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Sample records for active site chemistry

  1. Mimicking enzymatic active sites on surfaces for energy conversion chemistry.

    PubMed

    Gutzler, Rico; Stepanow, Sebastian; Grumelli, Doris; Lingenfelder, Magalí; Kern, Klaus

    2015-07-21

    Metal-organic supramolecular chemistry on surfaces has matured to a point where its underlying growth mechanisms are well understood and structures of defined coordination environments of metal atoms can be synthesized in a controlled and reproducible procedure. With surface-confined molecular self-assembly, scientists have a tool box at hand which can be used to prepare structures with desired properties, as for example a defined oxidation number and spin state of the transition metal atoms within the organic matrix. From a structural point of view, these coordination sites in the supramolecular structure resemble the catalytically active sites of metallo-enzymes, both characterized by metal centers coordinated to organic ligands. Several chemical reactions take place at these embedded metal ions in enzymes and the question arises whether these reactions also take place using metal-organic networks as catalysts. Mimicking the active site of metal atoms and organic ligands of enzymes in artificial systems is the key to understanding the selectivity and efficiency of enzymatic reactions. Their catalytic activity depends on various parameters including the charge and spin configuration in the metal ion, but also on the organic environment, which can stabilize intermediate reaction products, inhibits catalytic deactivation, and serves mostly as a transport channel for the reactants and products and therefore ensures the selectivity of the enzyme. Charge and spin on the transition metal in enzymes depend on the one hand on the specific metal element, and on the other hand on its organic coordination environment. These two parameters can carefully be adjusted in surface confined metal-organic networks, which can be synthesized by virtue of combinatorial mixing of building synthons. Different organic ligands with varying functional groups can be combined with several transition metals and spontaneously assemble into ordered networks. The catalytically active metal

  2. The hydrogen chemistry of the FeMo-co active site of nitrogenase.

    PubMed

    Dance, Ian

    2005-08-10

    The chemical mechanism by which nitrogenase enzymes catalyze the hydrogenation of N(2) (and other multiply bonded substrates) at the N(c)Fe(7)MoS(9)(homocitrate) active site (FeMo-co) is unknown, despite the accumulation of much data on enzyme reactivity and the influences of key amino acids surrounding FeMo-co. The mutual influences of H(2), substrates, and the inhibitor CO on reactivity are key experimental tests for postulated mechanisms. Fundamental to all aspects of mechanism is the accumulation of H atoms (from e(-) + H(+)) on FeMo-co, and the generation and influences of coordinated H(2). Here, I argue that the first introduction of H is via a water chain terminating at water 679 (PDB structure , Azotobacter vinelandii) to one of the mu(3)-S atoms (S3B) of FeMo-co. Next, using validated density functional calculations of a full chemical representation of FeMo-co and its connected residues (alpha-275(Cys), alpha-442(His)), I have characterized more than 80 possibilities for the coordination of up to three H atoms, and H(2), and H + H(2), on the S2A, Fe2, S2B, Fe6, S3B domain of FeMo-co, which is favored by recent targeted mutagenesis results. Included are calculated reaction profiles for movements of H atoms (between S and Fe, and between Fe and Fe), for the generation of Fe-H(2), for association and dissociation of Fe-H(2) at various reduction levels, and for H/H(2) exchange. This is new hydrogen chemistry on an unprecedented coordination frame, with some similarities to established hydrogen coordination chemistry, and with unexpected and unprecedented structures such as Fe(S)(3)(H(2))(2)(H) octahedral coordination. General principles for the hydrogen chemistry of FeMo-co include (1) the stereochemical mobility of H bound to mu(3)-S, (2) the differentiated endo- and exo- positions at Fe for coordination of H and/or H(2), and (3) coordinative allosteric influences in which structural and dynamic aspects of coordination at one Fe atom are affected by

  3. 'Unconventional' coordination chemistry by metal chelating fragments in a metalloprotein active site.

    PubMed

    Martin, David P; Blachly, Patrick G; Marts, Amy R; Woodruff, Tessa M; de Oliveira, César A F; McCammon, J Andrew; Tierney, David L; Cohen, Seth M

    2014-04-01

    The binding of three closely related chelators: 5-hydroxy-2-methyl-4H-pyran-4-thione (allothiomaltol, ATM), 3-hydroxy-2-methyl-4H-pyran-4-thione (thiomaltol, TM), and 3-hydroxy-4H-pyran-4-thione (thiopyromeconic acid, TPMA) to the active site of human carbonic anhydrase II (hCAII) has been investigated. Two of these ligands display a monodentate mode of coordination to the active site Zn(2+) ion in hCAII that is not recapitulated in model complexes of the enzyme active site. This unprecedented binding mode in the hCAII-thiomaltol complex has been characterized by both X-ray crystallography and X-ray spectroscopy. In addition, the steric restrictions of the active site force the ligands into a 'flattened' mode of coordination compared with inorganic model complexes. This change in geometry has been shown by density functional computations to significantly decrease the strength of the metal-ligand binding. Collectively, these data demonstrate that the mode of binding by small metal-binding groups can be significantly influenced by the protein active site. Diminishing the strength of the metal-ligand bond results in unconventional modes of metal coordination not found in typical coordination compounds or even carefully engineered active site models, and understanding these effects is critical to the rational design of inhibitors that target clinically relevant metalloproteins. PMID:24635441

  4. Environmental Chemistry Activities.

    ERIC Educational Resources Information Center

    Jackland, Thomas; And Others

    The authors of this curriculum supplement believe in a laboratory approach to chemistry and express the feeling that environmental chemistry provides the students an opportunity to apply theoretical chemistry to important practical problems. There are eighteen activities presented, each accompanied with behavioral objectives, one or more suggested…

  5. Experimental and computational investigation of acetic acid deoxygenation over oxophilic molybdenum carbide: Surface chemistry and active site identity

    DOE PAGESBeta

    Schaidle, Joshua A.; Blackburn, Jeffrey; Farberow, Carrie A.; Nash, Connor; Steirer, K. Xerxes; Clark, Jared; Robichaud, David J.; Ruddy, Daniel A.

    2016-01-21

    Ex situ catalytic fast pyrolysis (CFP) is a promising route for producing fungible biofuels; however, this process requires bifunctional catalysts that favor C–O bond cleavage, activate hydrogen at near atmospheric pressure and high temperature (350–500 °C), and are stable under high-steam, low hydrogen-to-carbon environments. Recently, early transition-metal carbides have been reported to selectively cleave C–O bonds of alcohols, aldehydes, and oxygenated aromatics, yet there is limited understanding of the metal carbide surface chemistry under reaction conditions and the identity of the active sites for deoxygenation. In this study, we evaluated molybdenum carbide (Mo2C) for the deoxygenation of acetic acid, anmore » abundant component of biomass pyrolysis vapors, under ex situ CFP conditions, and we probed the Mo2C surface chemistry, identity of the active sites, and deoxygenation pathways using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations.« less

  6. Solvent as a probe of active site motion and chemistry during the hydrogen tunnelling reaction in morphinone reductase.

    PubMed

    Hay, Sam; Pudney, Christopher R; Sutcliffe, Michael J; Scrutton, Nigel S

    2008-09-15

    The reductive half-reaction of morphinone reductase involves a hydride transfer from enzyme-bound beta-nicotinamide adenine dinucleotide (NADH) to a flavin mononucleotide (FMN). We have previously demonstrated that this step proceeds via a quantum mechanical tunnelling mechanism. Herein, we probe the effect of the solvent on the active site chemistry. The pK(a) of the reduced FMN N1 is 7.4+/-0.7, based on the pH-dependence of the FMN midpoint potential. We rule out that protonation of the reduced FMN N1 is coupled to the preceding H-transfer as both the rate and temperature-dependence of the reaction are insensitive to changes in solution pH above and below this pK(a). Further, the solvent kinetic isotope effect is approximately 1.0 and both the 1 degrees and 2 degrees KIEs are insensitive to solution pH. The effect of the solvent's dielectric constant is investigated and the rate of H-transfer is found to be unaffected by changes in the dielectric constant between approximately 60 and 80. We suggest that, while there is crystallographic evidence for some water in the active site, the putative promoting motion involved in the H-tunnelling reaction is insensitive to such changes. PMID:18668493

  7. Unique coupling of mono- and dioxygenase chemistries in a single active site promotes heme degradation.

    PubMed

    Matsui, Toshitaka; Nambu, Shusuke; Goulding, Celia W; Takahashi, Satoshi; Fujii, Hiroshi; Ikeda-Saito, Masao

    2016-04-01

    Bacterial pathogens must acquire host iron for survival and colonization. Because free iron is restricted in the host, numerous pathogens have evolved to overcome this limitation by using a family of monooxygenases that mediate the oxidative cleavage of heme into biliverdin, carbon monoxide, and iron. However, the etiological agent of tuberculosis, Mycobacterium tuberculosis, accomplishes this task without generating carbon monoxide, which potentially induces its latent state. Here we show that this unusual heme degradation reaction proceeds through sequential mono- and dioxygenation events within the single active center of MhuD, a mechanism unparalleled in enzyme catalysis. A key intermediate of the MhuD reaction is found to be meso-hydroxyheme, which reacts with O2 at an unusual position to completely suppress its monooxygenation but to allow ring cleavage through dioxygenation. This mechanistic change, possibly due to heavy steric deformation of hydroxyheme, rationally explains the unique heme catabolites of MhuD. Coexistence of mechanistically distinct functions is a previously unidentified strategy to expand the physiological outcome of enzymes, and may be applied to engineer unique biocatalysts. PMID:27006503

  8. Fog chemistry at three sites in Norway

    NASA Astrophysics Data System (ADS)

    Wang, Youliang; Zhang, Jinwei; Marcotte, Aurelie R.; Karl, Matthias; Dye, Christian; Herckes, Pierre

    2015-01-01

    Fog composition was investigated at three sites in Norway, one in suburban Oslo and two coastal sites in the area of the Mongstad refinery. Overall fog frequency during the study periods was low. Fog pH was around 5 with slightly lower values at Hakadal, the suburban site, compared to the coastal sites, which were slightly above 5. Major ions at the coastal sites were sodium and chloride consistent with the marine environment. The ion chemistry at the suburban site was dominated by ammonium, sulfate and nitrate, consistent with fogs in anthropogenically impacted environments. Overall concentrations of major ions were very low, orders of magnitude lower than those in polluted urban fogs. Organic matter concentrations were also low (< 3 mgC/L) consistent with limited anthropogenic impact and little biogenic activity in the winter months. Selected amine concentrations were determined and ranged from nanomolar concentrations for ethylamines to several hundred nanomolar concentrations for dimethylamine, the most abundant amine investigated. While N-nitrosodimehylamine was detected in fog, the concentrations were very low in the fogs.

  9. A ligand field chemistry of oxygen generation by the oxygen-evolving complex and synthetic active sites

    PubMed Central

    Betley, Theodore A; Surendranath, Yogesh; Childress, Montana V; Alliger, Glen E; Fu, Ross; Cummins, Christopher C; Nocera, Daniel G

    2007-01-01

    Oxygen–oxygen bond formation and O2 generation occur from the S4 state of the oxygen-evolving complex (OEC). Several mechanistic possibilities have been proposed for water oxidation, depending on the formal oxidation state of the Mn atoms. All fall under two general classifications: the AB mechanism in which nucleophilic oxygen (base, B) attacks electrophilic oxygen (acid, A) of the Mn4Ca cluster or the RC mechanism in which radical-like oxygen species couple within OEC. The critical intermediate in either mechanism involves a metal oxo, though the nature of this oxo for AB and RC mechanisms is disparate. In the case of the AB mechanism, assembly of an even-electron count, high-valent metal-oxo proximate to a hydroxide is needed whereas, in an RC mechanism, two odd-electron count, high-valent metal oxos are required. Thus the two mechanisms give rise to very different design criteria for functional models of the OEC active site. This discussion presents the electron counts and ligand geometries that support metal oxos for AB and RC O–O bond-forming reactions. The construction of architectures that bring two oxygen functionalities together under the purview of the AB and RC scenarios are described. PMID:17971328

  10. Chemistry: Experiments, Demonstrations and Other Activities Suggested for Chemistry.

    ERIC Educational Resources Information Center

    New York State Education Dept., Albany. Bureau of Secondary Curriculum Development.

    This publication is a handbook used in conjunction with the course of study in chemistry developed through the New York State Education Department and The University of the State of New York. It contains experiments, demonstrations, and other activities for a chemistry course. Areas covered include the science of chemistry, the atomic structure of…

  11. Fog chemistry at an urban midwestern site

    SciTech Connect

    Muir, P.S.; Wade, K.A.; Carter, B.H.; Armentano, T.V.; Pribush, R.A.

    1986-12-01

    The Holcomb Research Institute is monitoring fog chemistry in Indianapolis, Indiana and at sites in and near the heavily industrialized Ohio River Valley. Results reported here indicate that fogs in this area can be strongly acidic, and that further studies are warranted. We report 1) the ionic composition of three fog events, samples collected in Indianapolis between December 1985 and February 1986, and 2) the pH of three additional events, samples collected between November 1985 and February 1986. (The volume of fog collected during the latter three events was insufficient for chemical analysis other than pH.) The pH of the fog samples ranged from 2.85 to 4.06; some of this fell within the range known to damage foliage and yield of some plant species. It has been demonstrated that even one exposure to highly acidic mists (pH par. delta 2.5) can damage certain crop species; hence, it is important to document the occurrence of any events having acidity near this level.

  12. Student Active Learning Methods in Physical Chemistry

    NASA Astrophysics Data System (ADS)

    Hinde, Robert J.; Kovac, Jeffrey

    2001-01-01

    We describe two strategies for implementing active learning in physical chemistry. One involves supplementing a traditional lecture course with heavily computer-based active-learning exercises carried out by cooperative groups in a department computer lab. The other uses cooperative learning almost exclusively, supplemented by occasional mini-lectures. Both approaches seemed to result in better student learning and a more positive attitude toward the subject. On the basis of our respective experiences using active learning techniques, we discuss some of the strengths of these techniques and some of the challenges we encountered using the active-learning approach in teaching physical chemistry.

  13. Solar Energy Project, Activities: Chemistry & Physics.

    ERIC Educational Resources Information Center

    Tullock, Bruce, Ed.; And Others

    This guide contains lesson plans and outlines of science activities which present concepts of solar energy in the context of chemistry and physics experiments. Each unit presents an introduction to the unit; objectives; required skills and knowledge; materials; method; questions; recommendations for further work; and a teacher information sheet.…

  14. Supramolecular Chemistry And Self-assembly Special Feature: Selective immobilization of proteins to self-assembled monolayers presenting active site-directed capture ligands

    NASA Astrophysics Data System (ADS)

    Hodneland, Christian D.; Lee, Young-Sam; Min, Dal-Hee; Mrksich, Milan

    2002-04-01

    This paper describes a method for the selective and covalent immobilization of proteins to surfaces with control over the density and orientation of the protein. The strategy is based on binding of the serine esterase cutinase to a self-assembled monolayer presenting a phosphonate ligand and the subsequent displacement reaction that covalently binds the ligand to the enzyme active site. Surface plasmon resonance (SPR) spectroscopy showed that cutinase binds irreversibly to a monolayer presenting the capture ligand at a density of 1% mixed among tri(ethylene glycol) groups. The covalent immobilization is specific for cutinase, and the glycol-terminated monolayer effectively prevents unwanted nonspecific adsorption of proteins. To demonstrate that the method could be used to immobilize proteins of interest, a cutinase-calmodulin fusion protein was constructed and immobilized to the monolayer. SPR showed that calcineurin selectively associated with the immobilized calmodulin. This capture ligand immobilization method combines the advantages that the immobilization reaction is highly selective for the intended protein, the tether is covalent and, hence, stable, and the method avoids the need for synthetic modification and rigorous purification of proteins before immobilization. These characteristics make the method well suited to a range of applications and, in particular, for constructing protein microarrays.

  15. Rocky Mountain Snowpack Chemistry at Selected Sites, 2002

    USGS Publications Warehouse

    Ingersoll, George P.; Mast, M. Alisa; Nanus, Leora; Manthorne, David J.; Clow, David W.; Handran, Heather M.; Winterringer, Jesse A.; Campbell, Donald H.

    2004-01-01

    During spring 2002, the chemical composition of annual snowpacks in the Rocky Mountain region of the Western United States was analyzed. Snow samples were collected at 75 geographically distributed sites extending from New Mexico to Montana. Near the end of the 2002 snowfall season, the snow-water equivalent (SWE) in annual snowpacks sampled generally was below average in most of the region. Regional patterns in the concentrations of major ions (including ammonium, nitrate, and sulfate), mercury, and stable sulfur isotope ratios are presented. The 2002 snowpack chemistry in the region differed from the previous year. Snowpack ammonium concentrations were higher at 66 percent of sites in Montana compared to concentrations in the 2001 snowpack but were lower at 74 percent of sites in Wyoming, Colorado, and New Mexico. Nitrate was lower at all Montana sites and lower at all but one Wyoming site; nitrate was higher at all but two Colorado sites and higher at all New Mexico sites. Sulfate was lower across the region at 77 percent of sites. The range of mercury concentrations for the region was similar to those of 2001 but showed more variability than ammonium, nitrate, and sulfate concentrations. Concentrations of stable sulfur isotope ratios exhibited a strong regional pattern with values increasing northward from southern Colorado to northern Colorado and Wyoming.

