, suggesting that the combination of BEP and scaling relations may substantially reduce the cost of DFT calculations required...

Bronsted acid-functionalized choline chloride-butane sultone for the ...

Indian Academy of Sciences (India)

M P PADMA PRIYA

2018-03-21

Mar 21, 2018 ... Choline chloride and 1,4-butane sultone were combined to obtain a sulphonic acid-functionalized ..... Knifton J F and Sanderson J R 1990 Method for produc- ... alkenes via the Knoevenagel condensation Tetrahedron. Lett.

Surface acidity of calcium phosphate and calcium hydroxyapatite: FTIR spectroscopic study of low-temperature CO adsorption

International Nuclear Information System (INIS)

Pekounov, Yassen; Chakarova, Kristina; Hadjiivanov, Konstantin

2009-01-01

The surface properties of calcium phosphate precursor (CP) and crystalline calcium hydroxyapatite (HA) prepared biomimetically have been studied by IR spectroscopy of adsorbed CO. Both samples are characterized by the absence of Bronsted acidity. Low-temperature CO adsorption on CP evacuated at 523 K leads to formation of only one family of Ca 2+ -CO species (2168 cm -1 ). The analysis indicates that the respective calcium ions on the surface are not isolated. Similar spectra were obtained with HA evacuated at 573 K. In this case, however, the Ca 2+ -CO band was detected at 2165 cm -1 due to enhanced lateral interaction between the adsorbed CO molecules. Another family of Ca 2+ sites (Ca 2+ -CO band at 2178 cm -1 ) was created after evacuation of the HA sample at 673 K. These sites were assumed to be a result of sample dehydroxylation. The results demonstrate the absence of any protonic acidity of the samples (i.e. P-OH surface groups) and weak electrostatic Lewis acidity caused by coordinatively unsaturated Ca 2+ cations.

Quantitative 3D Fluorescence Imaging of Single Catalytic Turnovers Reveals Spatiotemporal Gradients in Reactivity of Zeolite H-ZSM-5 Crystals upon Steaming

NARCIS (Netherlands)

Ristanovic, Zoran|info:eu-repo/dai/nl/328233005; Hofmann, Jan P.|info:eu-repo/dai/nl/355351110; De Cremer, Gert; Kubarev, Alexey V.; Rohnke, Marcus; Meirer, Florian; Hofkens, Johan; Roeffaers, Maarten B. J.; Weckhuysen, Bert M.|info:eu-repo/dai/nl/285484397

2015-01-01

Optimizing the number, distribution, and accessibility of Bronsted acid sites in zeolite-based catalysts is of a paramount importance to further improve their catalytic performance. However, it remains challenging to measure real-time changes in reactivity of single zeolite catalyst particles by

Acidic and catalytic properties of hierarchical zeolites and hybrid ordered mesoporous materials assembled from MFI protozeolitic units

Czech Academy of Sciences Publication Activity Database

Serrano, D. P.; García, R. A.; Vicente, G.; Linares, M.; Vitvarová, Dana; Čejka, Jiří

2011-01-01

Roč. 279, č. 2 (2011), s. 366-380 ISSN 0021-9517 Institutional research plan: CEZ:AV0Z40400503 Keywords : hierarchical zeolites * hybrid zeolitic-mesostructured materials * Bronsted and Lewis acid centres Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.002, year: 2011

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

Science.gov (United States)

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…

The 11C-radioisotopic study of methanol conversion on V-MCM-41; the influence of methyl iodide on the transformation

International Nuclear Information System (INIS)

Sarkadi-Priboczki, E.; Szelecsenyi, F.; Kovacs, Z.; Solmaz, A.; Balci, S.; Dogu, T.

2007-01-01

Complete text of publication follows. The MCM-41 mesoporous material has Lewis and even Bronsted acid sites to produce dimethyl ether with some hydrocarbons, while over metal modified MCM-41 mostly formaldehyde and dimethoxy methane (i.e. methylal) or methyl formate are produced. In present experiments V incorporated basically mild acid sites of MCM-41 was prepared by low temperature direct synthesis. The V-MCM-41 has enough main active Lewis sites (by V-) to form formaldehyde and also light Bronsted acid sites to let the adsorbed formaldehyde eliminate and afterwards, with methanol, to form dimethoxy methane in nonoxidative environment. This V-MCM-41 has been tested by ethanol conversion in non-oxidative environments too and diethoxy methane as main product was detected. In present work the methanol conversion, as well as the methanol co-reaction with methyl iodide are studied from the same V-MCM-41 sample using 11 C-technique. The 11 C-labelled radioactive methanol has been already applied for determination of methanol conversion rates on Cu-modified MCM-41. The V-MCM-41 was prepared by direct hydrothermal synthesis method. The adsorption rate of 11 C-methanol and, after the reaction, the desorption rate of the remaining 11 C-derivatives on catalyst were continuously detected by gamma detectors. The derivatives were analyzed by radio-gas chromatography (gas chromatograph with FID coupled on-line with a radioactivity detector). Both dimethyl ether and hydrocarbon formation are also in slight degrees according to weak Lewis and Bronsted acidities. Since the conversion was carried out without added oxygen gas, only the frame oxygen can take part into catalysis. In presence of non-radioactive methyl iodide, the radioactive methanol is converted to radioactive methyl iodide on V-MCM-41. The radio-GC analysis confirmed that the iodide induced change of the reaction performance was reversible i.e. the radioactive methyl iodide was regenerated to non-radioactive methyl

SUPPLEMENTARY INFORMATION Bronsted acid functionalised ...

Indian Academy of Sciences (India)

raji

In the above spectrum, the broad peak at 3307 cm-1 was due to stretching vibrations of. –CH2–OH group. The broadness of the peak could be due to hydrogen bonding of hydroxyl group with chloride in the zwitter ion. The –CH2 stretching vibrations were observed at 1473 cm-1. The –CH3 stretching vibrations were ...

Effects of Bronsted acidity in the mechanism of selective oxidation of propane to acetone on CaY zeolite at room temperature.

NARCIS (Netherlands)

Xu, J.; Mojet, Barbara; van Ommen, J.G.; Lefferts, Leonardus

2005-01-01

The importance of Brønsted acid sites for partial oxidation of propane to acetone in CaY was investigated by in situ FTIR spectroscopy. With an increasing number of protons in Ca-Y, Volcano plots were observed for (1) amount of adsorbed propane; (2) initial acetone formation rate; (3) total amount

Structure–acidity correlation of supported tungsten(VI)-oxo-species: FT-IR and TPD studies of adsorbed pyridine and catalytic decomposition of 2-propanol

Energy Technology Data Exchange (ETDEWEB)

Zaki, M.I., E-mail: mizaki@mu.edu.eg; Mekhemer, G.A.H.; Fouad, N.E.; Rabee, A.I.M.

2014-07-01

The amount of 10 wt%-WO{sub 3} was supported on alumina, titania or silica by impregnation with aqueous solution of ammonium paratungstate and subsequent calcination at 500 °C for 10 h. Tungstate-related chemical and physical changes in the calcination products were resolved by ex-situ infrared (IR) spectroscopy. Nature of exposed surface acid sites were probed by in-situ IR spectroscopy of adsorbed pyridine (Py) molecules at room temperature (RT). The relative strength of the acid sites thus probed was gauged by combining results of temperature-programmed desorption (TPD) measurements of the RT-adsorbed Py with those communicated by in-situ IR spectra of residual Py on the surface after a brief thermoevacuation at high temperatures (100–300 °C). Reactivity of the surface acid sites was tested toward 2-propanal catalytic decomposition, and observed by in-situ IR gas phase spectra. Results obtained were correlated with predominant structures assumed by the supported tungstate species. Accordingly, polymerization of the supported tungstate into 2-/3-dimensional structures, was found to be relatively most advanced on favorable locations of titania surfaces as compared to the case on alumina or silica surfaces. Consequently, the Lewis acidity was strengthened, and strong Bronsted acidity was evolved, leading to a 2-propanol dehydration catalyst (tungstate/titania) of optimal activity and selectivity. Strong tungstate/support interfacial interactions were found to hamper the formation of the strongly acidic and catalytically active polymeric structures of the supported tungstate (i.e., the case on alumina or silica).

Structure–acidity correlation of supported tungsten(VI)-oxo-species: FT-IR and TPD studies of adsorbed pyridine and catalytic decomposition of 2-propanol

International Nuclear Information System (INIS)

Zaki, M.I.; Mekhemer, G.A.H.; Fouad, N.E.; Rabee, A.I.M.

2014-01-01

The amount of 10 wt%-WO 3 was supported on alumina, titania or silica by impregnation with aqueous solution of ammonium paratungstate and subsequent calcination at 500 °C for 10 h. Tungstate-related chemical and physical changes in the calcination products were resolved by ex-situ infrared (IR) spectroscopy. Nature of exposed surface acid sites were probed by in-situ IR spectroscopy of adsorbed pyridine (Py) molecules at room temperature (RT). The relative strength of the acid sites thus probed was gauged by combining results of temperature-programmed desorption (TPD) measurements of the RT-adsorbed Py with those communicated by in-situ IR spectra of residual Py on the surface after a brief thermoevacuation at high temperatures (100–300 °C). Reactivity of the surface acid sites was tested toward 2-propanal catalytic decomposition, and observed by in-situ IR gas phase spectra. Results obtained were correlated with predominant structures assumed by the supported tungstate species. Accordingly, polymerization of the supported tungstate into 2-/3-dimensional structures, was found to be relatively most advanced on favorable locations of titania surfaces as compared to the case on alumina or silica surfaces. Consequently, the Lewis acidity was strengthened, and strong Bronsted acidity was evolved, leading to a 2-propanol dehydration catalyst (tungstate/titania) of optimal activity and selectivity. Strong tungstate/support interfacial interactions were found to hamper the formation of the strongly acidic and catalytically active polymeric structures of the supported tungstate (i.e., the case on alumina or silica).

Selectivity Enhancement in methylamine synthesis via postsynthesis modification of bronsted acidic mordenite

NARCIS (Netherlands)

Grundling, C.; Gründling, Christian; Mirth, G.C.; Eder-Mirth, Gabriele C.; Lercher, J.A.

1996-01-01

Methylamine synthesis from methanol and ammonia over parent and modified Brønsted acidic mordenites is studied byin situinfrared spectroscopy and kinetic analysis to elucidate the role of elementary steps for activity and selectivity.In situinfrared spectroscopy reveals that all methylammonium ions

Oxidative dehydration of glycerol to acrylic acid over vanadium-impregnated zeolite beta

Energy Technology Data Exchange (ETDEWEB)

Pestana, Carolina F.M.; Guerra, Antonio C.O.; Turci, Cassia C. [Universidade Federal do Rio de Janeiro, RJ (Brazil). Inst. de Quimica; Ferreira, Glaucio B. [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Inst. de Quimica; Mota, Claudio J.A., E-mail: cmota@iq.ufrj.br [INCT Energia e Ambiente, Universidade Federal do Rio de Janeiro, RJ (Brazil)

2013-01-15

The oxidative dehydration of glycerol to acrylic acid was studied over vanadium-impregnated zeolite Beta. Catalysts were prepared by wet impregnation of ammonium metavanadate over ammonium-exchanged zeolite Beta, followed by air calcination at 823 K. Impregnation reduced the specific surface area, but did not significantly affected the acidity (Bronsted and Lewis) of the zeolites. The catalytic evaluation was carried out in a fixed bed flow reactor using air as the carrier and injecting glycerol by means of a syringe pump. Acrolein was the main product, with acetaldehyde and hydroxy-acetone (acetol) being also formed. Acrylic acid was formed with approximately 25% selectivity at 548 K over the impregnated zeolites. The result can be explained by XPS (X-ray photoelectron spectroscopy) measurements, which indicated a good dispersion of the vanadium inside the pores. (author)

Oxidative dehydration of glycerol to acrylic acid over vanadium-impregnated zeolite beta

International Nuclear Information System (INIS)

Pestana, Carolina F.M.; Guerra, Antonio C.O.; Turci, Cassia C.

2013-01-01

The oxidative dehydration of glycerol to acrylic acid was studied over vanadium-impregnated zeolite Beta. Catalysts were prepared by wet impregnation of ammonium metavanadate over ammonium-exchanged zeolite Beta, followed by air calcination at 823 K. Impregnation reduced the specific surface area, but did not significantly affected the acidity (Bronsted and Lewis) of the zeolites. The catalytic evaluation was carried out in a fixed bed flow reactor using air as the carrier and injecting glycerol by means of a syringe pump. Acrolein was the main product, with acetaldehyde and hydroxy-acetone (acetol) being also formed. Acrylic acid was formed with approximately 25% selectivity at 548 K over the impregnated zeolites. The result can be explained by XPS (X-ray photoelectron spectroscopy) measurements, which indicated a good dispersion of the vanadium inside the pores. (author)

Semi-quantitative estimation by IR of framework, extraframework and defect Al species of HBEA zeolites.

Science.gov (United States)

Marques, João P; Gener, Isabelle; Ayrault, Philippe; Lopes, José M; Ribeiro, F Ramôa; Guisnet, Michel

2004-10-21

A simple method based on the characterization (composition, Bronsted and Lewis acidities) of acid treated HBEA zeolites was developed for estimating the concentrations of framework, extraframework and defect Al species.

Integration of Chemical and Biological Catalysis

DEFF Research Database (Denmark)

Schwartz, Thomas J.; Goodman, Samuel M.; Osmundsen, Christian Mårup

2013-01-01

Furylglycolic acid (FA), a pseudoaromatic hydroxy-acid suitable for copolymerization with lactic acid, can be produced from glucose via enzymatically derived cortalcerone using a combination of Bronsted and Lewis acid catalysts. Cortalcerone is first converted to furylglyoxal hydrate (FH) over a ...

Study of MgO transformation into MgF2 in the presence of CF2Cl2•

Directory of Open Access Journals (Sweden)

Vedyagin Aleksey A.

2017-01-01

Full Text Available Alkaline-earth metal oxide aerogels prepared by sol–gel method followed by autoclave drying are nanocrystalline mesoporous materials with high reactivity. Bulk solid-state reaction of MgO aerogels with CF2Cl2 takes place after a long induction period, during which the active sites are accumulated on the surface of the nanoparticles. It was found that vanadium addition has a promoting effect on this reaction accelerating the process of the active sites formation. A method for characterization of electron-acceptor sites by electron spin resonance spectroscopy using perylene as the spin probe was developed. A good correlation was observed between the rate of the CF2Cl2 destructive sorption and the concentration of weak electron-acceptor sites. Simplified models of such sites were suggested. The acid sites on the modified MgO surface were supposed to be originated from separation of the charged fragments resulting in the surface polarization. Uncompensated oxygen substitution for chlorine and/or fluorine ions leads to appearance of Lewis acid sites while HCl/HF chemisorption results in Bronsted acid sites formation.

Dehydration of Glucose to 5-Hydroxymethylfurfural Using Nb-doped Tungstite

KAUST Repository

Yue, Chaochao

2016-08-05

Dehydration of glucose to 5-hydroxymethylfurfural (HMF) remains a significant problem in the context of the valorization of lignocellulosic biomass. Hydrolysis of WCl6 and NbCl5 leads to precipitation of Nb-containing tungstite (WO3H2O) at low Nb content and mixtures of tungstite and niobic acid at higher Nb content. Tungstite is a promising catalyst for the dehydration of glucose to HMF. Compared with Nb2O5, fewer by-products are formed because of the low BrOnsted acidity of the (mixed) oxides. In water, an optimum yield of HMF was obtained for Nb-W oxides with low Nb content owing to balanced Lewis and BrOnsted acidity. In THF/water, the strong Lewis acidity and weak BrOnsted acidity caused the reaction to proceed through isomerization to fructose and dehydration of fructose to a partially dehydrated intermediate, which was identified by LC-ESI-MS. The addition of HCl to the reaction mixture resulted in rapid dehydration of this intermediate to HMF. The HMF yield obtained in this way was approximately 56% for all tungstite catalysts. Density functional theory calculations show that the Lewis acid centers on the tungstite surface can isomerize glucose into fructose. Substitution of W by Nb lowers the overall activation barrier for glucose isomerization by stabilizing the deprotonated glucose adsorbate.

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

OpenAIRE

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 TixH3−4...

Sites that Can Produce Left-handed Amino Acids in the Supernova Neutrino Amino Acid Processing Model

Science.gov (United States)

Boyd, Richard N.; Famiano, Michael A.; Onaka, Takashi; Kajino, Toshitaka

2018-03-01

The Supernova Neutrino Amino Acid Processing model, which uses electron anti-neutrinos and the magnetic field from a source object such as a supernova to selectively destroy one amino acid chirality, is studied for possible sites that would produce meteoroids with partially left-handed amino acids. Several sites appear to provide the requisite magnetic field intensities and electron anti-neutrino fluxes. These results have obvious implications for the origin of life on Earth.

Sulfur tolerance of Pt/mordenites for benzene hydrogenation. Do Bronsted acid sites participate in hydrogenation?

NARCIS (Netherlands)

Simon, L.; van Ommen, J.G.; Jentys, A.; Lercher, J.A.

2002-01-01

The comparison of Pt electronic properties studied by in situ XANES and the kinetic study of benzene hydrogenation strongly suggests that the hydrogenation of benzene on Pt/mordenites occurs along two parallel reaction pathways. The routes proposed include (i) the monofunctional hydrogenation of

Synthesis and Characterization of Tin (IV Tungstate Nanoparticles – A Solid Acid Catalyst

Directory of Open Access Journals (Sweden)

Manoj Sadanandan

2012-12-01

Full Text Available Tin (IV tungstate, a tetravalent metal acid salt was synthesized in the nanoform by chemical coprecipitation method using EDTA as capping agent. The material was found to be stable in mineral acids, bases and organic solvents except  in HF and aquaregia. The material was characterized using EDS, TG/DTA, FTIR, XRD, SEM, HRTEM and BET surface area measurement. The molecular formula of the compound is 2SnO2 3WO3.5H2O determined from elemental analysis using TG/DTA. Surface morphology and particle size were obtained using SEM and HRTEM. The surface area was found to be 205-225m2/g. The Na+ exchange capacity found to be 3.8 meq/g, indicates the presence of surface hydroxyl group and hence the presence of Bronsted acid sites. The catalytic activity of the material was tested by using esterification and oxidation as model reactions. For the esterification of different alcohols, the percentage yield was found to be high for n-alcohol compared to isomeric alcohols. Oxidation of benzyl alcohol gives benzaldehyde and benzoic acid as the only products. Copyright © 2012 by BCREC UNDIP. All rights reservedReceived: 12nd June 2012, Revised: 23rd July 2012, Accepted: 29th July 2012[How to Cite: S. Manoj, R. Beena, (2012. Synthesis and Characterization of tin(IV Tungstate Nanoparticles – A Solid Acid Catalyst. Bulletin of Chemical Reaction Engineering & Catalysis, 7 (2: 105-111. doi:10.9767/bcrec.7.2.3622.105-111] [How to Link / DOI: http://dx.doi.org/10.9767/bcrec.7.2.3622.105-111 ] | View in 

Brønsted acid sites based on penta-coordinated aluminum species

Science.gov (United States)

Wang, Zichun; Jiang, Yijiao; Lafon, Olivier; Trébosc, Julien; Duk Kim, Kyung; Stampfl, Catherine; Baiker, Alfons; Amoureux, Jean-Paul; Huang, Jun

2016-12-01

Zeolites and amorphous silica-alumina (ASA), which both provide Brønsted acid sites (BASs), are the most extensively used solid acid catalysts in the chemical industry. It is widely believed that BASs consist only of tetra-coordinated aluminum sites (AlIV) with bridging OH groups in zeolites or nearby silanols on ASA surfaces. Here we report the direct observation in ASA of a new type of BAS based on penta-coordinated aluminum species (AlV) by 27Al-{1H} dipolar-mediated correlation two-dimensional NMR experiments at high magnetic field under magic-angle spinning. Both BAS-AlIV and -AlV show a similar acidity to protonate probe molecular ammonia. The quantitative evaluation of 1H and 27Al sites demonstrates that BAS-AlV co-exists with BAS-AlIV rather than replaces it, which opens new avenues for strongly enhancing the acidity of these popular solid acids.

Site-specific labeling of proteins with NMR-active unnatural amino acids

International Nuclear Information System (INIS)

Jones, David H.; Cellitti, Susan E.; Hao Xueshi; Zhang Qiong; Jahnz, Michael; Summerer, Daniel; Schultz, Peter G.; Uno, Tetsuo; Geierstanger, Bernhard H.

2010-01-01

A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame shift codon specifies the incorporation site in the protein to be studied. These unnatural amino acids can be isotopically labeled and provide unique opportunities for site-specific labeling of proteins for NMR studies. In this perspective, we discuss these opportunities including new photocaged unnatural amino acids, outline usage of metal chelating and spin-labeled unnatural amino acids and expand the approach to in-cell NMR experiments.

Absolute acidity of clay edge sites from ab-initio simulations

Science.gov (United States)

Tazi, Sami; Rotenberg, Benjamin; Salanne, Mathieu; Sprik, Michiel; Sulpizi, Marialore

2012-10-01

We provide a microscopic understanding of the solvation structure and reactivity of the edges of neutral clays. In particular we address the tendency to deprotonation of the different reactive groups on the (0 1 0) face of pyrophyllite. Such information cannot be inferred directly from titration experiments, which do not discriminate between different sites and whose interpretation resorts to macroscopic models. The determination of the corresponding pKa then usually relies on bond valence models, sometimes improved by incorporating some structural information from ab-initio simulations. Here we use density functional theory based molecular dynamics simulations, combined with thermodynamic integration, to compute the free energy of the reactions of water with the different surface groups, leading to a deprotonated site and an aqueous hydronium ion. Our approach consistently describes the clay and water sides of the interface and includes naturally electronic polarization effects. It also allows to investigate the structure and solvation of all sites separately. We find that the most acidic group is SiOH, due to its ability to establish strong hydrogen bonds with adsorbed water, as it also happens on the quartz and amorphous silica surfaces. The acidity constant of AlOH2 is only 1 pKa unit larger. Finally, the pKa of AlOH is outside the possible range in water and this site should not deprotonate in aqueous solution. We show that the solvation of surface sites and hence their acidity is strongly affected by the proximity of other sites, in particular for AlOH and AlOH2 which share the same Al. We discuss the implications of our findings on the applicability of bond valence models to predict the acidity of edge sites of clays.

Modification and characterization of sites giving acid cracking on aluminium oxide supports; Modification et caracterisation des sites responsables du craquage acide sur des supports a base d`alumine

Energy Technology Data Exchange (ETDEWEB)

Guillaume, D

1997-10-23

The aim of this work is to characterize the surface acid properties of {gamma} alumina, especially the nature, the amount, the strength and the environment of acid sites. The techniques that have been used are: the thermo-desorption of trimethyl-phosphine followed by {sup 31}P MAS NMR, the infrared spectroscopy, the n-heptane cracking, the modification of {gamma} alumina by the addition of chlorine, silicon and alkali (K{sup +}, Na{sup +}), alkaline-earths (Mg{sup 2+}, Ca{sup 2+}), lanthanum (La{sup 3+}) cations. The combination of these techniques has allowed to identify the surface acid properties of {gamma} alumina through the n-heptane transformation reactions under reforming conditions. We have shown that Lewis acidity is responsible for cracking reactions leading to C{sub 1}-C{sub 6} and C{sub 2}-C{sub 5} whereas the cracking of n-heptane producing C{sub 3}-C{sub 4} is due to Broensted acid sites. The isomerization and cyclization reactions both require weaker Broensted acid sites than cracking leading to C{sub 3}-C{sub 4}. The mechanisms involved in the formation of products of these reactions have been identified. Despite the complexity of surface acid properties of {gamma} alumina, this study has determined the environment of catalytically active sites, considering the presence of cation vacancies. (author) 206 refs.

The Variable Transition State in Polar Additions to Pi Bonds

Science.gov (United States)

Weiss, Hilton M.

2010-01-01

A vast majority of polar additions of Bronsted acids to alkynes involve a termolecular transition state. With strong acids, considerable positive charge is developed on carbon and Markovnikov addition predominates. In less acidic solutions, however, the reaction is much slower and the transition state more closely resembles the olefinic product.…

Ammonia IRMS-TPD study on the distribution of acid sites in mordenite.

Science.gov (United States)

Niwa, Miki; Suzuki, Katsuki; Katada, Naonobu; Kanougi, Tomonori; Atoguchi, Takashi

2005-10-13

Using an IRMS-TPD (temperature programmed desorption) of ammonia, we studied the nature, strength, crystallographic location, and distribution of acid sites of mordenite. In this method, infrared spectroscopy (IR) and mass spectroscopy (MS) work together to follow the thermal behavior of adsorbed and desorbed ammonia, respectively; therefore, adsorbed species were identified, and their thermal behavior was directly connected with the desorption of ammonia during an elevation of temperature. IR-measured TPD of the NH4(+) cation was similar to MS-measured TPD, thus showing the nature of Brønsted acidity. From the behavior of OH bands, it was found that the Brønsted acid sites consisted of two kinds of OH bands at high and low wavenumbers, ascribable to OH bands situated on 12- and 8-member rings (MR) of mordenite structure, respectively. The amount and strength of these Brønsted hydroxyls were measured quantitatively based on a theoretical equation using a curve fitting method. Up to ca. 30% of the exchange degree, NH4(+) was exchanged with Na+ on the 12-MR to arrive at saturation; therefore, in this region, the Brønsted acid site was situated on the large pore of 12-MR. The NH4(+) cation was then exchanged with Na+ on 8-MR, and finally exceeded the amount on 12-MR. In the 99% NH4-mordenite, Brønsted acid sites were located predominantly on the 8-MR more than on the 12-MR. Irrespective of the NH4(+) exchange degree, the strengths deltaH of Brønsted OH were 145 and 153 kJ mol(-1) on the 12- and 8-MR, respectively; that is, the strength of Brønsted acid site on the 8-MR was larger than that on the 12-MR. A density functional theory (DFT) calculation supported the difference in the strengths of the acid sites. Catalytic cracking activity of the Brønsted acid sites on the 8-MR declined rapidly, while that on the 12-MR was remarkably kept. The difference in strength and/or steric capacity may cause such a difference in the life of a catalyst.

Characterization of reference and site specific humic acids

International Nuclear Information System (INIS)

Kim, J.I.; Buckau, G.

1988-11-01

As a contribution to the interlaboratory exercise for the complexation of humic acid and colloid generation (COCO-Club activities) in the CEC project MIRAGE-II, the characterization of selected humic acids have been carried out at TU Muenchen, regarding their elemental compositions, inorganic impurities, spectroscopic properties, size distributions and proton exchange capacities. The commercial humic acid (Na salt) from Aldrich Co. is purified to a protonated form and used as reference material. Furthermore two humic acids extracted from groundwaters from Gorleben (FRG) and Boom Clay (B) are purified to protonated forms and taken as site specific materials. These three humic acids, together with the original Na salt from Aldrich Co., are included in the present characterization exercise. The results of characterization provide basic knowledge supporting the forthcoming study of complexation of actinides and fission products with humic acid and their migration processes in the geosphere. (orig.)

Characterization of reference and site specific human acids

International Nuclear Information System (INIS)

Kim, J.I.; Buckau, G.

1988-01-01

As a part of the interlaboratory exercise for the complexation of humic acid and colloid generation (COCO-Club activities) in the CEC project MIRAGE-II, the characterization of humic acids have been carried out, as for their elemental compositions, inorganic impurities, spectroscopic properties, size distributions and proton exchange capacities. The commercial humic acid (Na salt) from Aldrich Co. is purified to a protonated form and used as a reference material, and the humic acid extracted from one of Gorleben groundwaters is also purified to a protonated form and taken as a site specific material. These two humic acids, together with the original Na salt from Aldrich Co., are included for the characterization exercise. The results of characterization provide a basic knowledge that supports the forthcoming study of complexation of humic acids with actinides and fission products in their migration processes in the geosphere. (orig.)

Human acid β-glucosidase: isolation and amino acid sequence of a peptide containing the catalytic site

International Nuclear Information System (INIS)

Dinur, T.; Osiecki, K.M.; Legler, G.; Gatt, S.; Desnick, R.J.; Grabowski, G.A.

1986-01-01

Human acid β-glucosidase (D-glucosyl-N-acylsphingosine glucohydrolase, EC 3.2.1.45) cleaves the glucosidic bonds of glucosylceramide and synthetic β-glucosides. The deficient activity of this hydrolase is the enzymatic defect in the subtypes and variants of Gaucher disease, the most prevalent lysosomal storage disease. To isolate and characterize the catalytic site of the normal enzyme, brominated 3 H-labeled conduritol B epoxide ( 3 H-Br-CBE), which inhibits the enzyme by binding covalently to this site, was used as an affinity label. Under optimal conditions 1 mol of 3 H-Br-CBE bound to 1 mol of pure enzyme protein, indicating the presence of a single catalytic site per enzyme subunit. After V 8 protease digestion of the 3 H-Br-CBE-labeled homogeneous enzyme, three radiolabeled peptides, designated peptide A, B, or C, were resolved by reverse-phase HPLC. The partial amino acid sequence (37 residues) of peptide A (M/sub r/, 5000) was determined. The sequence of this peptide, which contained the catalytic site, had exact homology to the sequence near the carboxyl terminus of the protein, as predicted from the nucleotide sequence of the full-length cDNA encoding acid β-glucosidase

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

Science.gov (United States)

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

2015-09-16

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.

Aluminium and titanium modified mesoporous TUD-1: A bimetal acid catalyst for Biginelli reaction

Science.gov (United States)

Pasupathi, M.; Santhi, N.; Pachamuthu, M. P.; Alamelu Mangai, G.; Ragupathi, C.

2018-05-01

Using a simple, non-surfactant template triethanolamine (TEA), bimetal (Al3+ and Ti4+ ions) incorporated mesoporous catalyst AlTiTUD-1 (Si/Al+Ti = 50) was synthesized. The catalyst was characterized by XRD (Low and High angle), N2 Sorption, FTIR, SEM, TEM, DR UV Visible, and pyridine adsorbed FT-IR techniques. The XRD and N2 sorption studies confirmed its amorphous, mesoporous nature, which possessed a BET surface area of 590 m2 g-1 and pore diameter of 4.4 nm. The Al3+ and Ti4+ co-ordination within the TUD-1 was evaluated by DR UV-Vis. Pyridine adsorbed FTIR revealed both Bronsted (B) and Lewis (L) acidity, which is responsible for the catalytic activity. The acid catalyst showed a good catalytic performance in Biginelli type multicomponent coupling reaction for the substituted aldehydes, ethyl acetoacetate and thiourea to yield about 70% in reflux condition.

Development of catalytic materials for the synthesis of valuable chemical products via multifunctional and multisite reactions

International Nuclear Information System (INIS)

Apesteguia, C.R; Padro, C.L; Diez, V.K; Di Cosimo, J.I; Trasarti, A.F; Marchi, A.J

2004-01-01

This work reports on the successful development of solid catalytic materials carried out by our working group to obtain fine high yield chemical products. Specifically, a report is made of i) the development of metal/acid bi-functional catalysts to obtain racemic menthol from citral in a one step liquid phase process. This menthol is one of the most important chemical flavouring compounds in industry; ii) The use of acid zeolites containing a balanced concentration of Bronsted and Lewis heavy acid sites, which allow the selective synthesis of o-hydroxy acetophenone from the gas phase acylation of phenol with acetic acid. The o-hydroxy acetophenone is an intermediate compound in the production of 4-hydroxy coumarin and warfarin that are used as anticoagulants drugs; iii) The use of mixed MgAl x O y oxides containing dual acid-basic sites (Mg 2- O 2- and Al 3+ -O 2- ) to synthesize isoforone from acetone in gas phase. The isoforone is an intermediate key in the synthesis of vitamin E (CW)

Desulfurization of Hydrocarbon Fuels at Ambient Conditions Using Supported Silver Oxide-Titania Sorbents

Science.gov (United States)

2010-12-13

Potentiometric titration ------------------------------------------------------------------ 27 II.10 Equilibrium isotherms...chemisorption ------------------------------------------------ 104 VI.1.5 Potentiometric titration ...Figure VI.7. The relationship between bronsted surface acidity measured by potentiometric titration and sulfur adsorption capacity using JP5 fuel (1172

Nucleophilic addition to olefins. 7. Kinetic deuterium isotope effects as criterion for an enforced preassociation mechanism in the hydrolysis of substituted benzylidene Meldrum's acids

International Nuclear Information System (INIS)

Bernasconi, C.F.; Leonarduzzi, G.D.

1982-01-01

The hydrolysis of the title compounds occurs in four steps: (1) nucleophilic attack by water or hydroxide ion to form the addition complex T/sub OH/ - ; (2) carbon protonation of T/sub OH/ - to form T/sub OH/ 0 ; (3) oxygen deprotonation of T/sub OH/ 0 to form T/sub OH/ 0 - ; (4) collapse of the tetrahedral intermediate T/sub OH/ - into the respective benzaldehyde and Meldrum's acid anion. There is also a water-catalyzed collapse of T/sub OH/ 0 which becomes dominant in strongly acidic solution. In basic solution carbon protonation of T/sub OH/ - (step 2) is rate limiting; in strongly acidic media the water-catalyzed collapse of T/sub OH/ 0 is rate limiting for all substrates. In moderatly acidic solution two types of behavior were observed. With the p-nitro derivative step 4 is rate limiting at high, step 3 at low buffer concentrations. The latter situation is equivalent to a diffusion-controlled trapping mechanism in the reverse direction. With the parent and the p-methoxy derivative, collapse of T/sub OH/ 0 - occurs before the protonated base catalyst generated in step 3 can diffuse away; this is equivalent to an enforced preassociation mechanism in the reverse direction and is analogous to the reaction of thiol anions with acetaldehyde studied by Gilbert and Jencks. Our interpretation is strongly supported by (1) α secondary kinetic deuterium isotope effects which are large for the preassociation mechanism but essentially nil for the trapping mechanism and (2) by Bronsted #betta# values around 0.8 in the case of the preassociation mechanism and 1.0 for the trapping mechanism. The mechanism for the water-catalyzed collapse of T/sub OH/ 0 - is probably concerted, a conclusion which is supported by a large positive deviation from the Bronsted plot for base catalysis and by a large α secondary kinetic deuterium isotope effect

Sulfated polyborate: A mild, efficient catalyst for synthesis of N-tert ...

Indian Academy of Sciences (India)

chemsci

trityl protected amides via Ritter reaction of nitriles with tertiary alcohols in the presence of a sulfated polyborate catalyst under solvent-free conditions is described. The catalyst has the advantage of Lewis as well as Bronsted acidity and.

Acidity of edge surface sites of montmorillonite and kaolinite

Science.gov (United States)

Liu, Xiandong; Lu, Xiancai; Sprik, Michiel; Cheng, Jun; Meijer, Evert Jan; Wang, Rucheng

2013-09-01

Acid-base chemistry of clay minerals is central to their interfacial properties, but up to now a quantitative understanding on the surface acidity is still lacking. In this study, with first principles molecular dynamics (FPMD) based vertical energy gap technique, we calculate the acidity constants of surface groups on (0 1 0)-type edges of montmorillonite and kaolinite, which are representatives of 2:1 and 1:1-type clay minerals, respectively. It shows that tbnd Si-OH and tbnd Al-OH2OH groups of kaolinite have pKas of 6.9 and 5.7 and those of montmorillonite have pKas of 7.0 and 8.3, respectively. For each mineral, the calculated pKas are consistent with the experimental ranges derived from fittings of titration curves, indicating that tbnd Si-OH and tbnd Al-OH2OH groups are the major acidic sites responsible to pH-dependent experimental observations. The effect of Mg substitution in montmorillonite is investigated and it is found that Mg substitution increases the pKas of the neighboring tbnd Si-OH and tbnd Si-OH2 groups by 2-3 pKa units. Furthermore, our calculation shows that the pKa of edge tbnd Mg-(OH2)2 is as high as 13.2, indicating the protonated state dominates under common pH. Together with previous adsorption experiments, our derived acidity constants suggest that tbnd Si-O- and tbnd Al-(OH)2 groups are the most probable edge sites for complexing heavy metal cations.

Detecting coevolving amino acid sites using Bayesian mutational mapping

DEFF Research Database (Denmark)

Dimmic, Matthew W.; Hubisz, Melissa J.; Bustamente, Carlos D.

2005-01-01

Motivation: The evolution of protein sequences is constrained by complex interactions between amino acid residues. Because harmful substitutions may be compensated for by other substitutions at neighboring sites, residues can coevolve. We describe a Bayesian phylogenetic approach to the detection...

Radioisotopic Study of Methanol Transformation over H- and Fe-Beta Zeolites; Influence of Si/Al Ratio on Distribution of Products

International Nuclear Information System (INIS)

Sarkadi-Priboczki, E.; Kovacs, Z.; Kumar, N.; Murzin, D.Yu.

2006-01-01

Complete text of publication follows. The acid-basic properties of Beta zeolite can be modified by dealumination and/or ionexchange. The wide-pore H-Beta zeolite has strong Bronsted acid sites and other chemical environment which govern adsorption and conversion of methanol to dimethyl ether and hydrocarbons during catalysis [1-2]. Partly Fe-ion-exchanged Beta i.e. Fe-H-Beta zeolite keeps this behavior to a certain extent; however, the presence of Fe ions can modify the reaction pathway. In the present work, the methanol conversion was studied over H- and Fe-Beta zeolites at two different Si/Al ratios. 11 C-methanol was used to follow-up adsorption as well as desorption of methanol and its derivates. Therefore, a radioactivity detector was integrated to the gas chromatograph for exact identification of the labelled methanol and its derivates. H-Beta and Fe-Beta zeolites were applied at two different Si/Al ratios i.e. H-Beta(25) and H-Beta(300) and Fe-H-Beta(25) and Fe- H-Beta (300), respectively. A glass tube fixed-bed reactor was used as a closed static reactor. The 11 C-radioisotope (T 1/2 =20.4 min) was produced in 11 C-labelled carbon dioxide form by cyclotron. The 11 C-methanol tracer was produced by radiochemical process [3]. The mixture of 11 C-methanol and non-radioactive methanol was then introduced into zeolite by He gas flow. The volatile products of catalytic conversion of 11 C-methanol were analyzed by radio-gas chromatography (gas chromatograph with flame ionization detector (FID) coupled on-line with a radioactivity detector). The methanol conversion rate and product selectivities to dimethyl ether, hydrocarbons (methane, C 2 -C 6 olefins and paraffins), formaldehyde and carbon-oxides were measured and calculated over H- and Fe-Beta zeolites at two different Si/Al ratios at 250 and 350 deg C. Over H-Beta(25) C 2 -C 6 hydrocarbons (mostly as alkanes) with high conversion rate and some dimethyl ether were detected due to presence of strong Bronsted

Predicting protein amidation sites by orchestrating amino acid sequence features

Science.gov (United States)

Zhao, Shuqiu; Yu, Hua; Gong, Xiujun

2017-08-01

Amidation is the fourth major category of post-translational modifications, which plays an important role in physiological and pathological processes. Identifying amidation sites can help us understanding the amidation and recognizing the original reason of many kinds of diseases. But the traditional experimental methods for predicting amidation sites are often time-consuming and expensive. In this study, we propose a computational method for predicting amidation sites by orchestrating amino acid sequence features. Three kinds of feature extraction methods are used to build a feature vector enabling to capture not only the physicochemical properties but also position related information of the amino acids. An extremely randomized trees algorithm is applied to choose the optimal features to remove redundancy and dependence among components of the feature vector by a supervised fashion. Finally the support vector machine classifier is used to label the amidation sites. When tested on an independent data set, it shows that the proposed method performs better than all the previous ones with the prediction accuracy of 0.962 at the Matthew's correlation coefficient of 0.89 and area under curve of 0.964.

Synthesis of Diphenylamine Catalyzed by Zeolites

Czech Academy of Sciences Publication Activity Database

Hronec, M.; Cvengrošová, Z.; Čejka, Jiří

2003-01-01

Roč. 255, - (2003), s. 197-202 ISSN 0926-860X Institutional research plan: CEZ:AV0Z4040901 Keywords : zeolites beta * bentonite * Bronsted site Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.825, year: 2003

The hydroxyl species and acid sites on diatomite surface: a combined IR and Raman study

Science.gov (United States)

Yuan, P.; Wu, D. Q.; He, H. P.; Lin, Z. Y.

2004-04-01

Diffuse reflectance infrared Fourier transform spectroscopy (DRIFT), Raman spectroscopy of adsorbed pyridine molecules (Py-Raman) and in situ Py-IR have been used to investigate the hydroxyl species and acid sites on diatomite surfaces. The Lewis (L) and Brønsted (B) acid sites, and various hydroxyl species, including isolated hydroxyl groups, H-bonded hydroxyl groups and physically adsorbed water, are identified. The L acid sites in diatomite samples are resulted from the clay impurities, and the B acid sites are resulted from some moderate strength H-bonded hydroxyl groups. At room temperature, both of the isolated and H-bonded silanols associate with the physically adsorbed water by hydrogen bond. After calcination treatment, physically adsorbed water will be desorbed from the silanols, and the silanols will condense with the increase of temperature. Generally, the H-bonded silanols condense more easily than the isolated ones. The properties of surface hydroxyl species of diatomaceous silica are more similar to precipitated silica rather than fumed silica.

Location and nature of calcium-binding sites in salivary acidic proline-rich phosphoproteins

International Nuclear Information System (INIS)

Bennick, A.; McLaughlin, A.C.; Grey, A.A.; Madapallimattam, G.

1981-01-01

The location of the calcium-binding sites in the human acidic proline-rich proteins, salivary proteins A and C, was determined by equilibrium dialysis of the tryptic peptides with buffers containing 45 Ca. All the calcium-binding sites are located in the NH 2 -terminal tryptic peptide (TX peptide). The nature of the calcium binding sites in the TX peptide and native salivary proteins A and C, as well as dephosphorylated proteins was compared. Two types of sites can be distinguished in peptide TX. Type I sites have an apparent dissociation constant (K) of 38 μM and are responsible for the binding of 2.6 mol of Ca/mol of peptide. The corresponding figures for Type II sites are 780 μM and 5.3 mol of Ca/mol of peptide. In the native proteins, the amount of calcium bound at the type II sites decreases to 3.9 mol of Ca/mol of proteins A and C and K increases to 1100 μM. The amount of calcium bound at type I sites decreases to 1.5 mol/mol of protein A and 0.6 mol/mol of protein C, but there is no change in K. Dephosphorylation affects the calcium binding at both types of sites. The experiments indicate that the COOH-terminal parts of the native proteins affect the number and the nature of the protein calcium-binding sites. Proton and phosphorous NMR data demonstrate that β-COOH in aspartic acid, as well as phosphoserine, are part of the calcium-binding sites. The difference in calcium binding to salivary proteins A and C may be due at least partially to differences in the environment of one or more aspartic acids

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

Energy Technology Data Exchange (ETDEWEB)

Gangi Setty, Thanuja [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Cho, Christine [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Govindappa, Sowmya [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Apicella, Michael A. [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Ramaswamy, S., E-mail: ramas@instem.res.in [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India)

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.

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

International Nuclear Information System (INIS)

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

2014-01-01

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

Introduction to zeolite theory and modelling

NARCIS (Netherlands)

Santen, van R.A.; Graaf, van de B.; Smit, B.; Bekkum, van H.

2001-01-01

A review. Some of the recent advances in zeolite theory and modeling are present. In particular the current status of computational chem. in Bronsted acid zeolite catalysis, mol. dynamics simulations of mols. adsorbed in zeolites, and novel Monte Carlo technique are discussed to simulate the

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

Science.gov (United States)

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.

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

International Nuclear Information System (INIS)

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

1991-01-01

Binding of 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

Biodiesel forming reactions using heterogeneous catalysis

Science.gov (United States)

Liu, Yijun

other comparisons between the catalytic behaviors of liquid and solid acids suggests a common mode of operation of their Bronsted acid sites in carrying out esterification of a carboxylic acid with alcohol. The hypothesized Eley-Rideal type heterogeneous reaction mechanism involving a nucleophilic attack between adsorbed carboxylic acid and unadsorbed alcohol as the rate-limiting step was found to fit well the experimental observations and successfully predict the esterification rate obtained with SAC-13 as reaction progresses. The SAC-13 catalysis assay was also extended to carboxylic acids of higher molecular weights. A set of carboxylic acids with various alkyl chain lengths was used to investigate the structural effect of reacting carboxylic acids on heterogeneous catalyzed esterification. It was found that the reactivity of carboxylic acids was controlled by steric factors as the alkyl chain linearly lengthened. Despite their increased hydrophobicity, large carboxylic acids hardly impacted the deactivating effect of water on Bronsted acid sites. However, catalyst reusability and regeneration showed significant dependency on the size of the carboxylic acid used. With the use of larger reacting carboxylic acids, SAC-13 underwent more significant activity loss in consecutive reaction cycles due to stronger adsorption of the larger organics in the polymeric domains of the Nafion resin. In parallel to the research activity on acid catalyzed esterification, the use of strong solid bases with organic functionality (quarternary ammonium, QN+) was investigated from a fundamental perspective. Using triacetin as a model compound for TG molecules, the effectiveness of this Bronsted base functionality in transesterification was demonstrated even at mild reaction conditions. But its catalytic behavior including catalyst selectivity and deactivation was significantly affected by the nature of the adopted support. A purposive design of the immobilizing matrix is expected to

Interaction of Palmitic Acid with Metoprolol Succinate at the Binding Sites of Bovine Serum Albumin

Directory of Open Access Journals (Sweden)

Mashiur Rahman

2014-12-01

Full Text Available Purpose: The aim of this study was to characterize the binding profile as well as to notify the interaction of palmitic acid with metoprolol succinate at its binding site on albumin. Methods: The binding of metoprolol succinate to bovine serum albumin (BSA was studied by equilibrium dialysis method (ED at 27°C and pH 7.4, in order to have an insight in the binding chemistry of the drug to BSA in presence and absence of palmitic acid. The study was carried out using ranitidine as site-1 and diazepam as site-2 specific probe. Results: Different analysis of binding of metoprolol succinate to bovine serum albumin suggested two sets of association constants: high affinity association constant (k1 = 11.0 x 105 M-1 with low capacity (n1 = 2 and low affinity association (k2 = 4.0×105 M-1 constant with high capacity (n2 = 8 at pH 7.4 and 27°C. During concurrent administration of palmitic acid and metoprolol succinate in presence or absence of ranitidine or diazepam, it was found that palmitic acid displaced metoprolol succinate from its binding site on BSA resulting reduced binding of metoprolol succinate to BSA. The increment in free fraction of metoprolol succinate was from 26.27% to 55.08% upon the addition of increased concentration of palmitic acid at a concentration of 0×10-5 M to 16×10-5 M. In presence of ranitidine and diazepam, palmitic acid further increases the free fraction of metoprolol succinate from 33.05% to 66.95% and 40.68% to 72.88%, respectively. Conclusion: This data provided the evidence of interaction at higher concentration of palmitic acid at the binding sites on BSA, which might change the pharmacokinetic properties of metoprolol succinate.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Various reaction parameters were optimized and kinetics of the reaction was evaluated. This Bronsted acidic choline chloride-butane sultone-based ionic liquid was highly selective towards the conversion of cumene hydroperoxide to phenol. Ease of use and recovery, low environmental impact, and effective reduction of ...

Kinetic hydrogen isotope effects in the concerted mechanism for the hydrolysis of acetals, ketals, and ortho esters

International Nuclear Information System (INIS)

Eliason, R.; Kreevoy, M.M.

1978-01-01

The hydrolysis of many ortho esters, and some acetals and ketals, is general acid catalyzed, and in some examples these generate linear Bronsted plots over substantial ranges of catalyst acidity. This suggests that the reaction coordinate is primarily a reorganization of heavy atoms since proton transfer from one oxygen to another has been shown to generate strongly curved Bronsted plots. However, the isotopic fractionation factor for the catalytically active proton in these transition states is substantially less than 1.0; in several examples it is less than 0.5. Such values have been thought to require that the reaction coordinate be largely a motion of the hydrogen giving the low fractionation factor. This dilemma has been resolved by the observation and rationalization of fractionation factors as low as 0.28 for stable, hydrogen bridge-bonded complexes, AHA - . A similar, bounded coordinate is now suggested for the catalytically active protons in question. This permits the reaction coordinate to be pictured. 3 figures, 2 tables

Prediction of protein modification sites of pyrrolidone carboxylic acid using mRMR feature selection and analysis.

Directory of Open Access Journals (Sweden)

Lu-Lu Zheng

Full Text Available Pyrrolidone carboxylic acid (PCA is formed during a common post-translational modification (PTM of extracellular and multi-pass membrane proteins. In this study, we developed a new predictor to predict the modification sites of PCA based on maximum relevance minimum redundancy (mRMR and incremental feature selection (IFS. We incorporated 727 features that belonged to 7 kinds of protein properties to predict the modification sites, including sequence conservation, residual disorder, amino acid factor, secondary structure and solvent accessibility, gain/loss of amino acid during evolution, propensity of amino acid to be conserved at protein-protein interface and protein surface, and deviation of side chain carbon atom number. Among these 727 features, 244 features were selected by mRMR and IFS as the optimized features for the prediction, with which the prediction model achieved a maximum of MCC of 0.7812. Feature analysis showed that all feature types contributed to the modification process. Further site-specific feature analysis showed that the features derived from PCA's surrounding sites contributed more to the determination of PCA sites than other sites. The detailed feature analysis in this paper might provide important clues for understanding the mechanism of the PCA formation and guide relevant experimental validations.

Electrochemistry And Application Of Electrochemistry

International Nuclear Information System (INIS)

Jang, Hyang Dong

1990-02-01

This book introduces electrochemistry and applications of electrochemistry, SI unit system, solution, distribution ratios, concentration indicate, electrolyte and electrolytic dissociation, conduction of electrolyte dissolution, electrode potential such as gas electrode, Oxidation-reduction electrode and reversible cell, potential measurement by potentiometer law, acid-base like Bronsted-Lowry's acid-base and Lewis's acid-base, neutralization reaction and hydrolysis, zwitter ion, potentiometry, practical cell, polarization and electrolyte, electrolysis and electrical installation.

Catalytic Ozonation of Toluene Using Chilean Natural Zeolite: The Key Role of Brønsted and Lewis Acid Sites

Directory of Open Access Journals (Sweden)

Serguei Alejandro-Martín

2018-05-01

Full Text Available The influence of surface physical-chemical characteristics of Chilean natural zeolite on the catalytic ozonation of toluene is presented in this article. Surface characteristics of natural zeolite were modified by acid treatment with hydrochloric acid and ion-exchange with ammonium sulphate. Prior to catalytic ozonation assays, natural and chemically modified zeolite samples were thermally treated at 623 and 823 K in order to enhance Brønsted and Lewis acid sites formation, respectively. Natural and modified zeolite samples were characterised by N2 adsorption at 77 K, elemental analysis, X-ray fluorescence, and Fourier transform infrared (FTIR spectroscopy, using pyridine as a probe molecule. The highest values of the reaction rate of toluene oxidation were observed when NH4Z1 and 2NH4Z1 zeolite samples were used. Those samples registered the highest density values of Lewis acid sites compared to other samples used here. Results indicate that the presence of strong Lewis acid sites at the 2NH4Z1 zeolite surface causes an increase in the reaction rate of toluene oxidation, confirming the role of Lewis acid sites during the catalytic ozonation of toluene at room temperature. Lewis acid sites decompose gaseous ozone into atomic oxygen, which reacts with the adsorbed toluene at Brønsted acid sites. On the other hand, no significant contribution of Brønsted acid sites on the reaction rate was registered when NH4Z1 and 2NH4Z1 zeolite samples were used.

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

International Nuclear Information System (INIS)

Dittmer, L.M.

2006-01-01

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

Identification of nucleic acid binding sites on translin-associated factor X (TRAX protein.

Directory of Open Access Journals (Sweden)

Gagan Deep Gupta

Full Text Available Translin and TRAX proteins play roles in very important cellular processes such as DNA recombination, spatial and temporal expression of mRNA, and in siRNA processing. Translin forms a homomeric nucleic acid binding complex and binds to ssDNA and RNA. However, a mutant translin construct that forms homomeric complex lacking nucleic acid binding activity is able to form fully active heteromeric translin-TRAX complex when co-expressed with TRAX. A substantial progress has been made in identifying translin sites that mediate its binding activity, while TRAX was thought not to bind DNA or RNA on its own. We here for the first time demonstrate nucleic acid binding to TRAX by crosslinking radiolabeled ssDNA to heteromeric translin-TRAX complex using UV-laser. The TRAX and translin, photochemically crosslinked with ssDNA, were individually detected on SDS-PAGE. We mutated two motifs in TRAX and translin, designated B2 and B3, to help define the nucleic acid binding sites in the TRAX sequence. The most pronounced effect was observed in the mutants of B3 motif that impaired nucleic acid binding activity of the heteromeric complexes. We suggest that both translin and TRAX are binding competent and contribute to the nucleic acid binding activity.

Identification of Nucleic Acid Binding Sites on Translin-Associated Factor X (TRAX) Protein

Science.gov (United States)

Gupta, Gagan Deep; Kumar, Vinay

2012-01-01

Translin and TRAX proteins play roles in very important cellular processes such as DNA recombination, spatial and temporal expression of mRNA, and in siRNA processing. Translin forms a homomeric nucleic acid binding complex and binds to ssDNA and RNA. However, a mutant translin construct that forms homomeric complex lacking nucleic acid binding activity is able to form fully active heteromeric translin-TRAX complex when co-expressed with TRAX. A substantial progress has been made in identifying translin sites that mediate its binding activity, while TRAX was thought not to bind DNA or RNA on its own. We here for the first time demonstrate nucleic acid binding to TRAX by crosslinking radiolabeled ssDNA to heteromeric translin-TRAX complex using UV-laser. The TRAX and translin, photochemically crosslinked with ssDNA, were individually detected on SDS-PAGE. We mutated two motifs in TRAX and translin, designated B2 and B3, to help define the nucleic acid binding sites in the TRAX sequence. The most pronounced effect was observed in the mutants of B3 motif that impaired nucleic acid binding activity of the heteromeric complexes. We suggest that both translin and TRAX are binding competent and contribute to the nucleic acid binding activity. PMID:22427937

Molecular Design of a Chiral Brønsted Acid with Two Different Acidic Sites: Regio-, Diastereo-, and Enantioselective Hetero-Diels-Alder Reaction of Azopyridinecarboxylate with Amidodienes Catalyzed by Chiral Carboxylic Acid-Monophosphoric Acid.