  16. Using Art-Based Chemistry Activities to Improve Students' Conceptual Understanding in Chemistry

    ERIC Educational Resources Information Center

    Danipog, Dennis L.; Ferido, Marlene B.

    2011-01-01

    This study aimed to determine the effects of art-based chemistry activities (ABCA) on high school students' conceptual understanding in chemistry. The study used the pretest-posttest control group design. A total of 64 third-year high school students from two different chemistry classes participated in the study. One class was exposed to art-based…

  17. Rocky Mountain snowpack chemistry at selected sites for 2001

    USGS Publications Warehouse

    Ingersoll, George P.; Mast, M. Alisa; Clow, David W.; Nanus, Leora; Campbell, Donald H.; Handran, Heather

    2003-01-01

    Because regional-scale atmospheric deposition data in the Rocky Mountains are sparse, a program was designed by the U.S. Geological Survey, in cooperation with the National Park Service, U.S. Department of Agriculture Forest Service, and other agencies, to more thoroughly determine the chemical composition of precipitation and to identify sources of atmospherically deposited contaminants in a network of high-elevation sites. Samples of seasonal snowpacks at 57 geographically distributed sites, in a regional network from New Mexico to Montana, were collected and analyzed for major ions (including ammonium, nitrate, and sulfate), alkalinity, and dissolved organic carbon during 2001. Sites selected in this report have been sampled annually since 1993, enabling identification of increases or decreases in chemical concentrations from year to year. Spatial patterns in snowpack-chemical data for concentrations of ammonium, nitrate, and sulfate indicate that concentrations of these acid precursors in less developed areas of the region are lower than concentrations in the heavily developed areas. Results for the 2001 snowpack-chemistry analyses, however, indicate increases in concentrations of ammonium and nitrate in particular at sites where past concentrations typically were lower. Since 1993, concentrations of nitrate and sulfate were highest from snowpack samples in northern Colorado that were collected from sites adjacent to the Denver metropolitan area to the east and the coal-fired powerplants to the west. In 2001, relatively high concentrations of nitrate (12.3 to 23.0 microequivalents per liter (?eq/L) and sulfate (7.7 to 12.5 ?eq/L) were detected in Montana and Wyoming. Ammonium concentrations were highest in north-central Colorado (14.5 to 16.9 ?eq/L) and southwestern Montana (12.8 to 14.2 ?eq/L).

  18. Nighttime chemistry at a high altitude site above Hong Kong

    NASA Astrophysics Data System (ADS)

    Brown, Steven S.; Dubé, William P.; Tham, Yee Jun; Zha, Qiaozhi; Xue, Likun; Poon, Steven; Wang, Zhe; Blake, Donald R.; Tsui, Wilson; Parrish, David D.; Wang, Tao

    2016-03-01

    Nighttime reactions of nitrogen oxides influence ozone, volatile organic compounds, and aerosol and are thus important to the understanding of regional air quality. Despite large emissions and rapid recent growth of nitrogen oxide concentrations, there are few studies of nighttime chemistry in China. Here we present measurements of nighttime nitrogen oxides, NO3 and N2O5, from a coastal mountaintop site in Hong Kong adjacent to the megacities of the Pearl River Delta region. This is the first study of nighttime chemistry from a site within the residual layer in China. Key findings include the following. First, highly concentrated urban NOx outflow from the Pearl River Delta region was sampled infrequently at night, with N2O5 mixing ratios up to 8 ppbv (1 min average) or 12 ppbv (1 s average) in nighttime aged air masses. Second, the average N2O5 uptake coefficient was determined from a best fit to the available steady state lifetime data as γ(N2O5) = 0.014 ± 0.007. Although this determination is uncertain due to the difficulty of separating N2O5 losses from those of NO3, this value is in the range of previous residual layer determinations of N2O5 uptake coefficients in polluted air in North America. Third, there was a significant contribution of biogenic hydrocarbons to NO3 loss inferred from canister samples taken during daytime. Finally, daytime N2O5 mixing ratios were in accord with their predicted photochemical steady state. Heterogeneous uptake of N2O5 in fog is determined to be an important production mechanism for soluble nitrate, even during daytime.

  19. Neutron activation analysis in archaeological chemistry

    SciTech Connect

    Harbottle, G.

    1987-01-01

    Neutron activation analysis has proven to be a convenient way of performing the chemical analysis of archaeologically-excavated artifacts and materials. It is fast and does not require tedious laboratory operations. It is multielement, sensitive, and can be made nondestructive. Neutron activation analysis in its instrumental form, i.e., involving no chemical separation, is ideally suited to automation and conveniently takes the first step in data flow patterns that are appropriate for many taxonomic and statistical operations. The future will doubtless see improvements in the practice of NAA in general, but in connection with archaeological science the greatest change will be the filling, interchange and widespread use of data banks based on compilations of analytical data. Since provenience-oriented data banks deal with materials (obsidian, ceramics, metals, semiprecious stones, building materials and sculptural media) that participated in trade networks, the analytical data is certain to be of interest to a rather broad group of archaeologists. It is to meet the needs of the whole archaeological community that archaeological chemistry must now turn.

  20. Using Computational Chemistry Activities to Promote Learning and Retention in a Secondary School General Chemistry Setting

    ERIC Educational Resources Information Center

    Ochterski, Joseph W.

    2014-01-01

    This article describes the results of using state-of-the-art, research-quality software as a learning tool in a general chemistry secondary school classroom setting. I present three activities designed to introduce fundamental chemical concepts regarding molecular shape and atomic orbitals to students with little background in chemistry, such as…

  1. Writing Chemistry Jingles as an Introductory Activity in a High School Chemistry Class

    ERIC Educational Resources Information Center

    Heid, Peter F.

    2011-01-01

    Starting the school year in an introductory high school chemistry class can be a challenge. The topic and approach is new to the students; many of the early chapters in the texts can be a bit tedious; and for many students the activities are uninspiring. My goal in the first few weeks of school is to hook the students on chemistry by getting them…

  2. Active Learning Applications in the History of Chemistry: Pre-Service Chemistry Teachers' Level of Knowledge and Views

    ERIC Educational Resources Information Center

    Sendur, Gülten; Polat, Merve; Toku, Abdullah; Kazanci, Coskun

    2014-01-01

    This study aims to investigate the effects of a History and Philosophy of Chemistry-I course based on active learning applications on the level of knowledge of pre-service chemistry teachers about the history of chemistry. The views of pre-service chemistry teachers about these activities were also investigated. The study was carried out with 38…

  3. Single-Site Heterogeneous Catalysts: Innovations, Advantages, and Future Potential in Green Chemistry and Sustainable Technology

    NASA Astrophysics Data System (ADS)

    Raja, Robert; Thomas, John Meurig

    The advantages that flow from the availability of single-site heterogeneous catalysts are many. They facilitate the determination of the kinetics and mechanism of catalytic turnover and render accessible the energetics of various intermediates. More importantly, it is possible to prepare soluble molecular fragments that circumscribe the single site, thus enabling a direct comparison to be made between the catalytic performance of the same active site when functioning as a heterogeneous or a homogeneous catalyst. Our approach adopts the principles and practices of solid-state chemistry, augmented by lessons derived from enzymology, as well as computational chemistry. We have succeeded in designing a range of new catalysts to effect, inter alia, shape-selective, regioselective, bifunctional, and enantioselective catalytic conversions. In particular, large fractions of these catalysts are ideally suited for the era of clean technology in which single-step and/or solvent-free processes abound, and in which benign oxidants such as air or oxygen and inexpensive nanoporous materials are employed.

  4. Using Microcomputers in the Physical Chemistry Laboratory: Activation Energy Experiment.

    ERIC Educational Resources Information Center

    Touvelle, Michele; Venugopalan, Mundiyath

    1986-01-01

    Describes a computer program, "Activation Energy," which is designed for use in physical chemistry classes and can be modified for kinetic experiments. Provides suggestions for instruction, sample program listings, and information on the availability of the program package. (ML)

  5. Salt site performance assessment activities

    SciTech Connect

    Kircher, J.F.; Gupta, S.K.

    1983-01-01

    During this year the first selection of the tools (codes) for performance assessments of potential salt sites have been tentatively selected and documented; the emphasis has shifted from code development to applications. During this period prior to detailed characterization of a salt site, the focus is on bounding calculations, sensitivity and with the data available. The development and application of improved methods for sensitivity and uncertainty analysis is a focus for the coming years activities and the subject of a following paper in these proceedings. Although the assessments to date are preliminary and based on admittedly scant data, the results indicate that suitable salt sites can be identified and repository subsystems designed which will meet the established criteria for protecting the health and safety of the public. 36 references, 5 figures, 2 tables.

  6. Liaison activities with the Institute of Physical Chemistry, Russian Academy of Sciences: FY 1997

    SciTech Connect

    Delegard, C.H.; Elovich, R.J.

    1997-09-01

    The Institute of Physical Chemistry of the Russian Academy of Sciences is conducting a program of fundamental and applied research into the chemistry of the actinides and technetium in alkaline media such as are present in the Hanford Site underground waste storage tanks. This work is being coordinated and the results disseminated through a technical liaison maintained at the Pacific Northwest National Laboratory. The technical liaison is performing laboratory studies on plutonium chemistry in alkaline media. The activities at the Institute of Physical Chemistry and through the liaison are pursued to improve understanding of the chemical behavior of key long-lived radioactive elements under current operating and proposed tank waste processing conditions. Both activities are supported by the Efficient Separations and Processing Crosscutting Program under the Office of Science and Technology of the U.S. Department of Energy.

  7. Relating groundwater and sediment chemistry to microbial characterization at a BTEX-contaminated site

    SciTech Connect

    Pfiffner, S.M.; Palumbo, A.V.; McCarthy, J.F.; Gibson, T.

    1996-07-01

    The National Center for Manufacturing Science is investigating bioremediation of petroleum hydrocarbon at a site in Belleville, Michigan. As part of this study we examined the microbial communities to help elucidate biodegradative processes currently active at the site. We observed high densities of aerobic hydrocarbon degraders and denitrifiers in the less-contaminated sediments. Low densities of iron and sulfate reducers were measured in the same sediments. In contrast, the highly-contaminated sediments showed low densities of aerobic hydrocarbon degraders and denitrifiers and high densities of iron and sulfate reducers. Methanogens were also found in these highly-contaminated sediments. These contaminated sediments also showed a higher biomass, by phospholipid fatty acids, and greater ratios of phospholipid fatty acids which indicate stress within the microbial community. Aquifer chemistry analyses indicated that the more-contaminated area was more reduced and had lower sulfate than the less-contaminated area. These conditions suggest that the subsurface environment at the highly-contaminated area had progressed into sulfate reduction and methanogensis. The less-contaminated area, although less reduced, also appeared to be progressing into primarily iron- and sulfate-reducing microbial communities. The proposed treatment to stimulate bioremediation includes addition of oxygen and nitrate. Groundwater chemistry and microbial analyses revealed significant differences resulted from the injection of dissolved oxygen and nitrate in the subsurface. These differences included increases in pH and Eh and large decreases in BTEX, dissolved iron, and sulfate concentrations at the injection well.

  8. Teaching chemistry with neutron activation analysis at Dalhousie University

    SciTech Connect

    Holzbecher, J.; Chatt, A. )

    1991-11-01

    The Dalhousie University SLOWPOKE-2 Reactor (DUSR) has been operating since July 1976 and has proven to be an invaluable tool in many teaching programs. These reactors are inherently safe and are designed to serve teaching and research needs of the universities, research centers, hospitals, etc. Since the DUSR has been, from its inception, associated with the Trace Analysis Research Centre, which is the Analytical Chemistry Division of the Department of Chemistry, the main thrust of its use continues to be in the field of nuclear analytical chemistry. Both teaching and research programs involve trace element analysis by neutron activation.

  9. A study on the flexibility of enzyme active sites

    PubMed Central

    2011-01-01

    Background A common assumption about enzyme active sites is that their structures are highly conserved to specifically distinguish between closely similar compounds. However, with the discovery of distinct enzymes with similar reaction chemistries, more and more studies discussing the structural flexibility of the active site have been conducted. Results Most of the existing works on the flexibility of active sites focuses on a set of pre-selected active sites that were already known to be flexible. This study, on the other hand, proposes an analysis framework composed of a new data collecting strategy, a local structure alignment tool and several physicochemical measures derived from the alignments. The method proposed to identify flexible active sites is highly automated and robust so that more extensive studies will be feasible in the future. The experimental results show the proposed method is (a) consistent with previous works based on manually identified flexible active sites and (b) capable of identifying potentially new flexible active sites. Conclusions This proposed analysis framework and the former analyses on flexibility have their own advantages and disadvantage, depending on the cause of the flexibility. In this regard, this study proposes an alternative that complements previous studies and helps to construct a more comprehensive view of the flexibility of enzyme active sites. PMID:21342563

  10. Learning Activity Package, Chemistry I, (LAP) Study 29.

    ERIC Educational Resources Information Center

    Jones, Naomi

    Presented is a Learning Activity Package (LAP) study concerned with carbon and its compounds. This LAP in chemistry includes a rationale for studying the chemical element of carbon, a list of student objectives (stated in behavioral terms), of activities (reading, laboratory experiments, model construction, etc.), a two-page worksheet, a…

  11. Relating ground water and sediment chemistry to microbial characterization at a BTEX-contaminated site.

    PubMed

    Pfiffner, S M; Palumbo, A V; Gibson, T; Ringelberg, D B; McCarthy, J F

    1997-01-01

    The National Center for Manufacturing Science is investigating bioremediation of petroleum hydrocarbon at a site near Belleville, MI. As part of this study, we examined the microbial communities to help elucidate biodegradative processes currently active at the site. We observed high densities of aerobic hydrocarbon degraders and denitrifiers in the less-contaminated sediments. Low densities of iron and sulfate reducers were measured in the same sediments. In contrast, the highly contaminated sediments showed low densities of aerobic hydrocarbon degraders and denitrifiers, and high densities of iron and sulfate reducers. Methanogens were also found in these highly contaminated sediments. These contaminated sediments also showed a higher biomass, by the phospholipid fatty acids, and greater ratios of phospholipid fatty acids, which indicate stress within the microbial community. Aquifer chemistry analyses indicated that the highly contaminated area was more reduced and had lower sulfate than the less-contaminated area. These conditions suggest that the subsurface environment at the highly contaminated area had progressed into sulfate reduction and methanogenesis. The less-contaminated area, although less reduced, also appeared to be progressing into primarily iron- and sulfate-reducing microbial communities. The proposed treatment to stimulate bioremediation includes addition of oxygen and nitrate to the subsurface. Ground water chemistry and microbial analyses revealed significant differences that resulted from the injection of dissolved oxygen and nitrate. These differences included an increase in Eh, small decrease in pH, and large decreases in BTEX, dissolved iron, and sulfate concentrations at the injection well. Injected nitrate was rapidly utilized by the subsurface microbial communities, and significant nitrite amounts were observed in the injection well and in nearby down-gradient observation wells. Microbial and molecular analyses indicated an increase in

  12. Chemistry of proposed calcination/dissolution processing of Hanford Site tank wastes

    SciTech Connect

    Delegard, C.H.

    1995-01-01

    Plans exist to separate radioactive waste stored in underground tanks at the US Department of Energy`s Hanford Site in south central Washington State into low-level and high-level fractions, and to immobilize the separate fractions in high-integrity vitrified forms for long-term disposal. Calcination with water dissolution has been proposed as a possible treatment for achieving low/high-level separation. Chemistry development activities conducted since 1992 with simulated and genuine tank waste show that calcination/dissolution destroys organic carbon and converts nitrate and nitrite to hydroxide and benign offgases. The process also dissolves significant quantities of bulk chemicals (aluminum, chromium, and phosphate), allowing their redistribution from the high-level to the low-level fraction. Present studies of the chemistry of calcination/dissolution processing of genuine wastes, conducted in the period October 1993 to September 1994, show the importance of sodium fluoride phosphate double salt in controlling phosphate dissolution. Peptization of waste solids is of concern if extensive washing occurs. Strongly oxidizing conditions imposed by calcination reactions were found to convert transition metals to soluble anions in the order chromate > manganate > > ferrate. In analogy with manganese behavior, plutonium dissolution, presumably by oxidation to more soluble anionic species, also occurs by calcination/dissolution. Methods to remove plutonium from the product low-level solution stream must be developed.

  13. Rocky Mountain Snowpack Chemistry at Selected Sites, 2004

    USGS Publications Warehouse

    Ingersoll, George P.; Mast, M. Alisa; Nanus, Leora; Handran, Heather H.; Manthorne, David J.; Hultstrand, Douglas M.