Science.gov (United States)

Momiyama, Norie; Tabuse, Hideaki; Noda, Hirofumi; Yamanaka, Masahiro; Fujinami, Takeshi; Yamanishi, Katsunori; Izumiseki, Atsuto; Funayama, Kosuke; Egawa, Fuyuki; Okada, Shino; Adachi, Hiroaki; Terada, Masahiro

2016-09-07

A chiral Brønsted acid containing two different acidic sites, chiral carboxylic acid-monophosphoric acid 1a, was designed to be a new and effective concept in catalytic asymmetric hetero-Diels-Alder reactions of azopyridinecarboxylate with amidodienes. The multipoint hydrogen-bonding interactions among the carboxylic acid, monophosphoric acid, azopyridinecarboxylate, and amidodiene achieved high catalytic and chiral efficiency, producing substituted 1,2,3,6-tetrahydropyridazines with excellent stereocontrol in a single step. This constitutes the first example of regio-, diastereo-, and enantioselective azo-hetero-Diels-Alder reactions by chiral Brønsted acid catalysis.

Remediation of acid tar sludge at a Superfund site

International Nuclear Information System (INIS)

Grajczak, P.; McManus, R.W.

1995-01-01

An old refinery site in Texas was safely remediated a year before schedule and for 25% less than original engineering estimates through aggressive project management and the application of an innovative design. The authors planned to solidify the petroleum acid sludge and place it in an on-site, constructed landfill. Careful evaluation of available solidification technologies lead to selection of the DCR process, a patented stabilization process far waste treatment. The technology offered low expansion factor, low reagent to waste ratio, and low cost. The process also proved to be efficient and safe, implemented using a custom-designed, transportable treatment unit. High treatment rates and continuous uninterrupted operation resulted in early completion of the waste treatment task

Formation of Broensted acids sites in the reaction of cyclohexanol on NaCeY zeolites

International Nuclear Information System (INIS)

Vogt, O.; Nattich, M.; Datka, J.; Gil, B.

2002-01-01

This study was undertaken to elucidate why the catalytic activity of NaCeY in cyclohexanol reactions carried out in a pulse reactor increases with the pulse number. We studied therefore the effect of cyclohexanol and also of ethanol and water on catalytic activity NaCeY (of exchange degrees 36 and 72%) in cyclohexanol reactions: isomerization and disproportionation. We also studied the reaction of cyclohexanol and water with NaCeY zeolite by IR spectroscopy. Our results evidenced that new Broensted acid sites were formed by the reaction of cyclohexanol and water. This was shown by IR spectroscopy: the increase of Si-O 1 H-Al band 3638 cm -1 and in increase of ammonium ions band (upon ammonia adsorption). The new sites were formed by hydrolysis of Ce 3+ ions with water introduced in a pulse, or produced by dehydration of cyclohexanol catalyzed by acid sites. Formation of new Broensted acid sites resulted in an increase of catalytic activity of NaCeY in cyclohexane reaction as observed in this study and also in cyclohexanol reactions. (author)

Direct activation of microcrystalline zeolites

NARCIS (Netherlands)

Ortiz-Iniesta, Maria Jesus; Heeres, Hero Jan; Melian-Cabrera, Ignacio

2013-01-01

In this work a direct activation route of zeolites is assessed. It consists of NH4-exchanging the as-synthesized solids before removing the organic template. Calcination afterwards serves to combust the organic template and creates the Bronsted sites directly; thus applying merely a single thermal

Sulfated polyborate: A mild, efficient catalyst for synthesis of N-tert ...

Indian Academy of Sciences (India)

Rapid, efficient and inexpensive method for synthesis of N-tert-butyl/N-trityl protected amides via Ritter reaction of nitriles with tertiary alcohols in the presence of a sulfated polyborate catalyst under solvent-free conditions is described. The catalyst has the advantage of Lewis as well as Bronsted acidity and recyclability ...

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

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

2011-09-08

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.

Application of positron annihilation to the characterization of zeolites

International Nuclear Information System (INIS)

Nakanishi, H.; Ujihira, Y.

1982-01-01

Positron annihilation lifetime and Doppler-broadening measurements were carried out for synthetic zeolite 13X, SK-40, NH 4 -X, and NH 4 -Y by varying the evacuation temperature in order to study the character of the zeolite cages. Four components of the positron annihilation, derived from the lifetime spectra, were interpreted from the results of the authors' measurements and other studies on zeolites. The o-Ps lifetimes in the cages became longer as the desorption of water molecules proceeded. It was found that some active groups in zeolites interacted with o-Ps and reduced the o-Ps lifetime after all the water molecules had detected. Bronsted acid in the zeolite acted not only as an oxidizer but also as an inhibitor of Ps formation. An attempt was made to estimate the amount of Bronsted acids by the positron lifetime technique. The longest lifetime of 50 ns indicates o-Ps annihilation in a pore with 60 A free diameter, which seems to exist irregularly in the faujasite zeolites. It was found that o-Ps was oxidized in this large cavity

New insights into Cu/SSZ-13 SCR catalyst acidity. Part I: Nature of acidic sites probed by NH 3 titration

Energy Technology Data Exchange (ETDEWEB)

Luo, Jinyong; Gao, Feng; Kamasamudram, Krishna; Currier, Neal; Peden, Charles H. F.; Yezerets, Aleksey

2017-04-01

In this work we investigated an unusual acidity feature of a Cu/SSZ-13 catalyst used in selective catalytic reduction of NOx with NH3 (NH3-SCR). In particular, this catalyst showed two distinct NH3 desorption peaks in NH3-TPD measurements, in contrast to single, unresolved desorption peaks observed for other Cu-exchanged zeolites conventionally used in the SCR studies, including its isostructural but chemically different analogue Cu/SAPO-34. We further observed that the intensities of the two TPD peaks, which represented the amount of stored NH3, changed in opposite directions in response to progressive mild hydrothermal aging, while the total storage capacity was preserved. We proposed an explanation for this remarkable behavior, by using model reference samples and additional characterization techniques. At least three NH3 storage sites were identified: two distinct populations of Cu sites responsible for low-temperature NH3 storage, and Brønsted acid sites responsible for high-temperature NH3 storage. Contrary to the commonly accepted mechanism that Brønsted acid site loss during hydrothermal aging is driven by dealumination, we concluded that the decline in the number of Brønsted acid sites upon mild hydrothermal aging for Cu/SSZ-13 was not due to dealumination, but rather transformation of Cu sites, i.e., gradual conversion of ZCuOH (Cu2+ singly coordinated with Zeolite) to Z2Cu (Cu2+ doubly coordinated with Zeolite). This transformation was responsible for the increased low-temperature desorption peak in NH3-TPD since each ZCuOH adsorbed ~1 NH3 molecule while each Z2Cu adsorbed ~2 NH3 molecules under the conditions used here. These findings were used in Part II of this series of studies to develop a method for quantifying hydrothermal ageing of industrial Cu/SSZ-13 SCR catalysts. Authors would like to thank Randall Jines for his help with collecting the reactor data, Nancy W. Washton for measuring the NMR data and Tamas Varga for in-situ XRD measurements

A review of acid drainage from waste rock dumps and mine sites (Australian and Scandinavia)

International Nuclear Information System (INIS)

Harries, J.R.

1990-05-01

This report reviews the literature from Australia and Scandinavia on acid drainage from pyritic waste rock dumps with an emphasis on measurements and theory of processes that control the rage of oxidation and the release of pollutants. Conditions within waste rock dumps have been measured at several mine sites and a range of rehabilitation treatments have been tried to reduce the release of pollutants. A number of models have been proposed to calculate air flow, water transport and geochemistry. The data and experience at the mine sites are compared with predictions of the models. Details of Australian and Swedish mine sites where waste rock is a source of acid drainage are described in the Appendices. 92 refs., 2 tabs., 10 figs

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

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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.

Site directed mutagenesis of amino acid residues at the active site of mouse aldehyde oxidase AOX1.

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Silvia Schumann

Full Text Available Mouse aldehyde oxidase (mAOX1 forms a homodimer and belongs to the xanthine oxidase family of molybdoenzymes which are characterized by an essential equatorial sulfur ligand coordinated to the molybdenum atom. In general, mammalian AOs are characterized by broad substrate specificity and an yet obscure physiological function. To define the physiological substrates and the enzymatic characteristics of mAOX1, we established a system for the heterologous expression of the enzyme in Escherichia coli. The recombinant protein showed spectral features and a range of substrate specificity similar to the native protein purified from mouse liver. The EPR data of recombinant mAOX1 were similar to those of AO from rabbit liver, but differed from the homologous xanthine oxidoreductase enzymes. Site-directed mutagenesis of amino acids Val806, Met884 and Glu1265 at the active site resulted in a drastic decrease in the oxidation of aldehydes with no increase in the oxidation of purine substrates. The double mutant V806E/M884R and the single mutant E1265Q were catalytically inactive enzymes regardless of the aldehyde or purine substrates tested. Our results show that only Glu1265 is essential for the catalytic activity by initiating the base-catalyzed mechanism of substrate oxidation. In addition, it is concluded that the substrate specificity of molybdo-flavoenzymes is more complex and not only defined by the three characterized amino acids in the active site.

Synthesis of Trisubstituted Imidazoles Using Lewis and Bronsted Acid Catalysts

OpenAIRE

Hekmatshoar, Rahim; HEKMATSHOAR, Rahim; JAHANBAKHSHI, Hajar; MOUSAVIZADEH, Farnoosh; RAHNAMAFAR, Reyhane

2010-01-01

An efficient and one-pot method for the preparation of trisubstituted imidazoles by condensation of benzil, different aldehydes and ammonium acetate in the presence of  a catalytic amount of NiSO4.7H2O or H3BO3 under different conditions is reported.                    Key Words: Trisubstituted imidazoles, Multi-component &a...

Nucleic acid constructs containing orthogonal site selective recombinases (OSSRs)

Energy Technology Data Exchange (ETDEWEB)

Gilmore, Joshua M.; Anderson, J. Christopher; Dueber, John E.

2017-08-29

The present invention provides for a recombinant nucleic acid comprising a nucleotide sequence comprising a plurality of constructs, wherein each construct independently comprises a nucleotide sequence of interest flanked by a pair of recombinase recognition sequences. Each pair of recombinase recognition sequences is recognized by a distinct recombinase. Optionally, each construct can, independently, further comprise one or more genes encoding a recombinase capable of recognizing the pair of recombinase recognition sequences of the construct. The recombinase can be an orthogonal (non-cross reacting), site-selective recombinase (OSSR).

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

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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.

Creating diversity by site-selective peptide modification: a customizable unit affords amino acids with high optical purity.

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Romero-Estudillo, Ivan; Boto, Alicia

2013-11-15

The development of peptide libraries by site-selective modification of a few parent peptides would save valuable time and materials in discovery processes, but still is a difficult synthetic challenge. Herein natural hydroxyproline is introduced as a "convertible" unit for the production of a variety of optically pure amino acids, including expensive N-alkyl amino acids, and to achieve the mild, efficient, and site-selective modification of peptides.

A decade of monitoring at Swiss Long-Term Forest Ecosystem Research (LWF) sites: can we observe trends in atmospheric acid deposition and in soil solution acidity?

Science.gov (United States)

Pannatier, Elisabeth Graf; Thimonier, Anne; Schmitt, Maria; Walthert, Lorenz; Waldner, Peter

2011-03-01

Trends in atmospheric acid deposition and in soil solution acidity from 1995 or later until 2007 were investigated at several forest sites throughout Switzerland to assess the effects of air pollution abatements on deposition and the response of the soil solution chemistry. Deposition of the major elements was estimated from throughfall and bulk deposition measurements at nine sites of the Swiss Long-Term Forest Ecosystem Research network (LWF) since 1995 or later. Soil solution was measured at seven plots at four soil depths since 1998 or later. Trends in the molar ratio of base cations to aluminum (BC/Al) in soil solutions and in concentrations and fluxes of inorganic N (NO(3)-N + NH(4)-N), sulfate (SO(4)-S), and base cations (BC) were used to detect changes in soil solution chemistry. Acid deposition significantly decreased at three out of the nine study sites due to a decrease in total N deposition. Total SO(4)-S deposition decreased at the nine sites, but due to the relatively low amount of SO(4)-S load compared to N deposition, it did not contribute to decrease acid deposition significantly. No trend in total BC deposition was detected. In the soil solution, no trend in concentrations and fluxes of BC, SO(4)-S, and inorganic N were found at most soil depths at five out of the seven sites. This suggests that the soil solution reacted very little to the changes in atmospheric deposition. A stronger reduction in base cations compared to aluminum was detected at two sites, which might indicate that acidification of the soil solution was proceeding faster at these sites.

Vapor-Phase Hydrodeoxygenation of Guaiacol to Aromatics over Pt/HBeta: Identification of the Role of Acid Sites and Metal Sites on the Reaction Pathway

Energy Technology Data Exchange (ETDEWEB)

Nie, Lei [Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 P.R. China; Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Peng, Bo [Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Zhu, Xinli [Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 P.R. China

2018-02-05

Hydrodeoxygenation of guaiacol, a phenolic compound derived from lignin fraction of biomass, over a Pt/HBeta catalyst at 350 °C and atmospheric pressure produces benzene, toluene, xylenes, and C9+ aromatics with yield of 42%, 29%, 12%, and 5%, respectively. Reaction pathways for conversion of two functional groups (hydroxyl and methoxyl) over the bifunctional catalyst were studied. Both guaiacol and intermediate products (catechol and cyclopentanone) were fed onto zeolite HBeta and Pt/SiO2 to identify the individual role of acid site and metal site. Acid sites (mainly Brønsted acid site, BAS) catalyze transalkylation and dehydroxylation reactions in sequence, producing phenol, cresols and xylenols as the major products at high conversion. Pt sites catalyze demethylation reaction resulting in catechol as the primary product, which can either be deoxygenated to phenol followed by phenol to benzene, or decarbonylated to cyclopentanone and further to butane. The close proximity of Pt and BAS in bifunctional Pt/HBeta enables both transalkylation and deoxygenation reactions with inhibited demethylation and decarbonylation reactions, producing aromatics as major final products with a total yield > 85%. Both activity and stability of bifunctional Pt/HBeta during hydrodeoxygenation of guaiacol is improved compared to HBeta and Pt/SiO2. The addition of water to the feed further improves the activity and stability via hydrolysis of O-CH3 bond of guaiacol on BAS and removing coke around Pt.

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

Science.gov (United States)

Xie, Jianming [San Diego, CA; Wang, Lei [San Diego, CA; Wu, Ning [Boston, MA; Schultz, Peter G [La Jolla, CA

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.

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

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Li Karen

2008-12-01

Full Text Available Abstract Background Widely used substitution models for proteins, such as the Jones-Taylor-Thornton (JTT or Whelan and Goldman (WAG models, are based on empirical amino acid interchange matrices estimated from databases of protein alignments that incorporate the average amino acid frequencies of the data set under examination (e.g JTT + F. Variation in the evolutionary process between sites is typically modelled by a rates-across-sites distribution such as the gamma (Γ distribution. However, sites in proteins also vary in the kinds of amino acid interchanges that are favoured, a feature that is ignored by standard empirical substitution matrices. Here we examine the degree to which the pattern of evolution at sites differs from that expected based on empirical amino acid substitution models and evaluate the impact of these deviations on phylogenetic estimation. Results We analyzed 21 large protein alignments with two statistical tests designed to detect deviation of site-specific amino acid distributions from data simulated under the standard empirical substitution model: JTT+ F + Γ. We found that the number of states at a given site is, on average, smaller and the frequencies of these states are less uniform than expected based on a JTT + F + Γ substitution model. With a four-taxon example, we show that phylogenetic estimation under the JTT + F + Γ model is seriously biased by a long-branch attraction artefact if the data are simulated under a model utilizing the observed site-specific amino acid frequencies from an alignment. Principal components analyses indicate the existence of at least four major site-specific frequency classes in these 21 protein alignments. Using a mixture model with these four separate classes of site-specific state frequencies plus a fifth class of global frequencies (the JTT + cF + Γ model, significant improvements in model fit for real data sets can be achieved. This simple mixture model also reduces the long

Sulfonic-based precursors (SAPs for silica mesostructures: Advances in synthesis and applications

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Sadegh Rostamnia*

2016-01-01

Full Text Available Sulfonic acid-based precursors (SAP play an important role in tailoring mesoporous silica’s and convert them to a solid acid catalyst with a Bronsted-type nature. These kinds of solid acids contribute to sustainable and green chemistry by their heterogeneous, recyclable, and high efficiency features. Therefore, knowing the properties and reactivity of SAPs can guide us to manufacture a sulfonated mesostructures compatible with reaction type and conditions. In the present review, some of the important SAPs, their reactivity and mechanism of functionalization are discussed.

Prediction of citrullination sites by incorporating k-spaced amino acid pairs into Chou's general pseudo amino acid composition.

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Ju, Zhe; Wang, Shi-Yun

2018-04-22

As one of the most important and common protein post-translational modifications, citrullination plays a key role in regulating various biological processes and is associated with several human diseases. The accurate identification of citrullination sites is crucial for elucidating the underlying molecular mechanisms of citrullination and designing drugs for related human diseases. In this study, a novel bioinformatics tool named CKSAAP_CitrSite is developed for the prediction of citrullination sites. With the assistance of support vector machine algorithm, the highlight of CKSAAP_CitrSite is to adopt the composition of k-spaced amino acid pairs surrounding a query site as input. As illustrated by 10-fold cross-validation, CKSAAP_CitrSite achieves a satisfactory performance with a Sensitivity of 77.59%, a Specificity of 95.26%, an Accuracy of 89.37% and a Matthew's correlation coefficient of 0.7566, which is much better than those of the existing prediction method. Feature analysis shows that the N-terminal space containing pairs may play an important role in the prediction of citrullination sites, and the arginines close to N-terminus tend to be citrullinated. The conclusions derived from this study could offer useful information for elucidating the molecular mechanisms of citrullination and related experimental validations. A user-friendly web-server for CKSAAP_CitrSite is available at 123.206.31.171/CKSAAP_CitrSite/. Copyright © 2017. Published by Elsevier B.V.

Dynamic HypA zinc site is essential for acid viability and proper urease maturation in Helicobacter pylori.

Science.gov (United States)

Johnson, Ryan C; Hu, Heidi Q; Merrell, D Scott; Maroney, Michael J

2015-04-01

Helicobacter pylori requires urease activity in order to survive in the acid environment of the human stomach. Urease is regulated in part by nickelation, a process that requires the HypA protein, which is a putative nickel metallochaperone that is generally associated with hydrogenase maturation. However, in H. pylori, HypA plays a dual role. In addition to an N-terminal nickel binding site, HypA proteins also contain a structural zinc site that is coordinated by two rigorously conserved CXXC sequences, which in H. pylori are flanked by His residues. These structural Zn sites are known to be dynamic, converting from Zn(Cys)4 centers at pH 7.2 to Zn(Cys)2(His)2 centers at pH 6.3 in the presence of Ni(ii) ions. In this study, mutant strains of H. pylori that express zinc site variants of the HypA protein are used to show that the structural changes in the zinc site are important for the acid viability of the bacterium, and that a reduction in acid viability in these variants can be traced in large measure to deficient urease activity. This in turn leads to a model that connects the Zn(Cys)4 coordination to urease maturation.

Alkenylation of Arenes and Heteroarenes with Alkynes.

Science.gov (United States)

Boyarskiy, Vadim P; Ryabukhin, Dmitry S; Bokach, Nadezhda A; Vasilyev, Aleksander V

2016-05-25

This review is focused on the analysis of current data on new methods of alkenylation of arenes and heteroarenes with alkynes by transition metal catalyzed reactions, Bronsted/Lewis acid promoted transformations, and others. The synthetic potential, scope, limitations, and mechanistic problems of the alkenylation reactions are discussed. The insertion of an alkenyl group into aromatic and heteroaromatic rings by inter- or intramolecular ways provides a synthetic route to derivatives of styrene, stilbene, chalcone, cinnamic acid, various fused carbo- and heterocycles, etc.

GABAA [gamma-aminobutyric acid] type binding sites on membranes of spermatozoa

International Nuclear Information System (INIS)

Erdoe, S.L.; Wekerle, L.

1990-01-01

The binding of [ 3 H] gamma-aminobutyric acid (GABA) to seminal membranes of swines and rams was examined. Specific, GABA binding was demonstrated in both species, which showed the features of GABA A type receptors. The affinity of binding was similar in both species, whereas the density of seminal GABA binding sites was 5 times higher in swine. Our findings suggest that GABA may have a direct effect on spermatozoa

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

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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. Copyright © 2015 Elsevier B.V. All rights reserved.

Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites

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Sato Yukuto

2007-10-01

Full Text Available Abstract Background The partitioning of ancestral functions among duplicated genes by neutral evolution, or subfunctionalization, has been considered the primary process for the evolution of novel proteins (neofunctionalization. Nonetheless, how a subfunctionalized protein can evolve into a more adaptive protein is poorly understood, mainly due to the limitations of current analytical methods, which can detect only strong selection for amino acid substitutions involved in adaptive molecular evolution. In this study, we employed a comparative evolutionary approach to this question, focusing on differences in the structural properties of a protein, specifically the electric charge, encoded by fish-specific duplicated phosphoglucose isomerase (Pgi genes. Results Full-length cDNA cloning, RT-PCR based gene expression analyses, and comparative sequence analyses showed that after subfunctionalization with respect to the expression organ of duplicate Pgi genes, the net electric charge of the PGI-1 protein expressed mainly in internal tissues became more negative, and that of PGI-2 expressed mainly in muscular tissues became more positive. The difference in net protein charge was attributable not to specific amino acid sites but to the sum of various amino acid sites located on the surface of the PGI molecule. Conclusion This finding suggests that the surface charge evolution of PGI proteins was not driven by strong selection on individual amino acid sites leading to permanent fixation of a particular residue, but rather was driven by weak selection on a large number of amino acid sites and consequently by steady directional and/or purifying selection on the overall structural properties of the protein, which is derived from many modifiable sites. The mode of molecular evolution presented here may be relevant to various cases of adaptive modification in proteins, such as hydrophobic properties, molecular size, and electric charge.

Fatty Acid-Mediated Inhibition of Metal Binding to the Multi-Metal Site on Serum Albumin: Implications for Cardiovascular Disease.

Science.gov (United States)

Blindauer, Claudia A; Khazaipoul, Siavash; Yu, Ruitao; Stewart, Alan J

2016-01-01

Human serum albumin (HSA) is the major protein in blood plasma and is responsible for circulatory transport of a range of small molecules including fatty acids, metal ions and drugs. We previously identified the major plasma Zn2+ transport site on HSA and revealed that fatty-acid binding (at a distinct site called the FA2 site) and Zn2+ binding are interdependent via an allosteric mechanism. Since binding affinities of long-chain fatty acids exceed those of plasma Zn2+, this means that under certain circumstances the binding of fatty acid molecules to HSA is likely to diminish HSA Zn2+-binding, and hence affects the control of circulatory and cellular Zn2+ dynamics. This relationship between circulatory fatty acid and Zn2+ dynamics is likely to have important physiological and pathological implications, especially since it has been recognised that Zn2+ acts as a signalling agent in many cell types. Fatty acid levels in the blood are dynamic, but most importantly, chronic elevation of plasma fatty acid levels is associated with some metabolic disorders and disease states - including myocardial infarction and other cardiovascular diseases. In this article, we briefly review the metal-binding properties of albumin and highlight the importance of their interplay with fatty acid binding. We also consider the impact of this dynamic link upon levels and speciation of plasma Zn2+, its effect upon cellular Zn2+ homeostasis and its relevance to cardiovascular and circulatory processes in health and disease.

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

Science.gov (United States)

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.

Al-rich beta zeolites. Distribution of Al atoms in the framework 4 and related protonic and metal-ion species

Czech Academy of Sciences Publication Activity Database

Sazama, Petr; Tabor, Edyta; Klein, Petr; Wichterlová, Blanka; Sklenák, Štěpán; Mokrzycki, Lukasz; Pashková, Veronika; Ogura, M.; Dědeček, Jiří

2016-01-01

Roč. 333, JAN 2016 (2016), s. 102-114 ISSN 0021-9517 R&D Projects: GA ČR GA15-12113S; GA ČR GA15-13876S; GA ČR(CZ) GA15-14007S Institutional support: RVO:61388955 Keywords : Template-free BEA* * Framework Al * Lewis and Bronsted acid ity Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.844, year: 2016

N-Glycosylation Improves the Pepsin Resistance of Histidine Acid Phosphatase Phytases by Enhancing Their Stability at Acidic pHs and Reducing Pepsin's Accessibility to Its Cleavage Sites

Science.gov (United States)

Niu, Canfang; Luo, Huiying; Shi, Pengjun; Huang, Huoqing; Wang, Yaru; Yang, Peilong

2015-01-01

N-Glycosylation can modulate enzyme structure and function. In this study, we identified two pepsin-resistant histidine acid phosphatase (HAP) phytases from Yersinia kristensenii (YkAPPA) and Yersinia rohdei (YrAPPA), each having an N-glycosylation motif, and one pepsin-sensitive HAP phytase from Yersinia enterocolitica (YeAPPA) that lacked an N-glycosylation site. Site-directed mutagenesis was employed to construct mutants by altering the N-glycosylation status of each enzyme, and the mutant and wild-type enzymes were expressed in Pichia pastoris for biochemical characterization. Compared with those of the N-glycosylation site deletion mutants and N-deglycosylated enzymes, all N-glycosylated counterparts exhibited enhanced pepsin resistance. Introduction of the N-glycosylation site into YeAPPA as YkAPPA and YrAPPA conferred pepsin resistance, shifted the pH optimum (0.5 and 1.5 pH units downward, respectively) and improved stability at acidic pH (83.2 and 98.8% residual activities at pH 2.0 for 1 h). Replacing the pepsin cleavage sites L197 and L396 in the immediate vicinity of the N-glycosylation motifs of YkAPPA and YrAPPA with V promoted their resistance to pepsin digestion when produced in Escherichia coli but had no effect on the pepsin resistance of N-glycosylated enzymes produced in P. pastoris. Thus, N-glycosylation may improve pepsin resistance by enhancing the stability at acidic pH and reducing pepsin's accessibility to peptic cleavage sites. This study provides a strategy, namely, the manipulation of N-glycosylation, for improvement of phytase properties for use in animal feed. PMID:26637601

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

International Nuclear Information System (INIS)

STALLINGS, MARY

2004-01-01

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

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

Science.gov (United States)

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.

Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.

Science.gov (United States)

Jelínek, Jan; Škoda, Petr; Hoksza, David

2017-12-06

Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has been an active field of research for some time, the quality of in-silico methods is still far from perfect. We have developed a novel prediction method called INSPiRE which benefits from a knowledge base built from data available in Protein Data Bank. All proteins involved in PPIs were converted into labeled graphs with nodes corresponding to amino acids and edges to pairs of neighboring amino acids. A structural neighborhood of each node was then encoded into a bit string and stored in the knowledge base. When predicting PPIs, INSPiRE labels amino acids of unknown proteins as interface or non-interface based on how often their structural neighborhood appears as interface or non-interface in the knowledge base. We evaluated INSPiRE's behavior with respect to different types and sizes of the structural neighborhood. Furthermore, we examined the suitability of several different features for labeling the nodes. Our evaluations showed that INSPiRE clearly outperforms existing methods with respect to Matthews correlation coefficient. In this paper we introduce a new knowledge-based method for identification of protein-protein interaction sites called INSPiRE. Its knowledge base utilizes structural patterns of known interaction sites in the Protein Data Bank which are then used for PPI prediction. Extensive experiments on several well-established datasets show that INSPiRE significantly surpasses existing PPI approaches.

Site-specific estimates of water yield applied in regional acid sensitivity surveys across western Canada

Directory of Open Access Journals (Sweden)

Patrick D. SHAW

2010-08-01

Full Text Available Runoff or water yield is an important input to the Steady-State Water Chemistry (SSWC model for estimating critical loads of acidity. Herein, we present site-specific water yield estimates for a large number of lakes (779 across three provinces of western Canada (Manitoba, Saskatchewan, and British Columbia using an isotope mass balance (IMB approach. We explore the impact of applying site-specific hydrology as compared to use of regional runoff estimates derived from gridded datasets in assessing critical loads of acidity to these lakes. In general, the average water yield derived from IMB is similar to the long-term average runoff; however, IMB results suggest a much larger range in hydrological settings of the lakes, attributed to spatial heterogeneity in watershed characteristics and landcover. The comparison of critical loads estimates from the two methods suggests that use of average regional runoff data in the SSWC model may overestimate critical loads for the majority of lakes due to systematic skewness in the actual runoff distributions. Implications for use of site-specific hydrology in regional critical loads assessments across western Canada are discussed.

Catalysts for liquid phase oxidation of olefins and sulfur compounds; Catalyseurs pour l'oxydation en phase liquide d'olefines et de composes soufres

Energy Technology Data Exchange (ETDEWEB)

Palomeque Santiago, J.F.

2002-07-01

Several basic, acid and acid-base catalysts were studied for the epoxidation of olefins activated or not and dibenzo-thiophene.Hydrotalcite activation by thermic treatment and in situ re-hydration improves catalytic activity for 2-cyclohexene-1-one and isophorone. Bronsted basic sites were found to be more active than Lewis sites. Total conversion of 2-cyclohexene-1-one is reached in 1.5 h in polar solvents. W{sub 7}O{sub 24}{sup 6-} Iso-poly-anion was exchanged onto a meixnerite by a new preparation method, A meso-porous solid was obtained with good catalytic properties for cyclohexene epoxidation 100% selective to epoxide. W{sub 7}O{sub 24}{sup 6-} and WO{sub 5}{sup 2-} anions and phenyl and dodecyl-phospho-tungstates were grafted on hydrotalcites. Due to the acid-base characteristics of these solid catalysts, cyclohexene yields products of allylic reactions. Mg-La, and Mg-Al-La mixed oxides were synthesized and mixed phases were gotten. Their basic characteristics account for hydrogen peroxide decomposition which prevents DBT oxidation reaction to sulfone. On the contrary, Mg-Al re-hydrated hydrotalcites are very active for this reaction and remove 100% of sulfur compounds in 1 hour. New catalyst W-ZrO{sub 2} were synthesized with high acid properties. stable structure with temperature and high DBT conversion in less than 5 minutes of reaction. These catalytic systems can be applied for hydrocarbon desulfurization of fuels like naphtha, gas oil and kerosene. (author)

Treatment of acidic mine waters from the Solbec-Cupra site using the Mediaflex{trademark} process; Traitement des eaux minieres acides du site Solbec-Cupra par le procede Mediaflex{sub TM}

Energy Technology Data Exchange (ETDEWEB)

Belanger, M -C; Ross, A; Shoiry, J [Valoraction Inc., Sherbrooke, PQ (Canada)

1995-01-01

Applications and development of Mediaflex{trademark} filter treatment technology are described. The method combines physical, chemical, and biological processes into a technology suitable for purification of sanitary landfill leachates, septic tank sludge, and acidic mine waters. More than a dozen of the patented filters are in use. The treatment can reach 99.9% removal of heavy metals and phenolic compounds present in waste water. Since installation of the Mediaflex{sub TM} filter at the Cambior Solbec-Cupra mining site more than 50,000 cubic metres of acidic mine waste waters (pH 5.5) have been treated. After Mediaflex{sub TM} filtration, the pH is approximately 8.0, with the heavy metal content reduced substantially. 3 refs., 4 figs., 3 tabs.

Catalytic Pyrolysis of Chilean Oak: Influence of Brønsted Acid Sites of Chilean Natural Zeolite

Directory of Open Access Journals (Sweden)

Serguei Alejandro Martín

2017-11-01

Full Text Available This paper proposes the Chilean natural zeolite as catalyst on bio-oil upgrade processes. The aim of this study was to analyze chemical composition of bio-oil samples obtained from catalytic pyrolysis of Chilean native oak in order to increase bio-oil stability during storage. In order to identify chemical compounds before and after storage, biomass pyrolysis was carried out in a fixed bed reactor at 623 K and bio-oil samples were characterized by gas chromatography/mass spectrophotometry (GC/MS. A bio-oil fractionation method was successfully applied here. Results indicate that bio-oil viscosity decreases due to active sites on the zeolite framework. Active acids sites were associated with an increment of alcohols, aldehydes, and hydrocarbon content during storage. Higher composition on aldehydes and alcohols after storage could be attributed to the occurrence of carbonyl reduction reactions that promotes them. These reactions are influenced by zeolite surface characteristics and could be achieved via the direct contribution of Brønsted acid sites to Chilean natural zeolite.

Modifikasi Limbah Tulang Sapi Bali dan Pemanfaatannya untuk Adsorpsi Methylene Blue (MODIFICATION OF BALI COW BONE WASTE AND ITS APPLICATION TO ADSORPTION OF METHYLENE BLUE

Directory of Open Access Journals (Sweden)

I Nengah Simpen

2017-01-01

Full Text Available The research of modification, characterization, and application of nano-porous adsorbent base onBali cow bone waste to methylene blue (MB adsorption has been carried out. The modification was carriedout through extraction of hydroxyapatite (HA from cow bone, then its activated by 0.4 M NaOH solutionand coating to form active sites of Fe and Fe-Al oxides. The adsorbent was applied to know quantitativelyadsorption capacity coated-HA (CHA to MB as wastewaters simulation. Compound of CHA wascharacterized amount of active sites by base-acid titration, Bronsted-Lewis acid sites by FTIR spectroscopy,specific surface area by MB method and pore size by surface area analyzer gasorption nitrogen. While,amount of coated-Fe and Al by LIBS. Amount of MB adsorbed was analyzed by UV-Vis spectrophotometer.The results showed that coating of Fe and Fe-Al oxides increased amount of active sites, sites distributionof new Lewis acid site, everage nano pore size with pore volume is microporous (less than 2 nm, and Fe andFe-Al oxides was into HA crystal structure. The amount of active sites was the higest of T1-Fe-Al2O3 andall pores diameter less than 58.182 nm.While, the specific surface area increased T3-Fe2O3>T3-Fe-Al2O3>T2-Fe2O3 respectively. In the adsorption isotherm, coating on HA significantly increased ability of adsorbentand through Freundlich model (R2 > 0.77 with the higest adsorption capacity on T3-Fe2O3 (3.2019 mg/gthen T2-Fe-Al2O3 (2.7921 mg/g. Results of this research indicate that Fe and Fe-Al oxides HA-modifiedincreased adsorption ability.

Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149.

Science.gov (United States)

Tkavc, Rok; Matrosova, Vera Y; Grichenko, Olga E; Gostinčar, Cene; Volpe, Robert P; Klimenkova, Polina; Gaidamakova, Elena K; Zhou, Carol E; Stewart, Benjamin J; Lyman, Mathew G; Malfatti, Stephanie A; Rubinfeld, Bonnee; Courtot, Melanie; Singh, Jatinder; Dalgard, Clifton L; Hamilton, Theron; Frey, Kenneth G; Gunde-Cimerman, Nina; Dugan, Lawrence; Daly, Michael J

2017-01-01

Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE) production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans . However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute), heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.

Amino acid sequence surrounding the chondroitin sulfate attachment site of thrombomodulin regulates chondroitin polymerization.

Science.gov (United States)

Izumikawa, Tomomi; Kitagawa, Hiroshi

2015-05-01

Thrombomodulin (TM) is a cell-surface glycoprotein and a critical mediator of endothelial anticoagulant function. TM exists as both a chondroitin sulfate (CS) proteoglycan (PG) form and a non-PG form lacking a CS chain (α-TM); therefore, TM can be described as a part-time PG. Previously, we reported that α-TM bears an immature, truncated linkage tetrasaccharide structure (GlcAβ1-3Galβ1-3Galβ1-4Xyl). However, the biosynthetic mechanism to generate part-time PGs remains unclear. In this study, we used several mutants to demonstrate that the amino acid sequence surrounding the CS attachment site influences the efficiency of chondroitin polymerization. In particular, the presence of acidic residues surrounding the CS attachment site was indispensable for the elongation of CS. In addition, mutants defective in CS elongation did not exhibit anti-coagulant activity, as in the case with α-TM. Together, these data support a model for CS chain assembly in which specific core protein determinants are recognized by a key biosynthetic enzyme involved in chondroitin polymerization. Copyright © 2015 Elsevier Inc. All rights reserved.

iSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition.

Directory of Open Access Journals (Sweden)

Yan Xu

Full Text Available Posttranslational modifications (PTMs of proteins are responsible for sensing and transducing signals to regulate various cellular functions and signaling events. S-nitrosylation (SNO is one of the most important and universal PTMs. With the avalanche of protein sequences generated in the post-genomic age, it is highly desired to develop computational methods for timely identifying the exact SNO sites in proteins because this kind of information is very useful for both basic research and drug development. Here, a new predictor, called iSNO-PseAAC, was developed for identifying the SNO sites in proteins by incorporating the position-specific amino acid propensity (PSAAP into the general form of pseudo amino acid composition (PseAAC. The predictor was implemented using the conditional random field (CRF algorithm. As a demonstration, a benchmark dataset was constructed that contains 731 SNO sites and 810 non-SNO sites. To reduce the homology bias, none of these sites were derived from the proteins that had [Formula: see text] pairwise sequence identity to any other. It was observed that the overall cross-validation success rate achieved by iSNO-PseAAC in identifying nitrosylated proteins on an independent dataset was over 90%, indicating that the new predictor is quite promising. Furthermore, a user-friendly web-server for iSNO-PseAAC was established at http://app.aporc.org/iSNO-PseAAC/, by which users can easily obtain the desired results without the need to follow the mathematical equations involved during the process of developing the prediction method. It is anticipated that iSNO-PseAAC may become a useful high throughput tool for identifying the SNO sites, or at the very least play a complementary role to the existing methods in this area.

A cluster DFT study of NH{sub 3} and NO adsorption on the (MoO{sub 2}){sup 2+}/HZSM-5 surface: Lewis versus Brønsted acid sites

Energy Technology Data Exchange (ETDEWEB)

Yan, Zhifeng [College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); College of Material Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Zuo, Zhijun [Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Li, Zhe, E-mail: lizhe@tyut.edu.cn [College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China); Zhang, Jinshan [College of Material Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi (China)

2014-12-01

Graphical abstract: - Highlights: • NH{sub 3} adsorption is found to be more favorable energetically than NO adsorption on both Lewis and Brønsted acid sites. • Lewis and Brønsted acid sites are competitive energetically for NH{sub 3} adsorption. • Reduced-state Mo{sup 5+} is suggested to play a key role in adsorption and activation of NO{sub x} together with the adsorbed NH{sub 4}{sup +}. - Abstract: A systematic DFT study was carried out to investigate NH{sub 3} and NO adsorption on both Lewis and Brønsted acid sites of (MoO{sub 2}){sup 2+}/HZSM-5 catalyst by using cluster models. The adsorption energy results indicate that NH{sub 3} could strongly adsorb on both Lewis and Brønsted acid sites in the form of coordinated NH{sub 3} and NH{sub 4}{sup +}, respectively, whereas NO represents poorer adsorption ability. It is also found that Lewis and Brønsted acid sites are competitive energetically for NH{sub 3} adsorption. According to the difference in the proposed mechanisms for NH{sub 3} adsorption on different acid sites, particular attention has been focused on the first dissociation of coordinated NH{sub 3} for Lewis acid site and the effect of Mo site on the introduction of NO for Brønsted acid site. For the coordinated NH{sub 3} on Lewis acid site, the more electron donation from NH{sub 3} is, the greater its adsorption stability is and the higher active its H atoms are. In addition, DOS results show that stability of the H atoms is enhanced by interacting with framework oxygen and especially the H atoms chemical-bonded with framework oxygen. For the NH{sub 4}{sup +} on Brønsted acid site, reduced-state Mo{sup 5+} holds stronger reducibility and oxidizability than terminal oxygen, which is suggested to play a key role in adsorption and activation of NO{sub x} together with the adsorbed NH{sub 4}{sup +}.

Determination of the positions of aluminum atoms introduced into SSZ-35 and the catalytic properties of the generated Brønsted acid sites.

Science.gov (United States)

Miyaji, Akimitsu; Kimura, Nobuhiro; Shiga, Akinobu; Hayashi, Yoshihiro; Nishitoba, Toshiki; Motokura, Ken; Baba, Toshihide

2017-03-01

The positions of aluminum (Al) atoms in SSZ-35 together with the characteristics of the generated protons were investigated by 27 Al multiple quantum magic-angle spinning (MQ-MAS), 29 Si MAS, and 1 H MAS NMR data analyses accompanied by a variable temperature 1 H MAS NMR analysis. The origin of the acidic -OH groups (Brønsted acid sites) generated by introducing Al atoms into the T sites was investigated and the T sites introduced into the Al atoms were revealed. To further determine the catalytic properties of the acidic protons generated in SSZ-35, the influence of the concentration of the Al atoms on the catalytic activity and selectivity during the transformation of toluene was examined.

Identification of metal ion binding sites based on amino acid sequences.

Science.gov (United States)

Cao, Xiaoyong; Hu, Xiuzhen; Zhang, Xiaojin; Gao, Sujuan; Ding, Changjiang; Feng, Yonge; Bao, Weihua

2017-01-01

The identification of metal ion binding sites is important for protein function annotation and the design of new drug molecules. This study presents an effective method of analyzing and identifying the binding residues of metal ions based solely on sequence information. Ten metal ions were extracted from the BioLip database: Zn2+, Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+, K+ and Co2+. The analysis showed that Zn2+, Cu2+, Fe2+, Fe3+, and Co2+ were sensitive to the conservation of amino acids at binding sites, and promising results can be achieved using the Position Weight Scoring Matrix algorithm, with an accuracy of over 79.9% and a Matthews correlation coefficient of over 0.6. The binding sites of other metals can also be accurately identified using the Support Vector Machine algorithm with multifeature parameters as input. In addition, we found that Ca2+ was insensitive to hydrophobicity and hydrophilicity information and Mn2+ was insensitive to polarization charge information. An online server was constructed based on the framework of the proposed method and is freely available at http://60.31.198.140:8081/metal/HomePage/HomePage.html.

Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149

Directory of Open Access Journals (Sweden)

Rok Tkavc

2018-01-01

Full Text Available Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans. However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute, heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.

Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Triggered Isothermal Amplification for Site-Specific Nucleic Acid Detection.

Science.gov (United States)

Huang, Mengqi; Zhou, Xiaoming; Wang, Huiying; Xing, Da

2018-02-06

A novel CRISPR/Cas9 triggered isothermal exponential amplification reaction (CAS-EXPAR) strategy based on CRISPR/Cas9 cleavage and nicking endonuclease (NEase) mediated nucleic acids amplification was developed for rapid and site-specific nucleic acid detection. CAS-EXPAR was primed by the target DNA fragment produced by cleavage of CRISPR/Cas9, and the amplification reaction performed cyclically to generate a large number of DNA replicates which were detected using a real-time fluorescence monitoring method. This strategy that combines the advantages of CRISPR/Cas9 and exponential amplification showed high specificity as well as rapid amplification kinetics. Unlike conventional nucleic acids amplification reactions, CAS-EXPAR does not require exogenous primers, which often cause target-independent amplification. Instead, primers are first generated by Cas9/sgRNA directed site-specific cleavage of target and accumulated during the reaction. It was demonstrated this strategy gave a detection limit of 0.82 amol and showed excellent specificity in discriminating single-base mismatch. Moreover, the applicability of this method to detect DNA methylation and L. monocytogenes total RNA was also verified. Therefore, CAS-EXPAR may provide a new paradigm for efficient nucleic acid amplification and hold the potential for molecular diagnostic applications.

Remedial action at the Acid/Pueblo Canyon site, Los Alamos, New Mexico. Final report

International Nuclear Information System (INIS)

1984-10-01

The Acid/Pueblo Canyon site (TA-45) was designated in 1976 for remedial action under the Formerly Utilized Sites Remedial Action Program (FUSRAP). During the period 1943 to 1964 untreated and treated liquid wastes generated by nuclear weapons research activities at the Los Alamos Scientific Laboratory (LASL) were discharged into the two canyons. A survey of the site conducted by LASL in 1976 to 1977 identified two areas where radiological contamination exceeded criteria levels. The selected remedial action was based on extensive radiological characterization and comprehensive engineering assessments and comprised the excavation and disposal of 390 yd 3 of contaminated soil and rock. This document describes the background to the remedial action, the parties involved in administering and executing it, the chronology of the work, verification of the adequacy of the remedial action, and the cost incurred. 14 references, 5 figures, 5 tables

Triazacyclophane (TAC)-scaffolded histidine and aspartic acid residues as mimics of non-heme metalloenzyme active sites

NARCIS (Netherlands)

Albada, H.B.; Soulimani, F.; Jacobs, H.J.F.; Versluis, C.; Weckhuysen, B.M.; Liskamp, R.M.J.

2012-01-01

We describe the synthesis and coordination behaviour to copper(II) of two close structural triazacyclophane-based mimics of two often encountered aspartic acid and histidine containing metalloenzyme active sites. Coordination of these mimics to copper(I) and their reaction with molecular oxygen

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

International Nuclear Information System (INIS)

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

1985-01-01

125 I-Lysergic acid diethylamide ( 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. 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 125 I-LSD binding site appears to represent a new type of serotonergic site which is located on non-neuronal cells in this tissue

Soil degradation by sulfuric acid disposition on uranium producing sites in south Bulgaria

International Nuclear Information System (INIS)

Atanasov, I.; Gribachev, P.

1997-01-01

This study assesses the damage of soils caused by spills of sulfuric acid solutions used for in situ leaching of uranium at eight uranium producing (by open-cast method) sites (total area of approximately 220 ha) in the region of Momino-Rakovski (South Bulgaria). The upper soil layer is cinnamonic pseudopodzolic ( or Eutric Planosols by FAO Legend, 1974). The results of the investigation show that the sulfuric acid spills caused strong acidification of upper (0-20 cm) and subsurface (20-60 cm) soil horizons which is expressed as decreasing of pH (H 2 O) to 2.9-3.5 and increasing of exchangeable H + and Al 3+ to 18 and 32% from CEC. Acid degradation of soils is combined with reducing of organic matter content. The average concentration of the total heavy metal content in the upper soil horizon (in ppm) is: Cd=1.5; Cu=30; Pb=25; Zn=40 and U=8. No significant differences were detected between the upper and subsurface soil layers . The heavy metal concentration did not exceed the Bulgarian standards for heavy metals and uranium content of soils. But the coarse texture of the top soil layers, the lack of carbonates, The low CEC and strong acidity determine a low buffering capacity of the investigated soils and this can be considered as hazardous for plants. This indicates that a future soil monitoring should be carried out in the region together with measures for neutralizing of soil acidity

Modulation of salivation and heartburn in response to the site of acid infusion in the human oesophagus.

Science.gov (United States)

Dutta, S K; Agrawal, K; Mahmoud, M A

2010-09-01

The pathogenesis of gastro-oesophageal reflux disease includes increased acid reflux, reduced salivation and impaired peristalsis. This may depend upon the height of acid wave and magnitude of oesophageal mucosal exposure. Interestingly, the effect of site of acid infusion upon salivary secretion and heartburn has not been examined in any detail. To examine whether acid infusion in the upper oesophagus may cause increased salivation and heartburn as compared with acid infusion in the lower oesophagus. Twelve healthy male subjects (mean age 30) received infusions of HCl, citric acid and acetic acid at 10 and 20 cm above the lower oesophageal sphincter (LES) for fixed time periods. Parotid saliva collected periodically and heartburn severity scored using standardized scale. Standard statistical methods (paired t-tests, analysis of variance) were used to determine the significance of results. Acid infusion in the upper oesophagus increased parotid flow rate as compared with that in the lower oesophagus (P heartburn score at 20 cm as well as 10 cm above LES (P heartburn in response to acid infusion in the upper vs. lower part of the oesophagus. 2010 Blackwell Publishing Ltd.

Enzyme active site mimics based on TriAzaCyclophane (TAC)-scaffolded peptides and amino acid residues

NARCIS (Netherlands)

Albada, H.B.

2009-01-01

This thesis describes the scope and limitations of the application of TriAzaCyclophane (TAC)-scaffolded peptides or amino acid residues as enzyme active site mimics, as ligands in asymmetric catalysis and as hydrolysis catalysts attached to vancomycin. For the mimicry of functional group enzymes, of

Spontaneous dispersion of PdO onto acid sites of zeolites studied by in situ DXAFS

CERN Document Server

Okumura, K; Niwa, M; Yokota, S; Kato, K; Tanida, H; Uruga, T

2003-01-01

The generation of highly dispersed PdO over zeolite supports was studied using in situ energy-dispersive XAFS (DXAFS) technique. From the comparison with the Na-ZSM-5, it was found that the oxidation as well as the spontaneous dispersion of Pd was promoted through the interaction between PdO and acid sites of H-form zeolites. (author)

Complexes of metal chlorides with proton donors — promising polyfunctional catalysts for electrophilic processes

Science.gov (United States)

Minsker, Karl S.; Ivanova, S. R.; Biglova, Raisa Z.

1995-05-01

The Bronsted acids formed as a result of the interaction of aluminium chlorides with Group I and II metal chlorides in the presence of proton-donating compounds are promising polyfunctional catalysts for electrophilic processes (polymerisation, depolymerisation and degradation of macromolecules, alkylation, desulfurisation, and hydrogenation). The factor determing the electrophilic activity and selectivity of the action of the catalysts is their acidity. This makes it possible to predict the direction of the changes in the activity and selectivity of the catalyst in specific chemical processes in conformity with the opposite variation rule: with increase in the acidity of the electrophilic catalyst, their activity increases but the selectivity of their action diminishes. The bibliography includes 72 references.

Enhancement of the catalytic activity of ferulic acid decarboxylase from Enterobacter sp. Px6-4 through random and site-directed mutagenesis.

Science.gov (United States)

Lee, Hyunji; Park, Jiyoung; Jung, Chaewon; Han, Dongfei; Seo, Jiyoung; Ahn, Joong-Hoon; Chong, Youhoon; Hur, Hor-Gil

2015-11-01

The enzyme ferulic acid decarboxylase (FADase) from Enterobacter sp. Px6-4 catalyzes the decarboxylation reaction of lignin monomers and phenolic compounds such as p-coumaric acid, caffeic acid, and ferulic acid into their corresponding 4-vinyl derivatives, that is, 4-vinylphenol, 4-vinylcatechol, and 4-vinylguaiacol, respectively. Among various ferulic acid decarboxylase enzymes, we chose the FADase from Enterobacter sp. Px6-4, whose crystal structure is known, and produced mutants to enhance its catalytic activity by random and site-directed mutagenesis. After three rounds of sequential mutations, FADase(F95L/D112N/V151I) showed approximately 34-fold higher catalytic activity than wild-type for the production of 4-vinylguaiacol from ferulic acid. Docking analyses suggested that the increased activity of FADase(F95L/D112N/V151I) could be due to formation of compact active site compared with that of the wild-type FADase. Considering the amount of phenolic compounds such as lignin monomers in the biomass components, successfully bioengineered FADase(F95L/D112N/V151I) from Enterobacter sp. Px6-4 could provide an ecofriendly biocatalytic tool for producing diverse styrene derivatives from biomass.

Salicylic Acid and Jasmonic Acid Pathways are Activated in Spatially Different Domains Around the Infection Site During Effector-Triggered Immunity in Arabidopsis thaliana.

Science.gov (United States)

Betsuyaku, Shigeyuki; Katou, Shinpei; Takebayashi, Yumiko; Sakakibara, Hitoshi; Nomura, Nobuhiko; Fukuda, Hiroo

2018-01-01

The innate immune response is, in the first place, elicited at the site of infection. Thus, the host response can be different among the infected cells and the cells surrounding them. Effector-triggered immunity (ETI), a form of innate immunity in plants, is triggered by specific recognition between pathogen effectors and their corresponding plant cytosolic immune receptors, resulting in rapid localized cell death known as hypersensitive response (HR). HR cell death is usually limited to a few cells at the infection site, and is surrounded by a few layers of cells massively expressing defense genes such as Pathogenesis-Related Gene 1 (PR1). This virtually concentric pattern of the cellular responses in ETI is proposed to be regulated by a concentration gradient of salicylic acid (SA), a phytohormone accumulated around the infection site. Recent studies demonstrated that jasmonic acid (JA), another phytohormone known to be mutually antagonistic to SA in many cases, is also accumulated in and required for ETI, suggesting that ETI is a unique case. However, the molecular basis for this uniqueness remained largely to be solved. Here, we found that, using intravital time-lapse imaging, the JA signaling pathway is activated in the cells surrounding the central SA-active cells around the infection sites in Arabidopsis thaliana. This distinct spatial organization explains how these two phythormone pathways in a mutually antagonistic relationship can be activated simultaneously during ETI. Our results re-emphasize that the spatial consideration is a key strategy to gain mechanistic insights into the apparently complex signaling cross-talk in immunity. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

Decontamination of chemical warfare sulfur mustard agent simulant by ZnO nanoparticles

Science.gov (United States)

Sadeghi, Meysam; Yekta, Sina; Ghaedi, Hamed

2016-07-01

In this study, zinc oxide nanoparticles (ZnO NPs) have been surveyed to decontaminate the chloroethyl phenyl sulfide as a sulfur mustard agent simulant. Prior to the reaction, ZnO NPs were successfully prepared through sol-gel method in the absence and presence of polyvinyl alcohol (PVA). PVA was utilized as a capping agent to control the agglomeration of the nanoparticles. The formation, morphology, elemental component, and crystalline size of nanoscale ZnO were certified and characterized by SEM/EDX, XRD, and FT-IR techniques. The decontamination (adsorption and destruction) was tracked by the GC-FID analysis, in which the effects of polarity of the media, such as isopropanol, acetone and n-hexane, reaction time intervals from 1 up to 18 h, and different temperatures, including 25, 35, 45, and 55 °C, on the catalytic/decontaminative capability of the surface of ZnO NPs/PVA were investigated and discussed, respectively. Results demonstrated that maximum decontamination (100 %) occurred in n-hexane solvent at 55 °C after 1 h. On the other hand, the obtained results for the acetone and isopropanol solvents were lower than expected. GC-MS chromatograms confirmed the formation of hydroxyl ethyl phenyl sulfide and phenyl vinyl sulfide as the destruction reaction products. Furthermore, these chromatograms proved the role of hydrolysis and elimination mechanisms on the catalyst considering its surface Bronsted and Lewis acid sites. A non-polar solvent aids material transfer to the reactive surface acid sites without blocking these sites.

Are carboxyl groups the most acidic sites in amino acids? Gas-phase acidities, photoelectron spectra, and computations on tyrosine, p-hydroxybenzoic acid, and their conjugate bases.