    2007-01-01

    During spring 2004, the U.S. Geological Survey in cooperation with the National Park Service and the U.S. Department of Agriculture, Forest Service collected and analyzed snowpack samples for 65 sites in the Rocky Mountain region from New Mexico to Montana. Snowpacks were sampled from late February through early April and generally had well-below-average- to near-average snow-water equivalent. Regionally, on April 1, snow-water equivalent ranged from 50 to 89 percent. At most regional sites monitored during 1993-2004, snowpack ammonium, nitrate, and sulfate concentrations for 2004 were lower than the 12-year averages. Snowpack ammonium concentrations in the region were lower than average concentrations for the period at 61 percent of sites in the region, but showed a new pattern compared to previous years with three of the four highest 2004 concentrations observed in northern Colorado. Nitrate concentrations in 2004 were lower than the 12-year average for the year at 53 percent of regional sites, and typically occurred at sites in Wyoming, Idaho, and Montana where powerplants and large industrial areas were limited. A regional decrease in sulfate concentrations across most of the Rocky Mountains (with concentrations lower than the 12-year average at 84 percent of snowpack sites) was consistent with other monitoring of atmospheric deposition in the Western United States. Total mercury concentrations, although data are only available for the past 3 years, decreased slightly for the region as a whole in 2004 relative to 2003. Ratios of stable sulfur isotopes indicated a similar regional pattern as observed in recent years with sulfur-34 (d34S) values generally increasing northward from northern New Mexico and southern Colorado to northern Colorado, Wyoming, Idaho, and Montana.

  14. Empowering Girls with Chemistry, Exercise and Physical Activity

    ERIC Educational Resources Information Center

    Clapham, Emily D.; Ciccomascolo, Lori E.; Clapham, Andrew J.

    2015-01-01

    Research suggests that a girl's career interests in the areas of science, technology, engineering and mathematics (STEM) declines between grades 6 and 8. Similarly, in middle school, there is a decrease in physical activity among girls. Researchers at the University of Rhode Island (URI) conducted a chemistry-based science camp that took place…

  15. Active Learning Strategies in the Analytical Chemistry Classroom.

    ERIC Educational Resources Information Center

    Ross, Michael R.; Fulton, Robert B.

    1994-01-01

    Describes an analytical chemistry course restructured around the use of cooperative groups to help students become active learners in a non-competitive environment. Five years of experience with the course indicates that the syllabus covers almost exactly the same content as old courses and that test scores compare favorably on the national level.…

  16. Chemistry and movement of ground water, Nevada Test Site

    USGS Publications Warehouse

    Schoff, S.L.; Moore, J.E.

    1964-01-01

    Three chemical types of ground water are distinguished at the Nevada Test Site and vicinity. A sodium-potassium water is related to tuff (in part zeolitized) and to alluvium containing detrital tuff. A calcium-magnesium water is related to limestone and dolomite, or to alluvium containing detritus of these rock types. A mixed chemical type, containing about as much sodium and potassium as calcium and magnesium, may result from the addition of one of the first two types of water to the other; to passage of water first through tuff and then through carbonate rock, or vice versa; and to ion-exchange during water travel. Consideration of the distribution of these water types, together with the distribution of sodium in the water and progressive changes in the dissolved solids, suggests that the ground water in the Nevada Test Site probably moves toward the Amargosa Desert, not into Indian Spring Valley and thence southeastward toward Las Vegas. The low dissolved solids content of ground-water reservoirs in alluvium and tuff of the enclosed basins indicates that recharge is local in origin.

  17. Female Faculty Members in University Chemistry Departments: Observations and Conclusions Based on Site Visits

    ERIC Educational Resources Information Center

    Chapman, Sally; Dixon, Felicia F.; Foster, Natalie; Kuck, Valerie J.; McCarthy, Deborah A.; Tooney, Nancy M.; Buckner, Janine P.; Nolan, Susan A.; Marzabadi, Cecilia H.

    2011-01-01

    Oral interviews in focus groups and written surveys were conducted with 877 men and women, including administrators, faculty members, postdoctoral associates, and graduate students, during one-day site visits to chemistry and chemical engineering departments at 28 Ph.D.-granting institutions. This report is a preliminary review of the perceptions…

  18. A General Chemistry Assignment Analyzing Environmental Contamination for the Depue, IL, National Superfund Site

    ERIC Educational Resources Information Center

    Saslow Gomez, Sarah A.; Faurie-Wisniewski, Danielle; Parsa, Arlen; Spitz, Jeff; Spitz, Jennifer Amdur; Loeb, Nancy C.; Geiger, Franz M.

    2015-01-01

    The classroom exercise outlined here is a self-directed assignment that connects students to the environmental contamination problem surrounding the DePue Superfund site. By connecting chemistry knowledge gained in the classroom with a real-world problem, students are encouraged to personally connect with the problem while simultaneously…

  19. Indoor Chemistry: Materials, Ventilation Systems, and Occupant Activities

    SciTech Connect

    Morrison, G.C.; Corsi, R.L.; Destaillats, H.; Nazaroff, W.W.; Wells, J.R.

    2006-05-01

    Chemical processes taking place in indoor environments can significantly alter the nature and concentrations of pollutants. Exposure to secondary contaminants generated in these reactions needs to be evaluated in association with many aspects of buildings to minimize their impact on occupant health and well-being. Focusing on indoor ozone chemistry, we describe alternatives for improving indoor air quality by controlling chemical changes related to building materials, ventilation systems, and occupant activities.

  20. Active Sites Environmental Monitoring Program: Program plan

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1990-10-01

    DOE Order 5820.2A requires that low-level waste (LLW) disposal sites active on or after September 1988 and all transuranic (TRU) waste storage sites be monitored periodically to assure that radioactive contamination does not escape from the waste sites and pose a threat to the public or to the environment. This plan describes such a monitoring program for the active LLW disposal sites in SWSA 6 and the TRU waste storage sites in SWSA 5 North. 14 refs., 8 figs.

  1. Ithaca MAP3S regional precipitation chemistry site. Annual progress report, 1 November 1984-31 October 1985

    SciTech Connect

    Butler, T.J.; Likens, G.E.

    1986-07-01

    Samples were collected at the MAP3S Regional Precipitation Chemistry Site located 15 km southwest of Ithaca, New York (Lat. 42/sup 0/ 24', Long. 76/sup 0/ 39') at an elevation of 503 m. The surrounding area is rural in nature and consists of gently rolling terrain, vegetated by deciduous forest, abandoned fields, pasture and some agricultural land. Local point sources of combustion products include a 250 mw coal-fired power plant, 23 km NNE of the site and the Cornell University steam-generating plant 16 km ENE of the site. The latter produces emissions of SO/sub 2/ and particulates comparable to a 50 mw coal-fired power plant. Both of these plants are in a quadrant that is consistently downwind of the sampling station. Other local potential sources of particles are from agricultural activity, road dust, and road salt during the winter. Data are collected September 1984 through September 1985.

  2. Modeling Feedbacks between Biogenic Emissions and Air Chemistry from Site to Globe

    NASA Astrophysics Data System (ADS)

    Butler, T. M.; Grote, R.

    2014-12-01

    We present the implementation of a new model describing light dependent emission of volatile organic compounds (BVOC) that derives isoprenoid production directly from the electron transport potential and consumption from photosynthesis. Photosynthesis information requirements are designed to be met by many recent land-surface models that apply the Farquhar assimilation scheme, e.g. JULES or CLM. The new approach has the advantages that 1) the commonly observed decrease of (isoprene) emission with increasing CO2 air concentration is considered by the competition on energy between photosynthesis and emission processes, and 2) air pollution impacts may be considered as inducing emissions by activating emission enzymes as well as decreasing substrate supply from photosynthesis, and 3) many environmental drivers of BVOC emissions are implicitly considered in the description of plant photosynthesis and phenology, reducing the demand for species-specific emission parameters. We investigate the parameter sensitivity of the suggested model as well as the sensitivity of emissions to a range of environmental conditions with a particular focus on CO2 responses. We present evaluation at the site level and compare the model with other approaches. Finally, we demonstrate the implementation into a coupled global-air chemistry model and discuss the requirements to appropriately parameterize plant functional types.

  3. Chemistry, biological activity, and uses of formamidine pesticides.

    PubMed Central

    Hollingworth, R M

    1976-01-01

    The formamidines, a relatively new group of acaricide-insecticides, are novel both in their range of biological activities and in their mode of action, which is presently unknown. This paper is a review of the historical development, properties, structures, uses, and chemistry of this group of pesticides, with particular emphasis on chlordimeform (Galecron or Fundal), N'-4-chloro-o-tolyl-N,N-dimethylformamidine, and amitraz, 1,3=di-(2,4-dimethylphenylimino)-2-methyl-2-azapropane. Their biological activity and uses are defined by their toxicity to spider mites, ticks, and certain insects, and they are particularly effective against juvenile and resistant forms of these organisms. A significant, but poorly understood feature of their field effectiveness is their breadth of toxic action which includes direct lethality, excitant-repellant behavioral effects, and chemosterilization. They are generally of low hazard for nontarget species with the significant exception of predaceous mites. Several aspects of the chemistry of these compounds are considered, including structure--activity relations, synthetic pathways, isomerism and configuration, and their chemical and environmental stability. A significant feature of the metabolism and toxicity of these agents is the possible activation of chlordimeform by N-demethylation in vivo. Strong evidence for this has been presented with the cattle tick, but recent results discussed here suggest that in other species, i.e., mice, German cockroaches or black cutworm eggs, N-demethylation is neither a strong activation nor a detoxication reaction. PMID:789070

  4. Geology, hydrology, chemistry, and microbiology of the in situ bioremediation demonstration site

    SciTech Connect

    Newcomer, D.R.; Doremus, L.A.; Hall, S.H.; Truex, M.J.; Vermeul, V.R.; Engelman, R.E.

    1995-03-01

    This report summarizes characterization information on the geology, hydrology, microbiology, contaminant distribution, and ground-water chemistry to support demonstration of in situ bioremediation at the Hanford Site. The purpose of this information is to provide baseline conditions, including a conceptual model of the aquifer being utilized for in situ bioremediation. Data were collected from sampling and other characterization activities associated with three wells drilled in the upper part of the suprabasalt aquifer. Results of point-dilution tracer tests, conducted in the upper 9 m (30 ft) of the aquifer, showed that most ground-water flow occurs in the upper part of this zone, which is consistent with hydraulic test results and geologic and geophysical data. Other tracer test results indicated that natural ground-water flow velocity is equal to or less than about 0.03 m/d (0.1 ft/d). Laboratory hydraulic conductivity measurements, which represent the local distribution of vertical hydraulic conductivity, varied up to three orders of magnitude. Based on concentration data from both the vadose and saturated zone, it is suggested that most, if not all, of the carbon tetrachloride detected is representative of the aqueous phase. Concentrations of carbon tetrachloride, associated with a contaminant plume in the 200-West Area, ranged from approximately 500 to 3,800 {mu}g/L in the aqueous phase and from approximately 10 to 290 {mu}g/L in the solid phase at the demonstration site. Carbon tetrachloride gas was detected in the vadose zone, suggesting volatilization and subsequent upward migration from the saturated zone.

  5. Statistical methodology for exploring elevational differences in precipitation chemistry. [Dependence on site and elevation

    SciTech Connect

    Warren, W.G.; Boehm, M.; Link, D.

    1992-01-01

    A statistical methodology for exploring the relationships between elevation and precipitation chemistry is outlined and illustrated. The methodology utilizes maximum likelihood estimates and likelihood ratio tests with contour ellipses of assumed bivariate lognormal distributions used to assist in interpretation. The approach was illustrated using 12 NADP/NTN sites located in six study areas in the Wyoming and Colorado Rockies. These sites are part of the Rocky Mountain Deposition Monitoring Project (RMDMP), which was initiated in 1986 to investigate the relationships between elevation and the chemistry of precipitation. The results indicate differences in sulfate concentrations between airsheds, between snow and rain, and between higher and lower elevations. In general, sulfate concentrations in snow are greater at lower elevations and this difference is independent of concentration. A similar relationship for rain was not well established. In addition there is evidence that, overall, the sulfate concentrations differed between the six study areas, although pairwise differences were not always significant.

  6. Ammonia removal using activated carbons: effect of the surface chemistry in dry and moist conditions.

    PubMed

    Gonçalves, Maraisa; Sánchez-García, Laura; Oliveira Jardim, Erika de; Silvestre-Albero, Joaquín; Rodríguez-Reinoso, Francisco

    2011-12-15

    The effect of surface chemistry (nature and amount of oxygen groups) in the removal of ammonia was studied using a modified resin-based activated carbon. NH(3) breakthrough column experiments show that the modification of the original activated carbon with nitric acid, that is, the incorporation of oxygen surface groups, highly improves the adsorption behavior at room temperature. Apparently, there is a linear relationship between the total adsorption capacity and the amount of the more acidic and less stable oxygen surface groups. Similar experiments using moist air clearly show that the effect of humidity highly depends on the surface chemistry of the carbon used. Moisture highly improves the adsorption behavior for samples with a low concentration of oxygen functionalities, probably due to the preferential adsorption of ammonia via dissolution into water. On the contrary, moisture exhibits a small effect on samples with a rich surface chemistry due to the preferential adsorption pathway via Brønsted and Lewis acid centers from the carbon surface. FTIR analyses of the exhausted oxidized samples confirm both the formation of NH(4)(+) species interacting with the Brønsted acid sites, together with the presence of NH(3) species coordinated, through the lone pair electron, to Lewis acid sites on the graphene layers. PMID:22049916

  7. Site selective syntheses of [(3)H]omeprazole using hydrogen isotope exchange chemistry.

    PubMed

    Pollack, Scott R; Schenk, David J

    2015-01-01

    Omeprazole (Prilosec®) is a selective and irreversible proton pump inhibitor used to treat various medical conditions related to the production of excess stomach acids. It functions by suppressing secretion of those acids. Radiolabeled compounds are commonly employed in the drug discovery and development process to support efforts including library screening, target identification, receptor binding, assay development and validation and safety assessment. Herein, we describe synthetic approaches to the controlled and selective labeling of omeprazole with tritium via hydrogen isotope exchange chemistry. The chemistry may also be used to prepare tritium labeled esomeprazole (Nexium®), the active pure (S)-enantiomer of omeprazole. PMID:26380956

  8. Educational Activity Sites for High School Students

    ERIC Educational Resources Information Center

    Troutner, Joanne

    2005-01-01

    Finding quality Internet resources for high school students is a continuing challenge. Several high-quality web sites are presented for educators and students. These sites offer activities to learn how an art conservator looks at paintings, create a newspaper, research and develop an end product, build geometry and physics skills, explore science…

  9. Low dielectric response in enzyme active site

    PubMed Central

    Mertz, Edward L.; Krishtalik, Lev I.

    2000-01-01

    The kinetics of charge transfer depend crucially on the dielectric reorganization of the medium. In enzymatic reactions that involve charge transfer, atomic dielectric response of the active site and of its surroundings determines the efficiency of the protein as a catalyst. We report direct spectroscopic measurements of the reorganization energy associated with the dielectric response in the active site of α-chymotrypsin. A chromophoric inhibitor of the enzyme is used as a spectroscopic probe. We find that water strongly affects the dielectric reorganization in the active site of the enzyme in solution. The reorganization energy of the protein matrix in the vicinity of the active site is similar to that of low-polarity solvents. Surprisingly, water exhibits an anomalously high dielectric response that cannot be described in terms of the dielectric continuum theory. As a result, sequestering the active site from the aqueous environment inside low-dielectric enzyme body dramatically reduces the dielectric reorganization. This reduction is particularly important for controlling the rate of enzymatic reactions. PMID:10681440

  10. Probing the promiscuous active site of myo-inositol dehydrogenase using synthetic substrates, homology modeling, and active site modification.

    PubMed

    Daniellou, Richard; Zheng, Hongyan; Langill, David M; Sanders, David A R; Palmer, David R J

    2007-06-26

    The active site of myo-inositol dehydrogenase (IDH, EC 1.1.1.18) from Bacillus subtilis recognizes a variety of mono- and disaccharides, as well as 1l-4-O-substituted inositol derivatives. It catalyzes the NAD+-dependent oxidation of the axial alcohol of these substrates with comparable kinetic constants. We have found that 4-O-p-toluenesulfonyl-myo-inositol does not act as a substrate for IDH, in contrast to structurally similar compounds such as those bearing substituted benzyl substituents in the same position. X-ray crystallographic analysis of 4-O-p-toluenesulfonyl-myo-inositol and 4-O-(2-naphthyl)methyl-myo-inositol, which is a substrate for IDH, shows a distinct difference in the preferred conformation of the aryl substituent. Conformational analysis of known substrates of IDH suggests that this conformational difference may account for the difference in reactivity of 4-O-p-toluenesulfonyl-myo-inositol in the presence of IDH. A sequence alignment of IDH with the homologous glucose-fructose oxidoreductase allowed the construction of an homology model of inositol dehydrogenase, to which NADH and 4-O-benzyl-scyllo-inosose were docked and the active site energy minimized. The active site model is consistent with all experimental results and suggests that a conserved tyrosine-glycine-tyrosine motif forms the hydrophobic pocket adjoining the site of inositol recognition. Y233F and Y235F retain activity, while Y233R and Y235R do not. A histidine-aspartate pair, H176 and D172, are proposed to act as a dyad in which H176 is the active site acid/base. The enzyme is inactivated by diethyl pyrocarbonate, and the mutants H176A and D172N show a marked loss of activity. Kinetic isotope effect experiments with D172N indicate that chemistry is rate-determining for this mutant. PMID:17539607

  11. Comparing the Chemistry for the Pathfinder, MER and MSL Martian Landing Sites with APXS

    NASA Astrophysics Data System (ADS)

    Gellert, R.; Arvidson, R. E.; Clark, B. C.; Grotzinger, J. P.; Squyres, S. W.; Yen, A. S.

    2013-12-01

    The Alpha-Particle-X-ray Spectrometer is part of the science payload of all recent NASA Mars rover missions. It allows detailed comparison of the chemical composition and overall findings from rocks and soils at 4 landing sites. It can be even extended to the soil measurements performed with XRF on the two Viking landers. Typical soils at all 6 landing sites are very similar in chemical composition as well as mineralogy from instruments like Moessbauer on MER and CHEMIN on MSL. Beside a dominant basaltic composition the soil contains a significant altered and volatile rich component that is characterized by a constant S/Cl ratio in the APXS data. The overall similarity of the soils as well as the finding that soils around the 30 wt % SO3 rich bedrocks at Meridiani are not elevated in S, indicates the presence of a global distributed or at least large scale homogenized component in the Martian soil. This allows extending the SAM and CHEMIN findings in the altered and volatile components in the Gale Rocknest soils to other landing sites. However, in Gusev Crater anomalous subsurface soils were found - silica and hydrated ferric sulfate rich - that could indicate local fumarole and leaching activities. The sulfate rich Meridiani bedrock, called Burns formations, was documented to be remarkably homogeneous over the ~ 15 miles from the landing site at Eagle Crater to the base of the rim at Endurance Crater. Here for the first time a rover entered an area where evidence for clays is given by orbital CRISM data. With Opportunity's mineralogy instruments out of commission, the APXS was used to document the chemistry of the encountered outcrops. Having a composition close to the average Mars, one main characteristic feature of rocks at the rim is the low sulfur content compared to the younger Meridiani bedrock. The outcrops show post depositional cracks and veins filled with Calciumsulfate and Chlorine rich surface alteration rinds. A smaller outcrop called Esperance has

  12. DOTA derivatives for site-specific biomolecule-modification via click chemistry: synthesis and comparison of reaction characteristics.

    PubMed

    Wängler, Carmen; Schäfer, Martin; Schirrmacher, Ralf; Bartenstein, Peter; Wängler, Björn

    2011-06-15

    Due to the high stability of its complexes with many M(2+) and M(3+)-ions, DOTA (1,4,7,10-tetraazacyclododecane-N,N',N″,N‴-tetraacetic acid) is the most commonly used chelator for the derivatization and radiolabeling of bioactive molecules. Most of the currently used DOTA derivatives comprise amine-reactive functionalities, limiting their application to the derivatization of fully protected molecules or otherwise resulting in randomly distributed conjugation sites of undefined number. Click chemistry reactions are a valuable alternative to this unspecific conjugation as they proceed efficiently and chemoselectively under mild conditions allowing a site-specific derivatization of unprotected biomolecules. In this work, we describe straightforward syntheses of DOTA derivatives containing thiol, maleimide, aminooxy, aldehyde, alkyne, and azide functionalities, amenable to the currently most often used click chemistry reactions. Furthermore, the efficiency of the respective click reactions introducing DOTA into bioactive molecules was investigated. For each of the synthesized DOTA synthons, the site-specific and efficient conjugation to Tyr(3)-octreotate could be shown. Among these, the addition and oxime formation reactions proceeded fast and without side reactions, giving the products in high yields of 64-83% after purification. The copper-catalyzed triazole formation reactions produced some side-products, giving the desired products in lower, but still reasonable overall yields of 19-25%. All synthesized peptide-DOTA-conjugates were labeled with (68)Ga in high radiochemical yields of 96-99% and high specific activities providing compounds of high purity, demonstrating the applicability of all synthons for biomolecule modification and subsequent radiolabeling. PMID:21620712

  13. Litter chemistry prevails over litter consumers in mediating effects of past steel industry activities on leaf litter decomposition.

    PubMed

    Lucisine, Pierre; Lecerf, Antoine; Danger, Michaël; Felten, Vincent; Aran, Delphine; Auclerc, Apolline; Gross, Elisabeth M; Huot, Hermine; Morel, Jean-Louis; Muller, Serge; Nahmani, Johanne; Maunoury-Danger, Florence

    2015-12-15

    Soil pollution has adverse effects on the performance and life history traits of microorganisms, plants, and animals, yet evidence indicates that even the most polluted sites can support structurally-complex and dynamic ecosystems. The present study aims at determining whether and how litter decomposition, one of the most important soil ecological processes leaf, is affected in a highly trace-metal polluted site. We postulated that past steel mill activities resulting in soil pollution and associated changes in soil characteristics would influence the rate of litter decomposition through two non-exclusive pathways: altered litter chemistry and responses of decomposers to lethal and sub-lethal toxic stress. We carried out a litter-bag experiment using Populus tremula L. leaf litter collected at, and allowed to decompose in, a trace metal polluted site and in three unpolluted sites used as controls. We designed a fully-factorial transplant experimental design to assess effects of litter origin and exposure site on the rate of litter decomposition. We further determined initial litter chemistry, fungal biomass, mesofauna abundance in litter bags, and the soil macrofauna community. Irrespective of the site of litter exposure, litter originating from the polluted site had a two-fold faster decomposition than litter from the unpolluted sites. Litter chemistry, notably the lignin content, seemed most important in explaining the degradation rate of the leaf litter. Abundance of meso and macro-detritivores was higher at the polluted site than at the unpolluted sites. However, litter decomposition proceeded at similar rates in polluted and unpolluted sites. Our results show that trace metal pollution and associated soil and litter changes do not necessarily weaken consumer control on litter decomposition through lethal and sub-lethal toxic stress. PMID:26282755

  14. Chemistry, biogenesis, and biological activities of Cinnamomum zeylanicum.

    PubMed

    Jayaprakasha, G K; Rao, L Jagan Mohan

    2011-07-01

    The genus Cinnamomum comprises of several hundreds of species, which are distributed in Asia and Australia. Cinnamomum zeylanicum, the source of cinnamon bark and leaf oils, is an indigenous tree of Sri Lanka, although most oil now comes from cultivated areas. C. zeylanicum is an important spice and aromatic crop having wide applications in flavoring, perfumery, beverages, and medicines. Volatile oils from different parts of cinnamon such as leaves, bark, fruits, root bark, flowers, and buds have been isolated by hydro distillation/steam distillation and supercritical fluid extraction. The chemical compositions of the volatile oils have been identified by GC and GC-MS. More than 80 compounds were identified from different parts of cinnamon. The leaf oil has a major component called eugenol. Cinnamaldehyde and camphor have been reported to be the major components of volatile oils from stem bark and root bark, respectively. Trans-cinnamyl acetate was found to be the major compound in fruits, flowers, and fruit stalks. These volatile oils were found to exhibit antioxidant, antimicrobial, and antidiabetic activities. C. zeylanicum bark and fruits were found to contain proanthocyandins with doubly linked bis-flavan-3-ol units in the molecule. The present review provides a coherent presentation of scattered literature on the chemistry, biogenesis, and biological activities of cinnamon. PMID:21929331

  15. Operation and research at the Ithaca MAP3S regional precipitation chemistry site

    SciTech Connect

    Butler, T.J.; Likens, G.E.

    1991-07-01

    Annual precipitation chemistry data from network start-up through 1988 is presented for the nine MAP3S sites. Time trends show significant negative linear regressions (P < 0.10) for SO{sub 4}{sup 2-} at 2 sites, H{sup +} at 4 sites, Ca{sup ++} at 1 site, and Na{sup +} at 1 site. Significant positive regressions over time include: NH{sub 4}{sup +} at 2 sites, Ca{sup ++} at 1 site, K{sup +} at 4 sites, and Cl{sup {minus}} at 2 sites. The Ithaca site shows the highest number of significant trends, with positive trends for Cl{sup {minus}}, NH{sub 4}{sup +}, Ca{sup ++}, and K{sup +}, and a negative trend for H{sup +}. Linear regressions of annual SO{sub 4}{sup 2-} concentrations on SO2 emissions show a significant positive relationship for Whiteface, Illinois, and Ohio at p < 0.10, 0.02, and 0.05 respectively. Overall for all MAP3S sites, plus Hubbard Brook a 25% decline in SO2 emissions over the region has been accompanied by a 16.5% decline in annual precipitation concentrations of SO{sub 4}{sup 2-}. For the region as a whole, a 20% decline in combined emissions has been accompanied to a 20% decline in H{sup +} concentrations. Thus a linear relationship exists between combined emissions and precipitation H{sup +} concentrations. No strong relationship exists for NOx emissions and precipitation NO{sub 3}{sup {minus}} concentration at the annual, seasonal or monthly level. Removing the NOx transportation sector, removing high and low precipitation values, or high pH values also does little to improve the NOx -- NO{sub 3}{sup {minus}} concentration relationships. Dry deposition components such a PAN, NO2, gaseous HNO{sub 3}, or aerosol NO{sub 3}{sup {minus}} should be included in the future with precipitation NO{sub 3}{sup {minus}} to relate emissions of NOx to nitrogen deposition. 11 refs., 27 figs.,1 tab.

  16. Cyclopenta[c]phenanthrenes--chemistry and biological activity.

    PubMed

    Brzuzan, Paweł; Góra, Maciej; Luczyński, Michał K; Woźny, Maciej

    2013-06-25

    Despite cyclopenta-fused polycyclic aromatic hydrocarbons (CP-PAHs) having been detected in the environment, the ability of these compounds to induce cellular and tissue responses remains poorly characterized. In this review, we look at the chemistry and biological activity of the cyclopenta[c]phenanthrenes (CP[c]Phs) as potential chemicals of concern in the process of risk assessment. The first part of the review deals with the environmental occurrence and chemistry of CP-PAHs, focusing on available methods of CP[c]Ph chemical synthesis. The most interesting structural feature of the CP[c]Ph is the presence of a pseudo fjord-region constructed by the cyclopentane ring. This compound can be treated either as a structurally similar one to B[c]Ph, or as a phenanthrene skeleton with an electrodonating alkyl substituent in the bay-region of the molecule. The second thread, providing available data on the adverse effects of CP[c]Ph compounds on cells and tissues of living organisms, mainly fish, improves our understanding of these possible environmental hazards. The data show that CP[c]Ph is less potent at inducing CYP1A gene expression in rainbow trout than benzo[a]pyrene (B[a]P), a well-known Ah-receptor agonist. Interestingly, the CP[c]Ph dependent up-regulation of CYP1A mRNA is positively correlated with the incidences of clastogenic changes in rainbow trout erythrocytes. CP[c]Ph has, comparably to B[a]P, a potential to repress expression of tumor suppressor p53, in the head kidney of rainbow trout. Furthermore, estrogen responsive genes in fish liver, ERα and VTG, are not induced by CP[c]Ph, suggesting that the compound has no endocrine disrupting potential. However, some CP[c]Phs show mutagenic activity when investigated in the Ames test, and exhibit genotoxic properties in in vitro micronucleus assay. The above characteristics suggest that CP-PAHs are chemicals of concern for which potential pathways of exposure should be further identified. PMID:23628509

  17. Active site specificity of plasmepsin II.

    PubMed Central

    Westling, J.; Cipullo, P.; Hung, S. H.; Saft, H.; Dame, J. B.; Dunn, B. M.

    1999-01-01

    Members of the aspartic proteinase family of enzymes have very similar three-dimensional structures and catalytic mechanisms. Each, however, has unique substrate specificity. These distinctions arise from variations in amino acid residues that line the active site subsites and interact with the side chains of the amino acids of the peptides that bind to the active site. To understand the unique binding preferences of plasmepsin II, an enzyme of the aspartic proteinase class from the malaria parasite, Plasmodium falciparum, chromogenic octapeptides having systematic substitutions at various positions in the sequence were analyzed. This enabled the design of new, improved substrates for this enzyme (Lys-Pro-Ile-Leu-Phe*Nph-Ala/Glu-Leu-Lys, where * indicates the cleavage point). Additionally, the crystal structure of plasmepsin II was analyzed to explain the binding characteristics. Specific amino acids (Met13, Ser77, and Ile287) that were suspected of contributing to active site binding and specificity were chosen for site-directed mutagenesis experiments. The Met13Glu and Ile287Glu single mutants and the Met13Glu/Ile287Glu double mutant gain the ability to cleave substrates containing Lys residues. PMID:10548045

  18. Planet Chemistry. Hands-on Activities for Kids from All Planets.

    ERIC Educational Resources Information Center

    Kenney, Michael, Ed.

    This publication issues a challenge to students to collect data in a nationwide analysis of water hardness. Background information on the chemistry of hard water is presented using a cartoon format, and each of the four activities contains an explanation about the chemistry illustrated in the activity. The effect of hard water on soap, the effect…

  19. Turkish Chemistry Teachers' Views about an Implementation of the Active Learning Approaches in Their Lessons

    ERIC Educational Resources Information Center

    Karamustafaoglu, Sevilay; Costu, Bayram; Ayas, Alipasa

    2006-01-01

    Active learning is advocated as a better way of teaching for several decades in science education. The purpose of this study was to determine chemistry teachers' thinking and views about student-centered activities applicable in chemistry teaching and learning in the study context. A case study approach was used in this research. At the beginning,…

  20. Evaluation of Potential Impacts of Microbial Activity on Drift Chemistry

    SciTech Connect

    Y. Wang

    2004-11-18

    ''Evaluation of Potential Impacts of Microbial Activity on Drift Chemistry'' focuses on the potential for microbial communities that could be active in repository emplacement drifts to influence the in-drift bulk chemical environment. This report feeds analyses to support the inclusion or exclusion of features, events, and processes (FEPs) in the total system performance assessment (TSPA) for the license application (LA), but this work is not expected to generate direct feeds to the TSPA-LA. The purpose was specified by, and the evaluation was performed and is documented in accordance with, ''Technical Work Plan For: Near-Field Environment and Transport In-Drift Geochemistry Analyses'' (BSC 2004 [DIRS 172402], Section 2.1). This report addresses all of the FEPs assigned by the technical work plan (TWP), including the development of exclusion arguments for FEPs that are not carried forward to the TSPA-LA. Except for an editorial correction noted in Section 6.2, there were no other deviations from the TWP. This report documents the completion of all assigned tasks, as follows (BSC 2004 DIRS 172402, Section 1.2.1): (1) Perform analyses to evaluate the potential for microbial activity in the waste emplacement drift under the constraints of anticipated physical and chemical conditions. (2) Evaluate uncertainties associated with these analyses. (3) Determine whether the potential for microbes warrants a feed to TSPA-LA to account for predicted effects on repository performance. (4) Provide information to address the ''Yucca Mountain Review Plan, Final Report'' (NUREG-1804) (NRC 2003 [DIRS 163274]) and Key Technical Issues and agreements, as appropriate. (5) Develop information for inclusion or exclusion of FEPs.

  1. An Assessment of a Physical Chemistry Online Activity

    NASA Astrophysics Data System (ADS)

    Hamby Towns, Marcy; Kreke, Kelley; Sauder, Deborah; Stout, Roland; Long, George; Zielinski, Theresa Julia

    1998-12-01

    A questionnaire and list server archive were used to investigate the perception of students and faculty who took part in a physical chemistry online project. Students at four universities worked cooperatively in their own classrooms and collaborated as a larger team on the Internet via a list server to determine the best mathematical model to describe the PV behavior of a gas at a specified temperature. The strengths of the project were the interaction among students, the use of Mathcad and modern technology, and the experience of authentic problem-solving. The weaknesses were the problems with the technology, the facilitation of interaction, and the student's ability to ask questions to solve an ill-defined problem. The suggestions for improvements focused on facilitating interuniversity interaction between students, clarifying tasks and goals, and implementation of the online activities. We discuss how our evaluation of the project guided and informed the design of a subsequent online project, and our planning for future projects. In addition, we describe the professional learning community that evolved among faculty who participated in this project.

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

    PubMed

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

    2016-08-18

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

  3. Pollution Prevention Plan for the Y-12 Analytical Chemistry Organization Off-Site Union Valley Facility

    SciTech Connect

    Jackson, J. G.