Science.gov (United States)

Tian, Zhixin; Wang, Xue-Bin; Wang, Lai-Sheng; Kass, Steven R

2009-01-28

Deprotonation of tyrosine in the gas phase was found to occur preferentially at the phenolic site, and the conjugate base consists of a 70:30 mixture of phenoxide and carboxylate anions at equilibrium. This result was established by developing a chemical probe for differentiating these two isomers, and the presence of both ions was confirmed by photoelectron spectroscopy. Equilibrium acidity measurements on tyrosine indicated that deltaG(acid)(o) = 332.5 +/- 1.5 kcal mol(-1) and deltaH(acid)(o) = 340.7 +/- 1.5 kcal mol(-1). Photoelectron spectra yielded adiabatic electron detachment energies of 2.70 +/- 0.05 and 3.55 +/- 0.10 eV for the phenoxide and carboxylate anions, respectively. The H/D exchange behavior of deprotonated tyrosine was examined using three different alcohols (CF3CH2OD, C6H5CH2OD, and CH3CH2OD), and incorporation of up to three deuterium atoms was observed. Two pathways are proposed to account for these results, and all of the experimental findings are supplemented with B3LYP/aug-cc-pVDZ and G3B3 calculations. In addition, it was found that electrospray ionization of tyrosine from a 3:1 (v/v) CH3OH/H2O solution using a commercial source produces a deprotonated [M-H]- anion with the gas-phase equilibrium composition rather than the structure of the ion that exists in aqueous media. Electrospray ionization from acetonitrile, however, leads largely to the liquid-phase (carboxylate) structure. A control molecule, p-hydroxybenzoic acid, was found to behave in a similar manner. Thus, the electrospray conditions that are employed for the analysis of a compound can alter the isomeric composition of the resulting anion.

Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction.

Science.gov (United States)

López, Yosvany; Sharma, Alok; Dehzangi, Abdollah; Lal, Sunil Pranit; Taherzadeh, Ghazaleh; Sattar, Abdul; Tsunoda, Tatsuhiko

2018-01-19

Post-translational modification is considered an important biological mechanism with critical impact on the diversification of the proteome. Although a long list of such modifications has been studied, succinylation of lysine residues has recently attracted the interest of the scientific community. The experimental detection of succinylation sites is an expensive process, which consumes a lot of time and resources. Therefore, computational predictors of this covalent modification have emerged as a last resort to tackling lysine succinylation. In this paper, we propose a novel computational predictor called 'Success', which efficiently uses the structural and evolutionary information of amino acids for predicting succinylation sites. To do this, each lysine was described as a vector that combined the above information of surrounding amino acids. We then designed a support vector machine with a radial basis function kernel for discriminating between succinylated and non-succinylated residues. We finally compared the Success predictor with three state-of-the-art predictors in the literature. As a result, our proposed predictor showed a significant improvement over the compared predictors in statistical metrics, such as sensitivity (0.866), accuracy (0.838) and Matthews correlation coefficient (0.677) on a benchmark dataset. The proposed predictor effectively uses the structural and evolutionary information of the amino acids surrounding a lysine. The bigram feature extraction approach, while retaining the same number of features, facilitates a better description of lysines. A support vector machine with a radial basis function kernel was used to discriminate between modified and unmodified lysines. The aforementioned aspects make the Success predictor outperform three state-of-the-art predictors in succinylation detection.

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

Science.gov (United States)

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 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 process in treatment of acid impaired waters that were previously not amenable to low cost limestone treatment.

Possible site-specific reagent for the general amino acid transport system of Saccharomyces cerevisiae.

Science.gov (United States)

Larimore, F S; Roon, R J

1978-02-07

The general amino acid transport system of Saccharomyces cerevisiae functions in the uptake of neutral, basic, and acidic amino acids. The amino acid analogue N-delta-chloroacetyl-L-ornithine (NCAO) has been tested as potential site specific reagent for this system. L-Tryptophan, which is transported exclusively by the general transport system, was used as a substrate. In the presence of glucose as an energy source, NCAO inhibited tryptophan transport competitively (Ki = 80 micrometer) during short time intervals (1-2 min), but adding 100 micrometer NCAO to a yeast cell suspension resulted in a time-dependent activation of tryptophan transport during the first 15 min of treatment. Following the activation a time-dependent decay of tryptophan transport activity occurred. Approximately 80% inactivation of the system was observed after 90 min. When a yeast cell suspension was treated with NCAO in the absence of an energy source, an 80% inactivation of tryptophan transport occurred in 90 min. The inactivation was noncompetitive (Ki congruent to 60 micrometer) and could not be reversed by the removal of the NCAO. Addition of a five-fold excess of L-lysine during NCAO treatment or prevented inactivation of tryptophan transport. Under parallel conditions of incubation, other closely related transport systems were not inhibited by NCAO.

SiteFind: A software tool for introducing a restriction site as a marker for successful site-directed mutagenesis

Directory of Open Access Journals (Sweden)

Evans Paul M

2005-12-01

Full Text Available Abstract Background Site-directed mutagenesis is a widely-used technique for introducing mutations into a particular DNA sequence, often with the goal of creating a point mutation in the corresponding amino acid sequence but otherwise leaving the overall sequence undisturbed. However, this method provides no means for verifying its success other than sequencing the putative mutant construct: This can quickly become an expensive method for screening for successful mutations. An alternative to sequencing is to simultaneously introduce a restriction site near the point mutation in manner such that the restriction site has no effect on the translated amino acid sequence. Thus, the novel restriction site can be used as a marker for successful mutation which can be quickly and easily assessed. However, finding a restriction site that does not disturb the corresponding amino acid sequence is a time-consuming task even for experienced researchers. A fast and easy to use computer program is needed for this task. Results We wrote a computer program, called SiteFind, to help us design a restriction site within the mutation primers without changing the peptide sequence. Because of the redundancy of genetic code, a given peptide can be encoded by many different DNA sequences. Since the list of possible restriction sites for a given DNA sequence is not always obvious, SiteFind automates this task. The number of possible sequences a computer program must search through increases exponentially as the sequence length increases. SiteFind uses a novel "moving window" algorithm to reduce the number of possible sequences to be searched to a manageable level. The user enters a nucleotide sequence, specifies what amino acid residues should be changed in the mutation, and SiteFind generates a list of possible restriction sites and what nucleotides must be changed to introduce that site. As a demonstration of its use, we successfully generated a single point mutation

The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Haemophilus influenzae contains two active-site histidine residues.

Science.gov (United States)

Gillner, Danuta M; Bienvenue, David L; Nocek, Boguslaw P; Joachimiak, Andrzej; Zachary, Vincentos; Bennett, Brian; Holz, Richard C

2009-01-01

The catalytic and structural properties of the H67A and H349A dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) from Haemophilus influenzae were investigated. On the basis of sequence alignment with the carboxypeptidase from Pseudomonas sp. strain RS-16, both H67 and H349 were predicted to be Zn(II) ligands. The H67A DapE enzyme exhibited a decreased catalytic efficiency (180-fold) compared with wild-type (WT) DapE towards N-succinyldiaminopimelic acid. No catalytic activity was observed for H349A under the experimental conditions used. The electronic paramagnetic resonance (EPR) and electronic absorption data indicate that the Co(II) ion bound to H349A-DapE is analogous to that of WT DapE after the addition of a single Co(II) ion. The addition of 1 equiv of Co(II) to H67A DapE provides spectra that are very different from those of the first Co(II) binding site of the WT enzyme, but that are similar to those of the second binding site. The EPR and electronic absorption data, in conjunction with the kinetic data, are consistent with the assignment of H67 and H349 as active-site metal ligands for the DapE from H. influenzae. Furthermore, the data suggest that H67 is a ligand in the first metal binding site, while H349 resides in the second metal binding site. A three-dimensional homology structure of the DapE from H. influenzae was generated using the X-ray crystal structure of the DapE from Neisseria meningitidis as a template and superimposed on the structure of the aminopeptidase from Aeromonas proteolytica (AAP). This homology structure confirms the assignment of H67 and H349 as active-site ligands. The superimposition of the homology model of DapE with the dizinc(II) structure of AAP indicates that within 4.0 A of the Zn(II) binding sites of AAP all of the amino acid residues of DapE are nearly identical.

Impact of ursodeoxycholic acid on a CCK1R cholesterol-binding site may contribute to its positive effects in digestive function.

Science.gov (United States)

Desai, Aditya J; Dong, Maoqing; Harikumar, Kaleeckal G; Miller, Laurence J

2015-09-01

Dysfunction of the type 1 cholecystokinin (CCK) receptor (CCK1R) as a result of increased gallbladder muscularis membrane cholesterol has been implicated in the pathogenesis of cholesterol gallstones. Administration of ursodeoxycholic acid, which is structurally related to cholesterol, has been shown to have beneficial effects on gallstone formation. Our aims were to explore the possible direct effects and mechanism of action of bile acids on CCK receptor function. We studied the effects of structurally related hydrophobic chenodeoxycholic acid and hydrophilic ursodeoxycholic acid in vitro on CCK receptor function in the setting of normal and elevated membrane cholesterol. We also examined their effects on a cholesterol-insensitive CCK1R mutant (Y140A) disrupting a key site of cholesterol action. The results show that, similar to the impact of cholesterol on CCK receptors, bile acid effects were limited to CCK1R, with no effects on CCK2R. Chenodeoxycholic acid had a negative impact on CCK1R function, while ursodeoxycholic acid had no effect on CCK1R function in normal membranes but was protective against the negative impact of elevated cholesterol on this receptor. The cholesterol-insensitive CCK1R mutant Y140A was resistant to effects of both bile acids. These data suggest that bile acids compete with the action of cholesterol on CCK1R, probably by interacting at the same site, although the conformational impact of each bile acid appears to be different, with ursodeoxycholic acid capable of correcting the abnormal conformation of CCK1R in a high-cholesterol environment. This mechanism may contribute to the beneficial effect of ursodeoxycholic acid in reducing cholesterol gallstone formation. Copyright © 2015 the American Physiological Society.

Active site - a site of binding of affinity inhibitors in baker's yeast inorganic pyrophosphatase

International Nuclear Information System (INIS)

Svyato, I.E.; Sklyankina, V.A.; Avaeva, S.M.

1986-01-01

The interaction of the enzyme-substrate complex with methyl phosphate, O-phosphoethanolamine, O-phosphopropanolamine, N-acetylphosphoserine, and phosphoglyolic acid, as well as pyrophosphatase, modified by monoesters of phosphoric acid, with pyrophosphate and tripolyphosphate, was investigated. It was shown that the enzyme containing the substrate in the active site does not react with monophosphates, but modified pyrophosphatase entirely retains the ability to bind polyanions to the regulatory site. It is concluded that the inactivation of baker's yeast inorganic pyrophosphatase by monoesters of phosphoric acid, which are affinity inhibitors of it, is the result of modification of the active site of the enzyme

NOx Control Options and Integration for US Coal Fired Boilers

Energy Technology Data Exchange (ETDEWEB)

Mike Bockelie; Kevin Davis; Temi Linjewile; Connie Senior; Eric Eddings; Kevin Whitty; Larry Baxter; Calvin Bartholomew; William Hecker; Stan Harding

2004-06-30

This is the sixteenth Quarterly Technical Report for DOE Cooperative Agreement No: DEFC26-00NT40753. The goal of the project is to develop cost effective analysis tools and techniques for demonstrating and evaluating low NOx control strategies and their possible impact on boiler performance for boilers firing US coals. The Electric Power Research Institute (EPRI) is providing co-funding for this program. During an unplanned outage, damage occurred to the electrochemical noise corrosion probes installed at the AEP Gavin plant; testing is expected to resume in August. The KEMCOP corrosion coupons were not affected by the unplanned outage; the coupons were removed and sent for analysis. BYU conducted a series of tests before the ISSR lab was relocated. Ammonia adsorption experiments provided clear evidence of the types of acidic sites present on catalyst surfaces. Data collected this quarter indicate that surface sulfation decreases Lewis acid site concentrations for all catalysts thus far studied, confirming that catalytic activity under commercial coal-based SCR conditions occurs primarily on Br{o}nsted acid sites and would be susceptible to basic impurities such as alkali and alkaline earth oxides, chlorides, and sulfates. SCR activity tests based on MS analysis showed that increasing sulfation generally increases NO reduction activity for both 0% and 1% vanadia catalysts. During this quarter, the slipstream reactor at Rockport operated for 720 hours on flue gas. Catalyst exposure time reached 4500 hours since installation. The reactor is out of service at the Rockport plant and plans are being made to move it to the Gadsden Plant. At Gadsden, modifications have begun in preparation for installation of the slipstream reactor next quarter.

Defining proximity relationships in the tertiary structure of the dopamine transporter. Identification of a conserved glutamic acid as a third coordinate in the endogenous Zn(2+)-binding site

DEFF Research Database (Denmark)

Løland, Claus Juul; Norregaard, L; Gether, U

1999-01-01

, high affinity Zn(2+)-binding site. To achieve further insight into the tertiary organization of hDAT, we set out to identify additional residues involved in Zn(2+) binding and subsequently to engineer artificial Zn(2+)-binding sites. Ten aspartic acids and glutamic acids, predicted...

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

Energy Technology Data Exchange (ETDEWEB)

Truex, Michael J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Szecsody, James E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Qafoku, Nikolla [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Serne, R. Jeffrey [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

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.

Design, Synthesis, and in Vitro Pharmacology of New Radiolabeled γ-Hydroxybutyric Acid Analogues Including Photolabile Analogues with Irreversible Binding to the High-Affinity γ-Hydroxybutyric Acid Binding Sites

DEFF Research Database (Denmark)

Sabbatini, Paola; Wellendorph, Petrine; Høg, Signe

2010-01-01

γ-Hydroxybutyric acid (GHB) is a psychotropic compound endogenous to the brain. Despite its potential physiological significance, the complete molecular mechanisms of action remain unexplained. To facilitate the isolation and identification of the high-affinity GHB binding site, we herein report ...

Site-Directed Spin-Labeling of Nucleic Acids by Click Chemistry. Detection of Abasic Sites in Duplex DNA by EPR Spectroscopy

DEFF Research Database (Denmark)

Sigurdsson, Snorri; Vogel, Stefan; Shelke, Sandip

2010-01-01

and the nitroxide spin label. The spin label was used to detect, for the first time, abasic sites in duplex DNA by X-band CW-EPR spectroscopy and give information about other structural deformations as well as local conformational changes in DNA. For example, reduced mobility of the spin label in a mismatched pair...... label out of the duplex and toward the solution. Thus, reposition of the spin label, when acting as a mercury(II)-controlled mechanical lever, can be readily detected by EPR spectroscopy. The ease of incorporation and properties of the new spin label make it attractive for EPR studies of nucleic acids...

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

Science.gov (United States)

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 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 process in treatment of acid impaired waters that were

Effect of Number of Various-Type Acid Sites Located on 20 % Co/ZrO2 • SiO2 Sample Surface on Parameters of Catalytic Process in Synthesis of High-Octane Motor Fuel Components

Directory of Open Access Journals (Sweden)

A. P. Nesenchouk

2011-01-01

Full Text Available The paper considers an effect of ZrO2 content in 20%Co/xZrO2∙(100 – xSiO2 (x = 0, 10, 15, 25, 30, 40 and 100 mass percent catalyst carriers on their catalytic properties. Temperature programmed desorption of NH3 has made it possible to determine relations between their acid and catalytic properties. The paper reveals the TPD spectrum is the result of 4 overlapping peaks originating during NH3 desorption from the respective groups of acid sites. Total acidity of samples and contribution of separate acid site groups into the given acidity have been have been determined in the paper. The paper contains graphical dependences of a various-type acid site number on  content of zirconium oxide in the carrier. Correlations between change in various-type acid site number and catalytic process parameters (CO conversion, C5+ hydrocarbon output and  C5+ isoparaffin output have been found in the paper. The paper shows that the highest values of CO conversion and C5+ hydrocarbon output correspond to maximum number of acid sites, and that number accounts for a peak of desorbed ammonia at Tmax = 122 °C, while the lowest isoparaffin output corresponds to minimum number of acid sites, which characterizes a peak of desorbed ammonia at Tmax = 224–257 °C. 

Ion binding by humic and fulvic acids: A computational procedure based on functional site heterogeneity and the physical chemistry of polyelectrolyte solutions

International Nuclear Information System (INIS)

Marinsky, J.A.; Reddy, M.M.; Ephraim, J.; Mathuthu, A.

1988-04-01

Ion binding equilibria for humic and fulvic acids are examined from the point of view of functional site heterogeneity and the physical chemistry of polyelectrolyte solutions. A detailed explanation of the potentiometric properties of synthetic polyelectrolytes and ion-exchange gels is presented first to provide the basis for a parallel consideration of the potentiometric properties exhibited by humic and fulvic acids. The treatment is then extended to account for functional site heterogeneity. Sample results are presented for analysis of the ion-binding reactions of a standard soil fulvic acid (Armadale Horizons Bh) with this approach to test its capability for anticipation of metal ion removal from solution. The ultimate refined model is shown to be adaptable, after appropriate consideration of the heterogeneity and polyelectrolyte factors, to programming already available for the consideration of ion binding by inorganics in natural waters. (orig.)

TmiRUSite and TmiROSite scripts: searching for mRNA fragments with miRNA binding sites with encoded amino acid residues

OpenAIRE

Berillo, Olga; Régnier, Mireille; Ivashchenko, Anatoly

2014-01-01

microRNAs are small RNA molecules that inhibit the translation of target genes. microRNA binding sites are located in the untranslated regions as well as in the coding domains. We describe TmiRUSite and TmiROSite scripts developed using python as tools for the extraction of nucleotide sequences for miRNA binding sites with their encoded amino acid residue sequences. The scripts allow for retrieving a set of additional sequences at left and at right from the binding site. The scripts presents ...

Dehydroisomerization of n-butane over Pt-ZSMMMm5(I): effect of the metal loading and acid site concentration

NARCIS (Netherlands)

Pirngruber, G.D.; Seshan, Kulathuiyer; Lercher, J.A.

1999-01-01

The dehydroisomerization of n-butane to isobutene over Pt–ZSM5 catalysts with a high Si/Al ratio was studied. The catalytic activity increases with increasing metal loading. Butenes formed via dehydrogenation over the metallic particles are converted to isobutene over the Brønsted acid sites. The

Correction of a splice-site mutation in the beta-globin gene stimulated by triplex-forming peptide nucleic acids

DEFF Research Database (Denmark)

Chin, Joanna Y; Kuan, Jean Y; Lonkar, Pallavi S

2008-01-01

Splice-site mutations in the beta-globin gene can lead to aberrant transcripts and decreased functional beta-globin, causing beta-thalassemia. Triplex-forming DNA oligonucleotides (TFOs) and peptide nucleic acids (PNAs) have been shown to stimulate recombination in reporter gene loci in mammalian...... DNA fragments, can promote single base-pair modification at the start of the second intron of the beta-globin gene, the site of a common thalassemia-associated mutation. This single base pair change was detected by the restoration of proper splicing of transcripts produced from a green fluorescent...

Long chain fatty acids alter the interactive binding of ligands to the two principal drug binding sites of human serum albumin.

Directory of Open Access Journals (Sweden)

Keishi Yamasaki

Full Text Available A wide variety of drugs bind to human serum albumin (HSA at its two principal sites, namely site I and site II. A number of reports indicate that drug binding to these two binding sites are not completely independent, and that interactions between ligands of these two discrete sites can play a role. In this study, the effect of the binding of long-chain fatty acids on the interactive binding between dansyl-L-asparagine (DNSA; site I ligand and ibuprofen (site II ligand at pH6.5 was examined. Binding experiments showed that the binding of sodium oleate (Ole to HSA induces conformational changes in the molecule, which, in turn, changes the individual binding of DNSA and ibuprofen, as well as the mode of interaction between these two ligands from a 'competitive-like' allosteric interaction in the case of the defatted HSA conformer to a 'nearly independent' binding in the case of non-defatted HSA conformer. Circular dichroism measurements indicated that ibuprofen and Ole are likely to modify the spatial orientation of DNSA at its binding site. Docking simulations suggest that the long-distance electric repulsion between DNSA and ibuprofen on defatted HSA contributes to a 'competitive-like' allosteric interaction, whereas extending the distance between ligands and/or increasing the flexibility or size of the DNSA binding site in fatted HSA evokes a change in the interaction mode to 'nearly independent' binding. The present findings provide further insights into the structural dynamics of HSA upon the binding of fatty acids, and its effects on drug binding and drug-drug interactions that occur on HSA.

Metal-Free, Site-Selective Peptide Modification by Conversion of "Customizable" Units into β-Substituted Dehydroamino Acids.

Science.gov (United States)

Saavedra, Carlos J; Hernández, Dácil; Boto, Alicia

2018-01-12

Our site-selective modification of serine or threonine units in peptides allows the generation of β-substituted dehydroamino acids, which increase peptide resistance to hydrolysis and may improve their biological properties. Both the terminal and internal positions can be modified, and different customizable units can be activated separately. Remarkably, high Z selectivity is achieved, even at internal positions. The conversion involves a one-pot oxidative radical scission/phosphorylation process by using the low-toxicity (diacetoxyiodo)benzene/iodine system as the scission reagent. The resulting α-amino phosphonates undergo a Horner-Wadsworth-Emmons reaction to produce the dehydroamino acid derivatives (in a Z/E ratio of usually >98:2) under mild and metal-free conditions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation.

Science.gov (United States)

Wang, Huai-Chun; Minh, Bui Quang; Susko, Edward; Roger, Andrew J

2018-03-01

Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum likelihood (ML) frameworks, their formidable computational time and memory usage severely limits their use in large phylogenomic analyses. Here we propose a posterior mean site frequency (PMSF) method as a rapid and efficient approximation to full empirical profile mixture models for ML analysis. The PMSF approach assigns a conditional mean amino acid frequency profile to each site calculated based on a mixture model fitted to the data using a preliminary guide tree. These PMSF profiles can then be used for in-depth tree-searching in place of the full mixture model. Compared with widely used empirical mixture models with $k$ classes, our implementation of PMSF in IQ-TREE (http://www.iqtree.org) speeds up the computation by approximately $k$/1.5-fold and requires a small fraction of the RAM. Furthermore, this speedup allows, for the first time, full nonparametric bootstrap analyses to be conducted under complex site-heterogeneous models on large concatenated data matrices. Our simulations and empirical data analyses demonstrate that PMSF can effectively ameliorate long-branch attraction artefacts. In some empirical and simulation settings PMSF provided more accurate estimates of phylogenies than the mixture models from which they derive.

Sulfur-Hz(CHx)y(z = 0,1) functionalized metal oxide nanostructure decorated interfaces: Evidence of Lewis base and Brönsted acid sites – Influence on chemical sensing

International Nuclear Information System (INIS)

Laminack, William; Baker, Caitlin; Gole, James

2015-01-01

Nanostructure metal oxide decorated n-type extrinsic porous silicon (PS) semiconductor interfaces are modified through in-situ interaction with acidic ethane and butane thiols (EtSH, BuSH) and basic diethyl sulfide (Et 2 S). Highly sensitive conductometric sensor evaluations and X-ray Photoelectron Spectroscopy demonstrate the effect of sulfur group functionalization modifying the acidity of the metal oxides and their interaction with NH 3 . SEM micrographs demonstrate that the sulfur treated particles are less than 30 nm in size. EDAX studies confirm the chemical composition of the modified nanoparticles and suggest the surface interaction of the sulfides and thiols. The acidic thiols can form Brönsted acidic sites enhancing the acidity of the metal oxides, thus broadening the initial metal oxide acidity range. The sulfides interact to lower the Lewis acidity of nanostructured metal oxide sites. Conductometric response matrices with NH 3 at room temperature, corresponding to the thiol and sulfide treated nanostructures of the metal oxides TiO 2 , SnO x , Ni x O, Cu x O, and Au x O (x >> 1) are evaluated for a dominant electron transduction process forming the basis for reversible chemical sensing in the absence of chemical bond formation. Treatment with the acidic thiols enhances the metal center acidity. It is suggested that the thiols can interact to increase the Brönsted acidity of the doped metal oxide surface if they maintain SH bonds. This process may account for the shift in Lewis acidity as the Brönsted acid sites counter the decrease in Lewis acidity resulting from the interaction of S-(CH x ) y groups. In contrast, treatment with basic Et 2 S decreases the Lewis acidity of the metal oxide sites, enhancing the basicity of the decorated interface. XPS measurements indicate a change in binding energy (BE) of the metal and oxygen centers. The observed changes in conductometric response do not represent a simple increase in surface acidity or basicity but

Solid acid catalysis from fundamentals to applications

CERN Document Server

Hattori, Hideshi

2014-01-01

IntroductionTypes of solid acid catalystsAdvantages of solid acid catalysts Historical overviews of solid acid catalystsFuture outlookSolid Acids CatalysisDefinition of acid and base -Brnsted acid and Lewis acid-Acid sites on surfacesAcid strengthRole of acid sites in catalysisBifunctional catalysisPore size effect on catalysis -shape selectivity-Characterization of Solid Acid Catalysts Indicator methodTemperature programmed desorption (TPD) of ammoniaCalorimetry of adsorption of basic moleculesInfrare

Signaling-sensitive amino acids surround the allosteric ligand binding site of the thyrotropin receptor.

Science.gov (United States)

Kleinau, Gunnar; Haas, Ann-Karin; Neumann, Susanne; Worth, Catherine L; Hoyer, Inna; Furkert, Jens; Rutz, Claudia; Gershengorn, Marvin C; Schülein, Ralf; Krause, Gerd

2010-07-01

The thyrotropin receptor [thyroid-stimulating hormone receptor (TSHR)], a G-protein-coupled receptor (GPCR), is endogenously activated by thyrotropin, which binds to the extracellular region of the receptor. We previously identified a low-molecular-weight (LMW) agonist of the TSHR and predicted its allosteric binding pocket within the receptor's transmembrane domain. Because binding of the LMW agonist probably disrupts interactions or leads to formation of new interactions among amino acid residues surrounding the pocket, we tested whether mutation of residues at these positions would lead to constitutive signaling activity. Guided by molecular modeling, we performed site-directed mutagenesis of 24 amino acids in this spatial region, followed by functional characterization of the mutant receptors in terms of expression and signaling, measured as cAMP accumulation. We found that mutations V421I, Y466A, T501A, L587V, M637C, M637W, S641A, Y643F, L645V, and Y667A located in several helices exhibit constitutive activity. Of note is mutation M637W at position 6.48 in transmembrane helix 6, which has a significant effect on the interaction of the receptor with the LMW agonist. In summary, we found that a high proportion of residues in several helices surrounding the allosteric binding site of LMW ligands in the TSHR when mutated lead to constitutively active receptors. Our findings of signaling-sensitive residues in this region of the transmembrane bundle may be of general importance as this domain appears to be evolutionarily retained among GPCRs.

The Degradation of 14C-Glutamic Acid by L-Glutamic Acid Decarboxylase.

Science.gov (United States)

Dougherty, Charles M; Dayan, Jean

1982-01-01

Describes procedures and semi-micro reaction apparatus (carbon dioxide trap) to demonstrate how a particular enzyme (L-Glutamic acid decarboxylase) may be used to determine the site or sites of labeling in its substrate (carbon-14 labeled glutamic acid). Includes calculations, solutions, and reagents used. (Author/SK)

Mechanistic Effects of Water on the Fe-Catalyzed Hydrodeoxygenation of Phenol. The Role of Brønsted Acid Sites

Energy Technology Data Exchange (ETDEWEB)

Hensley, Alyssa J. R. [The; amp, Linda Voiland School of Chemical Engineering and Bioengineering, ∥Department of Physics; Institute for Integrated Catalysis and §Fundamental and; Wang, Yong [The; amp, Linda Voiland School of Chemical Engineering and Bioengineering, ∥Department of Physics; Institute for Integrated Catalysis and §Fundamental and; Mei, Donghai [The; amp, Linda Voiland School of Chemical Engineering and Bioengineering, ∥Department of Physics; Institute for Integrated Catalysis and §Fundamental and; McEwen, Jean-Sabin [The; amp, Linda Voiland School of Chemical Engineering and Bioengineering, ∥Department of Physics; Institute for Integrated Catalysis and §Fundamental and

2018-01-30

A mechanistic understanding of the roles of water is essential for developing highly active and selective catalysts for hydrodeoxygenation (HDO) reactions since water is ubiquitous in such reaction systems. Here, we present a study for phenol HDO on Fe catalysts using density functional theory which examines the effect of water on three elementary pathways for phenol HDO using an explicit solvation model. The presence of water is found to significantly decrease activation barriers required by hydrogenation reactions via two pathways. First, the proton transfer in the hydrogen bonding network of the liquid water phase is nearly barrierless, which significantly promotes the direct through space tautomerization of phenol. Second, due to the high degree of oxophilicity on Fe, liquid water molecules are found to be easily dissociated into surface hydroxyl groups that can act as Brønsted acid sites. These sites dramatically promote hydrogenation reactions on the Fe surface. As a result, the hydrogen assisted dehydroxylation becomes the dominant phenol HDO pathway. This work provides new fundamental insights into aqueous phase HDO of biomass-derived oxygenates over Fe-based catalysts; e.g., the activity of Fe-based catalysts can be optimized by tuning the surface coverage of Brønsted acid sites via surface doping.

The dependence of natural regeneration of forest trees on upper soil conditions and acidity at damaged sites in the Black Forest, Germany

International Nuclear Information System (INIS)

Littek, T.

1993-06-01

It was the goal of this study to investigate the influence of different upper soil conditions on the germination and establishment, as well as the growth, of young plants of various tree species. For this purpose, four test plots in the region of the Black Forest were laid out, in which, by various means of site preparation and fertilization, the upper soils were changed. Natural seeding of common spruce, European silver-fir, beech, sycamore maple, European mountainash, and grey alder was simulated by means of controlled sowing. For comparison, a greenhouse experiment was carried out, examining the germination and development of the same tree species in various soil substrata, using different fertilizers, and under the influence of artificial acid rain. The most important results - with a high level of variation depending on the tree species examined - can be summarized as follows: Based on the results of field and greenhouse experiments, as well as on the investigations of other authors, it can be concluded that natural regeneration of forest stands is considerably impeded under conditions of increasing soil acidity and by high acid depositions. This is seen directly as the result of unfavorable chemical conditions in the upper soil, as well as indirectly due to deteriorating competitiveness against other vegetation. Site preparation and lime or dolomite fertilization can be important measures in the practice of forestry, to encourage natural regeneration in highly acidic sites with an unfavourable humus layer and a high presence of competing vegetation. (orig./UWA). 2 figs., 85 tabs., 269 refs [de

Gamma-aminobutyric acid-modulated benzodiazepine binding sites in bacteria

International Nuclear Information System (INIS)

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 [ 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 [ 3 H]diazepam binding are those that are active in displacing [ 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

Phenylacetic acids and the structurally related non-steroidal anti-inflammatory drug diclofenac bind to specific gamma-hydroxybutyric acid sites in rat brain

DEFF Research Database (Denmark)

Wellendorph, Petrine; Høg, Signe; Skonberg, Christian

2009-01-01

with a twofold higher affinity than GHB. Measuring the affinities of structurally related NSAIDs for the [(3)H]NCS-382 site identified diclofenac, a clinically relevant NSAID (Voltaren, Diclon) of the phenylacetic acid (PAA) type, as a GHB ligand (K(i) value of 5.1 microM). Other non-NSAID PAAs also exhibited...... affinities similar to GHB. Our data raise the interesting possibility that the widely used over-the-counter drug compound, diclofenac, might affect GHB binding at relevant clinical dosages. Furthermore, the identification of PAAs as GHB ligands supplies new information about the structural preferences...

Molecular distribution, seasonal variation, chemical transformation and sources of dicarboxylic acids and related compounds in atmospheric aerosols at remote marine Gosan site, Jeju Island

Science.gov (United States)

Kundu, S.; Kawamura, K.; Lee, M.

2009-12-01

: A homologous series of C2-C12 α, ω-dicarboxylic acids, ω-oxocarboxylic acids (C2-C9), pyruvic acid and α-dicarbonyls (C2-C3) were detected in atmospheric aerosols collected between April 2003 and April 2004 from remote marine Gosan site (33°29‧ N, 126°16‧ E) located in Jeju Island, South Korea. They were determined using a GC-FID and GC/MS. Total diacid concentration ranged from 130 to 1911 ng m-3 (av. 642 ng m-3), whereas total oxoacid concentration ranged from 7 to 155 ng m-3 (av. 43 ng m-3), and pyruvic acid and α-dicarbonyls ranged from 0.5 to 15 ng m-3 (av. 5 ng m-3) and 2-108 ng m-3 (av. 17.3 ng m-3), respectively. Oxalic (C2) acid was the most abundant in all seasons followed by malonic (C3) or succinic (C4) acid, and phthalic (Ph) acid. The concentration of diacids decreased with an increase in carbon number except for azelaic (C9) acid, which was more abundant than suberic (C8) acid. Glyoxylic acid was predominant ω-oxoacid contributing to 92% of total ω-oxoacid. Total diacids, oxoacids and dicarbonyls showed maximum concentrations in spring and occasionally in winter, while minimum concentrations were observed in summer. Air mass trajectory analysis suggests that either spring or winter maxima can be explained by strong continental outflow associated with cold front passages, while summer minima are associated with warm southerly flows, which transport clean marine air from low latitudes to Jeju Island. The comparison between total diacid concentration level of this study and other study results of urban and remote sites of East Asia reveals that Gosan site is more heavily influenced by the continental outflow from China. The seasonal variation of malonic/succinic (C3/C4), malic/succinic (hC4/C4), fumaric/maleic (F/M), oxalic/pyruvic (C2/Py) and oxalic/Glyoxal (C2/Gly) ratios showed maxima in summer due to an enhanced photo-production and degradation of diacids and related compounds. Throughout all seasons C3/C4 ratio at Gosan site, located

Ibotenic acid and thioibotenic acid

DEFF Research Database (Denmark)

Hermit, Mette B; Greenwood, Jeremy R; Nielsen, Birgitte

2004-01-01

In this study, we have determined and compared the pharmacological profiles of ibotenic acid and its isothiazole analogue thioibotenic acid at native rat ionotropic glutamate (iGlu) receptors and at recombinant rat metabotropic glutamate (mGlu) receptors expressed in mammalian cell lines....... Thioibotenic acid has a distinct pharmacological profile at group III mGlu receptors compared with the closely structurally related ibotenic acid; the former is a potent (low microm) agonist, whereas the latter is inactive. By comparing the conformational energy profiles of ibotenic and thioibotenic acid...... with the conformations preferred by the ligands upon docking to mGlu1 and models of the other mGlu subtypes, we propose that unlike other subtypes, group III mGlu receptor binding sites require a ligand conformation at an energy level which is prohibitively expensive for ibotenic acid, but not for thioibotenic acid...

TmiRUSite and TmiROSite scripts: searching for mRNA fragments with miRNA binding sites with encoded amino acid residues.

Science.gov (United States)

Berillo, Olga; Régnier, Mireille; Ivashchenko, Anatoly

2014-01-01

microRNAs are small RNA molecules that inhibit the translation of target genes. microRNA binding sites are located in the untranslated regions as well as in the coding domains. We describe TmiRUSite and TmiROSite scripts developed using python as tools for the extraction of nucleotide sequences for miRNA binding sites with their encoded amino acid residue sequences. The scripts allow for retrieving a set of additional sequences at left and at right from the binding site. The scripts presents all received data in table formats that are easy to analyse further. The predicted data finds utility in molecular and evolutionary biology studies. They find use in studying miRNA binding sites in animals and plants. TmiRUSite and TmiROSite scripts are available for free from authors upon request and at https: //sites.google.com/site/malaheenee/downloads for download.

Samarium ion exchanged montmorillonite for high temperature cumene cracking reaction

International Nuclear Information System (INIS)

Binitha, N.N.

2009-01-01

Full text: Nano material Montmorillonite clay is cation exchanged with samarium and its catalytic influence in cumene cracking reaction is investigated. Effect of exchange with sodium ions on further exchange with samarium ions is also noted. Acidity measurements are done using TPD of ammonia. The retention of basic structure is proved from FTIR spectra and XRD patterns. Elemental analysis result shows that samarium exchange has occurred, which is responsible for the higher catalytic activity. Surface area and pore volume remains more or less unaffected upon exchange. Thermogravimetric analysis indicates the enhanced thermal stability on exchanging. Cumene cracking reaction is carried out at atmospheric pressure in a fixed bed glass reactor at 673 K. The predominance of Bronsted acidity is confirmed from high selectivity to benzene. (author)

Radiosynthesis and Evaluation of [(11)C]3-Hydroxycyclopent-1-enecarboxylic Acid as Potential PET Ligand for the High-Affinity γ-Hydroxybutyric Acid Binding Sites

DEFF Research Database (Denmark)

Jensen, Claus H; Hansen, Hanne D; Bay, Tina

2017-01-01

understanding of this population of binding sites. With its high specific affinity and monocarboxylate transporter (MCT1) mediated transport across the blood-brain barrier in pharmacological doses, 3-hydroxycyclopent-1-enecarboxylic acid (HOCPCA) seems like a suitable PET radiotracer candidate. Here, we report...... autoradiography on sections of pig brain was performed using [(3)H]HOCPCA. In vivo evaluation of [(11)C]HOCPCA showed no brain uptake, possibly due to a limited uptake of HOCPCA by the MCT1 transporter at tracer doses of [(11)C]HOCPCA....

USGS Tracks Acid Rain

Science.gov (United States)

Gordon, John D.; Nilles, Mark A.; Schroder, LeRoy J.

1995-01-01

The U.S. Geological Survey (USGS) has been actively studying acid rain for the past 15 years. When scientists learned that acid rain could harm fish, fear of damage to our natural environment from acid rain concerned the American public. Research by USGS scientists and other groups began to show that the processes resulting in acid rain are very complex. Scientists were puzzled by the fact that in some cases it was difficult to demonstrate that the pollution from automobiles and factories was causing streams or lakes to become more acidic. Further experiments showed how the natural ability of many soils to neutralize acids would reduce the effects of acid rain in some locations--at least as long as the neutralizing ability lasted (Young, 1991). The USGS has played a key role in establishing and maintaining the only nationwide network of acid rain monitoring stations. This program is called the National Atmospheric Deposition Program/National Trends Network (NADP/NTN). Each week, at approximately 220 NADP/NTN sites across the country, rain and snow samples are collected for analysis. NADP/NTN site in Montana. The USGS supports about 72 of these sites. The information gained from monitoring the chemistry of our nation's rain and snow is important for testing the results of pollution control laws on acid rain.

The dapE-encoded N-succinyl-L,L-Diaminopimelic Acid Desuccinylase from Haemophilus influenzae Contains two Active Site Histidine Residues

Science.gov (United States)

Gillner, Danuta M.; Bienvenue, David L.; Nocek, Boguslaw P.; Joachimiak, Andrzej; Zachary, Vincentos; Bennett, Brian; Holz, Richard C.

2009-01-01

The catalytic and structural properties of the H67A and H349A altered dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) from H. influenzae were investigated. Based on sequence alignment with CPG2 both H67 and H349 were predicted to be Zn(II) ligands. Catalytic activity was observed for the H67A altered DapE enzyme which exhibited kcat = 1.5 ± 0.5 sec−1 and Km = 1.4 ± 0.3 mM. No catalytic activity was observed for H349A under the experimental conditions used. The EPR and electronic absorption data indicate that the Co(II) ion bound to H349A-DapE is analogous to WT DapE after the addition of a single Co(II) ion. The addition of one equivalent of Co(II) to H67A altered DapE provides spectra that are very different from the first Co(II) binding site of the WT enzyme, but similar to the second binding site. The EPR and electronic absorption data, in conjunction with the kinetic data, are consistent with the assignment of H67 and H349 as active site metal ligands for the DapE from H. influenzae. Furthermore, the data suggest that H67 is a ligand in the first metal binding site while H349 resides in the second metal binding site. A three-dimensional homology structure of the DapE from H. influenzae was generated using the X-ray crystal structure of the DapE from N. meningitidis as a template and superimposed on the structure of AAP. This homology structure confirms the assignment of H67 and H349 as active site ligands. The superimposition of the homology model of DapE with the dizinc(II) structure of AAP indicates that within 4.0 Å of the Zn(II) binding sites of AAP, all of the amino acid residues of DapE are nearly identical. PMID:18712420

Selective aerobic alcohol oxidation method for conversion of lignin into simple aromatic compounds

Science.gov (United States)

Stahl, Shannon S; Rahimi, Alireza

2015-03-03

Described is a method to oxidize lignin or lignin sub-units. The method includes oxidation of secondary benzylic alcohol in the lignin or lignin sub-unit to a corresponding ketone in the presence of unprotected primarily aliphatic alcohol in the lignin or lignin sub-unit. The optimal catalyst system consists of HNO.sub.3 in combination with another Bronsted acid, in the absence of a metal-containing catalyst, thereby yielding a selectively oxidized lignin or lignin sub-unit. The method may be carried out in the presence or absence of additional reagents including TEMPO and TEMPO derivatives.

The acidic functional groups of humic acid

Energy Technology Data Exchange (ETDEWEB)

Shanxiang, Li; Shuhe, Sun; Zhai Zongxi, Wu Qihu

1983-09-01

The acidic functional groups content, pK value, DELTAH and DELTAS of humic acid (HA) and nitro-humic acid (NHA) were determined by potentiometry, conductometry and calorimetric titration. The thermodynamic parameters of carboxylic groups and phenolic hydroxyl groups of humic acid are similar to that of simple hydroxy-benzoic acid. The configuration sites of acidic functional groups in humic acid from different coals are different. The carbonyl groups on aromatic rings are probably ortho to phenolic -OH for HA and NHA extracted from Huangxian's brown coal and Japanese lignite, while those from Lingshi's weathered coal are not. The weak -COOH groups of the latter possess higher chemical activity. The -COOH content in HA increases, phenolic -OH group decreases and the chemical acidity of acidic functional groups increases when HA is oxidized by nitric acid. (14 refs.)

Site-Specific Protein Labeling Utilizing Lipoic Acid Ligase (LplA) and Bioorthogonal Inverse Electron Demand Diels-Alder Reaction.

Science.gov (United States)

Baalmann, Mathis; Best, Marcel; Wombacher, Richard

2018-01-01

Here, we describe a two-step protocol for selective protein labeling based on enzyme-mediated peptide labeling utilizing lipoic acid ligase (LplA) and bioorthogonal chemistry. The method can be applied to purified proteins, protein in cell lysates, as well as living cells. In a first step a W37V mutant of the lipoic acid ligase (LplA W37V ) from Escherichia coli is utilized to ligate a synthetic chemical handle site-specifically to a lysine residue in a 13 amino acid peptide motif-a short sequence that can be genetically expressed as a fusion with any protein of interest. In a second step, a molecular probe can be attached to the chemical handle in a bioorthogonal Diels-Alder reaction with inverse electron demand (DA inv ). This method is a complementary approach to protein labeling using genetic code expansion and circumvents larger protein tags while maintaining label specificity, providing experimental flexibility and straightforwardness.

IMPROVED CATALYSTS FOR HEAVY OIL UPGRADING BASED ON ZEOLITE Y NANOPARTICLES ENCAPSULATED IN STABLE NANOPOROUS HOST

Energy Technology Data Exchange (ETDEWEB)

Conrad Ingram; Mark Mitchell

2005-11-15

Composite materials of SBA-15/zeolite Y were synthesized from zeolite Y precursor and a synthesis mixture of mesoporous silicate SBA-15 via a hydrothermal process in the presence of a slightly acidic media of pH 4-6 with 2M H{sub 2}SO{sub 4}. The SBA-15/ZY composites showed Type IV adsorption isotherms, narrow BJH average pore size distribution of 4.9 nm, surface areas up to 800 m{sup 2}2/g and pore volumes 1.03 cm{sup 3}, all comparable to pure SBA-15 synthesized under similar conditions. Chemical analysis revealed Si/Al ratio down to 8.5 in the most aluminated sample, and {sup 27}AlSS MAS NMR confirmed aluminum was in tetrahedral coordination. This method of introduction of Al in pure T{sub d} coordination is effective in comparison to other direct and post synthesis alumination methods. Bronsted acid sites were evident from a pyridinium peak at 1544 cm-1 in the FTIR spectrum after pyridine adsorption, and from NH{sub 3} -TPD experiments. SBA-15/ZY composites showed significant catalytic activities for the dealkylation of isopropylbenzene to benzene and propene, similar to those of commercial zeolite Y. It was observed that higher conversion for catalysts synthesized with high amount of ZY precursor mixture added to the SBA-15. Over all the composites has shown good catalytic activity. Further studies will be focused on gaining a better understand the nature of the precursor, and to characterize and to locate the acid sites in the composite material. The composite will also be evaluated for heavy oil conversion to naphtha and middle distillates.

Characterization of the N-Acetyl-5-neuraminic Acid-binding Site of the Extracytoplasmic Solute Receptor (SiaP) of Nontypeable Haemophilus influenzae Strain 2019

Energy Technology Data Exchange (ETDEWEB)

Johnston, Jason W.; Coussens, Nathan P.; Allen, Simon; Houtman, Jon C.D.; Turner, Keith H.; Zaleski, Anthony; Ramaswamy, S.; Gibson, Bradford W.; Apicella, Michael A. (Iowa); (Buck Inst.)

2012-11-14

Nontypeable Haemophilus influenzae is an opportunistic human pathogen causing otitis media in children and chronic bronchitis and pneumonia in patients with chronic obstructive pulmonary disease. The outer membrane of nontypeable H. influenzae is dominated by lipooligosaccharides (LOS), many of which incorporate sialic acid as a terminal nonreducing sugar. Sialic acid has been demonstrated to be an important factor in the survival of the bacteria within the host environment. H. influenzae is incapable of synthesizing sialic acid and is dependent on scavenging free sialic acid from the host environment. To achieve this, H. influenzae utilizes a tripartite ATP-independent periplasmic transporter. In this study, we characterize the binding site of the extracytoplasmic solute receptor (SiaP) from nontypeable H. influenzae strain 2019. A crystal structure of N-acetyl-5-neuraminic acid (Neu5Ac)-bound SiaP was determined to 1.4 {angstrom} resolution. Thermodynamic characterization of Neu5Ac binding shows this interaction is enthalpically driven with a substantial unfavorable contribution from entropy. This is expected because the binding of SiaP to Neu5Ac is mediated by numerous hydrogen bonds and has several buried water molecules. Point mutations targeting specific amino acids were introduced in the putative binding site. Complementation with the mutated siaP constructs resulted either in full, partial, or no complementation, depending on the role of specific residues. Mass spectrometry analysis of the O-deacylated LOS of the R127K point mutation confirmed the observation of reduced incorporation of Neu5Ac into the LOS. The decreased ability of H. influenzae to import sialic acid had negative effects on resistance to complement-mediated killing and viability of biofilms in vitro, confirming the importance of sialic acid transport to the bacterium.

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

Directory of Open Access Journals (Sweden)

Md Mehedi Hasan

Full Text Available 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/.

Identifying key controls on the behavior of an acidic-U(VI) plume in the Savannah River Site using reactive transport modeling.

Science.gov (United States)

Bea, Sergio A; Wainwright, Haruko; Spycher, Nicolas; Faybishenko, Boris; Hubbard, Susan S; Denham, Miles E

2013-08-01

Acidic low-level waste radioactive waste solutions were discharged to three unlined seepage basins at the F-Area of the Department of Energy (DOE) Savannah River Site (SRS), South Carolina, USA, from 1955 through 1989. Despite many years of active remediation, the groundwater remains acidic and contaminated with significant levels of U(VI) and other radionuclides. Monitored Natural Attenuation (MNA) is a desired closure strategy for the site, based on the premise that regional flow of clean background groundwater will eventually neutralize the groundwater acidity, immobilizing U(VI) through adsorption. An in situ treatment system is currently in place to accelerate this in the downgradient portion of the plume and similar measures could be taken upgradient if necessary. Understanding the long-term pH and U(VI) adsorption behavior at the site is critical to assess feasibility of MNA along with the in-situ remediation treatments. This paper presents a reactive transport (RT) model and uncertainty quantification (UQ) analyses to explore key controls on the U(VI)-plume evolution and long-term mobility at this site. Two-dimensional numerical RT simulations are run including the saturated and unsaturated (vadose) zones, U(VI) and H(+) adsorption (surface complexation) onto sediments, dissolution and precipitation of Al and Fe minerals, and key hydrodynamic processes are considered. UQ techniques are applied using a new open-source tool that is part of the developing ASCEM reactive transport modeling and analysis framework to: (1) identify the complex physical and geochemical processes that control the U(VI) plume migration in the pH range where the plume is highly mobile, (2) evaluate those physical and geochemical parameters that are most controlling, and (3) predict the future plume evolution constrained by historical, chemical and hydrological data. The RT simulation results show a good agreement with the observed historical pH and concentrations of U(VI), nitrates

CATALYTIC PROPERTIES AND ACIDITY OF MODIFIED MCM-41 ...

African Journals Online (AJOL)

Adsorption of pyridine and IR spectroscopy indicated various types of Lewis and Brönsted acid sites. The density distribution of acid sites was determined by TPD. Both Lewis and Brönsted acid sites were found to be active in the heptane isomerisation. The presence of aluminium (low Si/Al) combined to the ionic exchange ...

Aspartic acid 397 in subunit B of the Na+-pumping NADH:quinone oxidoreductase from Vibrio cholerae forms part of a sodium-binding site, is involved in cation selectivity, and affects cation-binding site cooperativity.

Science.gov (United States)

Shea, Michael E; Juárez, Oscar; Cho, Jonathan; Barquera, Blanca

2013-10-25

The Na(+)-pumping NADH:quinone complex is found in Vibrio cholerae and other marine and pathogenic bacteria. NADH:ubiquinone oxidoreductase oxidizes NADH and reduces ubiquinone, using the free energy released by this reaction to pump sodium ions across the cell membrane. In a previous report, a conserved aspartic acid residue in the NqrB subunit at position 397, located in the cytosolic face of this protein, was proposed to be involved in the capture of sodium. Here, we studied the role of this residue through the characterization of mutant enzymes in which this aspartic acid was substituted by other residues that change charge and size, such as arginine, serine, lysine, glutamic acid, and cysteine. Our results indicate that NqrB-Asp-397 forms part of one of the at least two sodium-binding sites and that both size and charge at this position are critical for the function of the enzyme. Moreover, we demonstrate that this residue is involved in cation selectivity, has a critical role in the communication between sodium-binding sites, by promoting cooperativity, and controls the electron transfer step involved in sodium uptake (2Fe-2S → FMNC).

Acid-base characteristics of powdered-activated-carbon surfaces

Energy Technology Data Exchange (ETDEWEB)

Reed, B.E. (West Virginia Univ., Morgantown (United States)); Jensen, J.N.; Matsumoto, M.R. (State Univ. of New York, Buffalo (United States))

Adsorption of heavy metals onto activated carbon has been described using the surface-complex-formation (SCF) model, a chemical equilibrium model. The SCF model requires a knowledge of the amphoteric nature of activated carbon prior to metal adsorption modeling. In the past, a single-diprotic-acid-site model had been employed to describe the amphoteric nature of activated-carbon surfaces. During this study, the amphoteric nature of two powdered activated carbons were investigated, and a three-monoprotic site surface model was found to be a plausible alternative. The single-diprotic-acid-site and two-monoprotic-site models did not describe the acid-base behavior of the two carbons studied adequately. The two-diprotic site was acceptable for only one of the study carbons. The acid-base behavior of activated carbon surfaces seem to be best modeled as a series of weak monoprotic acids.

Tannic acid and chromic chloride-induced binding of protein to red cells: a preliminary study of possible binding sites and reaction mechanisms.

Science.gov (United States)

Hunt, A F; Reed, M I

1990-07-01

The binding mechanisms and binding sites involved in the tannic acid and chromic chloride-induced binding of protein to red cells were investigated using the binding of IgA paraprotein to red cells as model systems. Inhibition studies of these model systems using amino acid homopolymers and compounds (common as red cell membrane constituents) suggest that the mechanisms involved are similar to those proposed for the conversion of hide or skin collagen to leather, as in commercial tanning. These studies also suggest that tannic acid-induced binding of IgA paraprotein to red cells involves the amino acid residues of L-arginine, L-lysine, L-histidine, and L-proline analogous to tanning with phenolic plant extracts. The amino acid residues of L-aspartate, L-glutamate and L-asparagine are involved in a similar manner in chronic chloride-induced binding of protein to red cells.

Decontamination of soil from the research reactor site

International Nuclear Information System (INIS)

Won, H. Z.; Kim, K. N.; Choi, W. K.; Jeong, J. H.; Oh, W. J.

2002-01-01

The two research reactors (TRIGA MARK II and III) in Korea are to be decommissioned in the near future. When the reactors are completely dismantled, the site may remain contaminated due to the long period of operation. We assume that the site is radioactively contaminated by Co-60. Soils gathered from the research reactor site were artificially contaminated with Co 2+ ion. The desorption characteristics of Co 2+ ion from the soil surface by citric acid solution were investigated. Decontamination performances of citric acid and EDTA on soil stored in the radioactive waste drums was examined. The feasibility test of recycling the citric acid was also performed. We concluded that the radioactive waste volume could be reduced significantly by soil washing with a citric acid solution

Savannah River Site Tank Cleaning: Corrosion Rate For One Versus Eight Percent Oxalic Acid Solution

International Nuclear Information System (INIS)

Ketusky, E.; Subramanian, K.

2011-01-01

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

Assessment of acid mine drainage remediation schemes on ground water flow regimes at a reclaimed mine site

International Nuclear Information System (INIS)

Gabr, M.A.; Bowders, J.J.