    2010-03-01

    The Y-12 Analytical Chemistry Organization (ACO) Off-Site Union Valley Facility (Union Valley Facility) is managed by Babcock and Wilcox Technical Services Y-12, L.L.C. (B and W Y-12) through the Y-12 National Security Complex organization. Accordingly, the Y-12 Pollution Prevention Program encompasses the operations conducted at the Union Valley Facility. The Y-12 Program is designed to fully comply with state, federal and U.S. Department of Energy (DOE) requirements concerning waste minimization/pollution prevention as documented in the Y-12 Pollution Prevention Program Plan. The Program is formulated to reduce the generation and toxicity of all Y-12 wastes in all media, including those wastes generated by the Union Valley Facility operations. All regulatory and DOE requirements are met by the Y-12 Program Plan.

  4. Corrosion Research And Web Site Activities

    NASA Technical Reports Server (NTRS)

    Heidersbach, Robert H.

    2001-01-01

    This report covers corrosion-related activities at the NASA Kennedy Space Center during the summer of 2000. The NASA Kennedy Space Center's corrosion web site, corrosion.ksc.nasa.gov, was updated with new information based on feedback over the past two years. The methodology for a two-year atmospheric exposure testing program to study the effectiveness of commercial chemicals sold for rinsing aircraft and other equipment was developed and some preliminary laboratory chemical analyses are presented.

  5. Corrosion Research and Web Site Activities

    NASA Technical Reports Server (NTRS)

    Heidersbach, Robert H.

    2002-01-01

    This report covers corrosion-related activities at the NASA Kennedy Space Center during the summer of 2000. The NASA Kennedy Space Center's corrosion web site, corrosion.ksc.nasa.gov, was updated with new information based on feedback over the past two years. The methodology for a two-year atmospheric exposure testing program to study the effectiveness of commercial chemicals sold for rinsing aircraft and other equipment was developed and some preliminary laboratory chemical analyses are presented.

  6. Elaboration of copper-oxygen mediated C-H activation chemistry in consideration of future fuel and feedstock generation.

    PubMed

    Lee, Jung Yoon; Karlin, Kenneth D

    2015-04-01

    To contribute solutions to current energy concerns, improvements in the efficiency of dioxygen mediated C-H bond cleavage chemistry, for example, selective oxidation of methane to methanol, could minimize losses in natural gas usage or produce feedstocks for fuels. Oxidative C-H activation is also a component of polysaccharide degradation, potentially affording alternative biofuels from abundant biomass. Thus, an understanding of active-site chemistry in copper monooxygenases, those activating strong C-H bonds is briefly reviewed. Then, recent advances in the synthesis-generation and study of various copper-oxygen intermediates are highlighted. Of special interest are cupric-superoxide, Cu-hydroperoxo and Cu-oxy complexes. Such investigations can contribute to an enhanced future application of C-H oxidation or oxygenation processes using air, as concerning societal energy goals. PMID:25756327

  7. Elaboration of Copper-Oxygen Mediated C–H Activation Chemistry in Consideration of Future Fuel and Feedstock Generation

    PubMed Central

    Lee, Jung Yoon; Karlin, Kenneth D

    2015-01-01

    To contribute solutions for current energy concerns, improvements in the efficiency of C-H bond cleavage chemistry, e.g., selective oxidation of methane to methanol, could minimize losses in natural gas usage or produce feedstocks for fuels. Oxidative C-H activation is also a component of polysaccharide degradation, affording alternative biofuels from abundant biomass. Thus, an understanding of active-site chemistry in copper monooxygenases, those activating strong C-H bonds is briefly reviewed. Then, recent advances in the synthesis-generation and study of various copper-oxygen intermediates are highlighted. Of special interest are cupric-superoxide, Cu-hydroperoxo and Cu-oxy complexes. Such investigations can contribute to an enhanced future application of C-H oxidation or oxygenation processes using air, as concerning societal energy goals. PMID:25756327

  8. Comparative analysis of click chemistry mediated activity-based protein profiling in cell lysates.

    PubMed

    Yang, Yinliang; Yang, Xiaomeng; Verhelst, Steven H L

    2013-01-01

    Activity-based protein profiling uses chemical probes that covalently attach to active enzyme targets. Probes with conventional tags have disadvantages, such as limited cell permeability or steric hindrance around the reactive group. A tandem labeling strategy with click chemistry is now widely used to study enzyme targets in situ and in vivo. Herein, the probes are reacted in live cells, whereas the ensuing detection by click chemistry takes place in cell lysates. We here make a comparison of the efficiency of the activity-based tandem labeling strategy by using Cu(I)-catalyzed and strain-promoted click chemistry, different ligands and different lysis conditions. PMID:24126377

  9. Dependence of grain boundary chemistry on the irradiation dose in low activation ferritics

    NASA Astrophysics Data System (ADS)

    Kimura, A.; Charlot, L. A.; Gelles, D. S.; Jones, R. H.

    1994-09-01

    Grain boundary chemistries in low activation 9%Cr-2%Mn-1%W and 12%Cr-6%Mn-1%W steels were measured by means of Auger electron spectroscopy (AES) after irradiations in the FFTF/MOTA at 638 K up to doses of 10 and 25 dpa. In 12%Cr-6%Mn-1%W steel, grain boundary concentration of Si increased with an increase in the irradiation dose from 10 to 25 dpa. Segregation of Mn, however, appeared to saturate or even decreased with the increase. The average size of grain boundary precipitates was increased during the irradiation from 10 to 25 dpa. It is considered that beyond the 10 dpa irradiation, Mn-rich precipitates at grain boundaries absorb Mn atoms segregated at grain boundaries, resulting in the growth of grain boundary precipitates and the reduction of segregated Mn atoms in elemental form at grain boundaries. It is possible that Si atoms which may compete site with Mn atoms at grain boundaries begin to segregate at grain boundaries. In contrast, no significant change in grain boundary chemistry was recognized in 9%Cr-2%Mn-1%W alloy with the increase in irradiation dose from 10 to 25 dpa.

  10. Solar Energy Education. Renewable energy activities for chemistry and physics

    SciTech Connect

    Not Available

    1985-01-01

    Information on renewable energy sources is provided for students in this teachers' guide. With the chemistry and physics student in mind, solar energy topics such as absorber plate coatings for solar collectors and energy collection and storage methods are studied. (BCS)

  11. Incorporating More Individual Accountability in Group Activities in General Chemistry

    ERIC Educational Resources Information Center

    Cox, Charles T., Jr.

    2015-01-01

    A modified model of cooperative learning known as the GIG model (for group-individual-group) designed and implemented in a large enrollment freshman chemistry course. The goal of the model is to establish a cooperative environment while emphasizing greater individual accountability using both group and individual assignments. The assignments were…

  12. Active site of ribulosebisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.; Stringer, C.D.; Milanez, S.; Lee, E.H.

    1985-01-01

    Previous affinity labeling studies and comparative sequence analyses have identified two different lysines at the active site of ribulosebisphosphate carboxylase/oxygenase and have suggested their essentiality to function. The essential lysines occupy positions 166 and 329 in the Rhodospirillum rubrum enzyme and positions 175 and 334 in the spinach enzyme. Based on the pH-dependencies of inactivations of the two enzymes by trinitrobenzene sulfonate, Lys-166 (R. rubrum enzyme) exhibits a pK/sub a/ of 7.9 and Lys-334 (spinach enzyme) exhibits a pK/sub a/ of 9.0. These low pK/sub a/ values as well as the enhanced nucleophilicities of the lysyl residues argue that both are important to catalysis rather than to substrate binding. Lys-166 may correspond to the essential base that initiates catalysis and that displays a pK/sub a/ of 7.5 in the pH-curve for V/sub max//K/sub m/. Cross-linking experiments with 4,4'-diisothiocyano-2,2'-disulfonate stilbene demonstrate that the two active-site lysines are within 12 A. 50 refs., 7 figs., 1 tab.

  13. Active Sites Environmental Monitoring Program: Program plan

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  14. The chemistry of biogenic hydrocarbons at a rural site in eastern Canada

    NASA Astrophysics Data System (ADS)

    Biesenthal, T. A.; Bottenheim, J. W.; Shepson, P. B.; Li, S.-M.; Brickell, P. C.

    1998-10-01

    An intensive field study was undertaken in southern Nova Scotia, on the east coast of Canada, for several weeks during the summer of 1996 as part of the North American Research Strategy for Tropospheric Ozone - Canada East (NARSTO-CE) 1996 field measurement campaign. Clean air conditions prevailed during most of the study period, which allowed an examination of biogenic hydrocarbon chemistry with minimal influence from anthropogenic pollutants. Low NOx mixing ratios during the study had an impact on the ratio of isoprene's oxidation products methyl vinyl ketone (MVK) and methacrolein (MACR) to isoprene. The effects include changes to the fate of isoprene peroxy radicals and to the concentration of OH compared to conditions of higher [NOx]. Comparison to other studies indicate that there is a relationship between the ratio (MVK+MACR)/isoprene and the mixing ratio of NOx. Biogenic hydrocarbons were the dominant reactive volatile organic compound (VOC) precursors to ozone production in this region, although the net ozone production rate predicted by a box-model simulation of the measurement data was only <1 ppbv h-1. The evidence confirms that ozone production at this site is very NOx-sensitive. Model simulations indicated that the ozonolysis of biogenic hydrocarbons is an important source of the hydroxyl radical at this site and that OH was, in fact, the dominant oxidant during the nighttime under the observed low NOx conditions. Although the OH source did affect the nighttime mixing ratios of biogenic hydrocarbons, it could not fully explain the rapid nocturnal decay of isoprene observed on most evenings.

  15. First hydrothermal discoveries on the Australian-Antarctic Ridge: Discharge sites, plume chemistry, and vent organisms

    NASA Astrophysics Data System (ADS)

    Hahm, Doshik; Baker, Edward T.; Siek Rhee, Tae; Won, Yong-Jin; Resing, Joseph A.; Lupton, John E.; Lee, Won-Kyung; Kim, Minjeong; Park, Sung-Hyun

    2015-09-01

    The Australian-Antarctic Ridge (AAR) is one of the largest unexplored regions of the global mid-ocean ridge system. Here, we report a multiyear effort to locate and characterize hydrothermal activity on two first-order segments of the AAR: KR1 and KR2. To locate vent sites on each segment, we used profiles collected by Miniature Autonomous Plume Recorders on rock corers during R/V Araon cruises in March and December of 2011. Optical and oxidation-reduction-potential anomalies indicate multiple active sites on both segments. Seven profiles on KR2 found 3 sites, each separated by ˜25 km. Forty profiles on KR1 identified 17 sites, some within a few kilometer of each other. The spatial density of hydrothermal activity along KR1 and KR2 (plume incidence of 0.34) is consistent with the global trend for a spreading rate of ˜70 mm/yr. The densest area of hydrothermal activity, named "Mujin," occurred along the 20 km-long inflated section near the segment center of KR1. Continuous plume surveys conducted in January-February of 2013 on R/V Araon found CH4/3He (1 - 15 × 106) and CH4/Mn (0.01-0.5) ratios in the plume samples, consistent with a basaltic-hosted system and typical of ridges with intermediate spreading rates. Additionally, some of the plume samples exhibited slightly higher ratios of H2/3He and Fe/Mn than others, suggesting that those plumes are supported by a younger hydrothermal system that may have experienced a recent eruption. The Mujin-field was populated by Kiwa crabs and seven-armed Paulasterias starfish previously recorded on the East Scotia Ridge, raising the possibility of circum-Antarctic biogeographic connections of vent fauna.

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

    SciTech Connect

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

    2011-10-18

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

  17. Self-Directed Activity-Based Learning and Achievement in High School Chemistry

    ERIC Educational Resources Information Center

    Bassett, Meighan M.; Martinez, James; Martin, Ellice P.

    2014-01-01

    The effects of student-directed activity-based learning (SDABL) were examined in two high school chemistry classes. Students in the SDABL class were given pretest results, a list of standards to be mastered, and a chart of learning activities categorized by difficulty level. They selected activities to meet their needs and preferences.…

  18. Limitations in determining redox chemistry in basalt groundwaters at the Hanford site

    SciTech Connect

    Dill, J.A.; Jones, T.E.; Marcy, A.D.; West, M.H.

    1986-03-01

    The oxidation-reduction (redox) chemistry of the basalt groundwater system will be an important factor governing both the design and performance of a high-level nuclear waste repository in basalt. Although the redox state of the basalt groundwater system is inherently difficult to measure, there are a number of types of measurements that provide valuable information on this subject. These measurements include concentrations of dissolved sulfide, ferrous iron, electrode redox potential, and groundwater reducing capacity. These measurements have been made on a limited basis in a number of different repository test horizons. Taken collectively, the results of these measurements suggest that both sulfide and ferrous iron play an important role in the establishment of the basalt groundwater redox condition. Thermodynamic calculations of redox potential (E/sub h/) based on these measurements are indicative of an E/sub h/ of -0.4 V. Additional measurements are proposed that will provide a more complete understanding of basalt groundwater redox conditions. The proposed measurements include a more in-depth analysis of redox active species as well as quantification of dissolved gas species such as oxygen and methane.

  19. Mixed valency and site-preference chemistry for cerium and its compounds: A predictive density-functional theory study

    SciTech Connect

    Alam, Aftab; Johnson, Duane D.

    2014-06-01

    Cerium and its technologically relevant compounds are examples of anomalous mixed valency, originating from two competing oxidation states—itinerant Ce4+ and localized Ce3+. Under applied stress, anomalous transitions are observed but not well understood. Here we treat mixed valency as an “alloy” problem involving two valences with competing and numerous site-occupancy configurations. We use density-functional theory with Hubbard U (i.e., DFT+U) to evaluate the effective valence and predict properties, including controlling the valence by pseudoternary alloying. For Ce and its compounds, such as (Ce,La)2(Fe,Co)14B permanent magnets, we find a stable mixed-valent α state near the spectroscopic value of νs=3.53. Ce valency in compounds depends on its steric volume and local chemistry. For La doping, Ce valency shifts towards γ-like Ce3+, as expected from steric volume; for Co doping, valency depends on local Ce-site chemistry and steric volume. Our approach captures the key origins of anomalous valency and site-preference chemistry in complex compounds.

  20. Mixed valency and site-preference chemistry for cerium and its compounds: A predictive density-functional theory study

    NASA Astrophysics Data System (ADS)

    Alam, Aftab; Johnson, D. D.

    2014-06-01

    Cerium and its technologically relevant compounds are examples of anomalous mixed valency, originating from two competing oxidation states—itinerant Ce4+ and localized Ce3+. Under applied stress, anomalous transitions are observed but not well understood. Here we treat mixed valency as an "alloy" problem involving two valences with competing and numerous site-occupancy configurations. We use density-functional theory with Hubbard U (i.e., DFT+U) to evaluate the effective valence and predict properties, including controlling the valence by pseudoternary alloying. For Ce and its compounds, such as (Ce,La)2(Fe,Co)14B permanent magnets, we find a stable mixed-valent α state near the spectroscopic value of νs=3.53. Ce valency in compounds depends on its steric volume and local chemistry. For La doping, Ce valency shifts towards γ-like Ce3+, as expected from steric volume; for Co doping, valency depends on local Ce-site chemistry and steric volume. Our approach captures the key origins of anomalous valency and site-preference chemistry in complex compounds.

  1. Chemistry For Kids: Pre-Chemistry Acid Rain Activities for Kids.

    ERIC Educational Resources Information Center

    Barrow, Lloyd H.

    1985-01-01

    Presents two activities on acid rain for students in intermediate grades. Materials needed and procedures used are included. Also describes "chemical magic" shows performed by high school students for sixth-grade students in seven elementary schools in Altus, Oklahoma. (JN)

  2. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1976

    1976-01-01

    Described are eight chemistry experiments and demonstrations applicable to introductory chemistry courses. Activities include: measure of lattice enthalpy, Le Chatelier's principle, decarboxylation of soap, use of pocket calculators in pH measurement, and making nylon. (SL)

  3. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Presents background information, laboratory procedures, classroom materials/activities, and chemistry experiments. Topics include sublimation, electronegativity, electrolysis, experimental aspects of strontianite, halide test, evaluation of present and future computer programs in chemistry, formula building, care of glass/saturated calomel…

  4. Precipitation chemistry and wet deposition in a remote wet savanna site in West Africa: Djougou (Benin)

    NASA Astrophysics Data System (ADS)

    Akpo, A. B.; Galy-Lacaux, C.; Laouali, D.; Delon, C.; Liousse, C.; Adon, M.; Gardrat, E.; Mariscal, A.; Darakpa, C.

    2015-08-01

    , biomass burning and biofuel combustions. The second highest contribution is the calcium ion (13.3 μeq·L-1), characteristic of dust aerosols from terrigenous sources, Calcium contributes up to 46% of the precipitation chemistry in Djougou. Finally, these results are compared to those obtained for other selected African sites representative of other main natural ecosystems: dry savanna and forest. The study of the African ecosystem transect indicates a pH gradient with more acidic pH in the forested ecosystem. Nitrogenous contribution to the chemical composition of rain in Lamto, wet savanna, (24%) is equivalent to the one estimated in Djougou (24%). The last contribution concerns organic acidity, which represents 7% of total ionic content of precipitation at Djougou. The relative particulate contribution PC and the relative gaseous contribution GC are calculated using the mean chemical composition measured in Djougou for the studied period. The comparison with other African sites gives 40% and 43% PC in wet savannas of Lamto (Côte d'Ivoire) and Djougou (Benin) respectively, 20% PC in the equatorial forest of Zoetele (Cameroon) and 80% PC in dry savanna of Banizoumbou (Niger). The results shown here indicate the existence of a North-South gradients of organic, marine, terrigenous and nitrogenous contributions along the transect in West and Central Africa.

  5. Active site densities, oxygen activation and adsorbed reactive oxygen in alcohol activation on npAu catalysts.

    PubMed

    Wang, Lu-Cun; Friend, C M; Fushimi, Rebecca; Madix, Robert J

    2016-07-01

    The activation of molecular O2 as well as the reactivity of adsorbed oxygen species is of central importance in aerobic selective oxidation chemistry on Au-based catalysts. Herein, we address the issue of O2 activation on unsupported nanoporous gold (npAu) catalysts by applying a transient pressure technique, a temporal analysis of products (TAP) reactor, to measure the saturation coverage of atomic oxygen, its collisional dissociation probability, the activation barrier for O2 dissociation, and the facility with which adsorbed O species activate methanol, the initial step in the catalytic cycle of esterification. The results from these experiments indicate that molecular O2 dissociation is associated with surface silver, that the density of reactive sites is quite low, that adsorbed oxygen atoms do not spill over from the sites of activation onto the surrounding surface, and that methanol reacts quite facilely with the adsorbed oxygen atoms. In addition, the O species from O2 dissociation exhibits reactivity for the selective oxidation of methanol but not for CO. The TAP experiments also revealed that the surface of the npAu catalyst is saturated with adsorbed O under steady state reaction conditions, at least for the pulse reaction. PMID:27376884

  6. Offering Community Engagement Activities to Increase Chemistry Knowledge and Confidence for Teachers and Students

    ERIC Educational Resources Information Center

    Sewry, Joyce D.; Glover, Sarah R.; Harrison, Timothy G.; Shallcross, Dudley E.; Ngcoza, Kenneth M.

    2014-01-01

    Given the emphasis on community engagement in higher education, academic departments need to become more involved in the community. This paper discusses a number of outreach activities undertaken by the chemistry department at Rhodes University, South Africa. The activities range from service learning to community engagement with teachers and…

  7. Using Laboratory Chemicals to Imitate Illicit Drugs in a Forensic Chemistry Activity

    ERIC Educational Resources Information Center

    Hasan, Shawn; Bromfield-Lee, Deborah; Oliver-Hoyo, Maria T.; Cintron-Maldonado, Jose A.

    2008-01-01

    This forensic chemistry activity utilizes presumptive forensic testing procedures and laboratory chemicals that produce screening results similar to controlled substances. For obvious reasons, obtaining heavily regulated controlled substances to create an undergraduate student activity is not practical for most educational institutions. We were…

  8. "SimChemistry" as an Active Learning Tool in Chemical Education

    ERIC Educational Resources Information Center

    Bolton, Kim; Saalman, Elisabeth; Christie, Michael; Ingerman, Ake; Linder, Cedric

    2008-01-01

    The publicly available free computer program, "SimChemistry," was used as an active learning tool in the chemical engineering curriculum at the University College of Boras, Sweden. The activity involved students writing their own simulation programs on topics in the area of molecular structure and interactions. Evaluation of the learning…

  9. Mutation at a Strictly-Conserved, Active-Site Tyrosine in the Copper Amine Oxidase Leads to Uncontrolled Oxygenase Activity†

    PubMed Central

    Chen, Zhi-wei; Datta, Saumen; DuBois, Jennifer L.; Klinman, Judith P.; Mathews, F. Scott

    2010-01-01

    The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ), and the subsequent oxidative deamination of substrate amines. Because the same active-site pocket must facilitate both reactions, individual active-site residues may serve multiple roles. We have examined the roles of a strictly-conserved active-site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically, and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild-type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy-intermediates in cofactor biogenesis, but also indicates the critical control of oxidation chemistry that can be conferred by a single active-site residue. PMID:20684524

  10. Final Report: Main Group Element Chemistry in Service of Hydrogen Storage and Activation

    SciTech Connect

    David A. Dixon; Anthony J. Arduengo, III

    2010-09-30

    Replacing combustion of carbon-based fuels with alternative energy sources that have minimal environmental impact is one of the grand scientific and technological challenges of the early 21st century. Not only is it critical to capture energy from new, renewable sources, it is also necessary to store the captured energy efficiently and effectively for use at the point of service when and where it is needed, which may not be collocated with the collection site. There are many potential storage media but we focus on the storage of energy in chemical bonds. It is more efficient to store energy on a per weight basis in chemical bonds. This is because it is hard to pack electrons into small volumes with low weight without the use of chemical bonds. The focus of the project was the development of new chemistries to enable DOE to meet its technical objectives for hydrogen storage using chemical hydrogen storage systems. We provided computational chemistry support in terms of thermodynamics, kinetics, and properties prediction in support of the experimental efforts of the DOE Center of Excellence for Chemical Hydrogen Storage. The goal of the Center is to store energy in chemical bonds involving hydrogen atoms. Once the hydrogen is stored in a set of X-H/Y-H bonds, the hydrogen has to be easily released and the depleted fuel regenerated very efficiently. This differs substantially from our current use of fossil fuel energy sources where the reactant is converted to energy plus CO2 (coal) or CO2 and H2O (gasoline, natural gas), which are released into the atmosphere. In future energy storage scenarios, the spent fuel will be captured and the energy storage medium regenerated. This places substantial additional constraints on the chemistry. The goal of the computational chemistry work was to reduce the time to design new materials and develop materials that meet the 2010 and 2015 DOE objectives in terms of weight percent, volume, release time, and regeneration ability. This

  11. Dissecting the active site of a photoreceptor protein

    NASA Astrophysics Data System (ADS)

    Hoff, Wouter; Hara, Miwa; Ren, Jie; Moghadam, Farzaneh; Xie, Aihua; Kumauchi, Masato

    While enzymes are quite large molecules, functionally important chemical events are often limited to a small region of the protein: the active site. The physical and chemical properties of residues at such active sites are often strongly altered compared to the same groups dissolved in water. Understanding such effects is important for unraveling the mechanisms underlying protein function and for protein engineering, but has proven challenging. Here we report on our ongoing efforts on using photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system for such effects. We will report on the following questions: How many residues affect active site properties? Are these residues in direct physical contact with the active site? Can functionally important residues be recognized in the crystal structure of a protein? What structural resolution is needed to understand active sites? What spectroscopic techniques are most informative? Which weak interactions dominate active site properties?

  12. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

    Presents background information, laboratory procedures, classroom materials/activities, and experiments for chemistry. Topics include superheavy elements, polarizing power and chemistry of alkali metals, particulate carbon from combustion, tips for the chemistry laboratory, interesting/colorful experiments, behavior of bismuth (III) iodine, and…

  13. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, Virginia C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program --now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history The missions will develop technology and acquire data necessary for eventual human Exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines be opportunities for the Mars community to provide input into the landing site selection process.

  14. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, V. C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program -- now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history. The missions will develop technology and acquire data necessary for eventual human exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines the opportunities for the Mars community to provide input into the landing site selection process.

  15. Eliciting Metacognitive Experiences and Reflection in a Year 11 Chemistry Classroom: An Activity Theory Perspective

    NASA Astrophysics Data System (ADS)

    Thomas, Gregory P.; McRobbie, Campbell J.

    2013-06-01

    Concerns regarding students' learning and reasoning in chemistry classrooms are well documented. Students' reasoning in chemistry should be characterized by conscious consideration of chemical phenomenon from laboratory work at macroscopic, molecular/sub-micro and symbolic levels. Further, students should develop metacognition in relation to such ways of reasoning about chemistry phenomena. Classroom change eliciting metacognitive experiences and metacognitive reflection is necessary to shift entrenched views of teaching and learning in students. In this study, Activity Theory is used as the framework for interpreting changes to the rules/customs and tools of the activity systems of two different classes of students taught by the same teacher, Frances, who was teaching chemical equilibrium to those classes in consecutive years. An interpretive methodology involving multiple data sources was employed. Frances explicitly changed her pedagogy in the second year to direct students attention to increasingly consider chemical phenomena at the molecular/sub-micro level. Additionally, she asked students not to use the textbook until toward the end of the equilibrium unit and sought to engage them in using their prior knowledge of chemistry to understand their observations from experiments. Frances' changed pedagogy elicited metacognitive experiences and reflection in students and challenged them to reconsider their metacognitive beliefs about learning chemistry and how it might be achieved. While teacher change is essential for science education reform, students are not passive players in change efforts and they need to be convinced of the viability of teacher pedagogical change in the context of their goals, intentions, and beliefs.

  16. The bifunctional active site of s-adenosylmethionine synthetase. Roles of the active site aspartates.

    PubMed

    Taylor, J C; Markham, G D

    1999-11-12

    S-Adenosylmethionine (AdoMet) synthetase catalyzes the biosynthesis of AdoMet in a unique enzymatic reaction. Initially the sulfur of methionine displaces the intact tripolyphosphate chain (PPP(i)) from ATP, and subsequently PPP(i) is hydrolyzed to PP(i) and P(i) before product release. The crystal structure of Escherichia coli AdoMet synthetase shows that the active site contains four aspartate residues. Aspartate residues Asp-16* and Asp-271 individually provide the sole protein ligand to one of the two required Mg(2+) ions (* denotes a residue from a second subunit); aspartates Asp-118 and Asp-238* are proposed to interact with methionine. Each aspartate has been changed to an uncharged asparagine, and the metal binding residues were also changed to alanine, to assess the roles of charge and ligation ability on catalytic efficiency. The resultant enzyme variants all structurally resemble the wild type enzyme as indicated by circular dichroism spectra and are tetramers. However, all have k(cat) reductions of approximately 10(3)-fold in AdoMet synthesis, whereas the MgATP and methionine K(m) values change by less than 3- and 8-fold, respectively. In the partial reaction of PPP(i) hydrolysis, mutants of the Mg(2+) binding residues have >700-fold reduced catalytic efficiency (k(cat)/K(m)), whereas the D118N and D238*N mutants are impaired less than 35-fold. The catalytic efficiency for PPP(i) hydrolysis by Mg(2+) site mutants is improved by AdoMet, like the wild type enzyme. In contrast AdoMet reduces the catalytic efficiency for PPP(i) hydrolysis by the D118N and D238*N mutants, indicating that the events involved in AdoMet activation are hindered in these methionyl binding site mutants. Ca(2+) uniquely activates the D271A mutant enzyme to 15% of the level of Mg(2+), in contrast to the approximately 1% Ca(2+) activation of the wild type enzyme. This indicates that the Asp-271 side chain size is a discriminator between the activating ability of Ca(2+) and the

  17. Fuzzy electron density fragments in macromolecular quantum chemistry, combinatorial quantum chemistry, functional group analysis, and shape-activity relations.

    PubMed

    Mezey, Paul G

    2014-09-16

    Conspectus Just as complete molecules have no boundaries and have "fuzzy" electron density clouds approaching zero density exponentially at large distances from the nearest nucleus, a physically justified choice for electron density fragments exhibits similar behavior. Whereas fuzzy electron densities, just as any fuzzy object, such as a thicker cloud on a foggy day, do not lend themselves to easy visualization, one may partially overcome this by using isocontours. Whereas a faithful representation of the complete fuzzy density would need infinitely many such isocontours, nevertheless, by choosing a selected few, one can still obtain a limited pictorial representation. Clearly, such images are of limited value, and one better relies on more complete mathematical representations, using, for example, density matrices of fuzzy fragment densities. A fuzzy density fragmentation can be obtained in an exactly additive way, using the output from any of the common quantum chemical computational techniques, such as Hartree-Fock, MP2, and various density functional approaches. Such "fuzzy" electron density fragments properly represented have proven to be useful in a rather wide range of applications, for example, (a) using them as additive building blocks leading to efficient linear scaling macromolecular quantum chemistry computational techniques, (b) the study of quantum chemical functional groups, (c) using approximate fuzzy fragment information as allowed by the holographic electron density theorem, (d) the study of correlations between local shape and activity, including through-bond and through-space components of interactions between parts of molecules and relations between local molecular shape and substituent effects, (e) using them as tools of density matrix extrapolation in conformational changes, (f) physically valid averaging and statistical distribution of several local electron densities of common stoichiometry, useful in electron density databank mining, for

  18. Chemistry and Biological Activities of Flavonoids: An Overview

    PubMed Central

    Kumar, Shashank; Pandey, Abhay K.

    2013-01-01

    There has been increasing interest in the research on flavonoids from plant sources because of their versatile health benefits reported in various epidemiological studies. Since flavonoids are directly associated with human dietary ingredients and health, there is need to evaluate structure and function relationship. The bioavailability, metabolism, and biological activity of flavonoids depend upon the configuration, total number of hydroxyl groups, and substitution of functional groups about their nuclear structure. Fruits and vegetables are the main dietary sources of flavonoids for humans, along with tea and wine. Most recent researches have focused on the health aspects of flavonoids for humans. Many flavonoids are shown to have antioxidative activity, free radical scavenging capacity, coronary heart disease prevention, hepatoprotective, anti-inflammatory, and anticancer activities, while some flavonoids exhibit potential antiviral activities. In plant systems, flavonoids help in combating oxidative stress and act as growth regulators. For pharmaceutical purposes cost-effective bulk production of different types of flavonoids has been made possible with the help of microbial biotechnology. This review highlights the structural features of flavonoids, their beneficial roles in human health, and significance in plants as well as their microbial production. PMID:24470791

  19. Processed Vietnamese ginseng: Preliminary results in chemistry and biological activity

    PubMed Central

    Le, Thi Hong Van; Lee, Seo Young; Kim, Tae Ryong; Kim, Jae Young; Kwon, Sung Won; Nguyen, Ngoc Khoi; Park, Jeong Hill; Nguyen, Minh Duc

    2013-01-01

    Background This study was carried out to investigate the effect of the steaming process on chemical constituents, free radical scavenging activity, and antiproliferative effect of Vietnamese ginseng. Methods Samples of powdered Vietnamese ginseng were steamed at 120°C for various times and their extracts were subjected to chemical and biological studies. Results Upon steaming, contents of polar ginsenosides, such as Rb1, Rc, Rd, Re, and Rg1, were rapidly decreased, whereas less polar ginsenosides such as Rg3, Rg5, Rk1, Rk3, and Rh4 were increased as reported previously. However, ocotillol type saponins, which have no glycosyl moiety at the C-20 position, were relatively stable on steaming. The radical scavenging activity was increased continuously up to 20 h of steaming. Similarly, the antiproliferative activity against A549 lung cancer cells was also increased. Conclusion It seems that the antiproliferative activity is closely related to the contents of ginsenoside Rg3, Rg5, and Rk1. PMID:24748840

  20. Natural Product Nitric Oxide Chemistry: New Activity of Old Medicines

    PubMed Central

    Jiang, Hong; Torregrossa, Ashley C.; Parthasarathy, Deepa K.; Bryan, Nathan S.

    2012-01-01

    The use of complementary and alternative medicine (CAM) as a therapy and preventative care measure for cardiovascular diseases (CVD) may prove to be beneficial when used in conjunction with or in place of conventional medicine. However, the lack of understanding of a mechanism of action of many CAMs limits their use and acceptance in western medicine. We have recently recognized and characterized specific nitric oxide (NO) activity of select alternative and herbal medicines that may account for many of their reported health benefits. The ability of certain CAM to restore NO homeostasis both through enhancing endothelial production of NO and by providing a system for reducing nitrate and nitrite to NO as a compensatory pathway for repleting NO bioavailability may prove to be a safe and cost-effective strategy for combating CVD. We will review the current state of science behind NO activity of herbal medicines and their effects on CVD. PMID:22548122

  1. Learning Activity Package, Chemistry I. LAP Numbers 22, 23, 24, 25, 26, 27, and 28.

    ERIC Educational Resources Information Center

    Jones, Naomi

    As a set of seven Learning Activity Packages (LAPs) for individualized instruction in chemistry, the units cover the unit system, matter, energy, atomic structures, chemical formulas, physical states of matter, solutions and suspensions, ionization, acids, bases, and salts. Each unit contains a rationale for the material; a list of behavioral…

  2. Insight in the Chemistry of Laser-Activated Dental Bleaching

    PubMed Central

    De Moor, Roeland Jozef Gentil; Meire, Maarten August; De Coster, Peter Jozef; Walsh, Laurence James

    2015-01-01

    The use of optical radiation for the activation of bleaching products has not yet been completely elucidated. Laser light is suggested to enhance the oxidizing effect of hydrogen peroxide. Different methods of enhancing hydrogen peroxide based bleaching are possible. They can be classified into six groups: alkaline pH environment, thermal enhancement and photothermal effect, photooxidation effect and direct photobleaching, photolysis effect and photodissociation, Fenton reaction and photocatalysis, and photodynamic effect. PMID:25874251

  3. Multiple active site residues are important for photochemical efficiency in the light-activated enzyme protochlorophyllide oxidoreductase (POR).