1994-01-01

Ground water modeling and a field monitoring program were conducted for a 35-acre reclaimed surface mine site that continues to produce acid mine drainage (AMD). The modeling effort was focused on predicting the effectiveness of various remedial measures implemented at the site for the abatement of AMD on predicting the effectiveness of various remedial measures implemented at the site for the abatement of AMD production. The field work included surface surveys and monitoring of ground water levels with time, seepage areas, and sedimentation ponds located on the site. The surveys provided the physical and topographic characteristics of the site. Pump tests conducted at the site provided general hydraulic conductivities (k) for two major areas of the site; undisturbed area (k ≅ 2.9 x 10 -5 ft/s) and disturbed area (k ≅ 3.3 x 10 -4 ft/s to 2.0 x 10 -3 ft/s). The monitored ground water data indicated rapid change in ground water levels during recharge events. Such behavior is indicative of flow regime that is dominated by fracture flow. Modeling of an approximately 700 ft by 1,500 ft area of the site was achieved using the US GS code MODFLOW, and ground water field measurements were used to calibrate the model. A hydraulic conductivity of about 1.15 x 10 -3 ft/s was estimated for the undisturbed area and 1.15 x 10 -2 ft/s for the reclaimed area. Remedial measures for diverting the ground water away from the areas of spoil included the use of a subsurface seepage cutoff wall and discrete sealing techniques. Modeling results indicated that the most effective remedial technique for this site is the use of a subsurface seepage cutoff wall installed at the interface (highwall) between the disturbed and undisturbed zones. Using this scheme caused a dewatering effect in the reclaimed area and therefore reduction in the volume of the AMD generated at the site

Comparison and trend study on acidity and acidic buffering capacity of particulate matter in China

Science.gov (United States)

Ren, Lihong; Wang, Wei; Wang, Qingyue; Yang, XiaoYang; Tang, Dagang

2011-12-01

The acidity of about 2000 particulate matter samples from aircraft and ground-based monitoring is analyzed by the method similar to soil acidity determination. The ground-based samples were collected at about 50 urban or background sites in northern and southern China. Moreover, the acidic buffering capacity of those samples is also analyzed by the method of micro acid-base titration. Results indicate that the acidity level is lower in most northern areas than those in the south, and the acidic buffering capacity showed inverse tendency, correspondingly. This is the most important reason why the pollution of acidic-precipitation is much more serious in Southern China than that in Northern China. The acidity increases and the acidic buffering capacity drops with the decreasing of the particle sizes, indicating that fine particle is the main influencing factor of the acidification. The ionic results show that Ca salt is the main alkaline substance in particulate matter, whereas the acidification of particulate matter is due to the SO 2 and NO x emitted from the fossil fuel burning. And among of them, coal burning is the main contributor of SO 2, however the contribution of NO x that emitted from fuel burning of motor vehicles has increased in recent years. By comparison of the experimental results during the past 20 years, it can be concluded that the acid precipitation of particulate matter has not been well controlled, and it even shows an increasing tendency in China lately. The acid precipitation of particulate matter has begun to frequently attack in part of the northern areas. Multiple regression analysis indicates that coefficient value of the ions is the lowest at the urban sites and the highest at the regional sites, whereas the aircraft measurement results are intermediate between those two kinds of sites.

Catalytic reduction of NO{sub x}; Katalytisk reduktion av NO{sub x}

Energy Technology Data Exchange (ETDEWEB)

Odenbrand, I. [Lund Univ. (Sweden). Dept. of Chemical Engineering

2001-10-01

after the washing procedure. Using photoelectron spectroscopy it was found that the sulphation of a fresh catalyst resulted in an almost doubling of the sulphur content on the surface from 0.9 to 1.5 weight percent. In both the fresh and the sulphated fresh catalyst the sulphur was in the form of sulphate. In the deactivated catalyst a certain shift in the peak position was observed showing that potassium has an effect on the chemical state of the sulphate groups. The amount of sulphur increased heavily on deactivation. A deactivated catalyst with 4.4 percent sulphur on the surface could be washed with water to 0.3 percent sulphur. The water thus effectively removes sulphur from a deactivated catalyst. FTIR studies of the adsorption of ammonia showed that an increased content of potassium lowered both the amount of adsorbed ammonia and its binding strength to the Bronsted acid sites. Sulphation of a fresh catalyst resulted in an increase of both amount and strength of ammonia adsorption. A correlation between the amount of Bronsted sites and the relative activity was shown. Temperature programmed desorption of ammonia showed results in concordance with other methods of investigation and showed that: a) the presence of potassium decreases the amount of strongly bound ammonia and thereby the closely correlated activity in the SCR reaction, b) sulphation increases the amount of strongly bound ammonia, c) washing with sulphuric acid gives a similar effect, d) so does also a water washing when it is combined with a gas phase sulphation.

The Cu2+-nitrilotriacetic acid complex improves loading of α-helical double histidine site for precise distance measurements by pulsed ESR

Science.gov (United States)

Ghosh, Shreya; Lawless, Matthew J.; Rule, Gordon S.; Saxena, Sunil

2018-01-01

Site-directed spin labeling using two strategically placed natural histidine residues allows for the rigid attachment of paramagnetic Cu2+. This double histidine (dHis) motif enables extremely precise, narrow distance distributions resolved by Cu2+-based pulsed ESR. Furthermore, the distance measurements are easily relatable to the protein backbone-structure. The Cu2+ ion has, till now, been introduced as a complex with the chelating agent iminodiacetic acid (IDA) to prevent unspecific binding. Recently, this method was found to have two limiting concerns that include poor selectivity towards α-helices and incomplete Cu2+-IDA complexation. Herein, we introduce an alternative method of dHis-Cu2+ loading using the nitrilotriacetic acid (NTA)-Cu2+ complex. We find that the Cu2+-NTA complex shows a four-fold increase in selectivity toward α-helical dHis sites. Furthermore, we show that 100% Cu2+-NTA complexation is achievable, enabling precise dHis loading and resulting in no free Cu2+ in solution. We analyze the optimum dHis loading conditions using both continuous wave and pulsed ESR. We implement these findings to show increased sensitivity of the Double Electron-Electron Resonance (DEER) experiment in two different protein systems. The DEER signal is increased within the immunoglobulin binding domain of protein G (called GB1). We measure distances between a dHis site on an α-helix and dHis site either on a mid-strand or a non-hydrogen bonded edge-strand β-sheet. Finally, the DEER signal is increased twofold within two α-helix dHis sites in the enzymatic dimer glutathione S-transferase exemplifying the enhanced α-helical selectivity of Cu2+-NTA.

Single-Atom Mn Active Site in a Triol-Stabilized β-Anderson Manganohexamolybdate for Enhanced Catalytic Activity towards Adipic Acid Production

Directory of Open Access Journals (Sweden)

Jianhui Luo

2018-03-01

Full Text Available Adipic acid is an important raw chemical for the commercial production of polyamides and polyesters. The traditional industrial adipic acid production utilizes nitric acid to oxidize KA oil (mixtures of cyclohexanone and cyclohexanol, leading to the emission of N2O and thus causing ozone depletion, global warming, and acid rain. Herein, we reported an organically functionalized β-isomer of Anderson polyoxometalates (POMs nanocluster with single-atom Mn, β-{[H3NC(CH2O3]2MnMo6O18}− (1, as a highly active catalyst to selectively catalyze the oxidation of cyclohexanone, cyclohexanol, or KA oil with atom economy use of 30% H2O2 for the eco-friendly synthesis of adipic acid. The catalyst has been characterized by single crystal and powder XRD, XPS, ESI-MS, FT-IR, and NMR. A cyclohexanone (cyclohexanol conversion of >99.9% with an adipic acid selectivity of ~97.1% (~85.3% could be achieved over catalyst 1 with high turnover frequency of 2427.5 h−1 (2132.5 h−1. It has been demonstrated that the existence of Mn3+ atom active site in catalyst 1 and the special butterfly-shaped topology of POMs both play vital roles in the enhancement of catalytic activity.

Deactivation of molybdate catalysts by nitrogen bases

Energy Technology Data Exchange (ETDEWEB)

Furimsky, E.

1982-10-01

Nitrogen bases present in petroleum deactivate the surface of molybdate catalysts. The detrimental effect is attributed either to interactions of the bases with Lewis sites via unpaired electrons on nitrogen or to their ability to remove proton from the surface. The later effect results in a decrease of concentration of Bronsted sites known to be active in catalytic reactions. This enhances rate of coke forming reactions. Resistence of molybdate catalysts to coke formation depends on the form and redistribution of active ingredients on the surface. This can be effected by conditions applied during preparation and pretreatment of the catalysts. Processing parameters used during catalytic hydrotreatment are also important; i.e., the coke formation is slow under conditions ensuring high rate of removal of basic nitrogen containing compounds.

Unusual binding of ursodeoxycholic acid to ileal bile acid binding protein: role in activation of FXRα[S

Science.gov (United States)

Fang, Changming; Filipp, Fabian V.; Smith, Jeffrey W.

2012-01-01

Ursodeoxycholic acid (UDCA, ursodiol) is used to prevent damage to the liver in patients with primary biliary cirrhosis. The drug also prevents the progression of colorectal cancer and the recurrence of high-grade colonic dysplasia. However, the molecular mechanism by which UDCA elicits its beneficial effects is not entirely understood. The aim of this study was to determine whether ileal bile acid binding protein (IBABP) has a role in mediating the effects of UDCA. We find that UDCA binds to a single site on IBABP and increases the affinity for major human bile acids at a second binding site. As UDCA occupies one of the bile acid binding sites on IBABP, it reduces the cooperative binding that is often observed for the major human bile acids. Furthermore, IBABP is necessary for the full activation of farnesoid X receptor α (FXRα) by bile acids, including UDCA. These observations suggest that IBABP may have a role in mediating some of the intestinal effects of UDCA. PMID:22223860

Site specific incorporation of keto amino acids into proteins

Science.gov (United States)

Schultz, Peter G [La Jolla, CA; Wang, Lei [San Diego, CA

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.

Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

Directory of Open Access Journals (Sweden)

Selbig Joachim

2009-04-01

Full Text Available Abstract Background Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites. Results We characterized the spatial context of phosphorylation sites and assessed its usability for improved phosphorylation site predictions. We identified 750 non-redundant, experimentally verified sites with three-dimensional (3D structural information available in the protein data bank (PDB and grouped them according to their respective kinase family. We studied the spatial distribution of amino acids around phosphorserines, phosphothreonines, and phosphotyrosines to extract signature 3D-profiles. Characteristic spatial distributions of amino acid residue types around phosphorylation sites were indeed discernable, especially when kinase-family-specific target sites were analyzed. To test the added value of using spatial information for the computational prediction of phosphorylation sites, Support Vector Machines were applied using both sequence as well as structural information. When compared to sequence-only based prediction methods, a small but consistent performance improvement was obtained when the prediction was informed by 3D-context information. Conclusion While local one-dimensional amino acid sequence information was observed to harbor most of the discriminatory power, spatial context information was identified as

Dephosphorylation of microtubule-binding sites at the neurofilament-H tail domain by alkaline, acid, and protein phosphatases.

Science.gov (United States)

Hisanaga, S; Yasugawa, S; Yamakawa, T; Miyamoto, E; Ikebe, M; Uchiyama, M; Kishimoto, T

1993-06-01

The dephosphorylation-induced interaction of neurofilaments (NFs) with microtubules (MTs) was investigated by using several phosphatases. Escherichia coli alkaline and wheat germ acid phosphatases increased the electrophoretic mobility of NF-H and NF-M by dephosphorylation, and induced the binding of NF-H to MTs. The binding of NFs to MTs was observed only after the electrophoretic mobility of NF-H approached the exhaustively dephosphorylated level when alkaline phosphatase was used. The number of phosphate remaining when NF-H began to bind to MTs was estimated by measuring phosphate bound to NF-H. NF-H did not bind to MTs even when about 40 phosphates from the total of 51 had been removed by alkaline phosphatase. The removal of 6 further phosphates finally resulted in the association of NF-H with MTs. A similar finding, that the restricted phosphorylation sites in the NF-H tail domain, but not the total amount of phosphates, were important for binding to MTs, was also obtained with acid phosphatases. In contrast to alkaline and acid phosphatases, four classes of protein phosphatases (protein phosphatases 1, 2A, 2B, and 2C) were ineffective for shifting the electrophoretic mobility of NF proteins and for inducing the association of NFs to MTs.

A flexible metal-organic framework with a high density of sulfonic acid sites for proton conduction

Science.gov (United States)

Yang, Fan; Xu, Gang; Dou, Yibo; Wang, Bin; Zhang, Heng; Wu, Hui; Zhou, Wei; Li, Jian-Rong; Chen, Banglin

2017-11-01

The design of stable electrolyte materials with high proton conductivity for use in proton exchange membrane fuel cells remains a challenge. Most of the materials explored have good conductivity at high relative humidity (RH), but significantly decreased conductivity at reduced RH. Here we report a chemically stable and structurally flexible metal-organic framework (MOF), BUT-8(Cr)A, possessing a three-dimensional framework structure with one-dimensional channels, in which high-density sulfonic acid (-SO3H) sites arrange on channel surfaces for proton conduction. We propose that its flexible nature, together with its -SO3H sites, could allow BUT-8(Cr)A to self-adapt its framework under different humid environments to ensure smooth proton conduction pathways mediated by water molecules. Relative to other MOFs, BUT-8(Cr)A not only has a high proton conductivity of 1.27 × 10-1 S cm-1 at 100% RH and 80 °C but also maintains moderately high proton conductivity at a wide range of RH and temperature.

Copper-zinc superoxide dismutase is activated through a sulfenic acid intermediate at a copper ion entry site.

Science.gov (United States)

Fetherolf, Morgan M; Boyd, Stefanie D; Taylor, Alexander B; Kim, Hee Jong; Wohlschlegel, James A; Blackburn, Ninian J; Hart, P John; Winge, Dennis R; Winkler, Duane D

2017-07-21

Metallochaperones are a diverse family of trafficking molecules that provide metal ions to protein targets for use as cofactors. The copper chaperone for superoxide dismutase (Ccs1) activates immature copper-zinc superoxide dismutase (Sod1) by delivering copper and facilitating the oxidation of the Sod1 intramolecular disulfide bond. Here, we present structural, spectroscopic, and cell-based data supporting a novel copper-induced mechanism for Sod1 activation. Ccs1 binding exposes an electropositive cavity and proposed "entry site" for copper ion delivery on immature Sod1. Copper-mediated sulfenylation leads to a sulfenic acid intermediate that eventually resolves to form the Sod1 disulfide bond with concomitant release of copper into the Sod1 active site. Sod1 is the predominant disulfide bond-requiring enzyme in the cytoplasm, and this copper-induced mechanism of disulfide bond formation obviates the need for a thiol/disulfide oxidoreductase in that compartment. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Study on antimony oxide self-assembled inside HZSM-5

International Nuclear Information System (INIS)

Li Bin; Li Shijie; Wang Yingxia; Li Neng; Liu Xiyao; Lin Bingxiong

2005-01-01

Sb/ZSM-5 was obtained by solid-state reaction with the mixture of Sb 2 O 3 and zeolite HZSM-5 under a dry nitrogen flow at 773K. Characterization of the treated zeolite was undertaken with XRD, 27 Al MAS NMR, BET, TGA and FT-IR. The results revealed that part of the antimony oxides migrated into the channels of zeolite, and decreased the Bronsted acid sites in Sb/ZSM-5 remarkably. The other part of antimony oxides together with the amorphous alumino-silicate in the products distributed on the external surface of zeolite ZSM-5 and modified it, while the framework of ZSM-5 in crystal phase was retained. The structure of occluded antimony oxide inside the channels of ZSM-5 was studied by XRD Rietveld method. The result showed that their structure can be described as a chain of non-perfect [Sb 5 O 5 (H 2 O) 2 ] n 5n+ , which is parallel to the straight channel of ZSM-5. There is about 0.6 [Sb 5 O 5 (H 2 O) 2 ] 5+ unit in every cell of the ZSM-5 on an average

Acquisition of a novel eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site confers intracellular cleavage of an H7N7 influenza virus hemagglutinin

International Nuclear Information System (INIS)

Hamilton, Brian S.; Sun, Xiangjie; Chung, Changik; Whittaker, Gary R.

2012-01-01

A critical feature of highly pathogenic avian influenza viruses (H5N1 and H7N7) is the efficient intracellular cleavage of the hemagglutinin (HA) protein. H7N7 viruses also exist in equine species, and a unique feature of the equine H7N7 HA is the presence of an eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site. Here, we show that three histidine residues within the unique insertion of the equine H7N7 HA are essential for intracellular cleavage. An asparagine residue within the insertion-derived glycosylation site was also found to be essential for intracellular cleavage. The presence of the histidine residues also appear to be involved in triggering fusion, since mutation of the histidine residues resulted in a destabilizing effect. Importantly, the addition of a tetrabasic site and the eleven amino acid insertion conferred efficient intracellular cleavage to the HA of an H7N3 low pathogenicity avian influenza virus. Our studies show that acquisition of the eleven amino acid insertion offers an alternative mechanism for intracellular cleavage of influenza HA.

Acquisition of a novel eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site confers intracellular cleavage of an H7N7 influenza virus hemagglutinin

Energy Technology Data Exchange (ETDEWEB)

Hamilton, Brian S.; Sun, Xiangjie; Chung, Changik [Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca NY 14853 (United States); New York Center of Excellence for Influenza Research and Surveillance, University of Rochester Medical Center, Rochester NY 14627 (United States); Whittaker, Gary R., E-mail: grw7@cornell.edu [Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca NY 14853 (United States); New York Center of Excellence for Influenza Research and Surveillance, University of Rochester Medical Center, Rochester NY 14627 (United States)

2012-12-05

A critical feature of highly pathogenic avian influenza viruses (H5N1 and H7N7) is the efficient intracellular cleavage of the hemagglutinin (HA) protein. H7N7 viruses also exist in equine species, and a unique feature of the equine H7N7 HA is the presence of an eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site. Here, we show that three histidine residues within the unique insertion of the equine H7N7 HA are essential for intracellular cleavage. An asparagine residue within the insertion-derived glycosylation site was also found to be essential for intracellular cleavage. The presence of the histidine residues also appear to be involved in triggering fusion, since mutation of the histidine residues resulted in a destabilizing effect. Importantly, the addition of a tetrabasic site and the eleven amino acid insertion conferred efficient intracellular cleavage to the HA of an H7N3 low pathogenicity avian influenza virus. Our studies show that acquisition of the eleven amino acid insertion offers an alternative mechanism for intracellular cleavage of influenza HA.

An active site mutant of Escherichia coli cyclopropane fatty acid synthase forms new non-natural fatty acids providing insights on the mechanism of the enzymatic reaction.

Science.gov (United States)

E, Guangqi; Drujon, Thierry; Correia, Isabelle; Ploux, Olivier; Guianvarc'h, Dominique

2013-12-01

We have produced and purified an active site mutant of the Escherichia coli cyclopropane fatty acid synthase (CFAS) by replacing the strictly conserved G236 within cyclopropane synthases, by a glutamate residue, which corresponds to E146 of the homologous mycolic acid methyltransferase, Hma, producing hydroxymethyl mycolic acids. The G236E CFAS mutant had less than 1% of the in vitro activity of the wild type enzyme. We expressed the G236E CFAS mutant in an E. coli (DE3) strain in which the chromosomal cfa gene had been deleted. After extraction of phospholipids and conversion into the corresponding fatty acid methyl esters (FAMEs), we observed the formation of cyclopropanated FAMEs suggesting that the mutant retained some of the normal activity in vivo. However, we also observed the formation of new C17 methyl-branched unsaturated FAMEs whose structures were determined using GC/MS and NMR analyses. The double bond was located at different positions 8, 9 or 10, and the methyl group at position 10 or 9. Thus, this new FAMEs are likely arising from a 16:1 acyl chain of a phospholipid that had been transformed by the G236E CFAS mutant in vivo. The reaction catalyzed by this G236E CFAS mutant thus starts by the methylation of the unsaturated acyl chain at position 10 or 9 yielding a carbocation at position 9 or 10 respectively. It follows then two competing steps, a normal cyclopropanation or hydride shift/elimination events giving different combinations of alkenes. This study not only provides further evidence that cyclopropane synthases (CSs) form a carbocationic intermediate but also opens the way to CSs engineering for the synthesis of non-natural fatty acids. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Concentrations of nitrous acid, nitric acid, nitrite and nitrate in the gas and aerosol phase at a site in the emission zone during ESCOMPTE 2001 experiment

Science.gov (United States)

Acker, K.; Möller, D.; Auel, R.; Wieprecht, W.; Kalaß, D.

2005-03-01

Ground-based measurements were performed at the "Expérience sur Site pour COntraindre les Modèles de Pollution atmosphérique et de Transport d`Emissions" (ESCOMPTE) field site E3 (Realtor) about 30 km north of the urban environment of Marseille and east of the industrial centre Berre pond to investigate the formation of nitrous and nitric acid and to detect the distribution of reactive N-species between the gas and particle phase during photochemical pollution events. A wet denuder sampling for gases followed by a steam jet collection for aerosols was both coupled to anion chromatographic analysis. The analytical system provided data continuously with 30-min time resolution between June 13 and July 13, 2001. Indications for heterogeneous formation of nitrous acid during nighttime and daytime on ground and aerosol surfaces were found, the average HNO 2/NO 2 ratio was 6%. Highest concentrations were observed during two episodes of strong pollution accumulation when sea breeze transported industrial, traffic and urban pollution land-inwards. After nocturnal heterogeneous formation (about 0.1 ppb v h -1 were estimated corresponding to increasing HNO 2/NO 2 ratios) and accumulation processes up to 1.2 ppb v HNO 2 were observed. Their photolysis produces up to 5-9×10 6 OH cm -3 s -1 and will contribute significantly to initiation of the daily photochemistry in the lowest part of the troposphere. For the key tropospheric species, HNO 3 daily peaks up to 4 ppb v were detected.

Imaging Preferential Flow Pathways of Contaminants from Passive Acid Mine Drainage Mitigation Sites Using Electrical Resistivity

Science.gov (United States)

Kelley, N.; Mount, G.; Terry, N.; Herndon, E.; Singer, D. M.

2017-12-01

The Critical Zone represents the surficial and shallow layer of rock, air, water, and soil where most interactions between living organisms and the Earth occur. Acid mine drainage (AMD) resulting from coal extraction can influence both biological and geochemical processes across this zone. Conservative estimates suggest that more than 300 million gallons of AMD are released daily, making this acidic solution of water and contaminants a common issue in areas with legacy or current coal extraction. Electrical resistivity imaging (ERI) provides a rapid and minimally invasive method to identify and monitor contaminant pathways from AMD remediation systems in the subsurface of the Critical Zone. The technique yields spatially continuous data of subsurface resistivity that can be inverted to determine electrical conductivity as a function of depth. Since elevated concentrations of heavy metals can directly influence soil conductivity, ERI data can be used to trace the flow pathways or perhaps unknown mine conduits and transport of heavy metals through the subsurface near acid mine drainage sources. This study aims to examine preferential contaminant migration from those sources through substrate pores, fractures, and shallow mine workings in the near subsurface surrounding AMD sites in eastern Ohio and western Pennsylvania. We utilize time lapse ERI measures during different hydrologic conditions to better understand the variability of preferential flow pathways in relation to changes in stage and discharge within the remediation systems. To confirm ERI findings, and provide constraint to geochemical reactions occurring in the shallow subsurface, we conducted Inductively Coupled Plasma (ICP) spectrometry analysis of groundwater samples from boreholes along the survey transects. Through these combined methods, we can provide insight into the ability of engineered systems to contain and isolate metals in passive acid mine drainage treatment systems.

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

International Nuclear Information System (INIS)

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

1986-01-01

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 ∼ 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

Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs

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Sheng Zhi-Ya

2008-02-01

Full Text Available Abstract Background As one of the most common protein post-translational modifications, glycosylation is involved in a variety of important biological processes. Computational identification of glycosylation sites in protein sequences becomes increasingly important in the post-genomic era. A new encoding scheme was employed to improve the prediction of mucin-type O-glycosylation sites in mammalian proteins. Results A new protein bioinformatics tool, CKSAAP_OGlySite, was developed to predict mucin-type O-glycosylation serine/threonine (S/T sites in mammalian proteins. Using the composition of k-spaced amino acid pairs (CKSAAP based encoding scheme, the proposed method was trained and tested in a new and stringent O-glycosylation dataset with the assistance of Support Vector Machine (SVM. When the ratio of O-glycosylation to non-glycosylation sites in training datasets was set as 1:1, 10-fold cross-validation tests showed that the proposed method yielded a high accuracy of 83.1% and 81.4% in predicting O-glycosylated S and T sites, respectively. Based on the same datasets, CKSAAP_OGlySite resulted in a higher accuracy than the conventional binary encoding based method (about +5.0%. When trained and tested in 1:5 datasets, the CKSAAP encoding showed a more significant improvement than the binary encoding. We also merged the training datasets of S and T sites and integrated the prediction of S and T sites into one single predictor (i.e. S+T predictor. Either in 1:1 or 1:5 datasets, the performance of this S+T predictor was always slightly better than those predictors where S and T sites were independently predicted, suggesting that the molecular recognition of O-glycosylated S/T sites seems to be similar and the increase of the S+T predictor's accuracy may be a result of expanded training datasets. Moreover, CKSAAP_OGlySite was also shown to have better performance when benchmarked against two existing predictors. Conclusion Because of CKSAAP

Assessment of surface acidity in mesoporous materials containing aluminum and titanium

Science.gov (United States)

Araújo, Rinaldo S.; Maia, Débora A. S.; Azevedo, Diana C. S.; Cavalcante, Célio L., Jr.; Rodríguez-Castellón, E.; Jimenez-Lopez, A.

2009-04-01

The surface acidity of mesoporous molecular sieves of aluminum and titanium was evaluated using four different techniques: n-butylamine volumetry, cyclohexylamine thermodesorption, temperature-programmed desorption of ammonia and adsorption of pyridine. The nature, strength and concentration of the acid sites were determined and correlated to the results of a probe reaction of anthracene oxidation to 9,10-anthraquinone (in liquid phase). In general, the surface acidity was highly influenced by the nature, location and coordination of the metal species (Al and Ti) in the mesoporous samples. Moderate to strong Brönsted acid sites were identified for the Al-MCM-41 sample in a large temperature range. For mesoporous materials containing Ti, the acidity was represented by a combination of weak to moderate Brönsted and Lewis acid sites. The Ti-HMS sample exhibits a higher acidity of moderate strength together with a well-balanced concentration of Brönsted and Lewis acid sites, which enhanced both conversion and selectivity in the oxidation reaction of anthracene.

Dual Mode Fluorophore-Doped Nickel Nitrilotriacetic Acid-Modified Silica Nanoparticles Combine Histidine-Tagged Protein Purification with Site-Specific Fluorophore Labeling

OpenAIRE

Kim, Sung Hoon; Jeyakumar, M.; Katzenellenbogen, John A.

2007-01-01

We present the first example of a fluorophore-doped nickel chelate surface- modified silica nanoparticle that functions in a dual mode, combining histidine-tagged protein purification with site-specific fluorophore labeling. Tetramethylrhodamine (TMR)-doped silica nanoparticles, estimated to contain 700–900 TMRs per ca. 23-nm particle, were surface modified with nitrilotriacetic acid (NTA), producing TMR-SiO2-NTA-Ni+2. Silica-embedded TMR retains very high quantum yield, is resistant to quenc...

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

Directory of Open Access Journals (Sweden)

Janire Mingo

Full Text Available 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.

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

Energy Technology Data Exchange (ETDEWEB)

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.

In-plane conductance of thin films as a probe of surface chemical environment: Adsorbate effects on film electronic properties of indium tin oxide and gold

Science.gov (United States)

Swint, Amy Lynn

Changes in the in-plane conductance of conductive thin films are observed as a result of chemical adsorption at the surface. Reaction of the indium tin oxide (ITO) surface with Bronsted acids (bases) leads to increases (decreases) in its in-plane conductance as measured by a four-point probe configuration. The conductance varies monotonically with pH suggesting that the degree of surface protonation or hydroxylation controls the surface charge density, which in turn affects the width of the n-type depletion layer, and ultimately the in-plane conductance. Measurements at constant pH with a series of tetraalkylammonium hydroxide species of varying cation size indicate that surface dipoles also affect ITO conductance by modulating the magnitude of the surface polarization. Modulating the double layer with varying aqueous salt solutions also affects ITO conductance, though not to the same degree as strong Bronsted acids and bases. Solvents of varying dielectric constant and proton donating ability (ethanol, dimethylformamide) decrease ITO conductance relative to H2O. In addition, changing solvent gives rise to thermally-derived conductance transients, which result from exothermic solvent mixing. The self-assembly of alkanethiols at the surface increases the conductance of ITO films, most likely through carrier population effects. In all cases examined the combined effects of surface charge, adsorbed dipole layer magnitude and carrier injection are responsible for altering the ITO conductance. Besides being directly applicable to the control of electronic properties, these results also point to the use of four-point probe resistance measurements in condensed phase sensing applications. Ultrasensitive conductance-based gas phase sensing of organothiol adsorption to gold nanowires is accomplished with a limit of detection in the 105 molecule range. Further refinement of the inherently low noise resistance measurement may lead to observation of single adsorption events at

The Acid-Base Balance Between Organic Acids and Circumneutral Ground Waters in Large Peatlands

Science.gov (United States)

Siegel, D. I.; Glaser, P. H.; So, J.

2006-05-01

Organic acids supply most of the acidity in the surface waters of bogs in peatlands. Yet, the fundamental geochemical properties of peatland organic acids are still poorly known. To assess the geochemical properties of typical organic acid assemblages in peatlands, we used a triprotic analog model for peat pore waters and surface waters in the Glacial Lake Agassiz Peatlands, optimizing on charge balance and calibrated to estimates of mole site density in DOC and triprotic acid dissociation constants. Before the calibration process, all bog waters and 76% of fen waters had more than +20% charge imbalance. After calibration, most electrochemically balanced within 20%. In the best calibration, the mole site denisty of bog DOC was estimated as ~0.05 mmol/mmol C., approximately 6 times smaller than that for fen DOC or the DOC in the fen deeper fen peats that underlie bogs. The three modeled de-protonation constants were; pKa1 = ~3.0, pKa2 = ~4.5 and pKa3 = ~7.0 for the bog DOC, and; pKa1 = ~5.2, pKa2 =~ 6.5 and pKa3 = ~7.0 for the fen DOC. Bog DOC, behaves as a strong acid despite its small mole site density. The DOC in bog runoff can therefore theoretically acidify the surface waters in adjacent fens wherever these waters do not receive sufficient buffering alkalinity from active groundwater seepage.

The Fatty Acid Profile Analysis of Cyperus laxus Used for Phytoremediation of Soils from Aged Oil Spill-Impacted Sites Revealed That This Is a C18:3 Plant Species.

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Noemí Araceli Rivera Casado

Full Text Available The effect of recalcitrant hydrocarbons on the fatty acid profile from leaf, basal corm, and roots of Cyperus laxus plants cultivated in greenhouse phytoremediation systems of soils from aged oil spill-impacted sites containing from 16 to 340 g/Kg total hydrocarbons (THC was assessed to investigate if this is a C18:3 species and if the hydrocarbon removal during the phytoremediation process has a relationship with the fatty acid profile of this plant. The fatty acid profile was specific to each vegetative organ and was strongly affected by the hydrocarbons level in the impacted sites. Leaf extracts of plants from uncontaminated soil produced palmitic acid (C16, octadecanoic acid (C18:0, unsaturated oleic acids (C18:1-C18:3, and unsaturated eichosanoic (C20:2-C20:3 acids with a noticeable absence of the unsaturated hexadecatrienoic acid (C16:3; this finding demonstrates, for the first time, that C. laxus is a C18:3 plant. In plants from the phytoremediation systems, the total fatty acid contents in the leaf and the corm were negatively affected by the hydrocarbons presence; however, the effect was positive in root. Interestingly, under contaminated conditions, unusual fatty acids such as odd numbered carbons (C15, C17, C21, and C23 and uncommon unsaturated chains (C20:3n6 and C20:4 were produced together with a remarkable quantity of C22:2 and C24:0 chains in the corm and the leaf. These results demonstrate that weathered hydrocarbons may drastically affect the lipidic composition of C. laxus at the fatty acid level, suggesting that this species adjusts the cover lipid composition in its vegetative organs, mainly in roots, in response to the weathered hydrocarbon presence and uptake during the phytoremediation process.

The Fatty Acid Profile Analysis of Cyperus laxus Used for Phytoremediation of Soils from Aged Oil Spill-Impacted Sites Revealed That This Is a C18:3 Plant Species

Science.gov (United States)

Montes Horcasitas, María del Carmen; Rodríguez Vázquez, Refugio; Esparza García, Fernando José; Pérez Vargas, Josefina; Ariza Castolo, Armando; Ferrera-Cerrato, Ronald; Gómez Guzmán, Octavio

2015-01-01

The effect of recalcitrant hydrocarbons on the fatty acid profile from leaf, basal corm, and roots of Cyperus laxus plants cultivated in greenhouse phytoremediation systems of soils from aged oil spill-impacted sites containing from 16 to 340 g/Kg total hydrocarbons (THC) was assessed to investigate if this is a C18:3 species and if the hydrocarbon removal during the phytoremediation process has a relationship with the fatty acid profile of this plant. The fatty acid profile was specific to each vegetative organ and was strongly affected by the hydrocarbons level in the impacted sites. Leaf extracts of plants from uncontaminated soil produced palmitic acid (C16), octadecanoic acid (C18:0), unsaturated oleic acids (C18:1-C18:3), and unsaturated eichosanoic (C20:2-C20:3) acids with a noticeable absence of the unsaturated hexadecatrienoic acid (C16:3); this finding demonstrates, for the first time, that C. laxus is a C18:3 plant. In plants from the phytoremediation systems, the total fatty acid contents in the leaf and the corm were negatively affected by the hydrocarbons presence; however, the effect was positive in root. Interestingly, under contaminated conditions, unusual fatty acids such as odd numbered carbons (C15, C17, C21, and C23) and uncommon unsaturated chains (C20:3n6 and C20:4) were produced together with a remarkable quantity of C22:2 and C24:0 chains in the corm and the leaf. These results demonstrate that weathered hydrocarbons may drastically affect the lipidic composition of C. laxus at the fatty acid level, suggesting that this species adjusts the cover lipid composition in its vegetative organs, mainly in roots, in response to the weathered hydrocarbon presence and uptake during the phytoremediation process. PMID:26473488

The Fatty Acid Profile Analysis of Cyperus laxus Used for Phytoremediation of Soils from Aged Oil Spill-Impacted Sites Revealed That This Is a C18:3 Plant Species.

Science.gov (United States)

Rivera Casado, Noemí Araceli; Montes Horcasitas, María del Carmen; Rodríguez Vázquez, Refugio; Esparza García, Fernando José; Pérez Vargas, Josefina; Ariza Castolo, Armando; Ferrera-Cerrato, Ronald; Gómez Guzmán, Octavio; Calva Calva, Graciano

2015-01-01

The effect of recalcitrant hydrocarbons on the fatty acid profile from leaf, basal corm, and roots of Cyperus laxus plants cultivated in greenhouse phytoremediation systems of soils from aged oil spill-impacted sites containing from 16 to 340 g/Kg total hydrocarbons (THC) was assessed to investigate if this is a C18:3 species and if the hydrocarbon removal during the phytoremediation process has a relationship with the fatty acid profile of this plant. The fatty acid profile was specific to each vegetative organ and was strongly affected by the hydrocarbons level in the impacted sites. Leaf extracts of plants from uncontaminated soil produced palmitic acid (C16), octadecanoic acid (C18:0), unsaturated oleic acids (C18:1-C18:3), and unsaturated eichosanoic (C20:2-C20:3) acids with a noticeable absence of the unsaturated hexadecatrienoic acid (C16:3); this finding demonstrates, for the first time, that C. laxus is a C18:3 plant. In plants from the phytoremediation systems, the total fatty acid contents in the leaf and the corm were negatively affected by the hydrocarbons presence; however, the effect was positive in root. Interestingly, under contaminated conditions, unusual fatty acids such as odd numbered carbons (C15, C17, C21, and C23) and uncommon unsaturated chains (C20:3n6 and C20:4) were produced together with a remarkable quantity of C22:2 and C24:0 chains in the corm and the leaf. These results demonstrate that weathered hydrocarbons may drastically affect the lipidic composition of C. laxus at the fatty acid level, suggesting that this species adjusts the cover lipid composition in its vegetative organs, mainly in roots, in response to the weathered hydrocarbon presence and uptake during the phytoremediation process.

Site-specific incorporation of redox active amino acids into proteins

Science.gov (United States)

Alfonta, Lital [San Diego, CA; Schultz, Peter G [La Jolla, CA; Zhang, Zhiwen [San Diego, CA

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.

Site-specific incorporation of redox active amino acids into proteins

Energy Technology Data Exchange (ETDEWEB)

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

2017-10-10

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.

CHARACTERIZATION OF SORBENT PRODUCED THROUGH IMMOBILIZATION OF HUMIC ACID ON CHITOSAN USING GLUTARALDEHYDE AS CROSS-LINKING AGENT AND Pb(II ION AS ACTIVE SITE PROTECTOR

Directory of Open Access Journals (Sweden)

Uripto Trisno Santoso

2010-12-01

Full Text Available Sorbent produced through immobilization of humic acid (HA on chitosan using glutaraldehyde as cross-linking agent and Pb(II ions as active site protector has been characterized. Active sorption site of HA was protected by reacting HA with Pb(II ion, and the protected-HA was then activated by glutaraldehyde, crosslinked onto chitosan, and deprotected by 0.1 M disodium ethylenediamine tetra-acetic acid (Na2EDTA. The protected-crosslinking method enhanced the content of immobilized-HA and its chemical stability. Based on the FTIR spectra, crosslinking of HA on chitosan probably occurred through a chemical reaction. The sorption capacity of sorbent still remains unchanged after the second regeneration, but some of HA start to be soluble. The latter shows that cross-linking reaction between HA and chitosan is through formation an unstable product. The effectiveness of sorbent regeneration can also be identified by the XRD pattern.

Conserved amino acid motifs from the novel Piv/MooV family of transposases and site-specific recombinases are required for catalysis of DNA inversion by Piv.

Science.gov (United States)

Tobiason, D M; Buchner, J M; Thiel, W H; Gernert, K M; Karls, A C

2001-02-01

Piv, a site-specific invertase from Moraxella lacunata, exhibits amino acid homology with the transposases of the IS110/IS492 family of insertion elements. The functions of conserved amino acid motifs that define this novel family of both transposases and site-specific recombinases (Piv/MooV family) were examined by mutagenesis of fully conserved amino acids within each motif in Piv. All Piv mutants altered in conserved residues were defective for in vivo inversion of the M. lacunata invertible DNA segment, but competent for in vivo binding to Piv DNA recognition sequences. Although the primary amino acid sequences of the Piv/MooV recombinases do not contain a conserved DDE motif, which defines the retroviral integrase/transposase (IN/Tnps) family, the predicted secondary structural elements of Piv align well with those of the IN/Tnps for which crystal structures have been determined. Molecular modelling of Piv based on these alignments predicts that E59, conserved as either E or D in the Piv/MooV family, forms a catalytic pocket with the conserved D9 and D101 residues. Analysis of Piv E59G confirms a role for E59 in catalysis of inversion. These results suggest that Piv and the related IS110/IS492 transposases mediate DNA recombination by a common mechanism involving a catalytic DED or DDD motif.

Tracking the Chemical Transformations at the Brønsted Acid Site upon Water-Induced Deprotonation in a Zeolite Pore

Energy Technology Data Exchange (ETDEWEB)

Vjunov, Aleksei; Wang, Meng; Govind, Niranjan; Huthwelker, Thomas; Shi, Hui; Mei, Donghai; Fulton, John L.; Lercher, Johannes A.

2017-10-23

We report the structural changes induced by Brønsted acidic site deprotonation in a zeolite with MFI structure as a function of temperature up to 430°C using in situ Al K-edge X-ray absorption fine structure spectroscopy (XAFS). At ambient conditions, the protons are present as hydrated hydronium ions (H3O+(H2O)n) that are ion-paired to the anionic, Al tetrahedral (T) site. At elevated temperatures, loss of water molecules hydrating the hydronium ions leads to an unstable free hydronium ion that disso-ciates to form the hydroxylated T-site. The formation of this (-O3)-Al-(OH-) species leads to the elongation of one of the four Al-O bonds and causes significant distortion of the tetrahedral symmetry about the Al atom. This distortion leads to the appearance of new pre-edge features in the Al K-edge X-ray absorption near edge structure (XANES) spectra. The pre-edge peak assignment is confirmed by time-dependent density functional theory calculation of the XANES spectrum. The XANES spectra are also sensitive to solutes or solvent that are in proximity to the T-site. A second structural transition occurs at about the same temperature, namely the conversion of a minor fraction of extra-framework octahedral Al present in the sample at ambient conditions to a tetrahedral species through the de-coordination of H2O-ligands. Both IR spectroscopy and thermogravimetric analysis (TGA) are further used to confirm the overall chemical transformation of the T-site.

Monitoring Replication Protein A (RPA) dynamics in homologous recombination through site-specific incorporation of non-canonical amino acids.

Science.gov (United States)

Pokhrel, Nilisha; Origanti, Sofia; Davenport, Eric Parker; Gandhi, Disha; Kaniecki, Kyle; Mehl, Ryan A; Greene, Eric C; Dockendorff, Chris; Antony, Edwin

2017-09-19

An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as a reporter of its dynamics on DNA in the presence of multiple other DNA binding proteins. Using RPAf, we describe the kinetics of facilitated self-exchange and exchange by Rad51 and mediator proteins during various stages in homologous recombination. RPAf is widely applicable to investigate its mechanism of action in processes such as DNA replication, repair and telomere maintenance. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Synthesis of biodiesel from waste vegetable oil with large amounts of free fatty acids using a carbon-based solid acid catalyst

Energy Technology Data Exchange (ETDEWEB)

Shu, Qing; Gao, Jixian; Nawaz, Zeeshan; Liao, Yuhui; Wang, Dezheng; Wang, Jinfu [Beijing Key Laboratory of Green Chemical Reaction Engineering and Technology, Department of Chemical Engineering, Tsinghua University, Beijing 100084 (China)

2010-08-15

A carbon-based solid acid catalyst was prepared by the sulfonation of carbonized vegetable oil asphalt. This catalyst was employed to simultaneously catalyze esterification and transesterification to synthesis biodiesel when a waste vegetable oil with large amounts of free fatty acids (FFAs) was used as feedstock. The physical and chemical properties of this catalyst were characterized by a variety of techniques. The maximum conversion of triglyceride and FFA reached 80.5 wt.% and 94.8 wt.% after 4.5 h at 220 C, when using a 16.8 M ratio of methanol to oil and 0.2 wt.% of catalyst to oil. The high catalytic activity and stability of this catalyst was related to its high acid site density (-OH, Broensted acid sites), hydrophobicity that prevented the hydration of -OH species, hydrophilic functional groups (-SO{sub 3}H) that gave improved accessibility of methanol to the triglyceride and FFAs, and large pores that provided more acid sites for the reactants. (author)

Modification of palygorskite surface by organofunctionalization for application in immobilization of H{sub 3}PW{sub 12}O{sub 40}

Energy Technology Data Exchange (ETDEWEB)

Zhang Lixia; Jin Qingzhe; Huang Jianhua; Liu Yuanfa; Shan Liang [State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu Province (China); Wang Xingguo, E-mail: wxg1002@hotmail.com [State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu Province (China)

2010-08-01

Modified palygorskite with 3-aminopropyltriethoxysilane (KH550) and N-(2-aminoethyl)-3-aminopropyltrimethoxysilane (KH792) were used as adsorbent supports for adsorption of 12-phosphotungstic acid (H{sub 3}PW{sub 12}O{sub 40}, HPW). The effect of some factors, such as adsorbent dosage, contact time, initial HPW concentration and temperature, was investigated. The experimental data were well fitted with the pseudo-second-order kinetic model and the Langmuir adsorption isotherm model at all studied temperatures. The physicochemical properties of the solids were characterized by using Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis-simultaneous differential thermal analysis (TGA-SDTA), and diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy analysis techniques. The characteristic results indicated that silylated-Pa was a suitable support for adsorption of HPW; and HPW was finely and effectively distributed on silylated-Pa and retained partly strong Bronsted acidity.

Cleaving Double-Stranded DNA with Peptide Nucleic Acids

DEFF Research Database (Denmark)

1997-01-01

Peptide nucleic acids and analogues of peptide nucleic acids are used to form duplex, triplex, and other structures with nucleic acids and to modify nucleic acids. The peptide nucleic acids and analogues thereof also are used to modulate protein activity through, for example, transcription arrest......, transcription initiation, and site specific cleavage of nucleic acids....

Synthesis, characterization and performance of NiMo catalysts supported on titania modified alumina for the hydroprocessing of different gas oils derived from Athabasca bitumen

Energy Technology Data Exchange (ETDEWEB)

Ferdous, D.; Bakhshi, N.N.; Dalai, A.K. [Catalysis and Chemical Reactor Engineering Laboratories, Department of Chemical Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, Sask. (Canada); Adjaye, J. [Syncrude Canada Ltd., Edmonton Research Center, No. 9421, 17th Avenue, Edmonton, Alta. (Canada)

2007-03-08

In this work, a series of NiMo/Al{sub 2}O{sub 3} catalyst was prepared using different Al{sub 2}O{sub 3} supports modified by titania (0-9 wt%). All modified supports and fresh catalysts were characterized by BET surface area, pore volume and pore diameter measurement, TPR, TPD, XRD, FTIR and Raman spectroscopy analyses. The initial activity of these catalysts were tested in a trickle-bed reactor using three different gas oils such as light gas oil (LGO), blended gas oil (blended: 50% LGO and 50% HGO) and heavy gas oil (HGO), all derived from Athabasca bitumen. Little structural change in alumina was observed with the incorporation of titania. XRD analysis showed the well dispersion of Ni and Mo on the support. Titania in alumina increased the formation of polymolybdenum oxide on the catalyst as evident from TPR and Raman analyses. Weak-intermediate-strong acid sites on the catalyst were observed at all titania concentrations. The Lewis and Bronsted acidity on the catalyst surface increased with the increase in titania concentration from 0 to 9 wt%. Nitrogen conversion increased from 57 to 71 wt%, from 83 to 93 wt% and from 75 to 80 wt% for LGO, blended and HGO, respectively and also sulfur conversion of LGO increased from 86 to 92 wt% when titania concentration was increased from 0 to 9 wt%. For blended and HGO, sulfur conversion was in the range 96-99 wt% at all titania concentrations. (author)

Influence of incorporation method of sulfated zirconia in MCM-41 molecular sieve

International Nuclear Information System (INIS)

Pereira, C.E.; Santos, J.S.B.; Cavalcante, J.N.A.; Andrade, M.R.A.; Sousa, B.V.

2016-01-01

Sulfated metal oxides and sulfated zirconia have attracted great attention in recent years due to its high catalytic activity. The sulfated zirconia has the function of assigning the acidic material, through the formation of Bronsted acids and Lewis sites. The incorporation of sulfated zirconia in MCM-41 molecular sieve was carried out through the techniques: dry and wet. The wet process involves the use of an excess of solution on the volume of the support pores. Therefore, the concentration of the metal precursor on the support depends on the solution concentration and the pore volume of the support. In the process of incorporating by dry, the volume of the solution containing the precursor does not exceed the pore volume of the support. After either procedure, the impregnated support must be dried in order to allow the precursor compound can be converted into a catalytically active phase. This study aims to evaluate two methods of incorporation of sulfated zirconia in the mesoporous molecular sieve MCM-41. The process of merger took for wet and dry impregnation. Through the XRD patterns it was possible to identify the presence of the hexagonal structure of the molecular sieve, as well as the tetragonal and monoclinic phases of zirconia. From the spectroscopic analysis in the infrared region to the method the wet, it was possible to identify the vibrational frequencies related to the merger of sulfated zirconia in the MCM-41 structure of the molecular sieve. (author)

Influence of incorporation method of sulfated zirconia in MCM-41 molecular sieve; Influencia do metodo de incorporacao da zirconia sulfatada na peneira molecular MCM-41

Energy Technology Data Exchange (ETDEWEB)

Pereira, C.E.; Santos, J.S.B.; Cavalcante, J.N.A.; Andrade, M.R.A.; Sousa, B.V., E-mail: eduardopereira.eq@gmail.com [Universidade Federal de Campina Grande (UFCG), PB (Brazil). Centro de Ciencia e Tecnologia

2016-07-01

Sulfated metal oxides and sulfated zirconia have attracted great attention in recent years due to its high catalytic activity. The sulfated zirconia has the function of assigning the acidic material, through the formation of Bronsted acids and Lewis sites. The incorporation of sulfated zirconia in MCM-41 molecular sieve was carried out through the techniques: dry and wet. The wet process involves the use of an excess of solution on the volume of the support pores. Therefore, the concentration of the metal precursor on the support depends on the solution concentration and the pore volume of the support. In the process of incorporating by dry, the volume of the solution containing the precursor does not exceed the pore volume of the support. After either procedure, the impregnated support must be dried in order to allow the precursor compound can be converted into a catalytically active phase. This study aims to evaluate two methods of incorporation of sulfated zirconia in the mesoporous molecular sieve MCM-41. The process of merger took for wet and dry impregnation. Through the XRD patterns it was possible to identify the presence of the hexagonal structure of the molecular sieve, as well as the tetragonal and monoclinic phases of zirconia. From the spectroscopic analysis in the infrared region to the method the wet, it was possible to identify the vibrational frequencies related to the merger of sulfated zirconia in the MCM-41 structure of the molecular sieve. (author)

Preparation and characterization Al3+-bentonite Turen Malang for esterification fatty acid (palmitic acid, oleic acid and linoleic acid)

Science.gov (United States)

Abdulloh, Abdulloh; Aminah, Nanik Siti; Triyono, Mudasir, Trisunaryanti, Wega

2016-03-01

Catalyst preparation and characterization of Al3+-bentonite for esterification of palmitic acid, oleic acid and linoleic acid has been done. Al3+-bentonite catalyst was prepared from natural bentonite of Turen Malang through cation exchange reaction using AlCl3 solution. The catalysts obtained were characterized by XRD, XRF, pyridine-FTIR and surface area analyser using the BET method. Catalyst activity test of Al3+-bentonite for esterification reaction was done at 65°C using molar ratio of metanol-fatty acid of 30:1 and 0.25 g of Al3+-bentonite catalyst for the period of ½, 1, 2, 3, 4 and 5 hours. Based on the characterization results, the Al3+-bentonite Turen Malang catalyst has a d-spacing of 15.63 Ǻ, acid sites of Brönsted and Lewis respectively of 230.79 µmol/g and 99.39 µmol/g, surface area of 507.3 m2/g and the average of radius pore of 20.09 Å. GC-MS analysis results of the oil phase after esterification reaction showed the formation of biodiesel (FAME: Fatty acid methyl ester), namely methyl palmitate, methyl oleate and methyl linoleate. The number of conversions resulted in esterification reaction using Al3+-bentonite Turen Malang catalyst was 74.61%, 37.75%, and 20, 93% for the esterification of palmitic acid, oleic acid and linoleic acid respectively.

Impact of germline and somatic missense variations on drug binding sites.

Science.gov (United States)

Yan, C; Pattabiraman, N; Goecks, J; Lam, P; Nayak, A; Pan, Y; Torcivia-Rodriguez, J; Voskanian, A; Wan, Q; Mazumder, R

2017-03-01

Advancements in next-generation sequencing (NGS) technologies are generating a vast amount of data. This exacerbates the current challenge of translating NGS data into actionable clinical interpretations. We have comprehensively combined germline and somatic nonsynonymous single-nucleotide variations (nsSNVs) that affect drug binding sites in order to investigate their prevalence. The integrated data thus generated in conjunction with exome or whole-genome sequencing can be used to identify patients who may not respond to a specific drug because of alterations in drug binding efficacy due to nsSNVs in the target protein's gene. To identify the nsSNVs that may affect drug binding, protein-drug complex structures were retrieved from Protein Data Bank (PDB) followed by identification of amino acids in the protein-drug binding sites using an occluded surface method. Then, the germline and somatic mutations were mapped to these amino acids to identify which of these alter protein-drug binding sites. Using this method we identified 12 993 amino acid-drug binding sites across 253 unique proteins bound to 235 unique drugs. The integration of amino acid-drug binding sites data with both germline and somatic nsSNVs data sets revealed 3133 nsSNVs affecting amino acid-drug binding sites. In addition, a comprehensive drug target discovery was conducted based on protein structure similarity and conservation of amino acid-drug binding sites. Using this method, 81 paralogs were identified that could serve as alternative drug targets. In addition, non-human mammalian proteins bound to drugs were used to identify 142 homologs in humans that can potentially bind to drugs. In the current protein-drug pairs that contain somatic mutations within their binding site, we identified 85 proteins with significant differential gene expression changes associated with specific cancer types. Information on protein-drug binding predicted drug target proteins and prevalence of both somatic and

Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection

DEFF Research Database (Denmark)

Yang, Ziheng; Wong, Wendy Shuk Wan; Nielsen, Rasmus

2005-01-01

, with > 1 indicating positive selection. Statistical distributions are used to model the variation in among sites, allowing a subset of sites to have > 1 while the rest of the sequence may be under purifying selection with ... probabilities that a site comes from the site class with > 1. Current implementations, however, use the naive EB (NEB) approach and fail to account for sampling errors in maximum likelihood estimates of model parameters, such as the proportions and ratios for the site classes. In small data sets lacking...... information, this approach may lead to unreliable posterior probability calculations. In this paper, we develop a Bayes empirical Bayes (BEB) approach to the problem, which assigns a prior to the model parameters and integrates over their uncertainties. We compare the new and old methods on real and simulated...

Mapping Substance P Binding Sites on the Neurokinin-1 Receptor Using Genetic Incorporation of a Photoreactive Amino Acid

DEFF Research Database (Denmark)

Valentin-Hansen, Louise; Park, Minyoung; Huber, Thomas

2014-01-01

that the binding site for SP includes multiple domains in the N-terminal (Nt) segment and the second extracellular loop (ECLII) of NK1. To map precisely the NK1 residues that interact with SP, we applied a novel receptor-based targeted photocross-linking approach. We used amber codon suppression to introduce...... the photoreactive unnatural amino acid p-benzoyl-l-phenylalanine (BzF) at 11 selected individual positions in the Nt tail (residues 11-21) and 23 positions in the ECLII (residues 170(C-10)-193(C+13)) of NK1. The 34 NK1 variants were expressed in mammalian HEK293 cells and retained the ability to interact...

The acid-base titration of montmorillonite

Science.gov (United States)

Bourg, I. C.; Sposito, G.; Bourg, A. C.