    PubMed

    Menon, Binuraj R K; Hardman, Samantha J O; Scrutton, Nigel S; Heyes, Derren J

    2016-08-01

    Protochlorophyllide oxidoreductase (POR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), an essential, regulatory step in chlorophyll biosynthesis. The unique requirement of the enzyme for light has provided the opportunity to investigate how light energy can be harnessed to power biological catalysis and enzyme dynamics. Excited state interactions between the Pchlide molecule and the protein are known to drive the subsequent reaction chemistry. However, the structural features of POR and active site residues that are important for photochemistry and catalysis are currently unknown, because there is no crystal structure for POR. Here, we have used static and time-resolved spectroscopic measurements of a number of active site variants to study the role of a number of residues, which are located in the proposed NADPH/Pchlide binding site based on previous homology models, in the reaction mechanism of POR. Our findings, which are interpreted in the context of a new improved structural model, have identified several residues that are predicted to interact with the coenzyme or substrate. Several of the POR variants have a profound effect on the photochemistry, suggesting that multiple residues are important in stabilizing the excited state required for catalysis. Our work offers insight into how the POR active site geometry is finely tuned by multiple active site residues to support enzyme-mediated photochemistry and reduction of Pchlide, both of which are crucial to the existence of life on Earth. PMID:27285815

  4. The active site of ribulose-bisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.

    1991-01-01

    The active site of ribulose-bisphosphate carboxylase/oxygenase requires interacting domains of adjacent, identical subunits. Most active-site residues are located within the loop regions of an eight-stranded {beta}/{alpha}-barrel which constitutes the larger C-terminal domain; additional key residues are located within a segment of the smaller N-terminal domain which partially covers the mouth of the barrel. Site-directed mutagenesis of the gene encoding the enzyme from Rhodospirillum rubrum has been used to delineate functions of active-site residues. 6 refs., 2 figs.

  5. Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

    SciTech Connect

    Zull, Lawrence M.; Yeniscavich, William

    2008-01-15

    The Defense Nuclear Facilities Safety Board (Board) is an independent federal agency established by Congress in 1988 to provide nuclear safety oversight of activities at U.S. Department of Energy (DOE) defense nuclear facilities. The activities under the Board's jurisdiction include the design, construction, startup, operation, and decommissioning of defense nuclear facilities at DOE sites. This paper reviews the Board's safety oversight of decommissioning activities at DOE sites, identifies the safety problems observed, and discusses Board initiatives to improve the safety of decommissioning activities at DOE sites. The decommissioning of former defense nuclear facilities has reduced the risk of radioactive material contamination and exposure to the public and site workers. In general, efforts to perform decommissioning work at DOE defense nuclear sites have been successful, and contractors performing decommissioning work have a good safety record. Decommissioning activities have recently been completed at sites identified for closure, including the Rocky Flats Environmental Technology Site, the Fernald Closure Project, and the Miamisburg Closure Project (the Mound site). The Rocky Flats and Fernald sites, which produced plutonium parts and uranium materials for defense needs (respectively), have been turned into wildlife refuges. The Mound site, which performed R and D activities on nuclear materials, has been converted into an industrial and technology park called the Mound Advanced Technology Center. The DOE Office of Legacy Management is responsible for the long term stewardship of these former EM sites. The Board has reviewed many decommissioning activities, and noted that there are valuable lessons learned that can benefit both DOE and the contractor. As part of its ongoing safety oversight responsibilities, the Board and its staff will continue to review the safety of DOE and contractor decommissioning activities at DOE defense nuclear sites.

  6. Electrostatic activation of prebiotic chemistry in substellar atmospheres

    NASA Astrophysics Data System (ADS)

    Stark, C. R.; Helling, Ch.; Diver, D. A.; Rimmer, P. B.

    2014-04-01

    Charged dust grains in the atmospheres of exoplanets may play a key role in the formation of prebiotic molecules, necessary to the origin of life. Dust grains submerged in an atmospheric plasma become negatively charged and attract a flux of ions that are accelerated from the plasma. The energy of the ions upon reaching the grain surface may be sufficient to overcome the activation energy of particular chemical reactions that would be unattainable via ion and neutral bombardment from classical, thermal excitation. As a result, prebiotic molecules or their precursors could be synthesized on the surface of dust grains that form clouds in exoplanetary atmospheres. This paper investigates the energization of the plasma ions, and the dependence on the plasma electron temperature, in the atmospheres of substellar objects such as gas giant planets. Calculations show that modest electron temperatures of ~1 eV (~104 K) are enough to accelerate ions to sufficient energies that exceed the activation energies required for the formation of formaldehyde, ammonia, hydrogen cyanide and the amino acid glycine.

  7. DOE site performance assessment activities. Radioactive Waste Technical Support Program

    SciTech Connect

    Not Available

    1990-07-01

    Information on performance assessment capabilities and activities was collected from eight DOE sites. All eight sites either currently dispose of low-level radioactive waste (LLW) or plan to dispose of LLW in the near future. A survey questionnaire was developed and sent to key individuals involved in DOE Order 5820.2A performance assessment activities at each site. The sites surveyed included: Hanford Site (Hanford), Idaho National Engineering Laboratory (INEL), Los Alamos National Laboratory (LANL), Nevada Test Site (NTS), Oak Ridge National Laboratory (ORNL), Paducah Gaseous Diffusion Plant (Paducah), Portsmouth Gaseous Diffusion Plant (Portsmouth), and Savannah River Site (SRS). The questionnaire addressed all aspects of the performance assessment process; from waste source term to dose conversion factors. This report presents the information developed from the site questionnaire and provides a comparison of site-specific performance assessment approaches, data needs, and ongoing and planned activities. All sites are engaged in completing the radioactive waste disposal facility performance assessment required by DOE Order 5820.2A. Each site has achieved various degrees of progress and have identified a set of critical needs. Within several areas, however, the sites identified common needs and questions.

  8. Savannah River Site prioritization of transition activities

    SciTech Connect

    Finley, R.H.

    1993-11-01

    Effective management of SRS conversion from primarily a production facility to other missions (or Decontamination and Decommissioning (D&D)) requires a systematic and consistent method of prioritizing the transition activities. This report discusses the design of a prioritizing method developed to achieve systematic and consistent methods of prioritizing these activities.

  9. The synthesis of active pharmaceutical ingredients (APIs) using continuous flow chemistry

    PubMed Central

    2015-01-01

    Summary The implementation of continuous flow processing as a key enabling technology has transformed the way we conduct chemistry and has expanded our synthetic capabilities. As a result many new preparative routes have been designed towards commercially relevant drug compounds achieving more efficient and reproducible manufacture. This review article aims to illustrate the holistic systems approach and diverse applications of flow chemistry to the preparation of pharmaceutically active molecules, demonstrating the value of this strategy towards every aspect ranging from synthesis, in-line analysis and purification to final formulation and tableting. Although this review will primarily concentrate on large scale continuous processing, additional selected syntheses using micro or meso-scaled flow reactors will be exemplified for key transformations and process control. It is hoped that the reader will gain an appreciation of the innovative technology and transformational nature that flow chemistry can leverage to an overall process. PMID:26425178

  10. Chemistry and biological activity of steroidal glycosides from the Lilium genus.

    PubMed

    Munafo, John P; Gianfagna, Thomas J

    2015-03-01

    Plants from the Lilium genus are a rich source of chemical diversity and have been the focus of natural products chemistry research for over twenty years. This manuscript provides a background on the chemistry and nomenclature of steroidal glycosides, as well as a chronological account of the progress between the years of 1989 up to 2014, with respect to their isolation and characterization from the genus. This review highlights the traditional use of lilies, as both food and medicine, and brings attention to the fact that the genus contains 110 accepted species of which the chemistry and biological activity of the steroidal glycosides from the majority have not been investigated to date. Thus, making the genus a relatively untapped resource that contains a potential treasure trove of chemical diversity waiting to be discovered. PMID:25407469

  11. Amazon acai: chemistry and biological activities: a review.

    PubMed

    Yamaguchi, Klenicy Kazumy de Lima; Pereira, Luiz Felipe Ravazi; Lamarão, Carlos Victor; Lima, Emerson Silva; da Veiga-Junior, Valdir Florêncio

    2015-07-15

    Acai (acai or assai) is one of the Amazon's most popular functional foods and widely used in the world. There are many benefits to its alleged use in the growing market for nutraceuticals. The acai extracts have a range of polyphenolic components with antioxidant properties, some of those present in greater quantity are orientin, isoorientin and vanillic acid, as well as anthocyanins cyanidin-3-glucoside and cyanidin-3-rutinoside. The presence of these substances is linked mainly to the antioxidant, anti- inflammatory, anti-proliferative and cardioprotective activities. Importantly, there are two main species of the Euterpe genus which produce acai. There are several differences between them but they are still quite unknown, from literature to producers and consumers. In this review are highlighted the chemical composition, botanical aspects, pharmacological, marketing and nutrition of these species based on studies published in the last five years in order to unify the current knowledge and dissimilarities between them. PMID:25722148

  12. Learning about Chemistry Concepts. Superific Science Book VIII. A Good Apple Science Activity Book for Grades 5-8+.

    ERIC Educational Resources Information Center

    Conway, Lorraine

    Based on the idea that active participation stimulates the processes by which learning takes place, this document provides teachers and students with a variety of information and learning activities dealing with chemistry. Basic concepts about chemistry are presented through the use of laboratory experiments, demonstrations, worksheet exercises…

  13. Ionizable Side Chains at Catalytic Active Sites of Enzymes

    PubMed Central

    Jimenez-Morales, David; Liang, Jie

    2012-01-01

    Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

  14. Site-specific antibody-drug conjugates: the nexus of bioorthogonal chemistry, protein engineering, and drug development.

    PubMed

    Agarwal, Paresh; Bertozzi, Carolyn R

    2015-02-18

    Antibody-drug conjugates (ADCs) combine the specificity of antibodies with the potency of small molecules to create targeted drugs. Despite the simplicity of this concept, generation of clinically successful ADCs has been very difficult. Over the past several decades, scientists have learned a great deal about the constraints on antibodies, linkers, and drugs as they relate to successful construction of ADCs. Once these components are in hand, most ADCs are prepared by nonspecific modification of antibody lysine or cysteine residues with drug-linker reagents, which results in heterogeneous product mixtures that cannot be further purified. With advances in the fields of bioorthogonal chemistry and protein engineering, there is growing interest in producing ADCs by site-specific conjugation to the antibody, yielding more homogeneous products that have demonstrated benefits over their heterogeneous counterparts in vivo. Here, we chronicle the development of a multitude of site-specific conjugation strategies for assembly of ADCs and provide a comprehensive account of key advances and their roots in the fields of bioorthogonal chemistry and protein engineering. PMID:25494884

  15. Site-Specific Antibody–Drug Conjugates: The Nexus of Bioorthogonal Chemistry, Protein Engineering, and Drug Development

    PubMed Central

    2015-01-01

    Antibody–drug conjugates (ADCs) combine the specificity of antibodies with the potency of small molecules to create targeted drugs. Despite the simplicity of this concept, generation of clinically successful ADCs has been very difficult. Over the past several decades, scientists have learned a great deal about the constraints on antibodies, linkers, and drugs as they relate to successful construction of ADCs. Once these components are in hand, most ADCs are prepared by nonspecific modification of antibody lysine or cysteine residues with drug-linker reagents, which results in heterogeneous product mixtures that cannot be further purified. With advances in the fields of bioorthogonal chemistry and protein engineering, there is growing interest in producing ADCs by site-specific conjugation to the antibody, yielding more homogeneous products that have demonstrated benefits over their heterogeneous counterparts in vivo. Here, we chronicle the development of a multitude of site-specific conjugation strategies for assembly of ADCs and provide a comprehensive account of key advances and their roots in the fields of bioorthogonal chemistry and protein engineering. PMID:25494884

  16. Chemistry in the Molecular Disks of Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Harada, Nanase; Herbst, Eric

    2010-06-01

    Active galactic nuclei (AGNs) are the centers of galaxies with supermassive blackholes whose accretion of mass causes very high luminosities of L˜1044-46erg s-1. An accretion disk has a molecular component that extends to hundreds of pc from the central AGN core. The question of how much central illumination affects the disk and how much star formation is present near the core have been astrophysical interests. Rotational lines from these disks at a sub-kpc scale have been observed for molecules such as CO, HCO+, HCN, and HNC. When ALMA becomes fully operational, it will be able to resolve these disks at much higher resolution than currently. Molecular observations at higher resolution may give some hints on the physics in the molecular disk. We modeled the chemical composition of a molecular disk in an AGN on a scale of tens of pc. To do this, we extended our standard gas-phase OSU network to include important processes at much higher temperatures, approaching 1000 K. We used the density model of Thompson et al., and determined the temperature by the blackbody approximation from the luminosity of the AGN core. The ionization by X-rays from the AGN core, by cosmic-rays from the AGN core, supernovae and stellar winds, and by UV-photons from OB stars are considered. We will briefly mention the effects from other factors that may change the molecular abundances such as shock waves and inhomogeneity of the density of the disk. T. Thompson, E. Quataert, and N. Murray, Astrophysical J. 630, 167 (2005)

  17. Metal-dithiocarbamate complexes: chemistry and biological activity.

    PubMed

    Hogarth, Graeme

    2012-10-01

    Dithiocarbamates are highly versatile mono-anionic chelating ligands which form stable complexes with all the transition elements and also the majority of main group, lanthanide and actinide elements. They are easily prepared from primary or secondary amines and depending upon the nature of the cation can show good solubility in water or organic solvents. They are related to the thiuram disulfides by a one-electron redox process (followed by dimerisation via sulfur-sulfur bond formation) which is easily carried out upon addition of iodide or ferric salts. Dithiocarbamates are lipophilic and generally bind to metals in a symmetrical chelate fashion but examples of other coordination modes are known, the monodentate and anisobidentate modes being most prevalent. They are planar sterically non-demanding ligands which can be electronically tuned by judicious choice of substituents. They stabilize metals in a wide range of oxidation states, this being attributed to the existence of soft dithiocarbamate and hard thioureide resonance forms, the latter formally resulting from delocalization of the nitrogen lone pair onto the sulfurs, and consequently their complexes tend to have a rich electrochemistry. Tetraethyl thiuramdisulfide (disulfiram or antabuse) has been used as a drug since the 1950s but it is only recently that dithiocarbamate complexes have been explored within the medicinal domain. Over the past two decades anti-cancer activity has been noted for gold and copper complexes, technetium and copper complexes have been used in PET-imaging, dithiocarbamates have been used to treat acute cadmium poisoning and copper complexes also have been investigated as SOD inhibitors. PMID:22931592

  18. Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design.

    PubMed

    Ehrt, Christiane; Brinkjost, Tobias; Koch, Oliver

    2016-05-12

    Modern rational drug design not only deals with the search for ligands binding to interesting and promising validated targets but also aims to identify the function and ligands of yet uncharacterized proteins having impact on different diseases. Additionally, it contributes to the design of inhibitors with distinct selectivity patterns and the prediction of possible off-target effects. The identification of similarities between binding sites of various proteins is a useful approach to cope with those challenges. The main scope of this perspective is to describe applications of different protein binding site comparison approaches to outline their applicability and impact on molecular design. The article deals with various substantial application domains and provides some outstanding examples to show how various binding site comparison methods can be applied to promote in silico drug design workflows. In addition, we will also briefly introduce the fundamental principles of different protein binding site comparison methods. PMID:27046190

  19. Active Sites Environmental Monitoring Program FY 1996 annual report

    SciTech Connect

    Morrissey, C.M.; Marshall, D.S.; Cunningham, G.R.

    1997-11-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1995 through September 1996. The Radioactive Solid Waste Operations Group (RSWOG) of the Waste Management and Remedial Action Division (WMRAD) and the Environmental Sciences Division (ESD) at Oak Ridge National Laboratory (ORNL) established ASEMP in 1989. The purpose of the program is to provide early detection and performance monitoring at active low-level waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 North as required by Chapters 2 and 3 of US Department of Energy Order 5820.2A.

  20. Active sites environmental monitoring Program - Program Plan: Revision 2

    SciTech Connect

    Morrissey, C.M.; Hicks, D.S.; Ashwood, T.L.; Cunningham, G.R.

    1994-05-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of active low-level-waste (LLW) and transuranic (TRU) waste facilities at Oak Ridge National Laboratory (ORNL). Several changes have recently occurred in regard to the sites that are currently used for waste storage and disposal. These changes require a second set of revisions to the ASEMP program plan. This document incorporates those revisions. This program plan presents the organization and procedures for monitoring the active sites. The program plan also provides internal reporting levels to guide the evaluation of monitoring results.

  1. Teaching chemistry concepts using differentiated instruction via tiered labs and activity menus

    NASA Astrophysics Data System (ADS)

    Collins, Betsy C.