2003-12-01

Proton binding to clay minerals plays an important role in the chemical reactivity of soils (e.g., acidification, retention of nutrients or pollutants). If should also affect the performance of clay barriers for waste disposal. The surface acidity of clay minerals is commonly modelled empirically by assuming generic amphoteric surface sites (>SOH) on a flat surface, with fitted site densities and acidity constant. Current advances in experimental methods (notably spectroscopy) are rapidly improving our understanding of the structure and reactivity of the surface of clay minerals (arrangement of the particles, nature of the reactive surface sites, adsorption mechanisms). These developments are motivated by the difficulty of modelling the surface chemistry of mineral surfaces at the macro-scale (e.g., adsorption or titration) without a detailed (molecular-scale) picture of the mechanisms, and should be progressively incorporated into surface complexation models. In this view, we have combined recent estimates of montmorillonite surface properties (surface site density and structure, edge surface area, surface electrostatic potential) with surface site acidities obtained from the titration of alpha-Al2O3 and SiO2, and a novel method of accounting for the unknown initial net proton surface charge of the solid. The model predictions were compared to experimental titrations of SWy-1 montmorillonite and purified MX-80 bentonite in 0.1-0.5 mol/L NaClO4 and 0.005-0.5 mol/L NaNO3 background electrolytes, respectively. Most of the experimental data were appropriately described by the model after we adjusted a single parameter (silanol sites on the surface of montmorillonite were made to be slightly more acidic than those of silica). At low ionic strength and acidic pH the model underestimated the buffering capacity of the montmorillonite, perhaps due to clay swelling or to the interlayer adsorption of dissolved aluminum. The agreement between our model and the experimental

Superior acidic catalytic activity and stability of Fe-doped HTaWO6 nanotubes

KAUST Repository

Liu, He

2017-07-26

Fe-doped HTaWO6 (H1-3xFexTaWO6, x = 0.23) nanotubes as highly active solid acid catalysts were prepared via an exfoliation-scrolling-exchange process. The specific surface area and pore volume of undoped nanotubes (20.8 m2 g-1, 0.057 cm3 g-1) were remarkably enhanced through Fe3+ ion-exchange (>100 m2 g-1, 0.547 cm3 g-1). Doping Fe ions into the nanotubes endowed them with improved thermal stability due to the stronger interaction between the intercalated Fe3+ ions and the host layers. This interaction also facilitated the preservation of effective Brønsted acid sites and the generation of new acid sites. The integration of these functional roles resulted in Fe-doped nanotubes with high acidic catalytic activities in the Friedel-Crafts alkylation of anisole and the esterification of acetic acid. Facile accessibility to active sites, generation of effective Brønsted acid sites, high stability of the tubular structure and strong acid sites were found to synergistically contribute to the excellent acidic catalytic efficiency. Additionally, the activity of cycled nanocatalysts can be easily recovered through annealing treatment.

Superior acidic catalytic activity and stability of Fe-doped HTaWO6 nanotubes

KAUST Repository

Liu, He; Zhang, Haitao; Fei, Linfeng; Ma, Hongbin; Zhao, Guoying; Mak, CheeLeung; Zhang, Xixiang; Zhang, Suojiang

2017-01-01

Fe-doped HTaWO6 (H1-3xFexTaWO6, x = 0.23) nanotubes as highly active solid acid catalysts were prepared via an exfoliation-scrolling-exchange process. The specific surface area and pore volume of undoped nanotubes (20.8 m2 g-1, 0.057 cm3 g-1) were remarkably enhanced through Fe3+ ion-exchange (>100 m2 g-1, 0.547 cm3 g-1). Doping Fe ions into the nanotubes endowed them with improved thermal stability due to the stronger interaction between the intercalated Fe3+ ions and the host layers. This interaction also facilitated the preservation of effective Brønsted acid sites and the generation of new acid sites. The integration of these functional roles resulted in Fe-doped nanotubes with high acidic catalytic activities in the Friedel-Crafts alkylation of anisole and the esterification of acetic acid. Facile accessibility to active sites, generation of effective Brønsted acid sites, high stability of the tubular structure and strong acid sites were found to synergistically contribute to the excellent acidic catalytic efficiency. Additionally, the activity of cycled nanocatalysts can be easily recovered through annealing treatment.

5'Azido-N-1-napthylphthalamic acid, a photolabile analog of N-1-naphthylphthalamic acid

International Nuclear Information System (INIS)

Voet, J.G.; Howley, K.S.; Shumsky, J.S.

1987-01-01

A photolabile analog of N-1-naphthylphthalamic acid (NPA), 5'-azido-N-1-naphthylphthalamic acid (Az-NPA), has been synthesized and characterized. This potential photoaffinity label for the plasma membrane NPA binding protein competes with [ 3 H]NPA for binding sites on Curcurbita pepo L. (zucchini) hypocotyl cell membranes with K/sub 0.5/ = 2.8 x 10 -7 molar. The K/sub 0.5/ for NPA under these conditions is 2 x 10 -8 molar, indicating that the affinity of Az-NPA for the membranes is only 14-fold lower than NPA. While the binding of Az-NPA to NPA binding sites is reversible in the dark, exposure of the Az-NPA treated membranes to light results in a 30% loss in [ 3 H]NPA binding ability. Pretreatment of the membranes with NPA protects the membranes against photodestruction of [ 3 H]NPA binding sites by Az-NPA supporting the conclusion that Az-NPA destroys these sites by specific covalent attachment

The effects of topically applied glycolic acid and salicylic acid on ultraviolet radiation-induced erythema, DNA damage and sunburn cell formation in human skin.

Science.gov (United States)

Kornhauser, Andrija; Wei, Rong-Rong; Yamaguchi, Yuji; Coelho, Sergio G; Kaidbey, Kays; Barton, Curtis; Takahashi, Kaoruko; Beer, Janusz Z; Miller, Sharon A; Hearing, Vincent J

2009-07-01

alpha-Hydroxy acids (alphaHAs) are reported to reduce signs of aging in the skin and are widely used cosmetic ingredients. Several studies suggest that alphaHA can increase the sensitivity of skin to ultraviolet radiation. More recently, beta-hydroxy acids (betaHAs), or combinations of alphaHA and betaHA have also been incorporated into antiaging skin care products. Concerns have also arisen about increased sensitivity to ultraviolet radiation following use of skin care products containing beta-HA. To determine whether topical treatment with glycolic acid, a representative alphaHA, or with salicylic acid, a betaHA, modifies the short-term effects of solar simulated radiation (SSR) in human skin. Fourteen subjects participated in this study. Three of the four test sites on the mid-back of each subject were treated daily Monday-Friday, for a total of 3.5 weeks, with glycolic acid (10%), salicylic acid (2%), or vehicle (control). The fourth site received no treatment. After the last treatment, each site was exposed to SSR, and shave biopsies from all four sites were obtained. The endpoints evaluated in this study were erythema (assessed visually and instrumentally), DNA damage and sunburn cell formation. Treatment with glycolic acid resulted in increased sensitivity of human skin to SSR, measured as an increase in erythema, DNA damage and sunburn cell formation. Salicylic acid did not produce significant changes in any of these biomarkers. Short-term topical application of glycolic acid in a cosmetic formulation increased the sensitivity of human skin to SSR, while a comparable treatment with salicylic acid did not.

Evaluating rare amino acid substitutions (RGC_CAMs in a yeast model clade.

Directory of Open Access Journals (Sweden)

Kenneth Polzin

Full Text Available When inferring phylogenetic relationships, not all sites in a sequence alignment are equally informative. One recently proposed approach that takes advantage of this inequality relies on sites that contain amino acids whose replacement requires multiple substitutions. Identifying these so-called RGC_CAM substitutions (after Rare Genomic Changes as Conserved Amino acids-Multiple substitutions requires that, first, at any given site in the amino acid sequence alignment, there must be a minimum of two different amino acids; second, each amino acid must be present in at least two taxa; and third, the amino acids must require a minimum of two nucleotide substitutions to replace each other. Although theory suggests that RGC_CAM substitutions are expected to be rare and less likely to be homoplastic, the informativeness of RGC_CAM substitutions has not been extensively evaluated in biological data sets. We investigated the quality of RGC_CAM substitutions by examining their degree of homoplasy and internode certainty in nearly 2.7 million aligned amino acid sites from 5,261 proteins from five species belonging to the yeast Saccharomyces sensu stricto clade whose phylogeny is well-established. We identified 2,647 sites containing RGC_CAM substitutions, a number that contrasts sharply with the 100,887 sites containing RGC_non-CAM substitutions (i.e., changes between amino acids that require only a single nucleotide substitution. We found that RGC_CAM substitutions had significantly lower homoplasy than RGC_non-CAM ones; specifically RGC_CAM substitutions showed a per-site average homoplasy index of 0.100, whereas RGC_non-CAM substitutions had a homoplasy index of 0.215. Internode certainty values were also higher for sites containing RGC_CAM substitutions than for RGC_non-CAM ones. These results suggest that RGC_CAM substitutions possess a strong phylogenetic signal and are useful markers for phylogenetic inference despite their rarity.

Coal mine site reclamation

Energy Technology Data Exchange (ETDEWEB)

NONE

2013-02-15

Coal mine sites can have significant effects on local environments. In addition to the physical disruption of land forms and ecosystems, mining can also leave behind a legacy of secondary detrimental effects due to leaching of acid and trace elements from discarded materials. This report looks at the remediation of both deep mine and opencast mine sites, covering reclamation methods, back-filling issues, drainage and restoration. Examples of national variations in the applicable legislation and in the definition of rehabilitation are compared. Ultimately, mine site rehabilitation should return sites to conditions where land forms, soils, hydrology, and flora and fauna are self-sustaining and compatible with surrounding land uses. Case studies are given to show what can be achieved and how some landscapes can actually be improved as a result of mining activity.

Application of the CPA equation of state to organic acids

DEFF Research Database (Denmark)

Derawi, Samer; Zeuthen, Frederik Jacob; Michelsen, Michael Locht

2004-01-01

a strong tendency to dimerise in the vapor phase at normal condition resulting in strong non-ideal behavior, even at low pressures. Pure compound parameters have been determined from vapor pressure and liquid density data for the three acids. Among the three tested association schemes (one-site, two......-site, and four-site), only the one-site association scheme describes satisfactorily the association in both the gas and the liquid phase. Second virial coefficients axe predicted well with the proposed one-site model. Excellent binary VLE and acceptable LLE correlations have been obtained for acid + aliphatic...

Doping phosphoric acid in polybenzimidazole membranes for high temperature proton exchange membrane fuel cells

DEFF Research Database (Denmark)

He, Ronghuan; Li, Qingfeng; Jensen, Jens Oluf

2007-01-01

Polybenzimidazole (PBI) membranes were doped in phosphoric acid solutions of different concentrations at room temperature. The doping chemistry was studied using the Scatchard method. The energy distribution of the acid complexation in polymer membranes is heterogeneous, that is, there are two...... different types of sites in PBI for the acid doping. The protonation constants of PBI by phosphoric acid are found to be 12.7 L mol(-1) (K-1) for acid complexing sites with higher affinity, and 0.19 L mol(-1) (K-2) for the sites with lower affinity. The dissociation constants for the complexing acid onto...... these two types of PBI sites are found to be 5.4 X 10(-4) and 3.6 X 10(-2), respectively, that is, about 10 times smaller than that of aqueous phosphoric acid in the first case but 5 times higher in the second. The proton conducting mechanism is also discussed....

Medium-chain fatty acid binding to albumin and transfer to phospholipid bilayers

International Nuclear Information System (INIS)

Hamilton, J.A.

1989-01-01

Temperature-dependent (5-42 degree C) 13 C NMR spectra of albumin complexes with 90% isotopically substituted [1- 13 C]octanoic or [1- 13 C]decanoic acids showed a single peak at >30 degree C but three peaks at lower temperatures. The chemical-shift differences result from different ionic and/or hydrogen-bonding interactions between amino acid side chains and the fatty acid carboxyl carbon. Rapid exchange of fatty acid among binding sites obscures these sites at temperatures >30 degree C. Rate constants for exchange at 33 degree C were 350 sec -1 for octanoate and 20 sec -1 for decanoate. Temperature-dependent data for octanoate showed an activation energy of 2 kcal/mol for exchange. Spectra of albumin complexes with the 12-carbon saturated fatty acid, lauric acid, had several narrow laurate carboxyl peaks at 35 degree C, indicating longer lifetimes in the different binding sites. Fatty acid exchange between albumin and model membranes (phosphatidylcholine bilayers) occurred on a time scale comparable to that for exchange among albumin binding sites, following the order octanoate > decanoate > laurate. The equilibrium distribution of fatty acid between lipid bilayers and protein was measured directly from NMR spectra. Decreasing pH increased the relative affinity of fatty acid for the lipid bilayer. The results predict that the relative affinity of octanoic acid for albumin and membranes will be similar to that of long-chain fatty acids, but the rate of equilibration will be ∼ 10 4 faster for octanoic acid

Modulation of the acidity of niobic acid by ion-doping: Effects of nature and amount of the dopant ions

Energy Technology Data Exchange (ETDEWEB)

Carniti, Paolo [Dipartimento di Chimica, Università degli Studi di Milano (UNIMI), Milano (Italy); Gervasini, Antonella, E-mail: antonella.gervasini@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano (UNIMI), Milano (Italy); Marzo, Matteo [Dipartimento di Chimica, Università degli Studi di Milano (UNIMI), Milano (Italy); Auroux, Aline [Université Lyon 1, CNRS, UMR 5256, (IRCELYON), Villeurbanne (France)

2013-09-10

Highlights: ► Mitigation of the surface acidity of niobic acid was pursued by K-, Ba-, and Nd-doping. ► Thermal techniques of study were effective for the acidity study. ► The nature of the dopant influences the effectiveness of the acidity tuning of niobic acid. ► The acidity of the doped surfaces decreased with increasing the dopant species added to niobic acid. ► The samples showed different acidity when measured in gas–solid phase (intrinsic acidity) and water (effective acidity). - Abstract: The acidity of niobic acid (NBO) has been successfully mitigated and tuned by addition of K{sup +}, Ba{sup 2+} and Nd{sup 3+} dopant species in amounts from 1 to 15 atom nm{sup −2}. The characterization of the intrinsic acid properties of the samples was performed by adsorption of NH{sub 3} in a volumetric–microcalorimetric coupled line and by temperature programmed desorption (TPD) of 2-phenylethylamine in a thermogravimetric apparatus. The K-dopant was more effective in decreasing the acidity of niobic acid than the Ba- and Nd-dopants. Complementary measurements of the effective acidity of the samples in water by base titrations with 2-phenylethylamine completed the study and revealed a different picture of the effect of the three dopants on the NBO acidity in water. All the results indicated that the K-dopant targeted more selectively the Brønsted acid sites, acting as an ion-exchanger, while Ba- and Nd-species predominantly acted on the Lewis acid sites of the NBO surface.

Acidity and origin of dissolved organic carbon in different vegetation zones

Science.gov (United States)

Hruška, Jakub; Oulehle, Filip; Myška, Oldřích; Chuman, Tomáš

2016-04-01

The acid/base character of aquatic dissolved organic carbon (DOC) has been studied intensively during recent decades with regard to the role of DOC in stream water acidity and the balance between natural acidity and anthropogenic acidification. Recently, DOC has been shown to play an important role in preindustrial surface waters. Studies focused on the acid/base properties of DOC have been carried out in mainly in Europe and North America and paint a conflicting picture. Some studies reported large differences in acid base properties, sometimes between quite similar and nearby localities, or between seasons at the same site. Other studies, however, found similar acid/base properties in waters from a variety of sites, sometimes far from each other as well as stable acid/base properties at the same site through different seasons or runoff events. Site density of DOC (amount of carboxylic groups per milligram of DOC) and SUVA was measured for streams (or small tundra ponds respectively) from the tundra in northern Alaska, boreal zone of Sweden, western Czech Republic (temperate region), and tropical Congo rain forest in central Africa. At least 10 samples from each region were taken from surface waters during the growing season. Titration of carboxylic groups after proton saturation on cation-exchange resin was used for site density determination. Despite very different climatic and vegetation properties and internal variation within a region, there was no statistically significant difference among regions for site density (it varied between 10.2-10.5 ueq/mg DOC) as well as for SUVA (tested by ANOVA). Results suggest that different vegetation and climate produced generally the same DOC in respect of acid/base character and SUVA. It also suggests that use of the one analytical technique was more important than differences between climatic zones itself.

Acid neutralizing capacity and leachate results for igneous rocks, with associated carbon contents of derived soils, Animas River AML site, Silverton, Colorado

Science.gov (United States)

Yager, Douglas B.; Stanton, Mark R.; Choate, LaDonna M.; Burchell,

2009-01-01

Mine planning efforts have historically overlooked the possible acid neutralizing capacity (ANC) that local igneous rocks can provide to help neutralize acidmine drainage. As a result, limestone has been traditionally hauled to mine sites for use in neutralizing acid drainage. Local igneous rocks, when used as part of mine life-cycle planning and acid mitigation strategy, may reduce the need to transport limestone to mine sites because these rocks can contain acid neutralizing minerals. Igneous hydrothermal events often introduce moderately altered mineral assemblages peripheral to more intensely altered rocks that host metal-bearing veins and ore bodies. These less altered rocks can contain ANC minerals (calcite-chlorite-epidote) and are referred to as a propylitic assemblage. In addition, the carbon contents of soils in areas of new mining or those areas undergoing restoration have been historically unknown. Soil organic carbon is an important constituent to characterize as a soil recovery benchmark that can be referred to during mine cycle planning and restoration. This study addresses the mineralogy, ANC, and leachate chemistry of propylitic volcanic rocks that host polymetallic mineralization in the Animas River watershed near the historical Silverton, Colorado, mining area. Acid titration tests on volcanic rocks containing calcite (2 – 20 wt %) and chlorite (6 – 25 wt %), have ANC ranging from 4 – 146 kg/ton CaCO3 equivalence. Results from a 6-month duration, kinetic reaction vessel test containing layered pyritic mine waste and underlying ANC volcanic rock (saturated with deionized water) indicate that acid generating mine waste (pH 2.4) has not overwhelmed the ANC of propylitic volcanic rocks (pH 5.8). Sequential leachate laboratory experiments evaluated the concentration of metals liberated during leaching. Leachate concentrations of Cu-Zn-As-Pb for ANC volcanic rock are one-to-three orders of magnitude lower when compared to leached solution from

Site-selective 13C labeling of proteins using erythrose

International Nuclear Information System (INIS)

Weininger, Ulrich

2017-01-01

NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with 13 C and/or 1 H, which is achieved in the most general way by using site-selectively 13 C-enriched glucose (1- and 2- 13 C) as the carbon source in bacterial expression systems. Using this strategy, multiple sites in side chains, including aromatics, become site-selectively labeled and suitable for relaxation studies. Here we systematically investigate the use of site-selectively 13 C-enriched erythrose (1-, 2-, 3- and 4- 13 C) as a suitable precursor for 13 C labeled aromatic side chains. We quantify 13 C incorporation in nearly all sites in all 20 amino acids and compare the results to glucose based labeling. In general the erythrose approach results in more selective labeling. While there is only a minor gain for phenylalanine and tyrosine side-chains, the 13 C incorporation level for tryptophan is at least doubled. Additionally, the Phe ζ and Trp η2 positions become labeled. In the aliphatic side chains, labeling using erythrose yields isolated 13 C labels for certain positions, like Ile β and His β, making these sites suitable for dynamics studies. Using erythrose instead of glucose as a source for site-selective 13 C labeling enables unique or superior labeling for certain positions and is thereby expanding the toolbox for customized isotope labeling of amino-acid side-chains.

Strong activation of bile acid-sensitive ion channel (BASIC) by ursodeoxycholic acid

Science.gov (United States)

Wiemuth, Dominik; Sahin, Hacer; Lefèvre, Cathérine M.T.; Wasmuth, Hermann E.; Gründer, Stefan

2013-01-01

Bile acid-sensitive ion channel (BASIC) is a member of the DEG/ENaC gene family of unknown function. Rat BASIC (rBASIC) is inactive at rest. We have recently shown that cholangiocytes, the epithelial cells lining the bile ducts, are the main site of BASIC expression in the liver and identified bile acids, in particular hyo- and chenodeoxycholic acid, as agonists of rBASIC. Moreover, it seems that extracellular divalent cations stabilize the resting state of rBASIC, because removal of extracellular divalent cations opens the channel. In this addendum, we demonstrate that removal of extracellular divalent cations potentiates the activation of rBASIC by bile acids, suggesting an allosteric mechanism. Furthermore, we show that rBASIC is strongly activated by the anticholestatic bile acid ursodeoxycholic acid (UDCA), suggesting that BASIC might mediate part of the therapeutic effects of UDCA. PMID:23064163

Microbial exoenzymes as bioindicators of acid rock drainage impacts in the Finniss River

International Nuclear Information System (INIS)

Hammerton, K.M.

2002-01-01

Sediment samples were collected from several sites along the East Branch of the Finniss River during the dry season (June, 1999), when the East Branch is drying into a series of ponds. The sites included those upstream from the Rum Jungle mine site (EB8A, EB8B, FCA, FCB), a site receiving acid leachate from the waste rock (WO), sites downstream from the mine that are impacted by acid and metal contamination (EB6, TCP, EB5D, EB4U, EB2) and reference sites not subject to acid rock drainage (HS, EB4S, LFRB). Exoenzyme activities were measured with a spectrofluorometric technique that involved measuring the increase in fluorescence when an artificial fluorogenic substrate (that mimics the natural substrate) is hydrolysed to a highly fluorescent product. The present findings indicate that the acid rock drainage impacted sediments contain acidophilic, heterotrophic microorganisms, bacteria and/or fungi, producing extracellular enzymes adapted to the acid conditions. This study has demonstrated that measurements of extracellular enzyme activities in river sediments provide a rapid, sensitive technique for determining microbial activity and productivity. In aquatic ecosystems some exoenzymes, particularly leucine-aminopeptidase, could be used as bioindicators of pollution from acid rock drainage

Catalytic properties of mineral ion-exchangers previously used in uranium ore wastes treatment. I. Ammoniac octylation in gaseous phase using Y-type faujasite catalysts containing mainly uranium

International Nuclear Information System (INIS)

Azzouz, A.; Nibou, D.; Abbad, B.; Achache, M.

1990-06-01

Y-type faujasite, previously used in purifying aqueous wastes containing radioactive elements, are studied as catalysts in heterogeneous reactions such as octanol amination. This process consists in alkylating ammoniac NH 3 by octanol-1 in a flow reactor containing a fixed bed of pelleted catalysts. Acidic catalysts like Y-type faujasite impregnated with low concentration leaching solution containing between 10 and 1000 ppm of uranium show interesting activities and selectivities in yielding primary, secondary and tertiary amines. High octanol conversions were obtained reaching 60 mol.% for appreciable selectivities for producing amines of about 60-80 mol.%. Compared to the non-active fresh zeolite, the catalysts obtained present good activities essentially due to the presence of uranyl cations UO 2 ++ . The latter seems to play the main role in activating the zeolite by enhancing its Bronsted surface acidity. Another interest of this process consists in obtaining Trioctylamine (TOA), an important extraction agent in uranium hydrometallurgy or its derivatives (MOA and DOA) which are very used in chemical industry

Periodic DFT study of acidic trace atmospheric gas molecule adsorption on Ca- and Fe-doped MgO(001) surface basic sites.

Science.gov (United States)

Baltrusaitis, Jonas; Hatch, Courtney; Orlando, Roberto

2012-08-02

The electronic properties of undoped and Ca- or Fe-doped MgO(001) surfaces, as well as their propensity toward atmospheric acidic gas (CO2, SO2, and NO2) uptake was investigated with an emphasis on gas adsorption on the basic MgO oxygen surface sites, O(surf), using periodic density functional theory (DFT) calculations. Adsorption energy calculations show that MgO doping will provide stronger interactions of the adsorbate with the O(surf) sites than the undoped MgO for a given adsorbate molecule. Charge transfer from the iron atom in Fe-doped MgO(001) to NO2 was shown to increase the binding interaction between adsorbate by an order of magnitude, when compared to that of undoped and Ca-doped MgO(001) surfaces. Secondary binding interactions of adsorbate oxygen atoms were observed with surface magnesium sites at distances close to those of the Mg-O bond within the crystal. These interactions may serve as a preliminary step for adsorption and facilitate further adsorbate transformations into other binding configurations. Impacts on global atmospheric chemistry are discussed as these adsorption phenomena can affect atmospheric gas budgets via altered partitioning and retention on mineral aerosol surfaces.

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

Energy Technology Data Exchange (ETDEWEB)

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.

The acidic complexation of tetracycline with sucralfate for its mucoadhesive preparation.

Science.gov (United States)

Higo, Shoichi; Takeuchi, Hirofumi; Yamamoto, Hiromitsu; Hino, Tomoaki; Kawashima, Yoshiaki

2004-08-01

The complex of antibiotics with sucralfate (SF) was prepared with acid. The mechanism of the complexation and some factors concerning the preparation, which influence the mucoadhering property, were studied. The complexation was confirmed by the change in color and instrumental analysis. The acidic complex appeared to be produced by reagglomeration of SF preliminary particles. It was suggested that the amide or amine groups of tetracycline (TC) and aluminum moieties of SF serve as the binding sites. The potential of multiple binding sites and a priority in them were suggested by the Scatchard plot analysis. The additional amounts of acid and the increase in the surface area increased the number of sites. The amount of the additional acid appeared to be the most important factor during the preparation of the acidic complex. The appropriate amount of acid added appeared to produce a complex rich in TC. However, an excess amount might cause the excess dissociation of aluminum moieties, which destroys the mucoadhesive paste-forming property.

Pharmacology of morphine and morphine-3-glucuronide at opioid, excitatory amino acid, GABA and glycine binding sites

Energy Technology Data Exchange (ETDEWEB)

Bartlett, S.E.; Smith, M.T. (Department of Pharmacy, The University of Queensland (Australia)); Dood, P.R. (Clinical Research Centre, Royal Brisbane Hospital Foundation, Brisbane (Australia))

1994-07-01

Morphine in high doses and its major metabolite, morphine-3-glucuronide, cause CNS excitation following intrathecal and intracerebroventricular administration by an unknown mechanism. This study investigated whether morphine and morphine-3-glucuronide interact at major excitatory (glutamate), major inhibitory (GABA or glycine), or opioid binding sites. Homogenate binding assays were performed using specific radioligands. At opioid receptors, morphine-3-glucuronide and morphine caused an equipotent sodium shift, consistent with morphine-3-glucuronide behaving as an agonist. This suggests that morphine-3-glucuronide-mediated excitation is not caused by an interaction at opioid receptors. Morphine-3-glucuronide and morphine caused a weak inhibition of the binding of [sup 3]H-MK801 (non-competitive antagonist) and [sup 125]I-ifenprodil (polyamine site antagonist), but at unphysiologically high concentrations. This suggests that CNS excitation would not result from an interaction of morphine-3-glucuronide and high-dose morphine with these sites on the NMDA receptor. Morphine-3-glucuronide and morphine inhibited the binding of [sup 3]H-muscimol (GABA receptor agonist), [sup 3]H-diazepam and [sup 3]H-flunitraxepam (benzodiazepine agonists) binding very weakly, suggesting the excitatory effects of morphine-3-glucuronide and high-dose morphine are not elicited through GABA[sub A] receptors. Morphine-3-glucuronide and high-dose morphine did not prevent re-uptake of glutamate into presynaptic nerve terminals. In addition, morphine-3-glucuronide and morphine did not inhibit the binding of [sup 3]H-strychnine (glycine receptor antagonist) to synaptic membranes prepared from bovine spinal cord. It is concluded that excitation caused by high-dose morphine and morphine-3-glucuronide is not mediated by an interaction with postsynaptic amino acid receptors. (au) (30 refs.).

Contamination by perfluorinated compounds in water near waste recycling and disposal sites in Vietnam.

Science.gov (United States)

Kim, Joon-Woo; Tue, Nguyen Minh; Isobe, Tomohiko; Misaki, Kentaro; Takahashi, Shin; Viet, Pham Hung; Tanabe, Shinsuke

2013-04-01

There are very few reports on the contamination by perfluorinated chemicals (PFCs) in the environment of developing countries, especially regarding their emission from waste recycling and disposal sites. This is the first study on the occurrence of a wide range of PFCs (17 compounds) in ambient water in Vietnam, including samples collected from a municipal dumping site (MD), an e-waste recycling site (ER), a battery recycling site (BR) and a rural control site. The highest PFC concentration was found in a leachate sample from MD (360 ng/L). The PFC concentrations in ER and BR (mean, 57 and 16 ng/L, respectively) were also significantly higher than those detected in the rural control site (mean, 9.4 ng/L), suggesting that municipal solid waste and waste electrical and electronic equipment are potential contamination sources of PFCs in Vietnam. In general, the most abundant PFCs were perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), and perfluoroundecanoic acid (PFUDA; waste materials.

Acid rock drainage in the uranium mining and milling site of Pocos de Caldas, Brazil -- duration assessment, pollutant generation modelling and remediation strategies

International Nuclear Information System (INIS)

Fernandes, H.M.; Franklin, M.R.

2002-01-01

This geochemical modeling work was carried out to simulate the acid drainage generation from one of the waste-rock piles at the Pocos de Caldas uranium mining site. The mathematical code STEADQYL was used. The estimated results were in good agreement for sulphate and uranium concentrations and the duration of the acid water generation was estimated to be about 500 years. The effect of covering the dump with a material that minimized oxygen diffusion was assessed. Projections indicated that covering the dump with a 1.0 m thickness of a material (like clay), which had an oxygen diffusion coefficient of 10 9 m 2 ·s 1 , would reduce the pollutant concentrations to acceptable values. The estimated cost, when using this strategy, would be about US $10 million. (author)

ETMB-RBF: discrimination of metal-binding sites in electron transporters based on RBF networks with PSSM profiles and significant amino acid pairs.

Science.gov (United States)

Ou, Yu-Yen; Chen, Shu-An; Wu, Sheng-Cheng

2013-01-01

Cellular respiration is the process by which cells obtain energy from glucose and is a very important biological process in living cell. As cells do cellular respiration, they need a pathway to store and transport electrons, the electron transport chain. The function of the electron transport chain is to produce a trans-membrane proton electrochemical gradient as a result of oxidation-reduction reactions. In these oxidation-reduction reactions in electron transport chains, metal ions play very important role as electron donor and acceptor. For example, Fe ions are in complex I and complex II, and Cu ions are in complex IV. Therefore, to identify metal-binding sites in electron transporters is an important issue in helping biologists better understand the workings of the electron transport chain. We propose a method based on Position Specific Scoring Matrix (PSSM) profiles and significant amino acid pairs to identify metal-binding residues in electron transport proteins. We have selected a non-redundant set of 55 metal-binding electron transport proteins as our dataset. The proposed method can predict metal-binding sites in electron transport proteins with an average 10-fold cross-validation accuracy of 93.2% and 93.1% for metal-binding cysteine and histidine, respectively. Compared with the general metal-binding predictor from A. Passerini et al., the proposed method can improve over 9% of sensitivity, and 14% specificity on the independent dataset in identifying metal-binding cysteines. The proposed method can also improve almost 76% sensitivity with same specificity in metal-binding histidine, and MCC is also improved from 0.28 to 0.88. We have developed a novel approach based on PSSM profiles and significant amino acid pairs for identifying metal-binding sites from electron transport proteins. The proposed approach achieved a significant improvement with independent test set of metal-binding electron transport proteins.

Dataset of cocoa aspartic protease cleavage sites

Directory of Open Access Journals (Sweden)

Katharina Janek

2016-09-01

Full Text Available The data provide information in support of the research article, “The cleavage specificity of the aspartic protease of cocoa beans involved in the generation of the cocoa-specific aroma precursors” (Janek et al., 2016 [1]. Three different protein substrates were partially digested with the aspartic protease isolated from cocoa beans and commercial pepsin, respectively. The obtained peptide fragments were analyzed by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS/MS and identified using the MASCOT server. The N- and C-terminal ends of the peptide fragments were used to identify the corresponding in-vitro cleavage sites by comparison with the amino acid sequences of the substrate proteins. The same procedure was applied to identify the cleavage sites used by the cocoa aspartic protease during cocoa fermentation starting from the published amino acid sequences of oligopeptides isolated from fermented cocoa beans. Keywords: Aspartic protease, Cleavage sites, Cocoa, In-vitro proteolysis, Mass spectrometry, Peptides

Probes of the catalytic site of cysteine dioxygenase.

Science.gov (United States)

Chai, Sergio C; Bruyere, John R; Maroney, Michael J

2006-06-09

The first major step of cysteine catabolism, the oxidation of cysteine to cysteine sulfinic acid, is catalyzed by cysteine dioxygenase (CDO). In the present work, we utilize recombinant rat liver CDO and cysteine derivatives to elucidate structural parameters involved in substrate recognition and x-ray absorption spectroscopy to probe the interaction of the active site iron center with cysteine. Kinetic studies using cysteine structural analogs show that most are inhibitors and that a terminal functional group bearing a negative charge (e.g. a carboxylate) is required for binding. The substrate-binding site has no stringent restrictions with respect to the size of the amino acid. Lack of the amino or carboxyl groups at the alpha-carbon does not prevent the molecules from interacting with the active site. In fact, cysteamine is shown to be a potent activator of the enzyme without being a substrate. CDO was also rendered inactive upon complexation with the metal-binding inhibitors azide and cyanide. Unlike many non-heme iron dioxygenases that employ alpha-keto acids as cofactors, CDO was shown to be the only dioxygenase known to be inhibited by alpha-ketoglutarate.

Analysis of digitalis genin receptor site in Na,K-ATPase

International Nuclear Information System (INIS)

Ahmed, K.; McParland, R.; Becker, R.; From, A.; Fullerton, D.S.

1987-01-01

Na,K-ATPase is believed to be the receptor for digitalis glycosides, with binding site located in the α-subunit. To identify this binding site, the enzyme was covalently labeled with a photoactive probe localized in C17 side group of the cardenolide ([ 3 H]24-azidodigitoxoside). 3 H-labeled α-subunit was purified, and subjected to trypsin digestion. Fractions containing 3 H-labeled material were pooled. Amino acid sequence analysis of this material suggested the presence of two peptides (residues 68-146; residues 263-342). Additional studies have employed purification of the 3 H-labeled material by chromatography on Sepharose-6B, and CNBr cleavage followed by chromatography on hydroxylapatite. Amino acid sequence analysis of the purified 3 H-labeled peptide thus isolated indicated sequence containing amino acid residues 263-342. These data suggest that this is the peptide containing the digitalis genin binding site, and rule out such a role for the other peptide (amino acids 68 - 146). Preliminary data also hint that binding of the 3 H-probe occurs at the leu residue in the sequence glu tyr thr try leu glu .. present in the peptide containing residues 263 - 342

Determination of acid–base properties of HCl acid activated palygorskite by Potentiometrie titration

OpenAIRE

N. FriniSrasra; E.Srasra

2008-01-01

The surface acidity of raw and acid activated palygorskite clay were studied by acid-base potentiometric titration. The Gran plot method was applied for the hydroxide titration and the total surface site (Hs) and the average number of protons reacted per surface site (Z) of palygorskite samples at a given ionic strength were calculated. Acid treatment increases the clay acidity and modifies its surface charge. The point of zero charge value, determined by the common crossing point of Z vs pH ...

Comparative study of the active sites in zeolites by different probe molecules

Directory of Open Access Journals (Sweden)

ALINE AUROUX

2005-03-01

Full Text Available This review summarizes some of the recently published results concerning the acid sites in the zeolites ZSM-5 and Y studied by temperature-programmed desorption (TPD and adsorption calorimetry using different probe molecules NH3, CO, N2O and n-hexane. For the first time it has been shown that the acid sites in hydrated zeolites are accessible for n-hexane adsorption

Development of METAL-ACTIVE SITE and ZINCCLUSTER tool to predict active site pockets.

Science.gov (United States)

Ajitha, M; Sundar, K; Arul Mugilan, S; Arumugam, S

2018-03-01

The advent of whole genome sequencing leads to increasing number of proteins with known amino acid sequences. Despite many efforts, the number of proteins with resolved three dimensional structures is still low. One of the challenging tasks the structural biologists face is the prediction of the interaction of metal ion with any protein for which the structure is unknown. Based on the information available in Protein Data Bank, a site (METALACTIVE INTERACTION) has been generated which displays information for significant high preferential and low-preferential combination of endogenous ligands for 49 metal ions. User can also gain information about the residues present in the first and second coordination sphere as it plays a major role in maintaining the structure and function of metalloproteins in biological system. In this paper, a novel computational tool (ZINCCLUSTER) is developed, which can predict the zinc metal binding sites of proteins even if only the primary sequence is known. The purpose of this tool is to predict the active site cluster of an uncharacterized protein based on its primary sequence or a 3D structure. The tool can predict amino acids interacting with a metal or vice versa. This tool is based on the occurrence of significant triplets and it is tested to have higher prediction accuracy when compared to that of other available techniques. © 2017 Wiley Periodicals, Inc.

From Unnatural Amino Acid Incorporation to Artificial Metalloenzymes

KAUST Repository

Makki, Arwa

2016-01-01

This thesis explores a novel strategy based on the site-selective incorporation of unnatural, metal binding amino acids into a host protein. The unnatural amino acids can either serve directly as metal binding centers can

Ligand exchange chromatography of free amino acids and proteins on porous microparticulate zirconium oxide

International Nuclear Information System (INIS)

Blackwell, J.A.; Carr, P.W.

1992-01-01

The Lewis acid sites present on the underlying zirconium oxide particles are responsible for the unusual elution sequence for amino acids on copper loaded, phosphated zirconium oxide supports reported in an earlier study. To more thoroughly examine the effect of these strong Lewis acid sites in this paper. The authors have studied ligand exchange chromatography on copper loaded zirconium oxide particles. It is shown here that carboxylate functional groups on amino acid solutes strongly interact with surface Lewis acid sites. Addition of competing hard Lewis bases to the eluent attenuates these specific interactions. The result is a chromatographic system with high selectivity which is also suitable for ligand exchange chromatography of proteins

Fatty acid composition and amino acid profile of two freshwater ...

African Journals Online (AJOL)

The proximate, fatty and amino acids composition of two commercially important freshwater fish species Clarias gariepinus and Tilapia zillii. purchased from local fishermen in two landing sites in Lagos State, Nigeria were determined. Live specimens of C. gariepinus were purchased while samples of T. zillii were stored in ...

Biosynthesis of N-glycolyneuraminic acid. The primary site of hydroxylation of N-acetylneuraminic acid is the cytosolic sugar nucleotide pool

Energy Technology Data Exchange (ETDEWEB)

Muchmore, E.A.; Milewski, M.; Varki, A.; Diaz, S. (San Diego Veterans Administration Medical Center, CA (USA))

1989-12-05

N-Glycolylneuraminic acid (Neu5Gc) is an oncofetal antigen in humans and is developmentally regulated in rodents. We have explored the biology of N-acetylneuraminic acid hydroxylase, the enzyme responsible for conversion of the parent sialic acid, N-acetylneuraminic acid (Neu5Ac) to Neu5Gc. We show that the major sialic acid in all compartments of murine myeloma cell lines is Neu5Gc. Pulse-chase analysis in these cells with the sialic acid precursor (6-3H)N-acetylmannosamine demonstrates that most of the newly synthesized Neu5Gc appears initially in the cytosolic low-molecular weight pool bound to CMP. The percentage of Neu5Gc on membrane-bound sialic acids closely parallels that in the CMP-bound pool at various times of chase, whereas that in the free sialic acid pool is very low initially, and rises only later during the chase. This implies that conversion from Neu5Ac to Neu5Gc occurs primarily while Neu5Ac is in its sugar nucleotide form. In support of this, the hydroxylase enzyme from a variety of tissues and cells converted CMP-Neu5Ac to CMP-Neu5Gc, but showed no activity towards free or alpha-glycosidically bound Neu5Ac. Furthermore, the majority of the enzyme activity is found in the cytosol. Studies with isolated intact Golgi vesicles indicate that CMP-Neu5Gc can be transported and utilized for transfer of Neu5Gc to glycoconjugates. The general properties of the enzyme have also been investigated. The Km for CMP-Neu5Ac is in the range of 0.6-2.5 microM. No activity can be detected against the beta-methylglycoside of Neu5Ac. On the other hand, inhibition studies suggest that the enzyme recognizes both the 5'-phosphate group and the pyrimidine base of the substrate. Taken together, the data allow us to propose pathways for the biosynthesis and reutilization of Neu5Gc.

Dual-mode fluorophore-doped nickel nitrilotriacetic acid-modified silica nanoparticles combine histidine-tagged protein purification with site-specific fluorophore labeling.

Science.gov (United States)

Kim, Sung Hoon; Jeyakumar, M; Katzenellenbogen, John A

2007-10-31

We present the first example of a fluorophore-doped nickel chelate surface-modified silica nanoparticle that functions in a dual mode, combining histidine-tagged protein purification with site-specific fluorophore labeling. Tetramethylrhodamine (TMR)-doped silica nanoparticles, estimated to contain 700-900 TMRs per ca. 23 nm particle, were surface modified with nitrilotriacetic acid (NTA), producing TMR-SiO2-NTA-Ni2+. Silica-embedded TMR retains very high quantum yield, is resistant to quenching by buffer components, and is modestly quenched and only to a certain depth (ca. 2 nm) by surface-attached Ni2+. When exposed to a bacterial lysate containing estrogen receptor alpha ligand binding domain (ERalpha) as a minor component, these beads showed very high specificity binding, enabling protein purification in one step. The capacity and specificity of these beads for binding a his-tagged protein were characterized by electrophoresis, radiometric counting, and MALDI-TOF MS. ERalpha, bound to TMR-SiO2-NTA-Ni++ beads in a site-specific manner, exhibited good activity for ligand binding and for ligand-induced binding to coactivators in solution FRET experiments and protein microarray fluorometric and FRET assays. This dual-mode type TMR-SiO2-NTA-Ni2+ system represents a powerful combination of one-step histidine-tagged protein purification and site-specific labeling with multiple fluorophore species.

Synthesis of acid-base bifunctional mesoporous materials by oxidation and thermolysis

Energy Technology Data Exchange (ETDEWEB)

Yu, Xiaofang [College of Chemistry, Jilin University, Jiefang Road 2519, Changchun 130023 (China); Zou, Yongcun [State Key Laboratory of Inoranic Synthesis and Preparative Chemistryg, College of Chemistry, Jilin University, Changchun 130012 (China); Wu, Shujie; Liu, Heng [College of Chemistry, Jilin University, Jiefang Road 2519, Changchun 130023 (China); Guan, Jingqi, E-mail: guanjq@jlu.edu.cn [College of Chemistry, Jilin University, Jiefang Road 2519, Changchun 130023 (China); Kan, Qiubin, E-mail: qkan@jlu.edu.cn [College of Chemistry, Jilin University, Jiefang Road 2519, Changchun 130023 (China)

2011-06-15

Graphical abstract: A novel and efficient method has been developed for the synthesis of acid-base bifunctional catalyst. The obtained sample of SO{sub 3}H-MCM-41-NH{sub 2} containing amine and sulfonic acids exhibits excellent catalytic activity in aldol condensation reaction. Research highlights: {yields} Synthesize acid-base bifunctional mesoporous materials SO{sub 3}H-MCM-41-NH{sub 2}. {yields} Oxidation and then thermolysis to generate acidic site and basic site. {yields} Exhibit good catalytic performance in aldol condensation reaction between acetone and various aldehydes. -- Abstract: A novel and efficient method has been developed for the synthesis of acid-base bifunctional catalyst SO{sub 3}H-MCM-41-NH{sub 2}. This method was achieved by co-condensation of tetraethylorthosilicate (TEOS), 3-mercaptopropyltrimethoxysilane (MPTMS) and (3-triethoxysilylpropyl) carbamicacid-1-methylcyclohexylester (3TAME) in the presence of cetyltrimethylammonium bromide (CTAB), followed by oxidation and then thermolysis to generate acidic site and basic site. X-ray diffraction (XRD) and transmission electron micrographs (TEM) show that the resultant materials keep mesoporous structure. Thermogravimetric analysis (TGA), X-ray photoelectron spectra (XPS), back titration, solid-state {sup 13}C CP/MAS NMR and solid-state {sup 29}Si MAS NMR confirm that the organosiloxanes were condensed as a part of the silica framework. The bifunctional sample (SO{sub 3}H-MCM-41-NH{sub 2}) containing amine and sulfonic acids exhibits excellent acid-basic properties, which make it possess high activity in aldol condensation reaction between acetone and various aldehydes.

Structure of a highly acidic β-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs+-selective binding site

International Nuclear Information System (INIS)

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Matsumoto, Fumiko; Shibazaki, Chie; Shimizu, Rumi; Yamada, Mitsugu; Adachi, Motoyasu; Tamada, Taro; Kawamoto, Masahide; Tokunaga, Hiroko; Ishibashi, Matsujiro; Blaber, Michael; Tokunaga, Masao; Kuroki, Ryota

2015-01-01

The tertiary structure of a β-lactamase derived from the halobacterium Chromohalobacter sp. 560 (HaBLA) was determined by X-ray crystallography. Three unique Sr 2+ -binding sites and one Cs + -binding site were discovered in the HaBLA molecule. Environmentally friendly absorbents are needed for Sr 2+ and Cs + , as the removal of the radioactive Sr 2+ and Cs + that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs + or Sr 2+ . The crystal structure of a halophilic β-lactamase from Chromohalobacter sp. 560 (HaBLA) was determined to resolutions of between 1.8 and 2.9 Å in space group P3 1 using X-ray crystallography. Moreover, the locations of bound Sr 2+ and Cs + ions were identified by anomalous X-ray diffraction. The location of one Cs + -specific binding site was identified in HaBLA even in the presence of a ninefold molar excess of Na + (90 mM Na + /10 mM Cs + ). From an activity assay using isothermal titration calorimetry, the bound Sr 2+ and Cs + ions do not significantly affect the enzymatic function of HaBLA. The observation of a selective and high-affinity Cs + -binding site provides important information that is useful for the design of artificial Cs + -binding sites that may be useful in the bioremediation of radioactive isotopes

Evaluation of Fe(II) oxidation at an acid mine drainage site using laboratory-scale reactors

Science.gov (United States)

Brown, Juliana; Burgos, William

2010-05-01

Acid mine drainage (AMD) is a severe environmental threat to the Appalachian region of the Eastern United States. The Susquehanna and Potomac River basins of Pennsylvania drain to the Chesapeake Bay, which is heavily polluted by acidity and metals from AMD. This study attempted to unravel the complex relationships between AMD geochemistry, microbial communities, hydrodynamic conditions, and the mineral precipitates for low-pH Fe mounds formed downstream of deep mine discharges, such as Lower Red Eyes in Somerset County, PA, USA. This site is contaminated with high concentrations of Fe (550 mg/L), Mn (115 mg/L), and other trace metals. At the site 95% of dissolved Fe(II) and 56% of total dissolved Fe is removed without treatment, across the mound, but there is no change in the concentration of trace metals. Fe(III) oxides were collected across the Red Eyes Fe mound and precipitates were analyzed by X-ray diffraction, electron microscopy and elemental analysis. Schwertmannite was the dominant mineral phase with traces of goethite. The precipitates also contained minor amounts of Al2O3, MgO,and P2O5. Laboratory flow-through reactors were constructed to quantify Fe(II) oxidation and Fe removal over time at terrace and pool depositional facies. Conditions such as residence time, number of reactors in sequence and water column height were varied to determine optimal conditions for Fe removal. Reactors with sediments collected from an upstream terrace oxidized more than 50% of dissolved Fe(II) at a ten hour residence time, while upstream pool sediments only oxidized 40% of dissolved Fe(II). Downstream terrace and pool sediments were only capable of oxidizing 25% and 20% of Fe(II), respectively. Fe(II) oxidation rates measured in the reactors were determined to be between 3.99 x 10-8and 1.94 x 10-7mol L-1s-1. The sediments were not as efficient for total dissolved Fe removal and only 25% was removed under optimal conditions. The removal efficiency for all sediments

Biosynthesis of N-glycolyneuraminic acid. The primary site of hydroxylation of N-acetylneuraminic acid is the cytosolic sugar nucleotide pool.

Science.gov (United States)

Muchmore, E A; Milewski, M; Varki, A; Diaz, S

1989-12-05

N-Glycolylneuraminic acid (Neu5Gc) is an oncofetal antigen in humans and is developmentally regulated in rodents. We have explored the biology of N-acetylneuraminic acid hydroxylase, the enzyme responsible for conversion of the parent sialic acid, N-acetylneuraminic acid (Neu5Ac) to Neu5Gc. We show that the major sialic acid in all compartments of murine myeloma cell lines is Neu5Gc. Pulse-chase analysis in these cells with the sialic acid precursor [6-3H]N-acetylmannosamine demonstrates that most of the newly synthesized Neu5Gc appears initially in the cytosolic low-molecular weight pool bound to CMP. The percentage of Neu5Gc on membrane-bound sialic acids closely parallels that in the CMP-bound pool at various times of chase, whereas that in the free sialic acid pool is very low initially, and rises only later during the chase. This implies that conversion from Neu5Ac to Neu5Gc occurs primarily while Neu5Ac is in its sugar nucleotide form. In support of this, the hydroxylase enzyme from a variety of tissues and cells converted CMP-Neu5Ac to CMP-Neu5Gc, but showed no activity towards free or alpha-glycosidically bound Neu5Ac. Furthermore, the majority of the enzyme activity is found in the cytosol. Studies with isolated intact Golgi vesicles indicate that CMP-Neu5Gc can be transported and utilized for transfer of Neu5Gc to glycoconjugates. The general properties of the enzyme have also been investigated. The Km for CMP-Neu5Ac is in the range of 0.6-2.5 microM. No activity can be detected against the beta-methylglycoside of Neu5Ac. On the other hand, inhibition studies suggest that the enzyme recognizes both the 5'-phosphate group and the pyrimidine base of the substrate. Taken together, the data allow us to propose pathways for the biosynthesis and reutilization of Neu5Gc, with initial conversion from Neu5Ac occurring primarily at the level of the sugar nucleotide. Subsequent release and reutilization of Neu5Gc could then account for the higher steady-state level

Site-selective {sup 13}C labeling of proteins using erythrose

Energy Technology Data Exchange (ETDEWEB)

Weininger, Ulrich, E-mail: ulrich.weininger@physik.uni-halle.de [Lund University, Department of Biophysical Chemistry, Center for Molecular Protein Science (Sweden)

2017-03-15

NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with {sup 13}C and/or {sup 1}H, which is achieved in the most general way by using site-selectively {sup 13}C-enriched glucose (1- and 2-{sup 13}C) as the carbon source in bacterial expression systems. Using this strategy, multiple sites in side chains, including aromatics, become site-selectively labeled and suitable for relaxation studies. Here we systematically investigate the use of site-selectively {sup 13}C-enriched erythrose (1-, 2-, 3- and 4-{sup 13}C) as a suitable precursor for {sup 13}C labeled aromatic side chains. We quantify {sup 13}C incorporation in nearly all sites in all 20 amino acids and compare the results to glucose based labeling. In general the erythrose approach results in more selective labeling. While there is only a minor gain for phenylalanine and tyrosine side-chains, the {sup 13}C incorporation level for tryptophan is at least doubled. Additionally, the Phe ζ and Trp η2 positions become labeled. In the aliphatic side chains, labeling using erythrose yields isolated {sup 13}C labels for certain positions, like Ile β and His β, making these sites suitable for dynamics studies. Using erythrose instead of glucose as a source for site-selective {sup 13}C labeling enables unique or superior labeling for certain positions and is thereby expanding the toolbox for customized isotope labeling of amino-acid side-chains.

Silica-supported sulfonic acids as recyclable catalyst for esterification of levulinic acid with stoichiometric amounts of alcohols

Directory of Open Access Journals (Sweden)

Raimondo Maggi

2016-10-01

Full Text Available Converting biomass into value-added chemicals holds the key to sustainable long-term carbon resource management. In this context, levulinic acid, which is easily obtained from cellulose, is valuable since it can be transformed into a variety of industrially relevant fine chemicals. Here we present a simple protocol for the selective esterification of levulinic acid using solid acid catalysts. Silica supported sulfonic acid catalysts operate under mild conditions and give good conversion and selectivity with stoichiometric amounts of alcohols. The sulfonic acid groups are tethered to the support using organic tethers. These tethers may help in preventing the deactivation of the active sites in the presence of water.

Analysis of digitalis genin receptor site in Na,K-ATPase

Energy Technology Data Exchange (ETDEWEB)

Ahmed, K.; McParland, R.; Becker, R.; From, A.; Fullerton, D.S.

1987-05-01

Na,K-ATPase is believed to be the receptor for digitalis glycosides, with binding site located in the ..cap alpha..-subunit. To identify this binding site, the enzyme was covalently labeled with a photoactive probe localized in C17 side group of the cardenolide ((/sup 3/H)24-azidodigitoxoside). /sup 3/H-labeled ..cap alpha..-subunit was purified, and subjected to trypsin digestion. Fractions containing /sup 3/H-labeled material were pooled. Amino acid sequence analysis of this material suggested the presence of two peptides (residues 68-146; residues 263-342). Additional studies have employed purification of the /sup 3/H-labeled material by chromatography on Sepharose-6B, and CNBr cleavage followed by chromatography on hydroxylapatite. Amino acid sequence analysis of the purified /sup 3/H-labeled peptide thus isolated indicated sequence containing amino acid residues 263-342. These data suggest that this is the peptide containing the digitalis genin binding site, and rule out such a role for the other peptide (amino acids 68 - 146). Preliminary data also hint that binding of the /sup 3/H-probe occurs at the leu residue in the sequence glu tyr thr try leu glu .. present in the peptide containing residues 263 - 342.

Inhibiting Effect of Nicotinic Acid Hydrazide on Corrosion of Aluminum and Mild Steel in Acidic Medium

Energy Technology Data Exchange (ETDEWEB)

Bhat, J. Ishwara [Mangalore Univ., Karnataka (India); Alva, Vijaya D. P. [Shree Devi Institute of Technology, Karnataka (India)

2014-02-15

The corrosion behavior of aluminum and mild steel in hydrochloric acid medium was studied using a nicotinic acid hydrazide as inhibitor by potentiodynamic polarization, electrochemical impedance spectroscopy technique and gravimetric methods. The effects of inhibitor concentration and temperature were investigated. The experimental results suggested, nicotinic acid hydrazide is a good corrosion inhibitor for both aluminum and mild steel in hydrochloric acid medium and the inhibition efficiency increased with increase in the inhibitor concentration. The polarization studies revealed that nicotinic acid hydrazide exhibits mixed type of inhibition. The inhibition was assumed to occur via adsorption of the inhibitor molecules on the aluminum and mild steel surface and inhibits corrosion by blocking the reaction sites on the surface of aluminum.

Inhibiting Effect of Nicotinic Acid Hydrazide on Corrosion of Aluminum and Mild Steel in Acidic Medium

International Nuclear Information System (INIS)

Bhat, J. Ishwara; Alva, Vijaya D. P.

2014-01-01

The corrosion behavior of aluminum and mild steel in hydrochloric acid medium was studied using a nicotinic acid hydrazide as inhibitor by potentiodynamic polarization, electrochemical impedance spectroscopy technique and gravimetric methods. The effects of inhibitor concentration and temperature were investigated. The experimental results suggested, nicotinic acid hydrazide is a good corrosion inhibitor for both aluminum and mild steel in hydrochloric acid medium and the inhibition efficiency increased with increase in the inhibitor concentration. The polarization studies revealed that nicotinic acid hydrazide exhibits mixed type of inhibition. The inhibition was assumed to occur via adsorption of the inhibitor molecules on the aluminum and mild steel surface and inhibits corrosion by blocking the reaction sites on the surface of aluminum

Food deprivation modulates gamma-aminobutyric acid receptors and peripheral benzodiazepine binding sites in rats.

Science.gov (United States)

Weizman, A; Bidder, M; Fares, F; Gavish, M

1990-12-03

The effect of 5 days of food deprivation followed by 5 days of refeeding on gamma-aminobutyric acid (GABA) receptors, central benzodiazepine receptors (CBR), and peripheral benzodiazepine binding sites (PBzS) was studied in female Sprague-Dawley rats. Starvation induced a decrease in the density of PBzS in peripheral organs: adrenal (35%; P less than 0.001), kidney (33%; P less than 0.01), and heart (34%; P less than 0.001). Restoration of [3H]PK 11195 binding to normal values was observed in all three organs after 5 days of refeeding. The density of PBzS in the ovary, pituitary, and hypothalamus was not affected by starvation. Food deprivation resulted in a 35% decrease in cerebellar GABA receptors (P less than 0.01), while CBR in the hypothalamus and cerebral cortex remained unaltered. The changes in PBzS observed in the heart and kidney may be related to the long-term metabolic stress associated with starvation and to the functional changes occurring in these organs. The down-regulation of the adrenal PBzS is attributable to the suppressive effect of hypercortisolemia on pituitary ACTH release. The reduction in cerebellar GABA receptors may be an adaptive response to food deprivation stress and may be relevant to the proaggressive effect of hunger.

Influence of porous texture and surface chemistry on the CO₂ adsorption capacity of porous carbons: acidic and basic site interactions.

Science.gov (United States)

Sánchez-Sánchez, Angela; Suárez-García, Fabián; Martínez-Alonso, Amelia; Tascón, Juan M D

2014-12-10

Doped porous carbons exhibiting highly developed porosity and rich surface chemistry have been prepared and subsequently applied to clarify the influence of both factors on carbon dioxide capture. Nanocasting was selected as synthetic route, in which a polyaramide precursor (3-aminobenzoic acid) was thermally polymerized inside the porosity of an SBA-15 template in the presence of different H3PO4 concentrations. The surface chemistry and the porous texture of the carbons could be easily modulated by varying the H3PO4 concentration and carbonization temperature. Porous texture was found to be the determinant factor on carbon dioxide adsorption at 0 °C, while surface chemistry played an important role at higher adsorption temperatures. We proved that nitrogen functionalities acted as basic sites and oxygen and phosphorus groups as acidic ones toward adsorption of CO2 molecules. Among the nitrogen functional groups, pyrrolic groups exhibited the highest influence, while the positive effect of pyridinic and quaternary functionalities was smaller. Finally, some of these N-doped carbons exhibit CO2 heats of adsorption higher than 42 kJ/mol, which make them excellent candidates for CO2 capture.

Anatomical and pharmacological characterization of excitatory amino acid receptors

International Nuclear Information System (INIS)

Monaghan, D.T.

1985-01-01

The majority of the excitatory neurotransmission in the vertebrate Central Nervous System is thought to be mediated by acidic amino acid neurotransmitters. However, relatively little is known about the excitatory amino acid receptors and their distribution within the CNS. By analyzing radioligand binding to purified synaptic plasma membranes and to thin tissue sections processed for autoradiography, multiple distinct binding sites were found. These binding sites exhibited the pharmacological properties indicative of the excitatory amino acid receptors, which had been identified by electrophysiological techniques. Specifically, L-[ 3 H]-glutamate and D-[ 3 H]-amino-5-phosphonopentanoate appear to label N-methyl-D-aspartate receptors, L-[ 3 H]-glutamate and [ 3 H]-kainic acid appear to label kainic acid receptors, and L-[ 3 H]-glutamate and [ 3 H]-amino-3-hydroxy-5-methyl-4-isoxazolepropionate appear to label quisqualate receptors. Together, these results confirm the three receptor scheme proposed for excitatory amino acid neurotransmission. These results also show that these transmitter-receptor systems are differentially distributed in the brain, and that the total distribution is consistent with that found by other markers for excitatory amino acid-using neurons

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

Science.gov (United States)

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.

Acid Sulfate Alteration on Mars

Science.gov (United States)

Ming, D. W.; Morris, R. V.

2016-01-01

A variety of mineralogical and geochemical indicators for aqueous alteration on Mars have been identified by a combination of surface and orbital robotic missions, telescopic observations, characterization of Martian meteorites, and laboratory and terrestrial analog studies. Acid sulfate alteration has been identified at all three landing sites visited by NASA rover missions (Spirit, Opportunity, and Curiosity). Spirit landed in Gusev crater in 2004 and discovered Fe-sulfates and materials that have been extensively leached by acid sulfate solutions. Opportunity landing on the plains of Meridiani Planum also in 2004 where the rover encountered large abundances of jarosite and hematite in sedimentary rocks. Curiosity landed in Gale crater in 2012 and has characterized fluvial, deltaic, and lacustrine sediments. Jarosite and hematite were discovered in some of the lacustrine sediments. The high elemental abundance of sulfur in surface materials is obvious evidence that sulfate has played a major role in aqueous processes at all landing sites on Mars. The sulfate-rich outcrop at Meridiani Planum has an SO3 content of up to 25 wt.%. The interiors of rocks and outcrops on the Columbia Hills within Gusev crater have up to 8 wt.% SO3. Soils at both sites generally have between 5 to 14 wt.% SO3, and several soils in Gusev crater contain around 30 wt.% SO3. After normalization of major element compositions to a SO3-free basis, the bulk compositions of these materials are basaltic, with a few exceptions in Gusev crater and in lacustrine mudstones in Gale crater. These observations suggest that materials encountered by the rovers were derived from basaltic precursors by acid sulfate alteration under nearly isochemical conditions (i.e., minimal leaching). There are several cases, however, where acid sulfate alteration minerals (jarosite and hematite) formed in open hydrologic systems, e.g., in Gale crater lacustrine mudstones. Several hypotheses have been suggested for the

Structure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exit Channel.

Science.gov (United States)

Bera, Asim K; Aukema, Kelly G; Elias, Mikael; Wackett, Lawrence P

2017-03-27

Cyanuric acid hydrolases are of industrial importance because of their use in aquatic recreational facilities to remove cyanuric acid, a stabilizer for the chlorine. Degradation of excess cyanuric acid is necessary to maintain chlorine disinfection in the waters. Cyanuric acid hydrolase opens the cyanuric acid ring hydrolytically and subsequent decarboxylation produces carbon dioxide and biuret. In the present study, we report the X-ray structure of TrzD, a cyanuric acid hydrolase from Acidovorax citrulli. The crystal structure at 2.19 Å resolution shows a large displacement of the catalytic lysine (Lys163) in domain 2 away from the active site core, whereas the two other active site lysines from the two other domains are not able to move. The lysine displacement is proposed here to open up a channel for product release. Consistent with that, the structure also showed two molecules of the co-product, carbon dioxide, one in the active site and another trapped in the proposed exit channel. Previous data indicated that the domain 2 lysine residue plays a role in activating an adjacent serine residue carrying out nucleophilic attack, opening the cyanuric acid ring, and the mobile lysine guides products through the exit channel.

Thioesterase activity and acyl-CoA/fatty acid cross-talk of hepatocyte nuclear factor-4{alpha}.

Science.gov (United States)

Hertz, Rachel; Kalderon, Bella; Byk, Tamara; Berman, Ina; Za'tara, Ghadeer; Mayer, Raphael; Bar-Tana, Jacob

2005-07-01

Hepatocyte nuclear factor-4alpha (HNF-4alpha) activity is modulated by natural and xenobiotic fatty acid and fatty acyl-CoA ligands as a function of their chain length, unsaturation, and substitutions. The acyl-CoA site of HNF-4alpha is reported here to consist of the E-F domain, to bind long-chain acyl-CoAs but not the respective free acids, and to catalyze the hydrolysis of bound fatty acyl-CoAs. The free acid pocket, previously reported in the x-ray structure of HNF-4alpha E-domain, entraps fatty acids but excludes acyl-CoAs. The acyl-CoA and free acid sites are distinctive and noncongruent. Free fatty acid products of HNF-4alpha thioesterase may exchange with free acids entrapped in the fatty acid pocket of HNF-4alpha. Cross-talk between the acyl-CoA and free fatty acid binding sites is abrogated by high affinity, nonhydrolyzable acyl-CoA ligands of HNF-4alpha that inhibit its thioesterase activity. Hence, HNF-4alpha transcriptional activity is controlled by its two interrelated acyl ligands and two binding sites interphased in tandem by the thioesterase activity. The acyl-CoA/free-acid and receptor/enzyme duality of HNF-4alpha extends the paradigm of nuclear receptors.

Direct NO decomposition over stepped transition-metal surfaces

DEFF Research Database (Denmark)

Falsig, Hanne; Bligaard, Thomas; Christensen, Claus H.

2007-01-01

We establish the full potential energy diagram for the direct NO decomposition reaction over stepped transition-metal surfaces by combining a database of adsorption energies on stepped metal surfaces with known Bronsted-Evans-Polanyi (BEP) relations for the activation barriers of dissociation...

Scanning mutagenesis of the amino acid sequences flanking phosphorylation site 1 of the mitochondrial pyruvate dehydrogenase complex

Directory of Open Access Journals (Sweden)

Nagib eAhsan

2012-07-01

Full Text Available The mitochondrial pyruvate dehydrogenase complex is regulated by reversible seryl-phosphorylation of the E1α subunit by a dedicated, intrinsic kinase. The phospho-complex is reactivated when dephosphorylated by an intrinsic PP2C-type protein phosphatase. Both the position of the phosphorylated Ser-residue and the sequences of the flanking amino acids are highly conserved. We have used the synthetic peptide-based kinase client assay plus recombinant pyruvate dehydrogenase E1α and E1α-kinase to perform scanning mutagenesis of the residues flanking the site of phosphorylation. Consistent with the results from phylogenetic analysis of the flanking sequences, the direct peptide-based kinase assays tolerated very few changes. Even conservative changes such as Leu, Ile, or Val for Met, or Glu for Asp, gave very marked reductions in phosphorylation. Overall the results indicate that regulation of the mitochondrial pyruvate dehydrogenase complex by reversible phosphorylation is an extreme example of multiple, interdependent instances of co-evolution.

Effects of mutagenesis of aspartic acid residues in the putative phosphoribosyl diphosphate binding site of Escherichia coli phosphoribosyl diphosphate synthetase on metal ion specificity and ribose-5-phosphate binding

DEFF Research Database (Denmark)

Willemoës, Martin; Nilsson, Dan; Hove-Jensen, Bjarne

1996-01-01

The three conserved aspartic acid residues of the 5-phospho-d-ribosyl a-1-diphosphate binding site (213-GRDCVLVDDMIDTGGT-228) of Escherichia coli phosphoribosyl diphosphate synthetase were studied by analysis of the mutant enzymes D220E, D220F, D221A, D224A, and D224S. The mutant enzymes showed...... enzymes were dependent on the metal ion present, suggesting a function of the investigated aspartic acid residues both in the binding of ribose 5-phosphate, possibly via a divalent metal ion, and in the interaction with a divalent metal ion during catalysis....

Sugar-binding sites of the HA1 subcomponent of Clostridium botulinum type C progenitor toxin.

Science.gov (United States)

Nakamura, Toshio; Tonozuka, Takashi; Ide, Azusa; Yuzawa, Takayuki; Oguma, Keiji; Nishikawa, Atsushi

2008-02-22

Clostridium botulinum type C 16S progenitor toxin contains a hemagglutinin (HA) subcomponent, designated HA1, which appears to play an important role in the effective internalization of the toxin in gastrointestinal epithelial cells and in creating a broad specificity for the oligosaccharide structure that corresponds to various targets. In this study, using the recombinant protein fused to glutathione S-transferase, we investigated the binding specificity of the HA1 subcomponent to sugars and estimated the binding sites of HA1 based on X-ray crystallography and soaking experiments using various sugars. N-Acetylneuraminic acid, N-acetylgalactosamine, and galactose effectively inhibited the binding that occurs between glutathione S-transferase-HA1 and mucins, whereas N-acetylglucosamine and glucose did not inhibit it. The crystal structures of HA1 complex with N-acetylneuraminic acid, N-acetylgalactosamine, and galactose were also determined. There are two sugar-binding sites, sites I and II. Site I corresponds to the electron densities noted for all sugars and is located at the C-terminal beta-trefoil domain, while site II corresponds to the electron densities noted only for galactose. An aromatic amino acid residue, Trp176, at site I has a stacking interaction with the hexose ring of the sugars. On the other hand, there is no aromatic residue at site II; thus, the interaction with galactose seems to be poor. The double mutant W176A at site I and D271F at site II has no avidity for N-acetylneuraminic acid but has avidity for galactose. In this report, the binding specificity of botulinum C16S toxin HA1 to various sugars is demonstrated based on its structural features.

Acidity characterization of a titanium and sulfate modified vermiculite

International Nuclear Information System (INIS)

Hernandez, W.Y.; Centeno, M.A.; Odriozola, J.A.; Moreno, S.; Molina, R.

2008-01-01

A natural vermiculite has been modified with titanium and sulfated by the intercalation and impregnation method in order to optimize the acidity of the clay mineral, and characterization of samples were analyzed by X-ray fluorescence (XRF), X-ray diffraction (XRD), nitrogen adsorption isotherms, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) and temperature programmed desorption with ammonia (TPD-NH 3 ). All the modified solids have a significantly higher number of acidic sites with respect to the parent material and in all of these, Broensted as well as Lewis acidity are identified. The presence of sulfate appears not to increase the number of acidic centers in the modified clay. For the materials sulfated with the intercalation method, it is observed that the strength of the acidic sites found in the material increases with the nominal sulfate/metal ratio. Nevertheless, when elevated quantities of sulfur are deposited, diffusion problems in the heptane reaction appear

Chemical characteristics of dicarboxylic acids and related organic compounds in PM2.5 during biomass-burning and non-biomass-burning seasons at a rural site of Northeast China.

Science.gov (United States)

Cao, Fang; Zhang, Shi-Chun; Kawamura, Kimitaka; Liu, Xiaoyan; Yang, Chi; Xu, Zufei; Fan, Meiyi; Zhang, Wenqi; Bao, Mengying; Chang, Yunhua; Song, Wenhuai; Liu, Shoudong; Lee, Xuhui; Li, Jun; Zhang, Gan; Zhang, Yan-Lin

2017-12-01

Fine particulate matter (PM2.5) samples were collected using a high-volume air sampler and pre-combusted quartz filters during May 2013 to January 2014 at a background rural site (47 ∘ 35 N, 133 ∘ 31 E) in Sanjiang Plain, Northeast China. A homologous series of dicarboxylic acids (C 2 -C 11 ) and related compounds (oxoacids, α-dicarbonyls and fatty acids) were analyzed by using a gas chromatography (GC) and GC-MS method employing a dibutyl ester derivatization technique. Intensively open biomass-burning (BB) episodes during the harvest season in fall were characterized by high mass concentrations of PM2.5, dicarboxylic acids and levoglucosan. During the BB period, mass concentrations of dicarboxylic acids and related compounds were increased by up to >20 times with different factors for different organic compounds (i.e., succinic (C 4 ) acid > oxalic (C 2 ) acid > malonic (C 3 ) acid). High concentrations were also found for their possible precursors such as glyoxylic acid (ωC 2 ), 4-oxobutanoic acid, pyruvic acid, glyoxal, and methylglyoxal as well as fatty acids. Levoglucosan showed strong correlations with carbonaceous aerosols (OC, EC, WSOC) and dicarboxylic acids although such good correlations were not observed during non-biomass-burning seasons. Our results clearly demonstrate biomass burning emissions are very important contributors to dicarboxylic acids and related compounds. The selected ratios (e.g., C 3 /C 4 , maleic acid/fumaric acid, C 2 /ωC 2 , and C 2 /levoglucosan) were used as tracers for secondary formation of organic aerosols and their aging process. Our results indicate that organic aerosols from biomass burning in this study are fresh without substantial aging or secondary production. The present chemical characteristics of organic compounds in biomass-burning emissions are very important for better understanding the impacts of biomass burning on the atmosphere aerosols. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fundamental thermochemical properties of amino acids: gas-phase and aqueous acidities and gas-phase heats of formation.

Science.gov (United States)

Stover, Michele L; Jackson, Virgil E; Matus, Myrna H; Adams, Margaret A; Cassady, Carolyn J; Dixon, David A

2012-03-08

The gas-phase acidities of the 20 L-amino acids have been predicted at the composite G3(MP2) level. A broad range of structures of the neutral and anion were studied to determine the lowest energy conformer. Excellent agreement is found with the available experimental gas-phase deprotonation enthalpies, and the calculated values are within experimental error. We predict that tyrosine is deprotonated at the CO(2)H site. Cysteine is predicted to be deprotonated at the SH but the proton on the CO(2)H is shared with the S(-) site. Self-consistent reaction field (SCRF) calculations with the COSMO parametrization were used to predict the pK(a)'s of the non-zwitterion form in aqueous solution. The differences in the non-zwitterion pK(a) values were used to estimate the free energy difference between the zwitterion and nonzwitterion forms in solution. The heats of formation of the neutral compounds were calculated from atomization energies and isodesmic reactions to provide the first reliable set of these values in the gas phase. Further calculations were performed on five rare amino acids to predict their heats of formation, acidities, and pK(a) values.

Acid monolayer functionalized iron oxide nanoparticle catalysts

Science.gov (United States)

Ikenberry, Myles

Superparamagnetic iron oxide nanoparticle functionalization is an area of intensely active research, with applications across disciplines such as biomedical science and heterogeneous catalysis. This work demonstrates the functionalization of iron oxide nanoparticles with a quasi-monolayer of 11-sulfoundecanoic acid, 10-phosphono-1-decanesulfonic acid, and 11-aminoundecanoic acid. The carboxylic and phosphonic moieties form bonds to the iron oxide particle core, while the sulfonic acid groups face outward where they are available for catalysis. The particles were characterized by thermogravimetric analysis (TGA), transmission electron microscopy (TEM), potentiometric titration, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), inductively coupled plasma optical emission spectrometry (ICP-OES), X-ray photoelectron spectrometry (XPS), and dynamic light scattering (DLS). The sulfonic acid functionalized particles were used to catalyze the hydrolysis of sucrose at 80° and starch at 130°, showing a higher activity per acid site than the traditional solid acid catalyst Amberlyst-15, and comparing well against results reported in the literature for sulfonic acid functionalized mesoporous silicas. In sucrose catalysis reactions, the phosphonic-sulfonic nanoparticles (PSNPs) were seen to be incompletely recovered by an external magnetic field, while the carboxylic-sulfonic nanoparticles (CSNPs) showed a trend of increasing activity over the first four recycle runs. Between the two sulfonic ligands, the phosphonates produced a more tightly packed monolayer, which corresponded to a higher sulfonic acid loading, lower agglomeration, lower recoverability through application of an external magnetic field, and higher activity per acid site for the hydrolysis of starch. Functionalizations with 11-aminoundecanoic acid resulted in some amine groups binding to the surfaces of iron oxide nanoparticles. This amine binding is commonly ignored in iron oxide

Binding of acyl CoA by fatty acid binding protein and the effect on fatty acid activation

International Nuclear Information System (INIS)

Burrier, R.E.; Manson, C.R.; Brecher, P.

1987-01-01

The ability of purified rat liver and heart fatty acid binding proteins (FABPs) to bind oleoyl CoA and modulate acyl CoA synthesis by microsomal membranes was investigated. Using binding assays employing either Lipidex 1000 or multilamellar liposomes to sequester unbound ligand, rat liver but not rat heart FABP was shown to bind radiolabeled acyl CoA. Binding studies suggest that liver FABP has a single binding site for acyl CoA which is separate from the two binding sites for fatty acids. Experiments were then performed to determine how binding may influence acyl CoA metabolism by liver microsomes or heart sarcoplasmic reticulum. Using liposomes as fatty acid donors, liver FABP stimulated acyl CoA production whereas heart FABP did not stimulate production over control values. 14 C-Fatty acid-FABP complexes were prepared, incubated with membranes and acyl CoA synthetase activity was determined. Up to 70% of the fatty acid could be converted to acyl CoA in the presence of liver FABP but in the presence of heart FABP, only 45% of the fatty acid was converted. The amount of product formed was not changed by additional membrane, enzyme cofactor, or incubation time. Liver but not heart FABP bound the acyl CoA formed and removed it from the membranes. These studies suggest that liver FABP can increase the amount of acyl CoA by binding this ligand thereby removing it from the membrane and possibly aiding transport within the cell

Binding of acyl CoA by fatty acid binding protein and the effect on fatty acid activation

Energy Technology Data Exchange (ETDEWEB)

Burrier, R.E.; Manson, C.R.; Brecher, P.

1987-05-01

The ability of purified rat liver and heart fatty acid binding proteins (FABPs) to bind oleoyl CoA and modulate acyl CoA synthesis by microsomal membranes was investigated. Using binding assays employing either Lipidex 1000 or multilamellar liposomes to sequester unbound ligand, rat liver but not rat heart FABP was shown to bind radiolabeled acyl CoA. Binding studies suggest that liver FABP has a single binding site for acyl CoA which is separate from the two binding sites for fatty acids. Experiments were then performed to determine how binding may influence acyl CoA metabolism by liver microsomes or heart sarcoplasmic reticulum. Using liposomes as fatty acid donors, liver FABP stimulated acyl CoA production whereas heart FABP did not stimulate production over control values. /sup 14/C-Fatty acid-FABP complexes were prepared, incubated with membranes and acyl CoA synthetase activity was determined. Up to 70% of the fatty acid could be converted to acyl CoA in the presence of liver FABP but in the presence of heart FABP, only 45% of the fatty acid was converted. The amount of product formed was not changed by additional membrane, enzyme cofactor, or incubation time. Liver but not heart FABP bound the acyl CoA formed and removed it from the membranes. These studies suggest that liver FABP can increase the amount of acyl CoA by binding this ligand thereby removing it from the membrane and possibly aiding transport within the cell.

Bedrock neutralization study for the Bruin Lagoon Superfund Site

International Nuclear Information System (INIS)

Patelunas, G.M.; Lenhardt, D.R.; Niece, J.E.

1989-01-01

The Bruin Lagoon site is located in Bruin Butler County, Pennsylvania, and is listed as No. 3 on the U.S. Environmental Protection Agencies' National Priority List. The Lagoon contains waste petroleum tars, sulfuric acid, coal combustion ash, spent bauxite and other waste materials. This paper reports on the bedrock neutralization study, conducted to assess the feasibility of injecting caustic solutions into acid-contaminated bedrock beneath the lagoon. The site is underlain by a fine to medium grain quartz sandstone which is contaminated with acid to depths in excess of 30 feet. For this investigation, Nx-cores were obtained and pressure tests conducted to a depth of 30 feet below the top of rock. Leach tests were conducted on contaminated core sections using sodium hydroxide and sodium carbonate solutions. A total of 12 core sections were exposed in 3-inch diameter test cylinders and permeated under a positive pressure of 25 to 50 psi. Measurements of leachate volume, temperature, pH, and hydraulic conductivity were recorded

Increase in D-tagatose production rate by site-directed mutagenesis of L-arabinose isomerase from Geobacillus thermodenitrificans.

Science.gov (United States)

Oh, Hyo-Jung; Kim, Hye-Jung; Oh, Deok-Kun

2006-02-01

Among single-site mutations of L-arabinose isomerase derived from Geobacillus thermodenitrificans, two mutants were produced having the lowest and highest activities of D-tagatose production. Site-directed mutagenesis at these sites showed that the aromatic ring at amino acid 164 and the size of amino acid 475 were important for D-tagatose production. Among double-site mutations, one mutant converted D-galactose into D-tagatose with a yield of 58% whereas the wild type gave 46% D-tagatose conversion after 300 min at 65 degrees C.

Computer analysis of protein functional sites projection on exon structure of genes in Metazoa.

Science.gov (United States)

Medvedeva, Irina V; Demenkov, Pavel S; Ivanisenko, Vladimir A

2015-01-01

Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and

Effects of water on the esterification of free fatty acids by acid catalysts

Energy Technology Data Exchange (ETDEWEB)

Park, Ji-Yeon; Kim, Deog-Keun; Lee, Jin-Suk [Korea Institute of Energy Research, 71-2, Jang-dong, Yuseong-gu, Daejeon 305-343 (Korea); Wang, Zhong-Ming [Guangzhou Institute of Energy Conversion, No. 2 Nengyuan Rd, Wushan, Tianhe, Guangzhou 510-640 (China)

2010-03-15

To maximize the production of biodiesel from soybean soapstock, the effects of water on the esterification of high-FFA (free fatty acid) oils were investigated. Oleic acid and high acid acid oil (HAAO) were esterified by reaction with methanol in the presence of Amberlyst-15 as a heterogeneous catalyst or sulfuric acid as a homogeneous catalyst. The yield of fatty acid methyl ester (FAME) was studied at oil to methanol molar ratios of 1:3 and 1:6 and reaction temperatures of 60 and 80 C. The rate of esterification of oleic acid significantly decreased as the initial water content increased to 20% of the oil. The activity of Amberlyst-15 decreased more rapidly than that of sulfuric acid, due to the direct poisoning of acid sites by water. Esterification using sulfuric acid was not affected by water until there was a 5% water addition at a 1:6 molar ratio of oil to methanol. FAME content of HAAO prepared from soapstock rapidly increased for the first 30 min of esterification. Following the 30-min mark, the rate of FAME production decreased significantly due to the accumulation of water. When methanol and Amberlyst-15 were removed from the HAAO after 30 min of esterification and fresh methanol and a catalyst were added, the time required to reach 85% FAME content was reduced from 6 h to 1.8 h. (author)

Hazardous waste operational plan for site 300

International Nuclear Information System (INIS)

Roberts, R.S.

1982-01-01

This plan outlines the procedures and operations used at LLNL's Site 300 for the management of the hazardous waste generated. This waste consists primarily of depleted uranium (a by-product of U-235 enrichment), beryllium, small quantities of analytical chemicals, industrial type waste such as solvents, cleaning acids, photographic chemicals, etc., and explosives. This plan details the operations generating this waste, the proper handling of this material and the procedures used to treat or dispose of the hazardous waste. A considerable amount of information found in this plan was extracted from the Site 300 Safety and Operational Manual written by Site 300 Facility personnel and the Hazards Control Department

Site and extent of amino acid digestion in dairy cattle fed with corn and its byproducts

Directory of Open Access Journals (Sweden)

Reginaldo Nassar Ferreira

2015-02-01

Full Text Available The study was conducted to evaluated the site and extent of dry matter (DM, crude protein (CP, methionine (Met, lysine (Lys, and threonine (Thr digestion of corn and byproducts obtained from corn germ mixed with different amounts of extruded or non-extruded ether extract (EE in dairy cattle. Treatments consisted in eight types of feed and two processing in a 4 × 2 factorial design. There were four feeds: corn grain cracked (Corn, corn germ meal with 1% EE (CG1, corn germ meal with 7% EE (CG7, and corn germ meal with 10% EE (CG10. The feeds were processed in one of two ways: extruded (Ex and not extruded. In situ techniques were used to determine DM, CP, Met, Lys, and Thr partial and total tract digestion. A basic diet was compounded of corn germ meal, soybean meal and coastcross hay in a 70:30 roughage to concentrate ratio. There was no interaction (P>0.05 between feeds and processing method. Extrusion improved (P0.05 for corn and corn germ meal mixed with 7 and 10% EE, regardless of EE processing method. The CP total tract digestibility of corn germ meal with 1% nonextruded EE was 16.62% higher (P<0.05 than that of the extruded form. The best total CP digestibility was obtained for corn germ meal with 7% EE, independently of the processing method. The effects of EE processing method on partial and total digestibility differed between amino acid. Corn and corn byproduct extrusion may improve dry matter digestibility, but do not necessarily influence crude protein digestion. Ruminal and intestinal digestibility of Met, Lys, and Thr depends on both feed type and processing method. Therefore, amino acid availability should be considered individually.

Deaminated zeolite, ITQ-6 as heterogeneous catalyst for Friedel crafts alkylation

International Nuclear Information System (INIS)

Zainab Ramli; Noor Ashikin Mohd Yusoff; Halimaton Hamdan

2007-01-01

The ability of ITQ-6, a kind of meso porous zeolitic material to replace microporous zeolite as catalyst has attracted particular attention. In this study, modification of a precursor of microporous ferrierite, PREFER to meso porous material, ITQ-6 was carried out by delamination technique. The XRD results show that the crystalline phase of PREFER diminished for the sample after delamination. Porosity study of the ITQ-6 sample shows formation of homogeneous meso pores in the size between 3.5-4.0 nm. The acidity study indicates that ITQ-6 still contains appreciable amounts of Bronsted and Lewis acidities. Catalytic evaluation of the resulting material, ITQ-6 was carried out in the alkylation of resorcinol with methyl tert-butyl ether which gave 4-tert-butyl resorcinol and 4, 6-di-tert-butyl resorcinol as main products. The conversion of resorcinol when using ITQ-6 was ten times higher than ferrierite, FER with similar selectivity of disubstituted product. It shows that the meso porosity of ITQ-6 was responsible for the higher activity of the catalyst in the reaction. (author)

One-step hydroprocessing of fatty acids into renewable aromatic hydrocarbons over Ni/HZSM-5: insights into the major reaction pathways.

Science.gov (United States)

Xing, Shiyou; Lv, Pengmei; Wang, Jiayan; Fu, Junying; Fan, Pei; Yang, Lingmei; Yang, Gaixiu; Yuan, Zhenhong; Chen, Yong

2017-01-25

For high caloricity and stability in bio-aviation fuels, a certain content of aromatic hydrocarbons (AHCs, 8-25 wt%) is crucial. Fatty acids, obtained from waste or inedible oils, are a renewable and economic feedstock for AHC production. Considerable amounts of AHCs, up to 64.61 wt%, were produced through the one-step hydroprocessing of fatty acids over Ni/HZSM-5 catalysts. Hydrogenation, hydrocracking, and aromatization constituted the principal AHC formation processes. At a lower temperature, fatty acids were first hydrosaturated and then hydrodeoxygenated at metal sites to form long-chain hydrocarbons. Alternatively, the unsaturated fatty acids could be directly deoxygenated at acid sites without first being saturated. The long-chain hydrocarbons were cracked into gases such as ethane, propane, and C 6 -C 8 olefins over the catalysts' Brønsted acid sites; these underwent Diels-Alder reactions on the catalysts' Lewis acid sites to form AHCs. C 6 -C 8 olefins were determined as critical intermediates for AHC formation. As the Ni content in the catalyst increased, the Brønsted-acid site density was reduced due to coverage by the metal nanoparticles. Good performance was achieved with a loading of 10 wt% Ni, where the Ni nanoparticles exhibited a polyhedral morphology which exposed more active sites for aromatization.

Propriedades ácido-base e de complexação de ácidos húmico e fúlvico isolados de vermicomposto Acid/base and complexation properties of humic and fulvic acids isolated from vermicompost

Directory of Open Access Journals (Sweden)

Sandro de Miranda Colombo

2007-10-01

Full Text Available Proton binding properties of humic and fulvic acids were studied by potentiometric titration. Carboxylic groups were the predominant ionizable sites in comparison to phenolic and amine groups. Total acidity of fulvic acid was 12 x 10-3 mol g-1, a number significantly higher than that obtained for humic acid (5.2 x 10-3 mol g-1. Copper ion binding was evaluated at pH 4, 5 and 6 by potentiometric titration with an ion selective electrode for Cu(II. Differential stability constants and complexation capacities were systematically higher for humic acid, despite its lower number of ionizable sites in comparison with fulvic acid.

The response of amino acid cycling to global change across multiple biomes: Feedbacks on soil nitrogen availability

Science.gov (United States)

Brzostek, E. R.; Finzi, A. C.

2010-12-01

The cycling of organic nitrogen (N) in soil links soil organic matter decomposition to ecosystem productivity. Amino acids are a key pool of organic N in the soil, whose cycling is sensitive to alterations in microbial demand for carbon and N. Further, the amino acids released from the breakdown of protein by proteolytic enzymes are an important source of N that supports terrestrial productivity. The objective of this study was to measure changes in amino acid cycling in response to experimental alterations of precipitation and temperature in twelve global change experiments during the 2009 growing season. The study sites ranged from arctic tundra to xeric grasslands. The treatments experimentally increased temperature, increased or decreased precipitation, or some combination of both factors. The response of amino acid cycling to temperature and precipitation manipulations tended to be site specific, but the responses could be placed into a common framework. Changes in soil moisture drove a large response in amino acid cycling. Precipitation augmentation in xeric and mesic sites increased both amino acid pool sizes and production. However, treatments that decreased precipitation drove decreases in amino acid cycling in xeric sites, but led to increases in amino acid cycling in more mesic sites. Across sites, the response to soil warming was horizon specific. Amino acid cycling in organic rich horizons responded positively to warming, while negative responses were exhibited in lower mineral soil horizons. The variable response likely reflects a higher availability of protein substrate to sustain high rates of proteolytic enzyme activity in organic rich horizons. Overall, these results suggest that soil moisture and the availability of protein substrate may be important factors that mediate the response of amino acid cycling to predicted increases in soil temperatures.

Structure of a highly acidic β-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs{sup +}-selective binding site

Energy Technology Data Exchange (ETDEWEB)

Arai, Shigeki; Yonezawa, Yasushi; Okazaki, Nobuo; Matsumoto, Fumiko; Shibazaki, Chie; Shimizu, Rumi; Yamada, Mitsugu; Adachi, Motoyasu; Tamada, Taro [Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195 (Japan); Kawamoto, Masahide [Kyushu Synchrotron Light Research Center, 8-7 Yayoigaoka, Tosu, Saga 841-0005 (Japan); Tokunaga, Hiroko; Ishibashi, Matsujiro [Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065 (Japan); Blaber, Michael [Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195 (Japan); Florida State University, 1115 West Call Street, Tallahassee, FL 32306-4300 (United States); Tokunaga, Masao [Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065 (Japan); Kuroki, Ryota, E-mail: kuroki.ryota@jaea.go.jp [Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195 (Japan)

2015-03-01

The tertiary structure of a β-lactamase derived from the halobacterium Chromohalobacter sp. 560 (HaBLA) was determined by X-ray crystallography. Three unique Sr{sup 2+}-binding sites and one Cs{sup +}-binding site were discovered in the HaBLA molecule. Environmentally friendly absorbents are needed for Sr{sup 2+} and Cs{sup +}, as the removal of the radioactive Sr{sup 2+} and Cs{sup +} that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs{sup +} or Sr{sup 2+}. The crystal structure of a halophilic β-lactamase from Chromohalobacter sp. 560 (HaBLA) was determined to resolutions of between 1.8 and 2.9 Å in space group P3{sub 1} using X-ray crystallography. Moreover, the locations of bound Sr{sup 2+} and Cs{sup +} ions were identified by anomalous X-ray diffraction. The location of one Cs{sup +}-specific binding site was identified in HaBLA even in the presence of a ninefold molar excess of Na{sup +} (90 mM Na{sup +}/10 mM Cs{sup +}). From an activity assay using isothermal titration calorimetry, the bound Sr{sup 2+} and Cs{sup +} ions do not significantly affect the enzymatic function of HaBLA. The observation of a selective and high-affinity Cs{sup +}-binding site provides important information that is useful for the design of artificial Cs{sup +}-binding sites that may be useful in the bioremediation of radioactive isotopes.

Solar electric power for instruments at remote sites

Science.gov (United States)

McChesney, P.J.

2000-01-01

Small photovoltaic (PV) systems are the preferred method to power instruments operating at permanent locations away from the electric power grid. The low-power PV power system consists of a solar panel or small array of panels, lead-acid batteries, and a charge controller. Even though the small PV power system is simple, the job of supplying power at a remote site can be very demanding. The equipment is often exposed to harsh conditions. The site may be inaccessible part of the year or difficult and expensive to reach at any time. Yet the system must provide uninterrupted power with minimum maintenance at low cost. This requires good design. Successful small PV systems often require modifications by a knowledgeable fieldworker to adapt to conditions at the site. Much information is available in many places about solar panels, lead-acid batteries, and charging systems but very little of it applies directly to low power instrument sites. The discussion here aims to close some of the gap. Each of the major components is described in terms of this application with particular attention paid to batteries. Site problems are investigated. Finally, maintenance and test procedures are given. This document assumes that the reader is engaged in planning or maintaining low-power PV sites and has basic electrical and electronic knowledge. The area covered by the discussion is broad. To help the reader with the many terms and acronyms used, they are shown in bold when first used and a glossary is provided at the end of the paper.

Observation of new particle formation and measurement of sulfuric acid, ammonia, amines and highly oxidized organic molecules at a rural site in central Germany

Directory of Open Access Journals (Sweden)

A. Kürten

2016-10-01

Full Text Available The exact mechanisms for new particle formation (NPF under different boundary layer conditions are not known yet. One important question is whether amines and sulfuric acid lead to efficient NPF in the atmosphere. Furthermore, it is not clear to what extent highly oxidized organic molecules (HOMs are involved in NPF. We conducted field measurements at a rural site in central Germany in the proximity of three larger dairy farms to investigate whether there is a connection between NPF and the presence of amines and/or ammonia due to the local emissions from the farms. Comprehensive measurements using a nitrate chemical ionization–atmospheric pressure interface time-of-flight (CI-APi-TOF mass spectrometer, a proton-transfer-reaction mass spectrometer (PTR-MS, particle counters and differential mobility analyzers (DMAs, as well as measurements of trace gases and meteorological parameters, were performed. We demonstrate here that the nitrate CI-APi-TOF is suitable for sensitive measurements of sulfuric acid, amines, a nitrosamine, ammonia, iodic acid and HOMs. NPF was found to correlate with sulfuric acid, while an anti-correlation with RH, amines and ammonia is observed. The anti-correlation between NPF and amines could be due to the efficient uptake of these compounds by nucleating clusters and small particles. Much higher HOM dimer (C19/C20 compounds concentrations during the night than during the day indicate that these HOMs do not efficiently self-nucleate as no nighttime NPF is observed. Observed iodic acid probably originates from an iodine-containing reservoir substance, but the iodine signals are very likely too low to have a significant effect on NPF.

Chloride binding site of neurotransmitter sodium symporters

DEFF Research Database (Denmark)

Kantcheva, Adriana Krassimirova; Quick, Matthias; Shi, Lei

2013-01-01

Neurotransmitter:sodium symporters (NSSs) play a critical role in signaling by reuptake of neurotransmitters. Eukaryotic NSSs are chloride-dependent, whereas prokaryotic NSS homologs like LeuT are chloride-independent but contain an acidic residue (Glu290 in LeuT) at a site where eukaryotic NSSs...

Bronstinductie bij schapen : vijf jaar onderzoek op de Waiboerhoeve = Oestrus induction with sheep : five years research on the Waiboerhoeve [Experimental Farm

NARCIS (Netherlands)

Ruiter, T.

1983-01-01

Vanaf augustus 1975 tot en met februari 1980 werden 8 proeven uitgevoerd met als doel een vruchtbare bronst op te wekken buiten het bronstseizoen. Daarmee is het mogelijk de ooien drie keer per twee jaar te laten aflammen. Het onderzoek werd zoveel mogelijk onder praktijkomstandigheden op de

Uric acid in multiple sclerosis

NARCIS (Netherlands)

Koch, M; De Keyser, J

Peroxynitrite, a reactive oxidant formed by the reaction of nitric oxide with superoxide at sites of inflammation in multiple sclerosis (MS), is capable of damaging tissues and cells. Uric acid, a natural scavenger of peroxynitrite, reduces inflammatory demyelination in experimental allergic

Detection of nucleic acid sequences by invader-directed cleavage

Science.gov (United States)

Brow, Mary Ann D.; Hall, Jeff Steven Grotelueschen; Lyamichev, Victor; Olive, David Michael; Prudent, James Robert

1999-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

Structural analysis and binding domain of albumin complexes with natural dietary supplement humic acid

International Nuclear Information System (INIS)

Ding Fei; Diao Jianxiong; Yang Xinling; Sun Ying

2011-01-01

Humic acid, a natural ionic molecule, is rapidly being recognized as one of the crucial elements in our modern diets of the new century. A biophysical protocol utilizing circular dichroism (CD), steady state and time-resolved fluorescence for the investigation of the complexation of the humic acid to the staple in vivo transporter, human serum albumin (HSA), as a model for protein-humic substances, is proclaimed. The alterations of CD and three-dimensional fluorescence suggest that the polypeptide chain of HSA partially folded after complexation with humic acid. The data of fluorescence emission displayed that the binding of humic acid to HSA is the formation of HSA-humic acid complex with an association constant of 10 4 M -1 ; this corroborates the fluorescence lifetime measurements that the static mechanism was operated. The precise binding domain of humic acid in HSA has been verified from the denaturation of albumin, hydrophobic ANS displacement, and site-specific ligands; subdomain IIA (Sudlow's site I) was earmarked to possess high-affinity for humic acid. The observations are relevant for other albumin-humic substance systems when the ligands have analogous configuration with humic acid. - Highlights: → Albumin structure partially folds upon humic acid complexation. → Static type is dominance for the diminution in the Trp-214 fluorescence.→ Subdomain IIA is designate to possess high-affinity site for humic acid.

Catalytic properties and acidity of modified MCM-41 mesoporous materials with low Si/Al ratio: heptane isomerisation

Directory of Open Access Journals (Sweden)

Ahmed Belhakem

2006-06-01

Full Text Available The catalytic properties and acidity of modified MCM-41 with a low Si/Al ratio and 0-95% NH4+ exchange were investigated. The samples were characterised by X-ray diffraction, scanning and transmission electron microscopy, and nitrogen adsorption. The acidity was studied by pyridine adsorption, temperature programmed desorption (TPD of ammonia, and infrared (IR spectroscopy. Adsorption of pyridine and IR spectroscopy indicated various types of Lewis and Brönsted acid sites. The density distribution of acid sites was determined by TPD. Both Lewis and Brönsted acid sites were found to be active in the heptane isomerisation. The presence of aluminium (low Si/Al combined to the ionic exchange between Na+ and NH4+ increases the acidity of MCM-41 materials. A close correlation between acidity and isomerisation was observed. Coke deposition, which reduces the activity, was also studied.

Allosteric ligands and their binding sites define γ-aminobutyric acid (GABA) type A receptor subtypes.

Science.gov (United States)

Olsen, Richard W

2015-01-01

GABAA receptors (GABA(A)Rs) mediate rapid inhibitory transmission in the brain. GABA(A)Rs are ligand-gated chloride ion channel proteins and exist in about a dozen or more heteropentameric subtypes exhibiting variable age and brain regional localization and thus participation in differing brain functions and diseases. GABA(A)Rs are also subject to modulation by several chemotypes of allosteric ligands that help define structure and function, including subtype definition. The channel blocker picrotoxin identified a noncompetitive channel blocker site in GABA(A)Rs. This ligand site is located in the transmembrane channel pore, whereas the GABA agonist site is in the extracellular domain at subunit interfaces, a site useful for low energy coupled conformational changes of the functional channel domain. Two classes of pharmacologically important allosteric modulatory ligand binding sites reside in the extracellular domain at modified agonist sites at other subunit interfaces: the benzodiazepine site and the high-affinity, relevant to intoxication, ethanol site. The benzodiazepine site is specific for certain GABA(A)R subtypes, mainly synaptic, while the ethanol site is found at a modified benzodiazepine site on different, extrasynaptic, subtypes. In the transmembrane domain are allosteric modulatory ligand sites for diverse chemotypes of general anesthetics: the volatile and intravenous agents, barbiturates, etomidate, propofol, long-chain alcohols, and neurosteroids. The last are endogenous positive allosteric modulators. X-ray crystal structures of prokaryotic and invertebrate pentameric ligand-gated ion channels, and the mammalian GABA(A)R protein, allow homology modeling of GABA(A)R subtypes with the various ligand sites located to suggest the structure and function of these proteins and their pharmacological modulation. © 2015 Elsevier Inc. All rights reserved.

A method to attenuate U(VI) mobility in acidic waste plumes using humic acids

Energy Technology Data Exchange (ETDEWEB)

Wan, J.; Dong, W.; Tokunaga, T.K.

2011-02-01

Acidic uranium (U) contaminated plumes have resulted from acid-extraction of plutonium during the Cold War and from U mining and milling operations. A sustainable method for in-situ immobilization of U under acidic conditions is not yet available. Here, we propose to use humic acids (HAs) for in-situ U immobilization in acidic waste plumes. Our laboratory batch experiments show that HA can adsorb onto aquifer sediments rapidly, strongly and practically irreversibly. Adding HA greatly enhanced U adsorption capacity to sediments at pH below 5.0. Our column experiments using historically contaminated sediments from the Savannah River Site under slow flow rates (120 and 12 m/y) show that desorption of U and HA were non-detectable over 100 pore-volumes of leaching with simulated acidic groundwaters. Upon HA-treatment, 99% of the contaminant [U] was immobilized at pH < 4.5, compared to 5% and 58% immobilized in the control columns at pH 3.5 and 4.5, respectively. These results demonstrated that HA-treatment is a promising in-situ remediation method for acidic U waste plumes. As a remediation reagent, HAs are resistant to biodegradation, cost effective, nontoxic, and easily introducible to the subsurface.

Mutable Lewis and Bronsted Acidity of Aluminated SBA-15 as Revealed by NMR of Adsorbed Pyridine-(15)N

Czech Academy of Sciences Publication Activity Database

Gurinov, A. A.; Rozhkova, Yu. A.; Zukal, Arnošt; Čejka, Jiří; Shenderovich, I, G.

2011-01-01

Roč. 27, č. 19 (2011), s. 12115-12123 ISSN 0743-7463 R&D Projects: GA AV ČR KAN100400701; GA ČR GA203/08/0604 Institutional research plan: CEZ:AV0Z40400503 Keywords : 15N NMR * post-synthesis alumination * phase Beckmann rearrangement Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.186, year: 2011

Synthesis and characterization of 12-phosphotungstic acid supported on BEA zeolite

Energy Technology Data Exchange (ETDEWEB)

Jović, A.; Bajuk-Bogdanović, D.; Nedić Vasiljević, B. [Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade (Serbia); Milojević-Rakić, M., E-mail: maja@ffh.bg.ac.rs [Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade (Serbia); Krajišnik, D. [Department of Pharmaceutical Technology and Cosmetology, University of Belgrade-Faculty of Pharmacy, Vojvode Stepe 450, 11000 Belgrade (Serbia); Dondur, V. [Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade (Serbia); Popa, A. [Institute of Chemistry Timisoara, Bl. Mihai Viteazul 24, 300223 Timisoara (Romania); Uskoković-Marković, S. [Department of Analytical Chemistry, University of Belgrade-Faculty of Pharmacy, Vojvode Stepe 450, 11000 Belgrade (Serbia); Holclajtner-Antunović, I. [Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade (Serbia)

2017-01-15

An optimized synthetic route for obtaining heteropoly acid (HPA) species supported on BEA zeolite was applied, and different samples, comprising 20 to 50 wt% of 12-phosphotungstic acid (HPW) were prepared. The as-synthesized supported HPW were subjected to different post-synthesis routes, which involved calcination and ultrasound treatment. Characterization of these materials was performed by means of Scanning Electron Microscopy, zeta potential measurements, Infrared Spectroscopy and X-ray Powder Diffraction analysis. Results suggest strong interaction of HPW with the support and revealed that ultrasound treatment resulted in better dispersion of active phase and thus homogeneous morphology of the samples. The zeta potential was found to be dependent on the preparation procedure and HPW content in these materials, while higher HPW loadings induced its agglomeration. Catalytic activity of the synthesized materials was investigated in an ethanol dehydration reaction, where lower HPW loadings induced higher ethanol conversion. Acid sites distribution and accessibility for ethanol molecules were found to be more essential for catalytic activity than HPW loadings, i.e., amount of active sites present in these hybrid materials. - Highlights: • An optimized route for supporting heteropoly acid on beta zeolite is applied. • Ultrasound treatment of the composites gives dispersed morphology. • Lower heteropoly acid amount induces higher conversion in ethanol dehydration. • Acid sites distribution and accessibility for ethanol are essential for catalytic activity.

Synthesis and characterization of 12-phosphotungstic acid supported on BEA zeolite

International Nuclear Information System (INIS)

Jović, A.; Bajuk-Bogdanović, D.; Nedić Vasiljević, B.; Milojević-Rakić, M.; Krajišnik, D.; Dondur, V.; Popa, A.; Uskoković-Marković, S.; Holclajtner-Antunović, I.

2017-01-01

An optimized synthetic route for obtaining heteropoly acid (HPA) species supported on BEA zeolite was applied, and different samples, comprising 20 to 50 wt% of 12-phosphotungstic acid (HPW) were prepared. The as-synthesized supported HPW were subjected to different post-synthesis routes, which involved calcination and ultrasound treatment. Characterization of these materials was performed by means of Scanning Electron Microscopy, zeta potential measurements, Infrared Spectroscopy and X-ray Powder Diffraction analysis. Results suggest strong interaction of HPW with the support and revealed that ultrasound treatment resulted in better dispersion of active phase and thus homogeneous morphology of the samples. The zeta potential was found to be dependent on the preparation procedure and HPW content in these materials, while higher HPW loadings induced its agglomeration. Catalytic activity of the synthesized materials was investigated in an ethanol dehydration reaction, where lower HPW loadings induced higher ethanol conversion. Acid sites distribution and accessibility for ethanol molecules were found to be more essential for catalytic activity than HPW loadings, i.e., amount of active sites present in these hybrid materials. - Highlights: • An optimized route for supporting heteropoly acid on beta zeolite is applied. • Ultrasound treatment of the composites gives dispersed morphology. • Lower heteropoly acid amount induces higher conversion in ethanol dehydration. • Acid sites distribution and accessibility for ethanol are essential for catalytic activity.

Interactions between Therapeutic Proteins and Acrylic Acid Leachable.

Science.gov (United States)

Liu, Dengfeng; Nashed-Samuel, Yasser; Bondarenko, Pavel V; Brems, David N; Ren, Da

2012-01-01

Leachables are chemical compounds that migrate from manufacturing equipment, primary containers and closure systems, and packaging components into biopharmaceutical and pharmaceutical products. Acrylic acid (at concentration around 5 μg/mL) was detected as leachable in syringes from one of the potential vendors (X syringes). In order to evaluate the potential impact of acrylic acid on therapeutic proteins, an IgG 2 molecule was filled into a sterilized X syringe and then incubated at 45 °C for 45 days in a pH 5 acetate buffer. We discovered that acrylic acid can interact with proteins at three different sites: (1) the lysine side chain, (2) the N-terminus, and (3) the histidine side chain, by the Michael reaction. In this report, the direct interactions between acrylic acid leachable and a biopharmaceutical product were demonstrated and the reaction mechanism was proposed. Even thought a small amount (from 0.02% to 0.3%) of protein was found to be modified by acrylic acid, the modified protein can potentially be harmful due to the toxicity of acrylic acid. After being modified by acrylic acid, the properties of the therapeutic protein may change due to charge and hydrophobicity variations. Acrylic acid was detected to migrate from syringes (Vendor X) into a therapeutic protein solution (at a concentration around 5 μg/mL). In this study, we discovered that acrylic acid can modify proteins at three different sites: (1) the lysine side chain, 2) the N-terminus, and 3) the histidine side chain, by the Michael reaction. In this report, the direct interactions between acrylic acid leachable and a biopharmaceutical product were demonstrated and the reaction mechanism was proposed.

Inhibition of telomerase by linear-chain fatty acids: a structural analysis.

Science.gov (United States)

Oda, Masako; Ueno, Takamasa; Kasai, Nobuyuki; Takahashi, Hirotada; Yoshida, Hiromi; Sugawara, Fumio; Sakaguchi, Kengo; Hayashi, Hideya; Mizushina, Yoshiyuki

2002-01-01

In the present study, we have found that mono-unsaturated linear-chain fatty acids in the cis configuration with C(18) hydrocarbon chains (i.e. oleic acid) strongly inhibited the activity of human telomerase in a cell-free enzymic assay, with an IC(50) value of 8.6 microM. Interestingly, fatty acids with hydrocarbon chain lengths below 16 or above 20 carbons substantially decreased the potency of inhibition of telomerase. Moreover, the cis-mono-unsaturated C(18) linear-chain fatty acid oleic acid was the strongest inhibitor of all the fatty acids tested. A kinetic study revealed that oleic acid competitively inhibited the activity of telomerase ( K (i)=3.06 microM) with respect to the telomerase substrate primer. The energy-minimized three-dimensional structure of the linear-chain fatty acid was calculated and modelled. A molecule width of 11.53-14.26 A (where 1 A=0.1 nm) in the C(16) to C(20) fatty acid structure was suggested to be important for telomerase inhibition. The three-dimensional structure of the telomerase active site (i.e. the substrate primer-binding site) appears to have a pocket that could bind oleic acid, with the pocket being 8.50 A long and 12.80 A wide. PMID:12121150

Lead/acid batteries in systems to improve power quality

Science.gov (United States)

Taylor, P.; Butler, P.; Nerbun, W.

Increasing dependence on computer technology is driving needs for extremely high-quality power to prevent loss of information, material, and workers' time that represent billions of dollars annually. This cost has motivated commercial and Federal research and development of energy storage systems that detect and respond to power-quality failures in milliseconds. Electrochemical batteries are among the storage media under investigation for these systems. Battery energy storage systems that employ either flooded lead/acid or valve-regulated lead/acid battery technologies are becoming commercially available to capture a share of this emerging market. Cooperative research and development between the US Department of Energy and private industry have led to installations of lead/acid-based battery energy storage systems to improve power quality at utility and industrial sites and commercial development of fully integrated, modular battery energy storage system products for power quality. One such system by AC Battery Corporation, called the PQ2000, is installed at a test site at Pacific Gas and Electric Company (San Ramon, CA, USA) and at a customer site at Oglethorpe Power Corporation (Tucker, GA, USA). The PQ2000 employs off-the-shelf power electronics in an integrated methodology to control the factors that affect the performance and service life of production-model, low-maintenance, flooded lead/acid batteries. This system, and other members of this first generation of lead/acid-based energy storage systems, will need to compete vigorously for a share of an expanding, yet very aggressive, power quality market.

Osteopontin: A uranium phosphorylated binding-site characterization

International Nuclear Information System (INIS)

Safi, Samir; Jeanson, Aurelie; Roques, Jerome; Simoni, Eric; Creff, Gaelle; Qi, Lei; Basset, Christian; Vidaud, Claude; Solari, Pier Lorenzo; Den Auwer, Christophe

2013-01-01

Herein, we describe the structural investigation of one possible uranyl binding site inside a non structured protein. This approach couples spectroscopy, thermodynamics, and theoretical calculations (DFT) and studies the interaction of uranyl ions with a phospho-peptide, thus mimicking a possible osteopontin (OPN) hydroxyapatite growth-inhibition site. Although thermodynamical aspects were investigated by using time-resolved laser fluorescence spectroscopy (TRLFS) and isothermal titration calorimetry (ITC), structural characterization was performed by extended X-ray absorption fine structure (EXAFS) at the U L(III)-edge combined with attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. From the vibrational and fluorescence spectra, several structural models of a UO 2 2+ /peptide complex were developed and subsequently refined by using theoretical calculations to fit the experimental EXAFS obtained. The structural effect of the pH value was also considered under acidic to moderately acidic conditions (pH 1.5-5.5). Most importantly, the uranyl/peptide coordination environment was similar to that of the native protein. (authors)

Environmental radioactivity assessment around old uranium mining sites near Mangualde (Viseu), Portugal

International Nuclear Information System (INIS)

Carvalho, Fernando P.; Torres, Lubelia M.; Oliveira, Joao M.

2007-01-01

Uranium ore was extracted in the surroundings of Mangualde city, North of Portugal, in the mines of Cunha Baixa, Quinta do Bispo and Espinho until a few years ago. Mining waste, milling tailings and acid mine waters are the on site remains of this extractive activity. Environmental radioactivity measurements were performed in and around these sites in order to assess the dispersal of radionuclides from uranium mining waste and the spread of acidic waters resulting from the in situ uranium leaching with sulphuric acid. Results show migration of acid waters into groundwater around the Cunha Baixa mine. This groundwater is tapped by irrigation wells in the agriculture area near the Cunha Baixa village. Water from wells displayed uranium ( 238 U) concentrations up to 19x10 3 mBq L -1 and sulphate ion concentrations up to 1070 mg L -1 . These enhanced concentrations are positively correlated with low water pH, pointing to a common origin for radioactivity, dissolved sulphate, and acidity in underground mining works. Radionuclide concentrations were determined in horticulture and farm products from this area also and results suggest low soil to plant transfer of radionuclides and low food chain transfer of radionuclides to man. Analysis of aerosols in surface air showed re suspension of dust from mining and milling waste heaps. Therefore, it is recommended to maintain mine water treatment and to plan remediation of these mine sites in order to prevent waste dispersal in the environment. (authors)

Glutamic Acid Selective Chemical Cleavage of Peptide Bonds.

Science.gov (United States)

Nalbone, Joseph M; Lahankar, Neelam; Buissereth, Lyssa; Raj, Monika

2016-03-04

Site-specific hydrolysis of peptide bonds at glutamic acid under neutral aqueous conditions is reported. The method relies on the activation of the backbone amide chain at glutamic acid by the formation of a pyroglutamyl (pGlu) imide moiety. This activation increases the susceptibility of a peptide bond toward hydrolysis. The method is highly specific and demonstrates broad substrate scope including cleavage of various bioactive peptides with unnatural amino acid residues, which are unsuitable substrates for enzymatic hydrolysis.

Molecular composition of dicarboxylic acids, ketocarboxylic acids, α-dicarbonyls and fatty acids in atmospheric aerosols from Tanzania, East Africa during wet and dry seasons

Science.gov (United States)

Mkoma, S. L.; Kawamura, K.

2013-02-01

Atmospheric aerosol samples of PM2.5 and PM10 were collected during the wet and dry seasons in 2011 from a rural site in Tanzania and analysed for water-soluble dicarboxylic acids, ketocarboxylic acids, α-dicarbonyls, and fatty acids using a gas chromatography/flame ionization detector (GC/FID) and GC/mass spectrometry. Here we report the molecular composition and sources of diacids and related compounds for wet and dry seasons. Oxalic acid (C2) was found as the most abundant diacid species followed by succinic and/or malonic acids whereas glyoxylic acid and glyoxal were the dominant ketoacid and α-dicarbonyl, respectively in both seasons in PM2.5 and PM10. Mean concentration of C2 in PM2.5 (121 ± 47 ng m-3) was lower in wet season than dry season (258 ± 69 ng m-3). Similarly, PM10 samples showed lower concentration of C2 (169 ± 42 ng m-3) in wet season than dry season (292 ± 165 ng m-3). Relative abundances of C2 in total diacids were 65% and 67% in PM2.5 and 65% and 64% in PM10 in the wet and dry seasons, respectively. Total concentrations of diacids (289-362 ng m-3), ketoacids (37.8-53.7 ng m-3), and α-dicarbonyls (5.7-7.8 ng m-3) in Tanzania are higher than those reported at a rural background site in Nylsvley (South Africa) but comparable or lower than those reported from sites in Asia and Europe. Diacids and ketoacids were found to be present mainly in PM2.5 in both seasons (total α-dicarbonyls in the dry season), suggesting a production of organic acids from pyrogenic sources and photochemical oxidations. Averaged contributions of total diacids to aerosol total carbon were 1.4% in PM2.5 and 2.1% in PM10 during wet season and 3.3% in PM2.5 and 3.9% in PM10 during dry season whereas those to water-soluble organic carbon were 2.2% and 4.7% in PM2.5 during wet season and 3.1% and 5.8% in PM10 during dry season. The higher ratios in dry season suggest an enhanced photochemical oxidation of organic precursors probably via heterogeneous reactions on

Amino acid analogs for tumor imaging

International Nuclear Information System (INIS)

Goodman, M.M.; Shoup, T.

1998-01-01

The invention provides novel amino acid compounds of use in detecting and evaluating brain and body tumors. These compounds combine the advantageous properties of 1-amino-cycloalkyl-1-carboxylic acids, namely, their rapid uptake and prolonged retention in tumors with the properties of halogen substituents, including certain useful halogen isotopes including fluorine-18, iodine-123, iodine-125, iodine-131, bromine-75, bromine-76, bromine-77 and bromine-82. In one aspect, the invention features amino acid compounds that have a high specificity for target sites when administered to a subject in vivo. Preferred amino acid compounds show a target to non-target ratio of at least 5:1, are stable in vivo and substantially localized to target within 1 hour after administration. An especially preferred amino acid compound is [ 18 F]-1-amino-3-fluorocyclobutane-1-carboxylic acid (FACBC). In another aspect, the invention features pharmaceutical compositions comprised of an α-amino acid moiety attached to either a four, five, or a six member carbon-chain ring. In addition, the invention features analogs of α-aminoisobutyric acid

The Consistency of Isotopologues of Ambient Atmospheric Nitric Acid in Passively Collected Samples

Science.gov (United States)

Bell, M. D.; Sickman, J. O.; Bytnerowicz, A.; Padgett, P.; Allen, E. B.

2012-12-01

Anthropogenic sources of nitrogen oxides have previously been shown to have distinctive isotopic signatures of oxygen and nitrogen. Nylon filters are currently used in passive sampling arrays to measure ambient atmospheric nitric acid concentrations and estimate deposition rates. This experiment measured the ability of nylon filters to consistently collect isotopologues of atmospheric nitric acid in the same ratios as they are present in the atmosphere. Samplers were deployed in continuous stirred tank reactors (CSTR) and at field sites across a nitrogen deposition gradient in Southern California. Filters were exposed over a four week period with individual filters being subjected to 1-4 week exposure times. Extracted nitric acid were measured for δ18O and δ15N ratios and compared for consistency based on length of exposure and amount of HNO3 collected. Filters within the CSTRs collected HNO3 at a consistent rate in both high and low concentration chambers. After two weeks of exposure, the mean δ18O values were within 0.5‰ of the δ18O of the source HNO3 solution. The mean of all weekly exposures were within 0.5‰ of the δ15N of the source solution, but after three weeks, the mean δ15N of adsorbed HNO3 was within 0.2‰. As the length of the exposure increased, the variability of measured delta values decreased for both elements. The field samplers collected HNO3 consistent with previously measured values along a deposition gradient. The mean δ18O at high deposition sites was 52.2‰ compared to 35.7‰ at the low deposition sites. Mean δ15N values were similar at all sites across the deposition gradient. Due to precipitation events occurring during the exposure period, the δ15N and δ18O of nitric acid were highly variable at all field sites. At single sites, changes in δ15N and δ18O were negatively correlated, consistent with two-sourcing mixing dynamics, but the slope of the regressions differed between high and low deposition sites. Anthropogenic

Assembly of barcode-like nucleic acid nanostructures.

Science.gov (United States)

Wang, Pengfei; Tian, Cheng; Li, Xiang; Mao, Chengde

2014-10-15

Barcode-like (BC) nanopatterns from programmed self-assembly of nucleic acids (DNA and RNA) are reported. BC nanostructures are generated by the introduction of open spaces at selected sites to an otherwise closely packed, plain, rectangle nucleic acid nanostructure. This strategy is applied to nanostructures assembled from both origami approach and single stranded tile approach. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dehydration of alcohols using solid acid catalysts

OpenAIRE

Cholerton, Mary

2014-01-01

Solid acid catalysts were prepared through silicon substitution into aluminophosphate frameworks. Silicon incorporation was confirmed using solid state nuclear magnetic resonance spectroscopy. The nature of the acid sites generated was determined using Fourier Transform infrared spectroscopy. These materials were tested as catalysts for the dehydration of ethanol to ethylene at low operating temperatures. The materials were active for dehydration of ethanol to ethylene with significant differ...

Investigations at the former sites of raw phosphate processing in Germany

International Nuclear Information System (INIS)

Reichelt, Andreas; Weiss, Dietmar; Feige, Sebastian; Wiegand, Jens; Gerler, Juergen

2008-01-01

Raw phosphates have been processed in an industrial scale in Germany approximately since the middle of the 19th century. During the centuries, huge amounts of residues with high mass specific activities have been accumulated. Within the framework of a historical study, we have determined the accumulated radionuclide inventory from 1865 to 2005. The consumption amounts to approx. 150 million tons raw phosphates (corresponds to approx. 2.22*10 14 Bq U-238) with a fraction of national production of approx. 1 million tons. A production of approx. 3 million tons of elemental phosphorus (calcium silicate slag: 3.6*10 13 Bq Ra-226) and approx. 12 million tons of phosphoric acid (phosphogypsum: 2.7*10 13 Bq Ra-226) had been achieved. In the next step, we have looked for the former sites with legacies of the raw phosphate processing industry. 92 sites of former production of phosphate fertilizers, 3 sites of former production of elemental phosphorus and 10 sites of former production of phosphoric acid had been identified. Some of them were selected for more detailed researches regarding the accumulated radionuclide inventory and on-site/laboratory radiological investigations. (author)

Investigation of secondary formation of formic acid: urban environment vs. oil and gas producing region

Science.gov (United States)

Yuan, B.; Veres, P. R.; Warneke, C.; Roberts, J. M.; Gilman, J. B.; Koss, A.; Edwards, P. M.; Graus, M.; Kuster, W. C.; Li, S.-M.; Wild, R. J.; Brown, S. S.; Dubé, W. P.; Lerner, B. M.; Williams, E. J.; Johnson, J. E.; Quinn, P. K.; Bates, T. S.; Lefer, B.; Hayes, P. L.; Jimenez, J. L.; Weber, R. J.; Zamora, R.; Ervens, B.; Millet, D. B.; Rappenglück, B.; de Gouw, J. A.

2015-02-01

Formic acid (HCOOH) is one of the most abundant carboxylic acids in the atmosphere. However, current photochemical models cannot fully explain observed concentrations and in particular secondary formation of formic acid across various environments. In this work, formic acid measurements made at an urban receptor site (Pasadena) in June-July 2010 during CalNex (California Research at the Nexus of Air Quality and Climate Change) and a site in an oil and gas producing region (Uintah Basin) in January-February 2013 during UBWOS 2013 (Uintah Basin Winter Ozone Studies) will be discussed. Although the VOC (volatile organic compounds) compositions differed dramatically at the two sites, measured formic acid concentrations were comparable: 2.3 ± 1.3 in UBWOS 2013 and 2.0 ± 1.0 ppb in CalNex. We determine that concentrations of formic acid at both sites were dominated by secondary formation (> 99%). A constrained box model using the Master Chemical Mechanism (MCM v3.2) underestimates the measured formic acid concentrations drastically at both sites (by a factor of > 10). Compared to the original MCM model that includes only ozonolysis of unsaturated organic compounds and OH oxidation of acetylene, when we updated yields of ozonolysis of alkenes and included OH oxidation of isoprene, vinyl alcohol chemistry, reaction of formaldehyde with HO2, oxidation of aromatics, and reaction of CH3O2 with OH, the model predictions for formic acid were improved by a factor of 6.4 in UBWOS 2013 and 4.5 in CalNex, respectively. A comparison of measured and modeled HCOOH/acetone ratios is used to evaluate the model performance for formic acid. We conclude that the modified chemical mechanism can explain 19 and 45% of secondary formation of formic acid in UBWOS 2013 and CalNex, respectively. The contributions from aqueous reactions in aerosol and heterogeneous reactions on aerosol surface to formic acid are estimated to be 0-6 and 0-5% in UBWOS 2013 and CalNex, respectively. We observe that

Site observational work plan for the UMTRA Project site at Spook, Wyoming

International Nuclear Information System (INIS)

1994-09-01

Ground water in the uppermost aquifer beneath and downgradient from the Spook site was contaminated by uranium-processing activities that occurred from 1962 until 1966. Contamination from the tailings pile and the acid pond (including uranium, selenium, nitrate, and radium-226 and -228) leached into the subsurface by infiltration and migrated into ground water, forming a plume extending approximately 2,500 feet (ft) (760 meters [m]) downgradient from the site. The surface remedial action at the Spook site under Subpart A of 40 CFR Part 192 consisted of stabilizing the uranium mill tailings and other residual radioactive materials in a disposal cell in the bottom of the Spook open-pit mine and covering the cell with overburden material. The ground water protection strategy was supplemental standards based on Class 3 ground water in the uppermost aquifer because of widespread ambient contamination. The proposed ground water protection strategy to comply with Subpart B of 40 CFR Part 192 at the Spook site is to perform no remediation. This strategy is based on ground water in the uppermost aquifer (also the zone of contamination) being classified as Class 3, which allows the application of supplemental standards. Class 3 ground water beneath the Spook site is neither a current nor a potential source of drinking water because of widespread, ambient contamination that cannot be cleaned up using treatment methods reasonably employed in public water supply systems

Pore-expanded SBA-15 sulfonic acid silicas for biodiesel synthesis.

Science.gov (United States)

Dacquin, J P; Lee, A F; Pirez, C; Wilson, K

2012-01-07

Here we present the first application of pore-expanded SBA-15 in heterogeneous catalysis. Pore expansion over the range 6-14 nm confers a striking activity enhancement towards fatty acid methyl ester (FAME) synthesis from triglycerides (TAG), and free fatty acid (FFA), attributed to improved mass transport and acid site accessibility. This journal is © The Royal Society of Chemistry 2012

Surface and interlayer base-characters in lepidocrocite titanate: The adsorption and intercalation of fatty acid

International Nuclear Information System (INIS)

Maluangnont, Tosapol; Arsa, Pornanan; Limsakul, Kanokporn; Juntarachairot, Songsit; Sangsan, Saithong; Gotoh, Kazuma; Sooknoi, Tawan

2016-01-01

While layered double hydroxides (LDHs) with positively-charged sheets are well known as basic materials, layered metal oxides having negatively-charged sheets are not generally recognized so. In this article, the surface and interlayer base-characters of O 2− sites in layered metal oxides have been demonstrated, taking lepidocrocite titanate K 0.8 Zn 0.4 Ti 1.6 O 4 as an example. The low basicity (0.04 mmol CO 2 /g) and low desorption temperature (50–300 °C) shown by CO 2 − TPD suggests that O 2− sites at the external surfaces is weakly basic, while those at the interlayer space are mostly inaccessible to CO 2 . The liquid-phase adsorption study, however, revealed the uptake as much as 37% by mass of the bulky palmitic acid (C 16 acid). The accompanying expansion of the interlayer space by ~0.1 nm was detected by PXRD and TEM. In an opposite manner to the external surfaces, the interlayer O 2− sites can deprotonate palmitic acid, forming the salt (i.e., potassium palmitate) occluded between the sheets. Two types of basic sites are proposed based on ultrafast 1 H MAS NMR and FTIR results. The interlayer basic sites in lepidocrocite titanate leads to an application of this material as a selective and stable two-dimensional (2D) basic catalyst, as demonstrated by the ketonization of palmitic acid into palmitone (C 31 ketone). Tuning of the catalytic activity by varying the type of metal (Zn, Mg, and Li) substituting at Ti IV sites was also illustrated. - Graphical abstract: Interlayer basic sites in lepidocrocite titanate, K 0.8 Zn 0.4 Ti 1.6 O 4 , lead to an intercalation of palmitic acid with a layer expansion. Display Omitted - Highlights: • K 0.8 Zn 0.4 Ti 1.6 O 4 intercalates palmitic acid, forming the occluded potassium salt. • The interlayer expansion is evidenced by PXRD patterns and TEM image. • Two types of basic sites are deduced from ultrafast 1 H MAS NMR. • Lepidocrocite titanate catalyses ketonization of palmitic acid to palmitone and

An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides.

Science.gov (United States)

Plummer, Chelsea E; Stover, Michele L; Bokatzian, Samantha S; Davis, John T M; Dixon, David A; Cassady, Carolyn J

2015-07-30

Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.

Mapping the active site of vaccinia virus RNA triphosphatase

International Nuclear Information System (INIS)

Gong Chunling; Shuman, Stewart

2003-01-01

The RNA triphosphatase component of vaccinia virus mRNA capping enzyme (the product of the viral D1 gene) belongs to a family of metal-dependent phosphohydrolases that includes the RNA triphosphatases of fungi, protozoa, Chlorella virus, and baculoviruses. The family is defined by two glutamate-containing motifs (A and C) that form the metal-binding site. Most of the family members resemble the fungal and Chlorella virus enzymes, which have a complex active site located within the hydrophilic interior of a topologically closed eight-stranded β barrel (the so-called ''triphosphate tunnel''). Here we queried whether vaccinia virus capping enzyme is a member of the tunnel subfamily, via mutational mapping of amino acids required for vaccinia triphosphatase activity. We identified four new essential side chains in vaccinia D1 via alanine scanning and illuminated structure-activity relationships by conservative substitutions. Our results, together with previous mutational data, highlight a constellation of six acidic and three basic amino acids that likely compose the vaccinia triphosphatase active site (Glu37, Glu39, Arg77, Lys107, Glu126, Asp159, Lys161, Glu192, and Glu194). These nine essential residues are conserved in all vertebrate and invertebrate poxvirus RNA capping enzymes. We discerned no pattern of clustering of the catalytic residues of the poxvirus triphosphatase that would suggest structural similarity to the tunnel proteins (exclusive of motifs A and C). We infer that the poxvirus triphosphatases are a distinct lineage within the metal-dependent RNA triphosphatase family. Their unique active site, which is completely different from that of the host cell's capping enzyme, recommends the poxvirus RNA triphosphatase as a molecular target for antipoxviral drug discovery

Method Development for Efficient Incorporation of Unnatural Amino Acids

KAUST Repository

Harris, Paul D.

2014-04-01

The synthesis of proteins bearing unnatural amino acids has the potential to enhance and elucidate many processes in biochemistry and molecular biology. There are two primary methods for site specific unnatural amino acid incorporation, both of which use the cell’s native protein translating machinery: in vitro chemical acylation of suppressor tRNAs and the use of orthogonal amino acyl tRNA synthetases. Total chemical synthesis is theoretically possible, but current methods severely limit the maximum size of the product protein. In vivo orthogonal synthetase methods suffer from the high cost of the unnatural amino acid. In this thesis I sought to address this limitation by increasing cell density, first in shake flasks and then in a bioreactor in order to increase the yield of protein per amount of unnatural amino acid used. In a parallel project, I used the in vitro chemical acylation system to incorporate several unnatural amino acids, key among them the fluorophore BODIPYFL, with the aim of producing site specifically fluorescently labeled protein for single molecule FRET studies. I demonstrated successful incorporation of these amino acids into the trial protein GFP, although incorporation was not demonstrated in the final target, FEN1. This also served to confirm the effectiveness of a new procedure developed for chemical acylation.

Method Development for Efficient Incorporation of Unnatural Amino Acids

KAUST Repository

Harris, Paul D.

2014-01-01

The synthesis of proteins bearing unnatural amino acids has the potential to enhance and elucidate many processes in biochemistry and molecular biology. There are two primary methods for site specific unnatural amino acid incorporation, both of which use the cell’s native protein translating machinery: in vitro chemical acylation of suppressor tRNAs and the use of orthogonal amino acyl tRNA synthetases. Total chemical synthesis is theoretically possible, but current methods severely limit the maximum size of the product protein. In vivo orthogonal synthetase methods suffer from the high cost of the unnatural amino acid. In this thesis I sought to address this limitation by increasing cell density, first in shake flasks and then in a bioreactor in order to increase the yield of protein per amount of unnatural amino acid used. In a parallel project, I used the in vitro chemical acylation system to incorporate several unnatural amino acids, key among them the fluorophore BODIPYFL, with the aim of producing site specifically fluorescently labeled protein for single molecule FRET studies. I demonstrated successful incorporation of these amino acids into the trial protein GFP, although incorporation was not demonstrated in the final target, FEN1. This also served to confirm the effectiveness of a new procedure developed for chemical acylation.

Implementation of an ex situ stabilization technique at the Sand Springs superfund site to solidify and stabilize acid tar sludges involving a quick-lime based stabilization process and innovative equipment design

International Nuclear Information System (INIS)

McManus, R.W.; Grajczak, P.; Wilcoxson, J.C.; Webster, S.D.

1997-01-01

An old refinery site was safely remediated a year before schedule and for 25% less than final engineering estimates for the stabilization remedy thanks to energetic project management and innovative design involving ex situ stabilization/solidification of acid tar sludges. A quicklime based process, Dispersion by Chemical Reaction (DCR trademark), was employed to solidify and stabilize (SS) over 103,000 cubic meters (135,000 cubic yards) of petroleum waste, mostly acidic tarry sludge. The SS process was selected over competing methods because it afforded minimal volume increase, could readily achieve Record of Decision (ROD) specified physical and chemical treatment goals, could be implemented with treatment equipment that minimized emissions, and could be performed with low reagent usage and at low cost. To ensure treatment goals were achieved and an accelerated schedule met, a custom designed and fabricated transportable treatment unit (TTU) was employed to implement the process. The treated material was visually soil-like in character, it was left in stockpiles for periods of time, and it was placed and compacted in the on site landfill using standard earth-moving equipment

Isolation and complete amino acid sequence of human thymopoietin and splenin

International Nuclear Information System (INIS)

Audhya, T.; Schlesinger, D.H.; Goldstein, G.

1987-01-01

Human thymopoietin and splenin were isolated from human thymus and spleen, respectively, by monitoring tissue fractionation with a bovine thymopoietin RIA cross-reactive with human thymopoietin and splenin. Bovine thymopoietin and splenin are 49-amino acid polypeptides that differ by only 2 amino acids at positions 34 and 43; the change at position 34 in the active-site region changes the receptor specificities and biological activities. The complete amino acid sequences of purified human thymopoietin and splenin were determined and shown to be 48-amino acid polypeptides differing at four positions. Ten amino acids, constant within each species for thymopoietin and splenin, differ between the human and bovine polypeptides. The pentapeptide active side of thymopoietin (residues 32-36) is constant between the human and bovine thymopoietins, but position 34 in the active site of splenin has changed from glutamic acid in bovine splenin to alanine in human splenin, accounting for the biological activity of the human but not the bovine splenin on the human T-cell line MOLT-4

Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity.

Science.gov (United States)

Wahba, Haytham M; Lecoq, Lauriane; Stevenson, Michael; Mansour, Ahmed; Cappadocia, Laurent; Lafrance-Vanasse, Julien; Wilkinson, Kevin J; Sygusch, Jurgen; Wilcox, Dean E; Omichinski, James G

2016-02-23

In bacterial resistance to mercury, the organomercurial lyase (MerB) plays a key role in the detoxification pathway through its ability to cleave Hg-carbon bonds. Two cysteines (C96 and C159; Escherichia coli MerB numbering) and an aspartic acid (D99) have been identified as the key catalytic residues, and these three residues are conserved in all but four known MerB variants, where the aspartic acid is replaced with a serine. To understand the role of the active site serine, we characterized the structure and metal binding properties of an E. coli MerB mutant with a serine substituted for D99 (MerB D99S) as well as one of the native MerB variants containing a serine residue in the active site (Bacillus megaterium MerB2). Surprisingly, the MerB D99S protein copurified with a bound metal that was determined to be Cu(II) from UV-vis absorption, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and electron paramagnetic resonance studies. X-ray structural studies revealed that the Cu(II) is bound to the active site cysteine residues of MerB D99S, but that it is displaced following the addition of either an organomercurial substrate or an ionic mercury product. In contrast, the B. megaterium MerB2 protein does not copurify with copper, but the structure of the B. megaterium MerB2-Hg complex is highly similar to the structure of the MerB D99S-Hg complexes. These results demonstrate that the active site aspartic acid is crucial for both the enzymatic activity and metal binding specificity of MerB proteins and suggest a possible functional relationship between MerB and its only known structural homologue, the copper-binding protein NosL.

On the Structure Sensitivity of Direct NO Decomposition over Low-Index Transition Metal Facets

DEFF Research Database (Denmark)

Falsig, Hanne; Shen, Juan; Khan, Tuhin Suvra

2014-01-01

We present a study of the dissociative chemisorption of NO, O2, and N2 over close-packed, stepped, kinked, and open (fcc {111}, {211}, {311}, {532}, {100}, and {110}) transition metal facets using density functional theory (DFT). The offset of the Bronsted-Evans-Polanyi (BEP) relations suggest......} rate. The ordering of the maximum activity over the facets is: {110} > {100} similar to {532} > {311} similar to {211} > {111}, which is in general agreement with the offset in the BEP relations. We show that the top-point location and shape of the volcano relations are approximately independent...... for generally obtaining quantitative agreement between theory and experiments is for the simulations to address in detail the propensities of the various types of active sites. Finally, we show that the ordering of NO decomposition rates among metals and facets is essentially unaltered when using BEP...

N-methyl-D-aspartic acid receptor agonists

DEFF Research Database (Denmark)

Madsen, U; Frydenvang, Karla Andrea; Ebert, B

1996-01-01

(R,S)-2-Amino-2-(3-hydroxy-5-methyl-4-isoxazolyl)acetic acid [(R,S)-AMAA, 4] is a potent and selective agonist at the N-methyl-D-aspartic acid (NMDA) subtype of excitatory amino acid receptors. Using the Ugi "four-component condensation" method, the two diastereomers (2R)- and (2S)-2-[3-(benzyloxy......) showed peak affinity for [3H]AMPA receptor sites (IC50 = 72 +/- 13 microM) and was shown to be a more potent inhibitor of [3H]CPP binding (IC50 = 3.7 +/- 1.5 microM) than (S)-AMAA (9) (IC50 = 61 +/- 6.4 microM). Neither enantiomer of AMAA affected [3H]kainic acid receptor binding significantly...

Aluminium release from acidic forest soil following deforestation and ...

African Journals Online (AJOL)

Acidic tropical soils often have high Al3+ concentrations in soil solutions, which can be toxic to plants and, thereby, reduce agricultural yields. This study focuses on the impact of deforestation and cultivation on the short and long-term Al geochemistry of acidic soils in Ghana, West Africa. Site-specific investigations were ...

Partitioning of metals in a degraded acid sulfate soil landscape: influence of tidal re-inundation.

Science.gov (United States)

Claff, Salirian R; Sullivan, Leigh A; Burton, Edward D; Bush, Richard T; Johnston, Scott G

2011-11-01

The oxidation and acidification of sulfidic soil materials results in the re-partitioning of metals, generally to more mobile forms. In this study, we examine the partitioning of Fe, Cr, Cu, Mn, Ni and Zn in the acidified surface soil (0-0.1 m) and the unoxidised sub-soil materials (1.3-1.5 m) of an acid sulfate soil landscape. Metal partitioning at this acidic site was then compared to an adjacent site that was previously acidified, but has since been remediated by tidal re-inundation. Differences in metal partitioning were determined using an optimised six-step sequential extraction procedure which targets the "labile", "acid-soluble", "organic", "crystalline oxide", "pyritic" and "residual" fractions. The surficial soil materials of the acidic site had experienced considerable losses of Cr, Cu, Mn and Ni compared to the underlying parent material due to oxidation and acidification, yet only minor losses of Fe and Zn. In general, the metals most depleted from the acidified surface soil materials exhibited the greatest sequestration in the surface soil materials of the tidally remediated site. An exception to this was iron, which accumulated to highly elevated concentrations in the surficial soil materials of the tidally remediated site. The "acid-soluble", "organic" and "pyritic" fractions displayed the greatest increase in metals following tidal remediation. This study demonstrates that prolonged tidal re-inundation of severely acidified acid sulfate soil landscapes leads to the immobilisation of trace metals through the surficial accumulation of iron oxides, organic material and pyrite. Copyright © 2011 Elsevier Ltd. All rights reserved.

Biogenic and Synthetic Peptides with Oppositely Charged Amino Acids as Binding Sites for Mineralization.

Science.gov (United States)

Lemloh, Marie-Louise; Altintoprak, Klara; Wege, Christina; Weiss, Ingrid M; Rothenstein, Dirk

2017-01-28

Proteins regulate diverse biological processes by the specific interaction with, e.g., nucleic acids, proteins and inorganic molecules. The generation of inorganic hybrid materials, such as shell formation in mollusks, is a protein-controlled mineralization process. Moreover, inorganic-binding peptides are attractive for the bioinspired mineralization of non-natural inorganic functional materials for technical applications. However, it is still challenging to identify mineral-binding peptide motifs from biological systems as well as for technical systems. Here, three complementary approaches were combined to analyze protein motifs consisting of alternating positively and negatively charged amino acids: (i) the screening of natural biomineralization proteins; (ii) the selection of inorganic-binding peptides derived from phage display; and (iii) the mineralization of tobacco mosaic virus (TMV)-based templates. A respective peptide motif displayed on the TMV surface had a major impact on the SiO₂ mineralization. In addition, similar motifs were found in zinc oxide- and zirconia-binding peptides indicating a general binding feature. The comparative analysis presented here raises new questions regarding whether or not there is a common design principle based on acidic and basic amino acids for peptides interacting with minerals.

Examining the role of glutamic acid 183 in chloroperoxidase catalysis

NARCIS (Netherlands)

Yi, X.; Conesa, A.; Punt, P.J.; Hager, L.P.

2003-01-01

Site-directed mutagenesis has been used to investigate the role of glutamic acid 183 in chloroperoxidase catalysis. Based on the x-ray crystallographic structure of chloroperoxidase, Glu-183 is postulated to function on distal side of the heme prosthetic group as an acid-base catalyst in

Biosynthetic origin of acetic acid using SNIF-NMR; Determinacao da origem biossintetica de acido acetico atraves da tecnica 'Site Specific Natural Isotopic Fractionation Studied by Nuclear Magnetic Resonance (SNIF-NMR)'

Energy Technology Data Exchange (ETDEWEB)

Boffo, Elisangela Fabiana; Ferreira, Antonio Gilberto [Sao Carlos Univ., SP (Brazil). Dept. de Quimica

2006-05-15

The main purpose of this work is to describe the use of the technique Site-Specific Natural Isotopic Fractionation of hydrogen (SNIF-NMR), using {sup 2}H and {sup 1}H NMR spectroscopy, to investigate the biosynthetic origin of acetic acid in commercial samples of Brazilian vinegar. This method is based on the deuterium to hydrogen ratio at a specific position (methyl group) of acetic acitained by fermentation, through different biosynthetic mechanisms, which result in different isotopic ratios. We measured the isotopic ratio of vinegars obtained through C{sub 3}, C{sub 4}, and CAM biosynthetic mechanisms, blends of C{sub 3} and C{sub 4} (agrins) and synthetic acetic acid. (author)

COMPOST-FREE BIOREACTOR TREATMENT OF ACID ROCK DRAINAGE - TECHNOLOGY CAPSULE

Science.gov (United States)

As part of the Superfund Innovative Technology Evaluation (SITE) program, an evaluation of the compost-free bioreactor treatment of acid rock drainage (ARD) from the Aspen Seep was conducted at the Leviathan Mine Superfund site located in a remote, high altitude area of Alpine Co...

Lipidization of Simple and di-Functional Amino Acids

International Nuclear Information System (INIS)

Zainab Idris; Mohd Wahid Samsudin; Salmiah Ahmad

2013-01-01

This paper discuss the modification of azelaic acid into its applicable form by attachment of both its carboxyl sites to N-terminal of amino acid ethyl ester forming amide linkages in anhydrous medium. Acylation of glycine ethyl ester hydrochloride with azelaic acid dichloride was best conducted in a 100 % anhydrous medium. L-amino acid ethyl ester bearing a primary hydroxyl group on its side chain gave mixtures of product and variation in composition depending on the mole ratio of reactants used. Reduction in purity was also observed for L-amino acid ethyl ester with primary -SH group on its side chain as compared to L-amino acid ethyl ester having -SCH 3 group on the L-amino acid side chain. The diamidoester of azelaic acid with L-alanine ethyl ester, L-valine ethyl ester, L-leucine ethyl ester and L-glutamic acid diethyl ester were in good yield when prepared through the modified Schotten-Baumann reaction conditions. (author)

Biogeochemical Regeneration of a Nodule Mining Disturbance Site: Trace Metals, DOC and Amino Acids in Deep-Sea Sediments and Pore Waters

Directory of Open Access Journals (Sweden)

Sophie A. L. Paul

2018-04-01

Full Text Available Increasing interest in deep-sea mineral resources, such as polymetallic nodules, calls for environmental research about possible impacts of mineral exploitation on the deep-sea ecosystem. So far, little geochemical comparisons of deep-sea sediments before and after mining induced disturbances have been made, and thus long-term environmental effects of deep-sea mining are unknown. Here we present geochemical data from sediment cores from an experimental disturbance area at 4,100 m water depth in the Peru Basin. The site was revisited in 2015, 26 years after a disturbance experiment mimicking nodule mining was carried out and compared to sites outside the experimental zone which served as a pre-disturbance reference. We investigated if signs of the disturbance are still visible in the solid phase and the pore water after 26 years or if pre-disturbance conditions have been re-established. Additionally, a new disturbance was created during the cruise and sampled 5 weeks later to compare short- and longer-term impacts. The particulate fraction and pore water were analyzed for major and trace elements to study element distribution and processes in the surface sediment. Pore water and bottom water samples were also analyzed for oxygen, nitrate, dissolved organic carbon, and dissolved amino acids, to examine organic matter degradation processes. The study area of about 11 km2 was found to be naturally more heterogeneous than expected, requiring an analysis of spatial variability before the disturbed and undisturbed sites can be compared. The disturbed sites exhibit various disturbance features: some surface sediments were mixed through, others had the top layer removed and some had additional material deposited on top. Pore water constituents have largely regained pre-disturbance gradients after 26 years. The solid phase, however, shows clear differences between disturbed and undisturbed sites in the top 20 cm so that the impact is still visible in the

Acid mine drainage in Australia: its extent and potential future liability. Supervising Scientist Report 125

International Nuclear Information System (INIS)

Harries, J.

1997-01-01

In order to better understand the impact of acid drainage in Australia and to provide a basis for assessing long-term management options, the Office of the Supervising Scientist (OSS) and the Australian Centre for Minesite Rehabilitation Research (ACMRR) initiated this study to prepare a status report on acid mine drainage in Australia. The study is supported by the Minerals Council of Australia. The coverage of this study includes all mine sites where sulphidic oxidation in mine wastes or mine workings leads to the release of contaminated drainage with off-site impacts. The objectives of the study were: 1. to quantify and characterise the generation of contaminated drainage by sulphidic oxidation from historic and current mining activities in Australia; 2. to develop a classification scheme to characterise the potential for off-site impacts from sulphidic oxidation in mine wastes; 3. to compare the cost at the national level of managing sulphidic oxidation in mine wastes and any resulting contaminated drainage with other mining and environmental costs; 4. to make recommendations based on the information received to improve the understanding and management of acid mine drainage in Australia. Information was collected on the extent and management of sulphidic oxidation and acid drainage at operating, historic and derelict mines in Australia. Mining operators, environmental officers, industry representatives, state government departments and others were asked about their experience with acid mine drainage and how it is currently managed at operating and historic mine sites. Based on the information collected, the additional cost of managing potentially acid generating wastes at operating mine sites is estimated to be about AUD 60 million per year. Potentially, the financial risk could be much greater if sulphide oxidation and release of pollutants is discovered after mine closure, as was the case for historic sites like Mt Lyell, Rum Jungle or Mt Morgan. The

Development of nonlinear optical materials using inorganic-organic complexes; Hisenkei kogaku zairyo to shite no yuki-muki fukugotai no kaihatsu

Energy Technology Data Exchange (ETDEWEB)

Mizuno, N. [Hokkaido University, Sapporo (Japan). Catalysis Research Center

1994-12-15

Development was attempted on organic-inorganic complexes as nonlinear optical materials. The objective is to develop elements with SHG activity (generating second harmonics) to change a visible ray into an ultraviolet ray by inserting P-nitroaniline (pNA) into such solid acids having strong static electric field as zeolite, laminar compounds, and heteropolyacid, and utilizing the static electric field and the molecule coordination field of inorganic compounds. Used for the pNA{center_dot}Bronsted acid composite are HBr, HCl, HNO3, and H2SO4. The pNA that has a center of symmetry in the crystalline structure and does not generate the second harmonics shows SHG when it is formed into a composite with HBr. No SHG is recognized in other acid composites. This difference is due to the difference in the crystalline structure. The SHG activity was generated when pNA is loaded onto alumina and silica as solid oxides. When zeolites are used as carriers, no SHG was observed. A composite of pNA{center_dot}AlCl3 has high SHG intensity, which reached a maximum when the pNA/AlCl3 ratio was two. This composite showed four new peaks that belong to the SHG activity phase. 8 refs., 2 figs., 2 tabs.

Size distributions of dicarboxylic acids, ketocarboxylic acids, α-dicarbonyls and fatty acids in atmospheric aerosols from Tanzania, East Africa during wet and dry seasons

Science.gov (United States)

Mkoma, S. L.; Kawamura, K.

2012-09-01

Atmospheric aerosol samples of PM2.5 and PM10 were collected during the wet and dry seasons in 2011 from a rural site in Tanzania and analysed for water-soluble dicarboxylic acids, ketocarboxylic acids, α-dicarbonyls and fatty acids using a gas chromatography (GC) and GC/mass spectrometry. Here we report the size distribution and sources of diacids and related compounds for wet and dry seasons. Oxalic acid (C2) was found as the most abundant diacid species followed by succinic and/or malonic acids whereas glyoxylic acid and glyoxal were the dominant ketoacids and α-dicarbonyls, respectively in both seasons in PM2.5 and PM10. Mean concentration of C2 in PM2.5 (121.5± 46.6 ng m-3) was lower in wet season than dry season (258.1± 69.5 ng m-3). Similarly, PM10 samples showed lower concentration of C2 (168.6 ± 42.4 ng m-3) in wet season than dry season (292.4± 164.8 ng m-3). Relative abundances of C2 in total diacids were 65.4% and 67.1% in PM2.5 and 64.6% and 63.9% in PM10 in the wet and dry seasons, respectively. Total concentrations of diacids (289-362 m-3), ketoacids (37.8-53.7ng m-3), and α-dicarbonyls (5.7-7.8 ng m-3) in Tanzania are higher to those reported at a rural background site in Nylsvley (South Africa) but comparable or lower to those reported from sites in Asia and Europe. Diacids and ketoacids were found to be present mainly in the fine fraction in both seasons (total α-dicarbonyls in the dry season), suggesting a production of organic aerosols from pyrogenic sources and photochemical oxidations. The averaged contributions of total diacid carbon to aerosol total carbon were 1.4% in PM2.5 and 2.1% in PM10 in wet season and 3.3% in PM2.5 and 3.9% in PM10 in dry season whereas those to water-soluble organic carbon were 2.2% and 4.7% inPM2.5 and 3.1% and 5.8% in PM10 during the wet and dry seasons, respectively. These ratios suggest an enhanced photochemical oxidation of organic precursors and heterogeneous reactions on aerosols under strong solar

Orthogonal use of a human tRNA synthetase active site to achieve multifunctionality.

Science.gov (United States)

Zhou, Quansheng; Kapoor, Mili; Guo, Min; Belani, Rajesh; Xu, Xiaoling; Kiosses, William B; Hanan, Melanie; Park, Chulho; Armour, Eva; Do, Minh-Ha; Nangle, Leslie A; Schimmel, Paul; Yang, Xiang-Lei

2010-01-01

Protein multifunctionality is an emerging explanation for the complexity of higher organisms. In this regard, aminoacyl tRNA synthetases catalyze amino acid activation for protein synthesis, but some also act in pathways for inflammation, angiogenesis and apoptosis. It is unclear how these multiple functions evolved and how they relate to the active site. Here structural modeling analysis, mutagenesis and cell-based functional studies show that the potent angiostatic, natural fragment of human tryptophanyl-tRNA synthetase (TrpRS) associates via tryptophan side chains that protrude from its cognate cellular receptor vascular endothelial cadherin (VE-cadherin). VE-cadherin's tryptophan side chains fit into the tryptophan-specific active site of the synthetase. Thus, specific side chains of the receptor mimic amino acid substrates and expand the functionality of the active site of the synthetase. We propose that orthogonal use of the same active site may be a general way to develop multifunctionality of human tRNA synthetases and other proteins.

Assessing the acidity of high silica chabazite H-SSZ-13 by FTIR using CO as molecular probe: Comparison with H-SAPO-34.

Science.gov (United States)

Bordiga, Silvia; Regli, Laura; Cocina, Donato; Lamberti, Carlo; Bjørgen, Morten; Lillerud, Karl Petter

2005-02-24

Zeolitic materials based on the chabazite topology, such as H-SAPO-34, possess unique shape-selectivity properties for converting methanol into light olefins. In addition to the topology, zeolite acidity is inherently linked to catalyst activity and selectivity. The acidic properties of high silica chabazite (H-SSZ-13) have attracted much attention in the past decade because the material represents an idealized model system having one acidic site per cage. Conclusions drawn so far have essentially been founded on quantum chemical methods. An experimentally based benchmark of the acidity of H-SSZ-13 has hitherto not been available. In this work, transmission FTIR spectroscopy provides a description of the different acidic sites of H-SSZ-13 by using CO as molecular probe at 70 K. The results demonstrate that H-SSZ-13 is a strongly Brønsted acidic material, essentially having two distinct families of acidic sites. In contrast to numerous preceding reports, we find it fundamental to consider proton distributions among all four possible sites, and do not delimit the interpretations to only two sites. The present data consistently suggest the most abundant family of protons to have three members being located on different crystalline positions on the eight-membered-ring window giving access to the chabazite cage. Consequently, these protons are exposed to two neighboring cages. The second, and less abundant family, is constituted by only one site that is situated on the six-membered ring defining the top/bottom of the barrel-shaped chabazite cage. This proton is therefore only exposed to one cage and requires a higher CO pressure to form adducts. Toward CO, both families of sites possess the same acidity. Parallel experiments were also carried out for the isostructural and commercially important H-SAPO-34 having an equal density of acidic sites. This is the first attempt to directly compare, on an experimental basis, the acidity of these two materials.

Surface and interlayer base-characters in lepidocrocite titanate: The adsorption and intercalation of fatty acid

Energy Technology Data Exchange (ETDEWEB)

Maluangnont, Tosapol, E-mail: tosapol.ma@kmitl.ac.th [College of Nanotechnology, King Mongkut' s Institute of Technology Ladkrabang, Bangkok 10520 (Thailand); Catalytic Chemistry Research Unit, Faculty of Science, King Mongkut' s Institute of Technology Ladkrabang, Bangkok 10520 (Thailand); Arsa, Pornanan [Catalytic Chemistry Research Unit, Faculty of Science, King Mongkut' s Institute of Technology Ladkrabang, Bangkok 10520 (Thailand); Department of Chemistry, Faculty of Science, King Mongkut' s Institute of Technology Ladkrabang, Bangkok 10520 (Thailand); Limsakul, Kanokporn; Juntarachairot, Songsit; Sangsan, Saithong [Department of Chemistry, Faculty of Science, King Mongkut' s Institute of Technology Ladkrabang, Bangkok 10520 (Thailand); Gotoh, Kazuma [Graduate School of Natural Science & Technology, Okayama University, 3-1-1 Tsushima-naka, Okayama 700-8530 (Japan); Sooknoi, Tawan, E-mail: kstawan@gmail.com [Catalytic Chemistry Research Unit, Faculty of Science, King Mongkut' s Institute of Technology Ladkrabang, Bangkok 10520 (Thailand); Department of Chemistry, Faculty of Science, King Mongkut' s Institute of Technology Ladkrabang, Bangkok 10520 (Thailand)

2016-06-15

While layered double hydroxides (LDHs) with positively-charged sheets are well known as basic materials, layered metal oxides having negatively-charged sheets are not generally recognized so. In this article, the surface and interlayer base-characters of O{sup 2−} sites in layered metal oxides have been demonstrated, taking lepidocrocite titanate K{sub 0.8}Zn{sub 0.4}Ti{sub 1.6}O{sub 4} as an example. The low basicity (0.04 mmol CO{sub 2}/g) and low desorption temperature (50–300 °C) shown by CO{sub 2}− TPD suggests that O{sup 2−} sites at the external surfaces is weakly basic, while those at the interlayer space are mostly inaccessible to CO{sub 2}. The liquid-phase adsorption study, however, revealed the uptake as much as 37% by mass of the bulky palmitic acid (C{sub 16} acid). The accompanying expansion of the interlayer space by ~0.1 nm was detected by PXRD and TEM. In an opposite manner to the external surfaces, the interlayer O{sup 2−} sites can deprotonate palmitic acid, forming the salt (i.e., potassium palmitate) occluded between the sheets. Two types of basic sites are proposed based on ultrafast {sup 1}H MAS NMR and FTIR results. The interlayer basic sites in lepidocrocite titanate leads to an application of this material as a selective and stable two-dimensional (2D) basic catalyst, as demonstrated by the ketonization of palmitic acid into palmitone (C{sub 31} ketone). Tuning of the catalytic activity by varying the type of metal (Zn, Mg, and Li) substituting at Ti{sup IV} sites was also illustrated. - Graphical abstract: Interlayer basic sites in lepidocrocite titanate, K{sub 0.8}Zn{sub 0.4}Ti{sub 1.6}O{sub 4}, lead to an intercalation of palmitic acid with a layer expansion. Display Omitted - Highlights: • K{sub 0.8}Zn{sub 0.4}Ti{sub 1.6}O{sub 4} intercalates palmitic acid, forming the occluded potassium salt. • The interlayer expansion is evidenced by PXRD patterns and TEM image. • Two types of basic sites are deduced from ultrafast

High-Yield Production of Levulinic Acid from Pretreated Cow Dung in Dilute Acid Aqueous Solution

Directory of Open Access Journals (Sweden)

Jialei Su

2017-02-01

Full Text Available Agricultural waste cow dung was used as feedstock for the production of a high value–added chemical levulinic acid (LA in dilute acid aqueous solutions. A high LA yield of 338.9 g/kg was obtained from the pretreated cow dung, which was much higher than that obtained from the crude cow dung (135 g/kg, mainly attributed to the breakage of the lignin fraction in the lignocellulose structure of the cow dung by potassium hydroxide (KOH pretreatment, and thus enhanced the accessibility of cow dung to the acid sites in the catalytic reaction. Meanwhile, another value-added chemical formic acid could be obtained with a yield of ca. 160 g/kg in the process, implying a total production of ca. 500 g/kg yield for LA and formic acid from the pretreated cow dung with the proposed process. The developed process was shown to be tolerant to high initial substrate loading with a satisfied LA yield. This work provides a promising strategy for the value-increment utilization of liglocellulosic agricultural residues.

Macroinvertebrate community response to acid mine drainage in rivers of the High Andes (Bolivia)

International Nuclear Information System (INIS)

Van Damme, Paul Andre; Hamel, Caroli; Ayala, Alfredo; Bervoets, Lieven

2008-01-01

Several High Andes Rivers are characterized by inorganic water pollution known as acid mine drainage (AMD). The aim of this study was to assess the relationship between metal concentrations in the sediments and the macroinvertebrate communities in two river basins affected by AMD. In general, the taxon diversity of the macroinvertebrate community at the family level was low. The concentrations of Cd, Cu, Zn, Pb and Ni at mining sites were higher than at unpolluted sites. The pH of the water was alkaline (7.0-8.5) in unpolluted sites, whereas it dropped to very low values (<3) at mining sites. Redundancy Analysis (RDA) showed that pH was the best predictor of macroinvertebrate community richness. The number of macroinvertebrate families decreased gradually with increasing acidity, both in pools and riffles, though it is suggested that riffle communities were more affected because they are in closer contact with the acid water. - Community response to AMD

5'-azido-N-1-naphthylphthalamic acid, a photolabile analog of the auxin transport inhibitor, N-1-naphthylphthalamic acid: synthesis and binding properties

International Nuclear Information System (INIS)

Voet, J.G.; Howley, K.; Shumsky, J.S.

1987-01-01

The polar transport of the plant growth regulator, auxin (indole-3-acetic acid, IAAH), is thought to involve the participation of several proteins in the plasma membrane, including a specific, saturable, voltage independent H + /IAA - efflux carrier located preferentially at the basal end of each cell. Auxin transport is specifically inhibited by the herbicide, N-1-naphthylphthalamic acid (NPA), which binds specifically to a protein in the plasma membrane, thought to be either the IAA - efflux carrier or an allosteric effector protein. They have synthesized and characterized a photolabile analog of NPA, 5'-azido-N-1-naphthylphthalamic acid (Az-NPA). This potential photoaffinity label for the NPA binding protein competes with 3 H-NPA for binding sites on Curcurbita pepo L. (zucchini) stem cell membranes with K/sub j/ = 1.5 x 10 -7 M. The K/sub i/ for NPA under these conditions is 2 x 10 -8 M, indicating that the affinity of Az-NPA for the membranes is only 7.5 fold lower than NPA. While the binding of 4.6 x 10 -6 M Az-NPA to NPA binding sites is reversible in the dark, exposure to light results in a 30% loss in 3 H-NPA binding ability. Pretreatment with 10 -4 M NPA protects the membranes against photodestruction of 3 H-NPA binding sites by Az-NPA, supporting the conclusion that Az-NPA destroys these sites by specific covalent attachment

A human fatty acid synthase inhibitor binds β-ketoacyl reductase in the keto-substrate site.

Science.gov (United States)

Hardwicke, Mary Ann; Rendina, Alan R; Williams, Shawn P; Moore, Michael L; Wang, Liping; Krueger, Julie A; Plant, Ramona N; Totoritis, Rachel D; Zhang, Guofeng; Briand, Jacques; Burkhart, William A; Brown, Kristin K; Parrish, Cynthia A

2014-09-01

Human fatty acid synthase (hFAS) is a complex, multifunctional enzyme that is solely responsible for the de novo synthesis of long chain fatty acids. hFAS is highly expressed in a number of cancers, with low expression observed in most normal tissues. Although normal tissues tend to obtain fatty acids from the diet, tumor tissues rely on de novo fatty acid synthesis, making hFAS an attractive metabolic target for the treatment of cancer. We describe here the identification of GSK2194069, a potent and specific inhibitor of the β-ketoacyl reductase (KR) activity of hFAS; the characterization of its enzymatic and cellular mechanism of action; and its inhibition of human tumor cell growth. We also present the design of a new protein construct suitable for crystallography, which resulted in what is to our knowledge the first co-crystal structure of the human KR domain and includes a bound inhibitor.

Phosphorus mobilization by sulfide oxidation in carbonate sediments from seagrass and unvegetated sites in the US Virgin Islands

DEFF Research Database (Denmark)

Jensen, Henning; Pedersen, Ole; Koch, M. R.

PHOSPHORUS MOBILIZATION BY SULFIDE OXIDATION IN CARBONATE SEDIMENTS FROM SEAGRASS AND UNVEGETATED SITES IN THE US VIRGIN ISLANDS Sulfide produced by sulfate reduction (SR) can be oxidized by seagrass root O2 flux in shallow carbonate sediments low in Fe. The sulfuric acid produced from sulfide...... oxidation, as well as metabolic acids from aerobic respiration, has the potential to mobilize solid phase phosphorus (P) pools in support of seagrass nutrition. Fresh sediments from four US Virgin Islands sites were modestly acidified to near-neutral pH in slurries. Following sulfuric acid amendments...

A MAS NMR and DRIFT study of the Ga species in Ga/H-ZSM5 catalysts and their effect on propane ammoxidation

Energy Technology Data Exchange (ETDEWEB)

Pal, P. [Indian Inst. of Petroleum, Dehradun (India). Catalysis Division; Quartararo, J. [Liverpool Univ., Liverpool (United Kingdom). Leverhulme Centre for Innovative Catalysis, Dept. of Chemistry; Abd Hamid, S.B. [Malaya Univ., Postgraduate School, Bangunan (Malaysia); Derouane, E.G. [Algarve Univ., Faro (Portugal). Faculdade de Ciencias e Tecnologia; Vedrine, J.C. [Laboratoire de Physico-Chimie des Surface, Paris (France). Faculdade de Ciencias e Tecnologia; Magusin, P.C.M.M.; Anderson, B.G. [Eindhoven Univ. of Technology, Eindhoven (Netherlands). Schuit Institute of Catalysis

2005-07-01

This paper presents the results of a study that sought information about the nature and environment of the gallium (Ga) species in Ga/H-ZSM5 zeolites following H{sub 2}-O{sub 2} redox treatments applied during their activation by use of magic-angle spinning (MAS) {sup 71}Ga, {sup 27}Al, and {sup 29}Si NMR spectroscopy (Ga coordination) complemented by diffuse reflectance FT IR (DRIFT) spectroscopy (Bronsted acidity). This information was then correlated with their catalytic behavior for the ammoxidation of propane. Ga species were observed in several environments: octahedrally coordinated gallium in small Ga{sub 2}O{sub 3} particles at the external surface of the zeolite crystals; octahedrally coordinated gallium in GaO(OH) or related species; and tetrahedrally coordinated gallium in cationic-exchange positions inside the zeolite. Redox (H{sub 2}-O{sub 2}) cycles promote the migration of gallium from the GaO(OH) or Ga{sub 2}O{sub 3} species at the external surface of the zeolite crystals to cationic-exchange sites within the zeolite channels. It was concluded that the redox treatment had a beneficial effect on its catalytic performance for the ammoxidation of propane, which occurs via a bifunctional mechanism. The main product was acetonitrile at high gallium and aluminium contents. It was suggested that higher yields in acrylonitrile could be obtained through Ga-modified zeolites with a higher gallium and lower aluminium content. 22 refs., 1 tab., 6 figs.

Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

Directory of Open Access Journals (Sweden)

Shu-ichi Nakano

2011-01-01

Full Text Available Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

Characterization and complexation of humic acid

International Nuclear Information System (INIS)

Kim, J.I.; Buckau, G.; Klenze, R.; Rhee, D.S.; Wimmer, H.

1990-05-01

This paper summarizes the research contributions to the CEC project MIRAGE II, particularly the research area: complexation and colloids (COCO). The first part of the paper comprises the characterization of humic and fulvic acids from different origins: a commercial product from Aldrich Co. used as a reference humic acid and site specific humic acids from Gorleben (FRG), Boom Clay (B) and Fanay Augeres (F) aquifer systems. The second part includes the complexation of trivalent actinides: Am(III) and Cm(III) with various humic acids. A number of different methods have been applied for the complexation study: spectrophotometry, ultrafiltration, laser-indused photoacoustic spectroscopy (LPAS) and time resolved laser fluorescence spectroscopy (TRLFS). The evaluation process of complexation constant is discussed extensively and the well consolidated results are presented, which can be directly used for the geochemical modelling of the radionuclide migration. (orig.)

Recycling abandoned lead battery sites

International Nuclear Information System (INIS)

Montgomery, A.H.

1993-01-01

In the past, automobile batteries were recycled principally for their lead content. The waste generated at battery wrecking facilities consisted of spent acid, crushed casings (ebonite and plastic), and where secondary smelting was involved, matte, slag, and carbon from the smelting process. These waste products were generally disposed in an on-site in a landfill or stored in piles. If the facility shut down because further commercial operations were not financially viable, the waste piles remained to be addressed at a later date through remedial action or reclamation programs. There are many of these facilities in the US. Nationally, about 28 sites have been discovered by the US Environmental Protection Agency (EPA) under the Superfund program and are under investigation or administrative orders for remedial action. A major remediation effort is now underway at the Gould Superfund Site in Portland, Oregon, which was operated as a secondary smelting facility between 1949 and 1981. This paper describes the nature of the contamination at the Gould site and the work conducted by Canonie Environmental Services Corp. (Canonie) to develop a process which would treat the waste from battery wrecking operations and produce revenue generating recyclable products while removing the source contamination (lead) from the site. The full-scale commercial plant is now operating and is expected to achieve a throughput rate of between 200 and 250 tons per day in the coming weeks

Hyaluronic acid-carboxymethylcellulose film and perianastomotic adhesions in previously irradiated rats.

Science.gov (United States)

Bowers, D; Raybon, R B; Wheeless, C R

1999-12-01

Postoperative intra-abdominal adhesions are a major source of postsurgical morbidity. Pelvic irradiation increases the likelihood of adhesion development. The purpose of this study was to evaluate the effects of hyaluronic acid-carboxymethylcellulose film, which was designed as a barrier to prevent adhesions, on the healing of ileal anastomoses performed on irradiated rat bowel. Sixty-eight female Sprague-Dawley rats underwent whole pelvic irradiation with a single fraction of 1700 cGy. Twenty weeks later the rats underwent exploratory laparotomy with segmental ileal resection and reanastomosis. Eighteen of the anastomoses were wrapped in hyaluronic acid-carboxymethylcellulose film. Fifty anastomoses were not treated with any adhesion-inhibiting barrier. On the fifth postoperative day the animals underwent another laparotomy for evaluation of the anastomotic sites. At the second laparotomy 93% of the rats treated with hyaluronic acid-carboxymethylcellulose film were found to have perianastomotic abscesses. In the non-hyaluronic acid-carboxymethylcellulose film group the perianastomotic abscess rate was 24% (P hyaluronic acid-carboxymethylcellulose film was associated with a markedly increased rate of abscess formation at the operative site.

Intestinal metabolism of sulfur amino acids

Science.gov (United States)

The gastrointestinal tract (GIT) is a metabolically significant site of sulfur amino acid (SAA) metabolism in the body and metabolizes approx. 20% of the dietary methionine intake that is mainly transmethylated to homocysteine and transsulfurated to cysteine. The GIT accounts for approx. 25% of the ...

Fluorescence quenching of graphene oxide combined with the site-specific cleavage of restriction endonuclease for deoxyribonucleic acid demethylase activity assay

Energy Technology Data Exchange (ETDEWEB)

Ji, Lijuan; Qian, Yingdan; Wu, Ping; Zhang, Hui; Cai, Chenxin, E-mail: cxcai@njnu.edu.cn

2015-04-15

Highlights: • An approach for sensitive and selective DNA demethylase activity assay is reported. • This assay is based on the fluorescence quenching of GO and site-specific cleavage of endonuclease. • It can determine as low as 0.05 ng mL{sup −1} of MBD2 with a linear range of 0.2–300 ng mL{sup −1}. • It has an ability to recognize MBD2 from other possibly coexisting proteins and cancer cell extracts. • It can avoid false signals, requiring no bisulfite conversion, PCR amplification, radioisotope-labeling. - Abstract: We report on the development of a sensitive and selective deoxyribonucleic acid (DNA) demethylase (using MBD2 as an example) activity assay by coupling the fluorescence quenching of graphene oxide (GO) with the site-specific cleavage of HpaII endonuclease to improve the selectivity. This approach was developed by designing a single-stranded probe (P1) that carries a binding region to facilitate the interaction with GO, which induces fluorescence quenching of the labeled fluorophore (FAM, 6-carboxyfluorescein), and a sensing region, which contains a hemi-methylated site of 5′-CmCGG-3′, to specifically recognize the target (T1, a 32-mer DNA from the promoter region of p53 gene) and hybridize with it to form a P1/T1 duplex. After demethylation with MBD2, the duplex can be specifically cleaved using HpaII, which releases the labeled FAM from the GO surface and results in the recovery of fluorescence. However, this cleavage is blocked by the hemi-methylation of this site. Thus, the magnitude of the recovered fluorescence signal is related to the MBD2 activity, which establishes the basis of the DNA demethylase activity assay. This assay can determine as low as ∼(0.05 ± 0.01) ng mL{sup −1} (at a signal/noise of 3) of MBD2 with a linear range of 0.2–300 ng mL{sup −1} and recognize MBD2 from other possibly coexisting proteins and cancer cell extracts. The advantage of this assay is its ability to avoid false signals and no

Specific labeling of the thyroxine binding site in thyroxine-binding globulin: determination of the amino acid composition of a labeled peptide fragment isolated from a proteolytic digest of the derivatized protein.

Science.gov (United States)

Tabachnick, M; Perret, V

1987-08-01

[125I] Thyroxine has been covalently bound to the thyroxine binding site in thyroxine-binding globulin by reaction with the bifunctional reagent, 1,5-difluoro-2,4-dinitrobenzene. An average of 0.47 mol of [125I] thyroxine was incorporated per mol protein; nonspecific binding amounted to 8%. A labeled peptide fragment was isolated from a proteolytic digest of the derivatized protein by HPLC and its amino acid composition was determined. Comparison with the amino acid sequence of thyroxine-binding globulin indicated partial correspondence of the labeled peptide with two possible regions in the protein. These regions also coincide with part of the barrel structure present in the closely homologous protein, alpha 1-antitrypsin.

Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA.

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Orr Ashenberg

2017-03-01

Full Text Available The innate-immune restriction factor MxA inhibits influenza replication by targeting the viral nucleoprotein (NP. Human influenza virus is more resistant than avian influenza virus to inhibition by human MxA, and prior work has compared human and avian viral strains to identify amino-acid differences in NP that affect sensitivity to MxA. However, this strategy is limited to identifying sites in NP where mutations that affect MxA sensitivity have fixed during the small number of documented zoonotic transmissions of influenza to humans. Here we use an unbiased deep mutational scanning approach to quantify how all single amino-acid mutations to NP affect MxA sensitivity in the context of replication-competent virus. We both identify new sites in NP where mutations affect MxA resistance and re-identify mutations known to have increased MxA resistance during historical adaptations of influenza to humans. Most of the sites where mutations have the greatest effect are almost completely conserved across all influenza A viruses, and the amino acids at these sites confer relatively high resistance to MxA. These sites cluster in regions of NP that appear to be important for its recognition by MxA. Overall, our work systematically identifies the sites in influenza nucleoprotein where mutations affect sensitivity to MxA. We also demonstrate a powerful new strategy for identifying regions of viral proteins that affect inhibition by host factors.

Signal peptide discrimination and cleavage site identification using SVM and NN.

Science.gov (United States)

Kazemian, H B; Yusuf, S A; White, K

2014-02-01

About 15% of all proteins in a genome contain a signal peptide (SP) sequence, at the N-terminus, that targets the protein to intracellular secretory pathways. Once the protein is targeted correctly in the cell, the SP is cleaved, releasing the mature protein. Accurate prediction of the presence of these short amino-acid SP chains is crucial for modelling the topology of membrane proteins, since SP sequences can be confused with transmembrane domains due to similar composition of hydrophobic amino acids. This paper presents a cascaded Support Vector Machine (SVM)-Neural Network (NN) classification methodology for SP discrimination and cleavage site identification. The proposed method utilises a dual phase classification approach using SVM as a primary classifier to discriminate SP sequences from Non-SP. The methodology further employs NNs to predict the most suitable cleavage site candidates. In phase one, a SVM classification utilises hydrophobic propensities as a primary feature vector extraction using symmetric sliding window amino-acid sequence analysis for discrimination of SP and Non-SP. In phase two, a NN classification uses asymmetric sliding window sequence analysis for prediction of cleavage site identification. The proposed SVM-NN method was tested using Uni-Prot non-redundant datasets of eukaryotic and prokaryotic proteins with SP and Non-SP N-termini. Computer simulation results demonstrate an overall accuracy of 0.90 for SP and Non-SP discrimination based on Matthews Correlation Coefficient (MCC) tests using SVM. For SP cleavage site prediction, the overall accuracy is 91.5% based on cross-validation tests using the novel SVM-NN model. © 2013 Published by Elsevier Ltd.

Combined fluorescence and electrochemical investigation on the binding interaction between organic acid and human serum albumin

Institute of Scientific and Technical Information of China (English)

CHEN Yan-Min; GUO Liang-Hong

2009-01-01

Human serum albumin (HSA) is a plasma protein responsible for the binding and transport of fatty acids and a variety of exogenous chemicals such as drugs and environmental pollutants. Such binding plays a crucial role in determining the ADME (absorption, distribution, metabolism, and excretion) and bioavailability of the pollutants. We report investigation on the binding interaction between HSA and acetic acid (C2), octanoic acid (C8) and dodecanoic acid (C12) by the combination of site-specific fluorescent probe, tryptophan intrinsic fluorescence and tyrosine electrochemistry. Two fluorescent probes, dansylamide and dansyl-L-proline, were employed in the displacement measurement to study fatty acid interaction with the two drug-binding sites on HSA. Intrinsic fluorescence of tryptophan in HSA was monitored upon addition of the fatty acids into HSA. Electrocatalyzed response of the tyrosine residues in HSA by a redox mediator was used to investigate the binding interaction. Qualitatively, observations made by the three approaches are very similar. HSA did not show any change in either fluorescence or electrochemistry after mixing with C2, suggesting there is no significant interaction with the short-chain fatty acid. For C8, the measured signal dropped in a single-exponential fashion, indicative of independent and non-cooperative binding. The calculated association constant and binding ratio is 3.1×106 L/mol and 1 with drug binding Site I, 1.1×107 L/mol and 1 with Site II, and 7.0×104 L/mol and 4 with the tryptophan site. The measurement with C12 displayed multiple phases of fluorescence change, suggesting cooperativity and allosteric effect of C12 binding. These results correlate well with those obtained by the established methods, and validate the new approach as a viable tool to study the interactions of environmental pollutants with biological molecules.

Catalytically important amino-acid residues of abalone alginate lyase HdAly assessed by site-directed mutagenesis

OpenAIRE

Yamamoto, Sayo; Sahara, Takehiko; Sato, Daisuke; Kawasaki, Kosei; Ohgiya, Satoru; Inoue, Akira; Ojima, Takao

2008-01-01

Alginate lyase is an enzyme that degrades alginate chains via β-elimination and has been used for the production of alginate oligosaccharides and protoplasts from brown algae. Previously, we deduced the amino-acid sequence of an abalone alginate lyase, HdAly, from its cDNA sequence and, through multiple amino-acid sequence alignment, found that several basic amino-acid residues were highly conserved among the polysaccharide-lyase family 14 (PL-14) enzymes including HdAly. In the present study...

Intestinal uptake of bile acids: effect of external abdominal irradiation

International Nuclear Information System (INIS)

Thomson, A.B.R.; Cheeseman, C.I.; Walker, K.

1984-01-01

Abdominal irradiation has recently been shown to influence the uptake of hexoses, amino acids, fatty acids and cholesterol into the jejunum of rats. The present studies were undertaken with a previously validated in vitro technique to determine the effect of abdominal irradiation from a cesium source on the rates of uptake of six bile acids into the jejunum, ileum, and colon. The results show that: 1) there likely are multiple ileal carriers for bile acids: 2) abdominal irradiation has a variable effect on these carriers; 3) the passive permeability to bile acids varies with the bile acid and with the site along the intestine; and 4) abdominal irradiation is associated with a rise in the colonic permeability to only some bile acids

Control of bovine hepatic fatty acid oxidation

International Nuclear Information System (INIS)

Jesse, B.W.; Emery, R.S.; Thomas, J.W.

1986-01-01

Fatty acid oxidation by bovine liver slices and mitochondria was examined to determine potential regulatory sites of fatty acid oxidation. Conversion of 1-[ 14 C]palmitate to 14 CO 2 and total [ 14 C]acid-soluble metabolites was used to measure fatty acid oxidation. Oxidation of palmitate (1 mM) was linear in both liver slice weight and incubation time. Carnitine stimulated palmitate oxidation; 2 mM dl-carnitine produced maximal stimulation of palmitate oxidation to both CO 2 and acid-soluble metabolites. Propionate (10 mM) inhibited palmitate oxidation by bovine liver slices. Propionate (.5 to 10 mM) had no effect on palmitate oxidation by mitochondria, but malonyl Coenzyme A, the first committed intermediate of fatty acid synthesis, inhibited mitochondrial palmitate oxidation (inhibition constant = .3 μM). Liver mitochonndrial carnitine palmitoyltransferase exhibited Michaelis constants for palmitoyl Coenzyme A and l-carnitine of 11.5 μM and .59 mM, respectively. Long-chain fatty acid oxidation in bovine liver is regulated by mechanisms similar to those in rats but adapted to the unique digestive physiology of the bovine

COMPOST-FREE BIOLOGICAL TREATMENT OF ACID ROCK DRAINAGE, TECHNICAL EVALUATION BULLETIN

Science.gov (United States)

As part of the Superfund Innovative Technology Evaluation (SITE) program, an evaluation of the compost-free bioreactor treatment of acid rock drainage (ARD) from the Aspen Seep was conducted at the Leviathan Mine Superfund site located in a remote, high altitude area of Alpine Co...

Acid-basic and complexation properties of a sedimentary humic acid. A study on the Barra Bonita reservoir of Tietê river, São Paulo State, Brazil

Directory of Open Access Journals (Sweden)

Abate Gilberto

2001-01-01

Full Text Available Acid-base and complexation properties of humic acid (HA isolated from a river sediment were studied by potentiometric titration, adopting the discrete site distribution model and the modified Gran functions for data fitting. Six classes of titratable groups were characterized, with pKa values between 2.4 and 10.2. Carboxylic groups accounted for 66% of the total of ionizable sites. The complexing properties were studied with regard to Cu2+, Pb2+, Cd2+ and Zn2+ ions by potentiometric titration using Cu ion selective electrode, or amalgam electrodes (Pb, Cd and Zn. The data treatment by the Scatchard method revealed two binding sites for copper and lead and one binding site for cadmium and zinc. The average stability constants were in the following order: log KHA-Cu > log KHA-Pb > log KHA-Cd @ log KHA-Zn, while the complexing capacity order, Cc, was: Pb > Cu > Cd @ Zn.

Internal ribosome entry site-mediated translation of a mammalian mRNA is regulated by amino acid availability

NARCIS (Netherlands)

Fernandez, J.; Yaman, I.; Mishra, R.; Merrick, W. C.; Snider, M. D.; Lamers, W. H.; Hatzoglou, M.

2001-01-01

The cationic amino acid transporter, Cat-1, facilitates the uptake of the essential amino acids arginine and lysine. Amino acid starvation causes accumulation and increased translation of cat-1 mRNA, resulting in a 58-fold increase in protein levels and increased arginine uptake. A bicistronic mRNA

Synthesis of α-MoC1-x Nanoparticles with a Surface-Modified SBA-15 Hard Template: Determination of Structure-Function Relationships in Acetic Acid Deoxygenation.

Science.gov (United States)

Baddour, Frederick G; Nash, Connor P; Schaidle, Joshua A; Ruddy, Daniel A

2016-07-25

Surface modification of mesoporous SBA-15 silica generated a hydrophobic environment for a molybdenum diamine (Mo-diamine) precursor solution, enabling direct growth of isolated 1.9±0.4 nm α-MoC1-x nanoparticles (NPs) inside the pores of the support. The resulting NP catalysts are bifunctional, and compared to bulk α-MoC1-x and β-Mo2 C, the NPs exhibit a greater acid-site:H-site ratio and a fraction of stronger acid sites. The greater acid-site:H-site ratio results in higher decarbonylation (DCO) selectivity during acetic acid hydrodeoxygenation (HDO) reactions, and the stronger acid sites lead to higher activity and ketonization (KET) selectivity at high temperatures. The hard-templating synthetic method could be a versatile route toward carbide NPs of varying size, composition, and phase, on a range of mesoporous oxide supports. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bronsted acidity of H-MCM-22 as probed by variable-temperature infrared spectroscopy of adsorbed CO and N-2

Czech Academy of Sciences Publication Activity Database

Delgado, M. R.; Bulánek, R.; Eliášová, Pavla; Arean, C. O.

2014-01-01

Roč. 227, MAY 2014 (2014), s. 45-49 ISSN 0920-5861 R&D Projects: GA ČR GBP106/12/G015 Institutional support: RVO:61388955 Keywords : adsorption * hydrogen bonding * IR probe molecules Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.893, year: 2014

NRMRL EVALUATES ACTIVE AND SEMI-PASSIVE TECHNOLOGIES FOR TREATING ACID MINE DRAINAGE

Science.gov (United States)

Two-page article describing three SITE demonstration projects underway on the Leviathan mine site in California. BiPhasic lime treatment, lime treatment lagoons and compost free BioReactors are being evaluated as innovative technologies for treating acid mine drainage.

Site-Specific Biomolecule Labeling with Gold Clusters

OpenAIRE

Ackerson, Christopher J.; Powell, Richard D.; Hainfeld, James F.

2010-01-01

Site-specific labeling of biomolecules in vitro with gold clusters can enhance the information content of electron cryomicroscopy experiments. This chapter provides a practical overview of well-established techniques for forming biomolecule/gold cluster conjugates. Three bioconjugation chemistries are covered: Linker-mediated bioconjugation, direct gold–biomolecule bonding, and coordination-mediated bonding of nickel(II) nitrilotriacetic acid (NTA)-derivatized gold clusters to polyhistidine (...

Oleic acid and linoleic acid from Tenebrio molitor larvae inhibit BACE1 activity in vitro: molecular docking studies.

Science.gov (United States)

Youn, Kumju; Yun, Eun-Young; Lee, Jinhyuk; Kim, Ji-Young; Hwang, Jae-Sam; Jeong, Woo-Sik; Jun, Mira

2014-02-01

In our ongoing research to find therapeutic compounds for Alzheimer's disease (AD) from natural resources, the inhibitory activity of the BACE1 enzyme by Tenebrio molitor larvae and its major compounds were evaluated. The T. molitor larvae extract and its fractions exhibited strong BACE1 suppression. The major components of hexane fraction possessing both high yield and strong BACE1 inhibition were determined by thin layer chromatography, gas chromatography, and nuclear magnetic resonance analysis. A remarkable composition of unsaturated long chain fatty acids, including oleic acid and linoleic acid, were identified. Oleic acid, in particular, noncompetitively attenuated BACE1 activity with a half-maximal inhibitory concentration (IC₅₀) value of 61.31 μM and Ki value of 34.3 μM. Furthermore, the fatty acids were stably interacted with BACE1 at different allosteric sites of the enzyme bound with the OH of CYS319 and the NH₃ of TYR320 for oleic acid and with the C=O group of GLN304 for linoleic acid. Here, we first revealed novel pharmacophore features of oleic acids and linoleic acid to BACE1 by in silico docking studies. The present findings would clearly suggest potential guidelines for designing novel BACE1 selective inhibitors.

Functional analysis of a potential regulatory K+-binding site in the Na+, K+-ATPase

DEFF Research Database (Denmark)

Schack, Vivien Rodacker; Vilsen, Bente

The Na+, K+-ATPase functions by actively transporting 3 Na+ ions out of and 2 K+ ions into the cell, thereby creating ion gradients crucial for many physiological processes. Recently, a combined structural and functional study of the closely related Ca2+-ATPase indicated the presence...... of a regulatory K+-binding site in the P-domain of the enzyme, identifying E732 as being of particular importance (Sorensen, Clausen et al. 2004). In addition, P709 is thought to play a significant role in the structural organization of this site. Both E732 and P709 are highly conserved among P-type ATPases (E732...... is present as either glutamic acid or aspartic acid), which supports their importance and additionally raises the question whether this site may play a general role among P-type ATPases. In Na+, K+-ATPase, K+ functions directly as a substrate for membrane binding sites, however, an additional regulatory...

Grafting on nuclear tracks using the active sites that remain after the etching process

International Nuclear Information System (INIS)

Mazzei, R.; Bermudez, G. Garcia; Chappa, V.C.; Grosso, M.F. del; Fernandez, A.

2006-01-01

Poly(propylene) foils were irradiated with Ag ions and then chemically etched to produce samples with structured surfaces. After the etching procedure the active sites that remain on the latent track were used to graft acrylic acid. Nuclear tracks before grafting were visualised using a transmission electron microscope. The grafting yields were determined by weight measurements as a function of ion fluence, etching and grafting time, and were also analysed using Fourier transform infrared spectroscopy. Both measurements suggest that the acrylic acid was grafted on etched tracks using the active sites produced by the swift heavy ion beam

Grafting on nuclear tracks using the active sites that remain after the etching process

Energy Technology Data Exchange (ETDEWEB)

Mazzei, R. [Unidad de Aplicaciones Tecnologicas y Agropecuarias, CNEA, 1429 Buenos Aires (Argentina) and Universidad Tecnologica Nacional, Buenos Aires (Argentina)]. E-mail: mazzei@cae.cnea.gov.ar; Bermudez, G. Garcia [U. A. de Fisica, Tandar, CNEA, 1429 Buenos Aires (Argentina); Escuela de Ciencia y Tecnologia, UNSAM, 1653 Buenos Aires (Argentina); Consejo Nacional de Investigaciones Cientificas y Tecnicas (Argentina); Chappa, V.C. [U. A. de Fisica, Tandar, CNEA, 1429 Buenos Aires (Argentina); Grosso, M.F. del [U. A. de Fisica, Tandar, CNEA, 1429 Buenos Aires (Argentina); U. A. de Materiales, CNEA, 1429 Buenos Aires (Argentina); Fernandez, A. [Universidad Tecnologica Nacional, Buenos Aires (Argentina)

2006-09-15

Poly(propylene) foils were irradiated with Ag ions and then chemically etched to produce samples with structured surfaces. After the etching procedure the active sites that remain on the latent track were used to graft acrylic acid. Nuclear tracks before grafting were visualised using a transmission electron microscope. The grafting yields were determined by weight measurements as a function of ion fluence, etching and grafting time, and were also analysed using Fourier transform infrared spectroscopy. Both measurements suggest that the acrylic acid was grafted on etched tracks using the active sites produced by the swift heavy ion beam.

Boosted surface acidity in TiO{sub 2} and Al{sub 2}O{sub 3}-TiO{sub 2} nanotubes as catalytic supports

Energy Technology Data Exchange (ETDEWEB)

Camposeco, R. [Molecular Engineering Program, Mexican Institute of Petroleum, 07730, México, D.F. (Mexico); Department of Chemistry, UAM-A, 55534, México, D.F. (Mexico); Castillo, S., E-mail: scastill@imp.mx [Molecular Engineering Program, Mexican Institute of Petroleum, 07730, México, D.F. (Mexico); Department of Chemical Engineering, ESIQIE-IPN, 75876, México, D.F. (Mexico); Mejía-Centeno, Isidro; Navarrete, J.; Nava, N. [Molecular Engineering Program, Mexican Institute of Petroleum, 07730, México, D.F. (Mexico)

2015-11-30

Graphical abstract: - Highlights: • Surface acidity of NTs was modified by adding alumina. • Brönsted acid sites remain constant but Lewis acid sites are increased remarkably. • IR characterization by lutidine and pyridine confirms the surface acidity of NTs. • 98% of NO conversion was reached between 380 and 480 °C on NT-5Al. • The boosted surface acidity of NT-Al improves the catalytic activity for SCR-NO. - Abstract: In this study, titanate nanotubes (NT) and titanate nanotubes with alumina (NT-Al) were studied as solid acid catalytic supports to show the relationship between the kind of acidity and catalytic activity. The supports were characterized by XRD, TEM, FTIR, XPS, and tested in the SCR-NO with NH{sub 3}. It was found that the amount of Brönsted acid sites was maintained and the Lewis acid sites were significantly affected by the addition of alumina (1, 3, 5 and 10 wt.%); such acidity was higher than that of the titanate nanotubes (NT) by two-fold. To confirm the formation of titanate nanotubes and titanate nanotubes with alumina, transmission electron microscopy (TEM) was used. X-ray diffraction (XRD) revealed the formation of the H{sub 2}Ti{sub 4}O{sub 9}·H{sub 2}O phase. All NT and NT-Al supports presented catalytic activity to remove NO with NH{sub 3} under lean conditions, confirming the presence of an important amount of Brönsted and Lewis acid sites in both NT and NT-Al supports.

Baseline and premining geochemical characterization of mined sites

Science.gov (United States)

Nordstrom, D. Kirk

2015-01-01

A rational goal for environmental restoration of new, active, or inactive mine sites would be ‘natural background’ or the environmental conditions that existed before any mining activities or other related anthropogenic activities. In a strictly technical sense, there is no such thing as natural background (or entirely non-anthropogenic) existing today because there is no part of the planet earth that has not had at least some chemical disturbance from anthropogenic activities. Hence, the terms ‘baseline’ and ‘pre-mining’ are preferred to describe these conditions. Baseline conditions are those that existed at the time of the characterization which could be pre-mining, during mining, or post-mining. Protocols for geochemically characterizing pre-mining conditions are not well-documented for sites already mined but there are two approaches that seem most direct and least ambiguous. One is characterization of analog sites along with judicious application of geochemical modeling. The other is reactive-transport modeling (based on careful synoptic sampling with tracer-injection) and subtracting inputs from known mining and mineral processing. Several examples of acidic drainage are described from around the world documenting the range of water compositions produced from pyrite oxidation in the absence of mining. These analog sites provide insight to the processes forming mineralized waters in areas untouched by mining. Natural analog water-chemistry data is compared with the higher metal concentrations, metal fluxes, and weathering rates found in mined areas in the few places where comparisons are possible. The differences are generally 1–3 orders of magnitude higher for acid mine drainage.

Applications of site-specific labeling to study HAMLET, a tumoricidal complex of α-lactalbumin and oleic acid.

Science.gov (United States)

Mercer, Natalia; Ramakrishnan, Boopathy; Boeggeman, Elizabeth; Qasba, Pradman K

2011-01-01

Alpha-lactalbumin (α-LA) is a calcium-bound mammary gland-specific protein that is found in milk. This protein is a modulator of β1,4-galactosyltransferase enzyme, changing its acceptor specificity from N-acetyl-glucosamine to glucose, to produce lactose, milk's main carbohydrate. When calcium is removed from α-LA, it adopts a molten globule form, and this form, interestingly, when complexed with oleic acid (OA) acquires tumoricidal activity. Such a complex made from human α-LA (hLA) is known as HAMLET (Human A-lactalbumin Made Lethal to Tumor cells), and its tumoricidal activity has been well established. In the present work, we have used site-specific labeling, a technique previously developed in our laboratory, to label HAMLET with biotin, or a fluoroprobe for confocal microscopy studies. In addition to full length hLA, the α-domain of hLA (αD-hLA) alone is also included in the present study. We have engineered these proteins with a 17-amino acid C-terminal extension (hLA-ext and αD-hLA-ext). A single Thr residue in this extension is glycosylated with 2-acetonyl-galactose (C2-keto-galactose) using polypeptide-α-N-acetylgalactosaminyltransferase II (ppGalNAc-T2) and further conjugated with aminooxy-derivatives of fluoroprobe or biotin molecules. We found that the molten globule form of hLA and αD-hLA proteins, with or without C-terminal extension, and with and without the conjugated fluoroprobe or biotin molecule, readily form a complex with OA and exhibits tumoricidal activity similar to HAMLET made with full-length hLA protein. The confocal microscopy studies with fluoroprobe-labeled samples show that these proteins are internalized into the cells and found even in the nucleus only when they are complexed with OA. The HAMLET conjugated with a single biotin molecule will be a useful tool to identify the cellular components that are involved with it in the tumoricidal activity.

Stabilization of bacterially expressed erythropoietin by single site-specific introduction of short branched PEG chains at naturally occurring glycosylation sites.

Science.gov (United States)

Hoffmann, E; Streichert, K; Nischan, N; Seitz, C; Brunner, T; Schwagerus, S; Hackenberger, C P R; Rubini, M

2016-05-24

The covalent attachment of polyethylene glycol (PEG) to therapeutic proteins can improve their physicochemical properties. In this work we utilized the non-natural amino acid p-azidophenylalanine (pAzF) in combination with the chemoselective Staudinger-phosphite reaction to install branched PEG chains to recombinant unglycosylated erythropoietin (EPO) at each single naturally occurring glycosylation site. PEGylation with two short 750 or 2000 Da PEG units at positions 24, 38, or 83 significantly decreased unspecific aggregation and proteolytic degradation while biological activity in vitro was preserved or even increased in comparison to full-glycosylated EPO. This site-specific bioconjugation approach permits to analyse the impact of PEGylation at single positions. These results represent an important step towards the engineering of site-specifically modified EPO variants from bacterial expression with increased therapeutic efficacy.

Stereoselective synthesis of stable-isotope-labeled amino acids

Energy Technology Data Exchange (ETDEWEB)

Unkefer, C.J.; Martinez, R.A.; Silks, L.A. III [Los Alamos National Laboratory, NM (United States); Lodwig, S.N. [Centralia College, WA (United States)

1994-12-01

For magnetic resonance and vibrational spectroscopies to reach their full potential, they must be used in combination with sophisticated site-specific stable isotope labeling of biological macromolecules. Labeled amino acids are required for the study of the structure and function of enzymes and proteins. Because there are 20 common amino acids, each with its own distinguishing chemistry, they remain a synthetic challenge. The Oppolzer chiral auxiliary provides a general tool with which to approach the synthesis of labeled amino acids. By using the Oppolzer auxiliary, amino acids can be constructed from several small molecules, which is ideal for stable isotope labeling. In addition to directing the stereochemistry at the {alpha}-carbon, the camphorsultam can be used for stereo-specific isotope labeling at prochiral centers in amino acids. By using the camphorsultam auxiliary we have the potential to synthesize virtually any isotopomer of all of the common amino acids.

Stereoselective synthesis of stable-isotope-labeled amino acids

International Nuclear Information System (INIS)

Unkefer, C.J.; Martinez, R.A.; Silks, L.A. III; Lodwig, S.N.

1994-01-01

For magnetic resonance and vibrational spectroscopies to reach their full potential, they must be used in combination with sophisticated site-specific stable isotope labeling of biological macromolecules. Labeled amino acids are required for the study of the structure and function of enzymes and proteins. Because there are 20 common amino acids, each with its own distinguishing chemistry, they remain a synthetic challenge. The Oppolzer chiral auxiliary provides a general tool with which to approach the synthesis of labeled amino acids. By using the Oppolzer auxiliary, amino acids can be constructed from several small molecules, which is ideal for stable isotope labeling. In addition to directing the stereochemistry at the α-carbon, the camphorsultam can be used for stereo-specific isotope labeling at prochiral centers in amino acids. By using the camphorsultam auxiliary we have the potential to synthesize virtually any isotopomer of all of the common amino acids

Molecular composition of dicarboxylic acids, ketocarboxylic acids, α-dicarbonyls and fatty acids in atmospheric aerosols from Tanzania, East Africa during wet and dry seasons

Directory of Open Access Journals (Sweden)

S. L. Mkoma

2013-02-01

Full Text Available Atmospheric aerosol samples of PM_2.5 and PM₁₀ were collected during the wet and dry seasons in 2011 from a rural site in Tanzania and analysed for water-soluble dicarboxylic acids, ketocarboxylic acids, α-dicarbonyls, and fatty acids using a gas chromatography/flame ionization detector (GC/FID and GC/mass spectrometry. Here we report the molecular composition and sources of diacids and related compounds for wet and dry seasons. Oxalic acid (C₂ was found as the most abundant diacid species followed by succinic and/or malonic acids whereas glyoxylic acid and glyoxal were the dominant ketoacid and α-dicarbonyl, respectively in both seasons in PM_2.5 and PM₁₀. Mean concentration of C₂ in PM_2.5 (121 ± 47 ng m⁻³ was lower in wet season than dry season (258 ± 69 ng m⁻³. Similarly, PM₁₀ samples showed lower concentration of C₂ (169 ± 42 ng m⁻³ in wet season than dry season (292 ± 165 ng m⁻³. Relative abundances of C₂ in total diacids were 65% and 67% in PM_2.5 and 65% and 64% in PM₁₀ in the wet and dry seasons, respectively. Total concentrations of diacids (289–362 ng m⁻³, ketoacids (37.8–53.7 ng m⁻³, and α-dicarbonyls (5.7–7.8 ng m⁻³ in Tanzania are higher than those reported at a rural background site in Nylsvley (South Africa but comparable or lower than those reported from sites in Asia and Europe. Diacids and ketoacids were found to be present mainly in PM_2.5 in both seasons (total α-dicarbonyls in the dry season, suggesting a production of organic acids from pyrogenic sources and photochemical oxidations. Averaged contributions of total diacids to aerosol total carbon were 1.4% in PM_2.5 and 2.1% in PM₁₀ during wet season and 3.3% in PM_2.5 and 3.9% in PM₁₀ during

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

Energy Technology Data Exchange (ETDEWEB)

Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan [Institute of Biotechnology CAS, Videnska 1083, 142 20 Prague (Czech Republic)

2015-10-27

The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

Study of the interactions between Eu(III) and Al2O3 particles in the presence of phenolic acids

International Nuclear Information System (INIS)

Moreau, P.

2012-01-01

In the framework of environmental pollution by radionuclides, this work was focused on the interactions occurring in systems containing europium(III) - as a chemical analogue for the actinides Am(III) and Cm(III) -, phenolic acids - lignin degradation products and anti-fungi, naturally occurring in soils, and alumina - representative of sorption sites found in the environment. This study was conducted at different scales of description: the macroscopic scale - to quantify Eu(III) and/or phenolic acids adsorption onto the mineral surface -, and the microscopic scale - to study the chemical environment of Eu(III) using Time-Resolved Luminescence Spectroscopy (TRLS). First, the binary systems, i.e. systems containing only two entities among the three previously cited, were characterized. Complexation constants of Eu(III) by three phenolic acids (4-hydroxybenzoic, 3,4-dihydroxybenzoic, and 3,4,5-trihydroxybenzoic acids) were determined and quantum calculations (DFT) were carried out on La(III)-acid complex analogues. Sorption of the acids onto aluminol sites was modelled using surface complexation concepts. Analyses of two ternary systems (containing 4-hydroxybenzoic and 3,4-dihydroxybenzoic acids) revealed synergistic processes for Eu(III) and phenolic acids sorption onto Al 2 O 3 . A spectral fingerprint of ternary complex involving Eu(III)/4-hydroxybenzoic acid/Al 2 O 3 surface sites was evidenced. (author) [fr

Wismut sites regeneration: Flooding of the former leaching mine 'Koenigstein'

International Nuclear Information System (INIS)

Runge, W.

2001-01-01

Flooding of abandoned mines was part of the regeneration programme for the Wismut sites. In January 2001, flooding was started at the Koenigstein mine, the easternmost site of the Wismut in Sachsen. The operations are scheduled for 5 - 6 years. Since 1984, this mine was operated in a leaching process involving sulphuric acid, so that a number of measures had to be taken to ensure that polluted flooding water will not contaminate the groundwater in this area [de

Increments to chiral recognition facilitating enantiomer separations of chiral acids, bases, and ampholytes using Cinchona-based zwitterion exchanger chiral stationary phases.

Science.gov (United States)

Wernisch, Stefanie; Pell, Reinhard; Lindner, Wolfgang

2012-07-01

The intramolecular distances of anion and cation exchanger sites of zwitterionic chiral stationary phases represent potential tuning sites for enantiomer selectivity. In this contribution, we investigate the influence of alkanesulfonic acid chain length and flexibility on enantiomer separations of chiral acids, bases, and amphoteric molecules for six Cinchona alkaloid-based chiral stationary phases in comparison with structurally related anion and cation exchangers. Employing polar-organic elution conditions, we observed an intramolecular counterion effect for acidic analytes which led to reduced retention times but did not impair enantiomer selectivities. Retention of amphoteric analytes is based on simultaneous double ion pairing of their charged functional groups with the acidic and basic sites of the zwitterionic selectors. A chiral center in the vicinity of the strong cation exchanger site is vital for chiral separations of bases. Sterically demanding side chains are beneficial for separations of free amino acids. Enantioseparations of free (un-derivatized) peptides were particularly successful in stationary phases with straight-chain alkanesulfonic acid sites, pointing to a beneficial influence of more flexible moieties. In addition, we observed pseudo-enantiomeric behavior of quinine and quinidine-derived chiral stationary phases facilitating reversal of elution orders for all analytes. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mesoporous (Ta, Nb3W7 Modified with Stearic Acid Used as Solid Acids for Esterification

Directory of Open Access Journals (Sweden)

Fei Chang

2017-01-01

Full Text Available Mesoporous solid acids Ta3W7 and Nb3W7 were prepared from TaCl5 and NbCl5 with WCl6 in the presence of stearic acid (SA via a sol-gel method, respectively. For comparison, mesoporous Ta3W7-P123 mixed oxides and mesoporous Nb3W7-P123 mixed oxides were synthesized in the same way. The catalysts were characterized through TGA, XRD, SEM, TEM, BET, and NH3-TPD. Experimental results showed that Ta3W7-SA and Nb3W7-SA exhibited several advantages such as higher activity, shorter preparation period, lower cost, stronger acid sites, and higher surface area, which had potential to be used as mesoporous heterogeneous catalysts in biodiesel production.

Improvement of surface acidity and structural regularity of Zr-modified mesoporous MCM-41

Energy Technology Data Exchange (ETDEWEB)

Chen, L.F. [Departamento de Ciencias Basicas, Universidad Autonoma Metropolitana-A, Av. San Pablo 180, Col. Reynosa-Tamaulipas, 02200 Mexico D.F. (Mexico)]. E-mail: chenlf2001@yahoo.com; Norena, L.E. [Departamento de Ciencias Basicas, Universidad Autonoma Metropolitana-A, Av. San Pablo 180, Col. Reynosa-Tamaulipas, 02200 Mexico D.F. (Mexico); Navarrete, J. [Grupo de Molecular Ingenieria, Instituto Mexicano del Petroleo, Eje Lazaro Cardenas 152, 07730 Mexico D.F. (Mexico); Wang, J.A. [Laboratorio de Catalisis y Materiales, SEPI-ESIQIE, Instituto Politecnico Nacional, Av. Politecnico S/N, Col. Zacatenco, 07738 Mexico D.F. (Mexico)

2006-06-10

This work reports the synthesis and surface characterization of a Zr-modified mesoporous MCM-41 solid with an ordered hexagonal arrangement, prepared through a templated synthesis route, using cetyltrimethylammonium chloride as the template. The surface features, crystalline structure, textural properties and surface acidity of the materials were characterized by in situ Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD), N{sub 2} physisorption isotherms, {sup 29}Si MAS-NMR and in situ FT-IR of pyridine adsorption. It is evident that the surfactant cations inserted into the network of the solids during the preparation could be removed by calcination of the sample above 500 deg. C. The resultant material showed a large surface area of 680.6 m{sup 2} g{sup -1} with a uniform pore diameter distribution in a very narrow range centered at approximately 2.5 nm. Zirconium incorporation into the Si-MCM-41 framework, confirmed by {sup 29}Si MAS-NMR analysis, increased not only the wall thickness of the mesopores but also the long-range order of the periodically hexagonal structure. Both, Lewis and Broensted acid sites, were formed on the surface of the Zr-modified MCM-41 solid. Compared to Si-MCM-41 on which only very weak Lewis acid sites were formed, the densities of both Lewis and Broensted acid sites and the strength of the acidity on the Zr-modified sample were significantly increased, indicating that the incorporation of zirconium greatly enhances the acidity of the material.

Acidity of clay edges from ab-initio simulations

International Nuclear Information System (INIS)

Tazi, Sami; Salanne, Mathieu; Rotenberg, Benjamin; Turq, Pierre; Sprik, Michiel; Sulpizi, Marialore

2012-01-01

Document available in extended abstract form only. One of the most important factor to understand and predict the sorption of cations on clay surfaces is the protonation state of the surface sites, which is difficult to determine experimentally. Indeed, titration provides a global measure only; it does not probe the status of different silanol (Si-OH) and aluminol sites (Al-OH and Al-OH 2 ) present along the edges of clay sheets in the presence of water. A novel method has been recently designed to quantify the acidity of chemical species. This method allows to estimate pKa values from First Principles Molecular Dynamics by thermodynamic integration. We have applied it to the case of pyrophyllite clay edge sites. These calculations will allow us to subsequently perform classical Molecular Dynamic simulations with realistic surface structures (protonated/deprotonated sites) for natural clays in the presence of water. After presenting the method, we show its application to the (010) edge of pyrophyllite. We find that the most acidic group is Si-OH while the least acidic one is Al-OH, which never deprotonates in water because of its high pKa value (22.1). We further provide a microscopic understanding of the solvation structure and reactivity of the edges of neutral clays. In particular we address the tendency to deprotonation of the different reactive groups on the (010) face of pyrophyllite, showing the important role of solvation and its rearrangements after deprotonation. Finally, we compare our results to the one predicted by the empiric method MUSIC and the estimate from deprotonation energies in the vacuum, confirming the important role of solvation in both the protonated and deprotonated states. (authors)

Searching for Extraterrestrial Amino Acids in a Contaminated Meteorite: Amino Acid Analyses of the Canakkale L6 Chondrite

Science.gov (United States)

Burton, A. S.; Elsila, J. E.; Glavin, D. P.; Dworkin, J. P.; Ornek, C. Y.; Esenoglu, H. H.; Unsalan, O.; Ozturk, B.

2016-01-01

Amino acids can serve as important markers of cosmochemistry, as their abundances and isomeric and isotopic compositions have been found to vary predictably with changes in parent body chemistry and alteration processes. Amino acids are also of astrobiological interest because they are essential for life on Earth. Analyses of a range of meteorites, including all groups of carbonaceous chondrites, along with H, R, and LL chondrites, ureilites, and a martian shergottite, have revealed that amino acids of plausible extraterrestrial origin can be formed in and persist after a wide range of parent body conditions. However, amino acid analyses of L6 chondrites to date have not provided evidence for indigenous amino acids. In the present study, we performed amino acid analysis on larger samples of a different L6 chondite, Canakkale, to determine whether or not trace levels of indigenous amino acids could be found. The Canakkale meteor was an observed fall in late July, 1964, near Canakkale, Turkey. The meteorite samples (1.36 and 1.09 g) analyzed in this study were allocated by C. Y. Ornek, along with a soil sample (1.5 g) collected near the Canakkale recovery site.

Binding of 3,4,5,6-Tetrahydroxyazepanes to the Acid-[beta]-glucosidase Active Site: Implications for Pharmacological Chaperone Design for Gaucher Disease

Energy Technology Data Exchange (ETDEWEB)

Orwig, Susan D.; Tan, Yun Lei; Grimster, Neil P.; Yu, Zhanqian; Powers, Evan T.; Kelly, Jeffery W.; Lieberman, Raquel L. (Scripps); (GIT)

2013-03-07

Pharmacologic chaperoning is a therapeutic strategy being developed to improve the cellular folding and trafficking defects associated with Gaucher disease, a lysosomal storage disorder caused by point mutations in the gene encoding acid-{beta}-glucosidase (GCase). In this approach, small molecules bind to and stabilize mutant folded or nearly folded GCase in the endoplasmic reticulum (ER), increasing the concentration of folded, functional GCase trafficked to the lysosome where the mutant enzyme can hydrolyze the accumulated substrate. To date, the pharmacologic chaperone (PC) candidates that have been investigated largely have been active site-directed inhibitors of GCase, usually containing five- or six-membered rings, such as modified azasugars. Here we show that a seven-membered, nitrogen-containing heterocycle (3,4,5,6-tetrahydroxyazepane) scaffold is also promising for generating PCs for GCase. Crystal structures reveal that the core azepane stabilizes GCase in a variation of its proposed active conformation, whereas binding of an analogue with an N-linked hydroxyethyl tail stabilizes GCase in a conformation in which the active site is covered, also utilizing a loop conformation not seen previously. Although both compounds preferentially stabilize GCase to thermal denaturation at pH 7.4, reflective of the pH in the ER, only the core azepane, which is a mid-micromolar competitive inhibitor, elicits a modest increase in enzyme activity for the neuronopathic G202R and the non-neuronopathic N370S mutant GCase in an intact cell assay. Our results emphasize the importance of the conformational variability of the GCase active site in the design of competitive inhibitors as PCs for Gaucher disease.

New insights into sulfur amino acids function in gut health and disease

Science.gov (United States)

The gastrointestinal tract (GIT) is a metabolically significant site of sulfur amino acids (SAAs) metabolism in the body. Aside from their role in protein synthesis, methionine and cysteine are involved in many biological functions and diseases. Methionine (MET) is an indispensable amino acid and is...

High frequency and large deposition of acid fog on high elevation forest.

Science.gov (United States)

Igawa, Manabu; Matsumura, Ko; Okochi, Hiroshi

2002-01-01

We have collected and analyzed fogwater on the mountainside of Mt. Oyama (1252 m) in the Tanzawa Mountains of Japan and observed the fog event frequency from the base of the mountain with a video camera. The fog event frequency increased with elevation and was observed to be present 46% of the year at the summit. The water deposition via throughfall increased with elevation because of the increase in fogwater interception and was about twice that via rain at the summit, where the air pollutant deposition via throughfall was several times that via rainwater. The dry deposition and the deposition via fogwater were dominant factors in the total ion deposition at high elevation sites. In a fog event, nitric acid, the major acid component on the mountain, is formed during the transport of the air mass from the base of the mountain along the mountainside, where gases including nitric acid deposit and are scavenged by fogwater. Therefore, high acidity caused by nitric acid and relatively low ion strength are observed in the fogwater at high elevation sites.

Probing the active site of MIO-dependent 2,3-aminomutases, key catalysts in the biosynthesis of beta-amino acids incorporated in secondary metabolites

Science.gov (United States)

Bruner, Steven D.; Cooke, Heather

2012-01-01

The tyrosine aminomutase SgTAM produces (S)-β-tyrosine from l-tyrosine in the biosynthesis of the enediyne antitumor antibiotic C-1027. This conversion is promoted by the methylideneimidazole-5-one (MIO) prosthetic group. MIO was first identified in the homologous family of ammonia lyases, which deaminate aromatic amino acids to form α,β-unsaturated carboxylates. Studies of substrate specificity have been described for lyases but there have been no reports in altering the substrate specificity of aminomutases. Furthermore, it remains unclear as to what structural properties are responsible for catalyzing the presumed readdition of the amino group into the α,β-unsaturated intermediates to form β-amino acids. Attempts to elucidate specificity and mechanistic determinants of SgTAM have also proved to be difficult as it is recalcitrant to perturbations to the active site via mutagenesis. An X-ray co-crystal structure of the SgTAM mutant of the catalytic base with l-tyrosine verified important substrate binding residues as well as the enzymatic base. Further mutagenesis revealed that removal of these crucial interactions renders the enzyme inactive. Proposed structural determinants for mutase activity probed via mutagenesis, time-point assays and X-ray crystallography revealed a complicated role for these residues in maintaining key quaternary structure properties that aid in catalysis. PMID:20577998

Pyrolusite Process® to remove acid mine drainage contaminants from Kimble Creek in Ohio: A pilot study

Science.gov (United States)

Shiv Hiremath; Kirsten Lehtoma; Mike Nicklow; Gary. Willison

2013-01-01

The Kimble Creek abandoned coal mine site, located on Wayne National Forest in southeastern Ohio, is among several abandoned coal mine sites that have been responsible for the acid mine drainage (AMD) polluting ground and surface water. Materials released by AMD include iron, aluminum, manganese, other hazardous substances, and acidity that are harmful to aquatic life...

Evaluating the effects of moving to a low maintenance ARD control strategy at the Victoria Junction coal tailings site

Energy Technology Data Exchange (ETDEWEB)

Ziemkiewicz, P.F. [Morgantown, WV (United States); Peckham, D.; Kehoe, A. [Enterprise Cape Breton Corp., Sydney, NS (Canada)

2010-07-01

The Victoria Junction Coal Preparation site located near Sydney, Nova Scotia has been a major source of acid rock drainage (ARD) to waterways and surrounding wetlands. A polymer cap placed on the pile in 2005 resulted in a rapid improvement in waterway and wetland health. An earlier water treatment system (WTS) remained in operation until an evaluation was conducted to determine if the WTS was needed to maintain water quality in the region. This paper described the acid base loading model used to develop a close-out plan for the WTS. A mass balance model was used to isolate and compare the effects of the WTS and the capping system. The effect of shutting down the WTS was monitored for 8 moths. The model used flow and net acidity rates to calculate loadings. Net acidity represented the mass of pure base expressed as a calcium carbonate equivalent needed to neutralize acid loads. Acidity was calculated base on pH and metal concentrations. Alkalinity was determined by titration. A comparison with analytical studies of collected water samples showed that the mass balance model underestimated the alkalinity produced at the site. Results of the study showed that the site is now a net alkalinity generator. 5 refs., 1 tab., 1 fig.

Sugar maple seedling anatomy and element localization at forest sites with differing nutrient levels

Science.gov (United States)

Carolyn J. McQuattie; Robert P. Long; Thomas J. Hall

1999-01-01

Sugar maple (Acer saccharum Marsh.) seedlings often have poor survival on acidic unglaciated portions of the Allegheny Plateau. Greater survival is found after lime treatment of unglaciated sites or on glaciated areas of the Plateau. The difference in survival rate may depend in part on the acidity or chemical composition of the soil.

Surface and interlayer base-characters in lepidocrocite titanate: The adsorption and intercalation of fatty acid

Science.gov (United States)

Maluangnont, Tosapol; Arsa, Pornanan; Limsakul, Kanokporn; Juntarachairot, Songsit; Sangsan, Saithong; Gotoh, Kazuma; Sooknoi, Tawan

2016-06-01

While layered double hydroxides (LDHs) with positively-charged sheets are well known as basic materials, layered metal oxides having negatively-charged sheets are not generally recognized so. In this article, the surface and interlayer base-characters of O2- sites in layered metal oxides have been demonstrated, taking lepidocrocite titanate K0.8Zn0.4Ti1.6O4 as an example. The low basicity (0.04 mmol CO2/g) and low desorption temperature (50-300 °C) shown by CO2- TPD suggests that O2- sites at the external surfaces is weakly basic, while those at the interlayer space are mostly inaccessible to CO2. The liquid-phase adsorption study, however, revealed the uptake as much as 37% by mass of the bulky palmitic acid (C16 acid). The accompanying expansion of the interlayer space by ~0.1 nm was detected by PXRD and TEM. In an opposite manner to the external surfaces, the interlayer O2- sites can deprotonate palmitic acid, forming the salt (i.e., potassium palmitate) occluded between the sheets. Two types of basic sites are proposed based on ultrafast 1H MAS NMR and FTIR results. The interlayer basic sites in lepidocrocite titanate leads to an application of this material as a selective and stable two-dimensional (2D) basic catalyst, as demonstrated by the ketonization of palmitic acid into palmitone (C31 ketone). Tuning of the catalytic activity by varying the type of metal (Zn, Mg, and Li) substituting at TiIV sites was also illustrated.

Nanoparticles for Site Specific Genome Editing

Science.gov (United States)

McNeer, Nicole Ali

Triplex-forming peptide nucleic acids (PNAs) can be used to coordinate the recombination of short 50-60 by "donor DNA" fragments into genomic DNA, resulting in site-specific correction of genetic mutations or the introduction of advantageous genetic modifications. Site-specific gene editing in hematopoietic stem and progenitor cells (HSPCs) could result in treatment or cure of inherited disorders of the blood such as beta-thalassemia. Gene editing in HSPCs and differentiated T cells could help combat HIV/AIDs by modifying receptors, such as CCR5, necessary for R5-tropic HIV entry. However, translation of genome modification technologies to clinical practice is limited by challenges in intracellular delivery, especially in difficult-to-transfect hematolymphoid cells. In vivo gene editing could also provide novel treatment for systemic monogenic disorders such as cystic fibrosis, an autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane receptor. Here, we have engineered biodegradable nanoparticles to deliver oligonucleotides for site-specific genome editing of disease-relevant genes in human cells, with high efficiency, low toxicity, and editing of clinically relevant cell types. We designed nanoparticles to edit the human beta-globin and CCR5 genes in hematopoietic cells. We show that poly(lactic-co-glycolic acid) (PLGA) nanoparticles can delivery PNA and donor DNA for site-specific gene modification in human hematopoietic cells in vitro and in vivo in NOD-scid IL2rgammanull mice. Nanoparticles delivered by tail vein localized to hematopoietic compartments in the spleen and bone marrow of humanized mice, resulting in modification of the beta-globin and CCR5 genes. Modification frequencies ranged from 0.005 to 20% of cells depending on the organ and cell type, without detectable toxicity. This project developed highly versatile methods for delivery of therapeutics to hematolymphoid cells and hematopoietic stem cells, and will help to