    Today's high school classrooms are composed of students with different levels of knowing and ways of understanding. Differentiating the type of work that they are asked to do to achieve the same objective is one way to meet each student's special circumstances on a somewhat equal playing field. By doing so, students are being challenged at their level rather than just blindly going through the same motions that they see others around them doing. Offering students choices to better understand a concept places the student in the driver seat of their educational journey. The purpose of this research project was to design and implement choice activities within the chemistry classroom to more appropriately teach and assess chemistry concepts and assess understanding of those concepts. These choice activities included tiered-laboratory investigations and activity menus. This project was implemented over the course of two trimesters in a high school chemistry classroom. Topics covered included calculating and interpreting density and applying significant figures, calculating and interpreting percent composition with the mole concept, and stoichiometry. The effectiveness of the tiered-labs and activity menus were evaluated using pre and post test comparisons, student surveys, and general in-class observations. Gains in conceptual understanding and student motivation were documented. These findings indicated that allowing choice and leveling of skills to achieve the same conceptual understanding promoted student learning and the overall enjoyment and motivation for learning.

  2. Recent activities of EC4 in the harmonization of clinical chemistry in the European Union.

    PubMed

    Sanders, G T; Jansen, R T; Beastall, G; Gurr, E; Kenny, D; Kohse, K P; Zérah, S

    1999-04-01

    This article describes the recent activities of the European Communities Confederation of Clinical Chemistry (EC4). Main goal of EC4 is harmonization of clinical chemistry in the European Union and Europe. EC4's actions connected to that are training and registration of professionals, and accreditation of laboratories. The 35000 professionals practising clinical chemistry in the EU have different backgrounds (medical, pharmaceutical, science-oriented, veterinary, or microbiological). Thus, for the harmonization of training of clinical chemists, EC4 has published a European Syllabus for Postgraduate Training, and instituted a European Union Register for Clinical Chemists. The Syllabus is an indication of the level of requirements in postgraduate training. The EC4 initiative to implement the European Register for Clinical Chemists is based on the 8 years vocational training necessary to obtain sufficient knowledge in clinical chemistry according to the European Syllabus. A guide to the EC4 Register has been published; registration leads to the title European Clinical Chemist (EurClinChem). The accreditation of laboratories must be based on a total quality management system. EC4 has described guidelines (essential criteria) which it judges appropriate for establishing the quality of medical laboratory service; it does not wish to fulfil the role of an accrediting body. Moreover, a working group has been set up to seek to harmonize the work of national accrediting bodies. Therefore, it is logical that EC4 monitors the activities of the different standardizing bodies that might influence the practice of clinical chemistry in the EU. Finally, some aspects concerning the future strategy of EC4 are brought forward. PMID:10369121

  3. The active site behaviour of electrochemically synthesised gold nanomaterials.

    PubMed

    Plowman, Blake J; O'Mullane, Anthony P; Bhargava, Suresh K

    2011-01-01

    Even though gold is the noblest of metals, a weak chemisorber and is regarded as being quite inert, it demonstrates significant electrocatalytic activity in its nanostructured form. It is demonstrated here that nanostructured and even evaporated thin films of gold are covered with active sites which are responsible for such activity. The identification of these sites is demonstrated with conventional electrochemical techniques such as cyclic voltammetry as well as a large amplitude Fourier transformed alternating current (FT-ac) method under acidic and alkaline conditions. The latter technique is beneficial in determining if an electrode process is either Faradaic or capacitive in nature. The observed behaviour is analogous to that observed for activated gold electrodes whose surfaces have been severely disrupted by cathodic polarisation in the hydrogen evolution region. It is shown that significant electrochemical oxidation responses occur at discrete potential values well below that for the formation of the compact monolayer oxide of bulk gold and are attributed to the facile oxidation of surface active sites. Several electrocatalytic reactions are explored in which the onset potential is determined by the presence of such sites on the surface. Significantly, the facile oxidation of active sites is used to drive the electroless deposition of metals such as platinum, palladium and silver from their aqueous salts on the surface of gold nanostructures. The resultant surface decoration of gold with secondary metal nanoparticles not only indicates regions on the surface which are rich in active sites but also provides a method to form interesting bimetallic surfaces. PMID:22455038

  4. Nicotinamide Cofactors Suppress Active-Site Labeling of Aldehyde Dehydrogenases.

    PubMed

    Stiti, Naim; Chandrasekar, Balakumaran; Strubl, Laura; Mohammed, Shabaz; Bartels, Dorothea; van der Hoorn, Renier A L

    2016-06-17

    Active site labeling by (re)activity-based probes is a powerful chemical proteomic tool to globally map active sites in native proteomes without using substrates. Active site labeling is usually taken as a readout for the active state of the enzyme because labeling reflects the availability and reactivity of active sites, which are hallmarks for enzyme activities. Here, we show that this relationship holds tightly, but we also reveal an important exception to this rule. Labeling of Arabidopsis ALDH3H1 with a chloroacetamide probe occurs at the catalytic Cys, and labeling is suppressed upon nitrosylation and oxidation, and upon treatment with other Cys modifiers. These experiments display a consistent and strong correlation between active site labeling and enzymatic activity. Surprisingly, however, labeling is suppressed by the cofactor NAD(+), and this property is shared with other members of the ALDH superfamily and also detected for unrelated GAPDH enzymes with an unrelated hydantoin-based probe in crude extracts of plant cell cultures. Suppression requires cofactor binding to its binding pocket. Labeling is also suppressed by ALDH modulators that bind at the substrate entrance tunnel, confirming that labeling occurs through the substrate-binding cavity. Our data indicate that cofactor binding adjusts the catalytic Cys into a conformation that reduces the reactivity toward chloroacetamide probes. PMID:26990764

  5. Amine Oxidative N-Dealkylation via Cupric Hydroperoxide Cu–OOH Homolytic Cleavage Followed by Site-Specific Fenton Chemistry

    PubMed Central

    Kim, Sunghee; Ginsbach, Jake W.; Lee, Jung Yoon; Peterson, Ryan L.; Liu, Jeffrey J.; Siegler, Maxime A.; Sarjeant, Amy A.; Solomon, Edward I.; Karlin, Kenneth D.

    2015-01-01

    Copper(II)-hydroperoxide species are significant intermediates in processes such as fuel cells and (bio)chemical oxidations, all involving stepwise reduction of molecular oxygen. We previously reported a CuII-OOH species that performs oxidative N-dealkylation on a dibenzylamino group that is appended to the 6-position of a pyridyl donor of a tripodal tetradentate ligand. To obtain insights into the mechanism of this process, reaction kinetics and products were determined employing ligand substrates with various para- substituent dibenzyl pairs (-H,-H; -H,-Cl; -H,-OMe and -Cl,-OMe), or with partially or fully deuterated dibenzyl N-(CH2Ph)2 moieties. A series of ligand-copper(II) bis-perchlorate complexes were synthesized, characterized, and the X-ray structures of the -H, -OMe analog was were determined. The corresponding metastable CuII-OOH species were generated by addition of H2O2/base in acetone at –90 °C. These convert (t1/2 ~ 53 s) to oxidatively N-dealkylated products, producing para-substituted benzaldehydes. Based on the experimental observations and supporting DFT calculations, a reaction mechanism involving dibenzylamine H-atom abstraction or electron-transfer oxidation by the CuII-OOH entity could be ruled out. It is concluded that the chemistry proceeds by rate limiting Cu–O homolytic cleavage of the CuII–(OOH) species, followed by site-specific copper Fenton chemistry. As a process of broad interest in copper as well as iron oxidative (bio)chemistries, a detailed computational analysis was performed, indicating that a CuIOOH species undergoes O–O homolytic cleavage to yield a hydroxyl radical and CuIIOH rather than heterolytic cleavage to yield water and a CuII-O•−. PMID:25706825

  6. Clay Chemistry's Influence on the Average Carbon Content and Particle Size at the Ninety-Six Historical Site, South Carolina

    NASA Astrophysics Data System (ADS)

    Lintz, L.; Werts, S. P.

    2014-12-01

    The Ninety-Six National Historic Site is located in Greenwood County, SC. Recent geologic mapping of this area has revealed differences in soil properties over short distances within the park. We studied the chemistry of the clay minerals found within the soils to see if there was a correlation between the amounts of soil organic carbon contained in the soil and particle size in individual soil horizons. Three different vegetation areas, including an old field, a deciduous forest, and a pine forest were selected to see what influence vegetation type had on the clay chemistry and carbon levels as well. Four samples containing the O, A, and B horizons were taken from each location and we studied the carbon and nitrogen content using an elemental analyzer, particle size using a Laser Diffraction Particle Size Analyzer, and clay mineralogy with powder X-ray diffraction of each soil sample. Samples from the old field and pine forest gave an overall negative correlation between carbon content and clay percentage, which is against the normal trend for Southern Piedmont Ultisols. The deciduous forest samples gave no correlation at all between its carbon content and clay percentage. Together, all three locations show the same negative relationship, while once separated into vegetation type and A and B horizons it shows even more abnormal relationships of negative while several show no correlation (R2= 0.007403- 0.56268). Using powder XRD, we ran clay samples from each A and B horizon for the clay mineralogy. All three vegetation areas had the same results of containing quartz, kaolinite, and Fe oxides, therefore, clay chemistry is not a reason behind the abnormal trend of a negative correlation between average carbon content and clay percentage. Considering that all three locations have the same climate, topography, and parent material of metagranite, it could be reasonable to assume these results are a factor of environmental and biological influences rather than clay type.

  7. Diversity of Secondary Metabolites from Marine Bacillus Species: Chemistry and Biological Activity

    PubMed Central

    Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Islam, Mohammad Tofazzal

    2013-01-01

    Marine Bacillus species produce versatile secondary metabolites including lipopeptides, polypeptides, macrolactones, fatty acids, polyketides, and isocoumarins. These structurally diverse compounds exhibit a wide range of biological activities, such as antimicrobial, anticancer, and antialgal activities. Some marine Bacillus strains can detoxify heavy metals through reduction processes and have the ability to produce carotenoids. The present article reviews the chemistry and biological activities of secondary metabolites from marine isolates. Side by side, the potential for application of these novel natural products from marine Bacillus strains as drugs, pesticides, carotenoids, and tools for the bioremediation of heavy metal toxicity are also discussed. PMID:23941823

  8. Diversity of secondary metabolites from marine Bacillus species: chemistry and biological activity.

    PubMed

    Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Islam, Mohammad Tofazzal

    2013-08-01

    Marine Bacillus species produce versatile secondary metabolites including lipopeptides, polypeptides, macrolactones, fatty acids, polyketides, and isocoumarins. These structurally diverse compounds exhibit a wide range of biological activities, such as antimicrobial, anticancer, and antialgal activities. Some marine Bacillus strains can detoxify heavy metals through reduction processes and have the ability to produce carotenoids. The present article reviews the chemistry and biological activities of secondary metabolites from marine isolates. Side by side, the potential for application of these novel natural products from marine Bacillus strains as drugs, pesticides, carotenoids, and tools for the bioremediation of heavy metal toxicity are also discussed. PMID:23941823

  9. The active site of low-temperature methane hydroxylation in iron-containing zeolites.

    PubMed

    Snyder, Benjamin E R; Vanelderen, Pieter; Bols, Max L; Hallaert, Simon D; Böttger, Lars H; Ungur, Liviu; Pierloot, Kristine; Schoonheydt, Robert A; Sels, Bert F; Solomon, Edward I

    2016-08-18

    An efficient catalytic process for converting methane into methanol could have far-reaching economic implications. Iron-containing zeolites (microporous aluminosilicate minerals) are noteworthy in this regard, having an outstanding ability to hydroxylate methane rapidly at room temperature to form methanol. Reactivity occurs at an extra-lattice active site called α-Fe(ii), which is activated by nitrous oxide to form the reactive intermediate α-O; however, despite nearly three decades of research, the nature of the active site and the factors determining its exceptional reactivity are unclear. The main difficulty is that the reactive species-α-Fe(ii) and α-O-are challenging to probe spectroscopically: data from bulk techniques such as X-ray absorption spectroscopy and magnetic susceptibility are complicated by contributions from inactive 'spectator' iron. Here we show that a site-selective spectroscopic method regularly used in bioinorganic chemistry can overcome this problem. Magnetic circular dichroism reveals α-Fe(ii) to be a mononuclear, high-spin, square planar Fe(ii) site, while the reactive intermediate, α-O, is a mononuclear, high-spin Fe(iv)=O species, whose exceptional reactivity derives from a constrained coordination geometry enforced by the zeolite lattice. These findings illustrate the value of our approach to exploring active sites in heterogeneous systems. The results also suggest that using matrix constraints to activate metal sites for function-producing what is known in the context of metalloenzymes as an 'entatic' state-might be a useful way to tune the activity of heterogeneous catalysts. PMID:27535535

  10. Precipitation-chemistry data at selected sites in northwestern Colorado, 1980-94

    USGS Publications Warehouse

    Ranalli, A.J.

    1997-01-01

    The chemical content of precipitation was monitored during the period 1980-94 at three sites at altitudes above 2,400 meters near the Piceance Basin in northwestern Colorado. Daily precipitation volumes, specific conductance, pH (in this report pH is expressed as hydrogen-ion concentration), concentrations of major cations and anions, calculated charge balance between cations and anions, and summary statistics of chemical concentrations are tabulated. Sampling sites are plotted on a map of the area. Seasonal variabilities of major cation and anion concentrations are presented graphically.

  11. Textbook Questions in Context-Based and Traditional Chemistry Curricula Analysed from a Content Perspective and a Learning Activities Perspective

    ERIC Educational Resources Information Center

    Overman, Michelle; Vermunt, Jan D.; Meijer, Paulien C.; Bulte, Astrid M. W.; Brekelmans, Mieke

    2013-01-01

    In this study, questions in context-based and traditional chemistry textbooks were analysed from two perspectives that are at the heart of chemistry curricula reforms: a content perspective and a learning activities perspective. To analyse these textbook questions, we developed an instrument for each perspective. In total, 971 textbook questions…

  12. Silent and Vocal Students in a Large Active Learning Chemistry Classroom: Comparison of Performance and Motivational Factors

    ERIC Educational Resources Information Center

    Obenland, Carrie A.; Munson, Ashlyn H.; Hutchinson, John S.

    2013-01-01

    Active learning is becoming more prevalent in large science classrooms, and this study shows the impact on performance of being vocal during Socratic questioning in a General Chemistry course. 800 college students over a two year period were given a pre and post-test using the Chemistry Concept Reasoning Test. The pre-test results showed that…

  13. S.E.A. Lab. Science Experiments and Activities. Marine Science for High School Students in Chemistry, Biology and Physics.

    ERIC Educational Resources Information Center

    Hart, Kathy, Ed.

    A series of science experiments and activities designed for secondary school students taking biology, chemistry, physics, physical science or marine science courses are outlined. Each of the three major sections--chemistry, biology, and physics--addresses concepts that are generally covered in those courses but incorporates aspects of marine…

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

    SciTech Connect

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

    1986-03-20

    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.

  15. The potential effects of CO2 leakage from CCS sites on soil leachate chemistry

    NASA Astrophysics Data System (ADS)

    Moonis, M.; Yoo, G.; Wenmei, H.; Kim, Y.

    2015-12-01

    Monitoring of potential leakages and its effect on the soil environment are essential to ensure long term feasibility of the carbon capture and storage (CCS) projects. When high concentration of CO2 is leaked into the soil system, the soil chemical environment will be changed. We hypothesized that soil pH will decrease sharply in response to the high soil CO2, but we also expect that it would gradually resume because of the buffering capacity of the soil. The mechanisms of the soil's buffering capacity could be dissolution of carbonate minerals and organic matter, which could result in production of dissolved organic and inorganic carbon (DOC and DIC) in the soil and leachate. In addition, changes in cation exchange capacity (CEC) induced by high CO2 can lead to mobilization of base cations due to replacement by H+, Al3+ and Mn2+. This study aims at investigating changes in soil leachate chemical parameters when the soil was injected with 100% CO2 for four weeks (28 days). Custom made plexiglass pots (30 cm × 20 cm × 20 cm) have been filled with organic rich soil (10 cmm depth) overlaid with mineral soil (15 cm). The pots were injected with 100% CO2 at a flow rate of 400 cm3 min-1. Separate control groups were made with no injection and N2 injection. All the treatments have 9 replicates. The 300 ml of tap water was watered down in the pots three times a week. Leachates collected are analyzed for the soil pH and EC. Leachates are filtered through 0.2 μm membranes for analysis of DOC, DIC, and metal concentrations. After 4 wk of incubation, organic and mineral soils will be destructively sampled and analyzed for total organic and inorganic carbon and CEC. Knowledge of changes in leachate chemistry will allow us to quantify the mobilization of chemical parameters in well-drained soils under the potential influence of high soil CO2. Furthermore, effect on leaching may give indirect information about consequent changes in groundwater chemistry.

  16. Use of a World Wide Web Site Evaluation Tool in Chemistry.

    ERIC Educational Resources Information Center

    Yates, Paul C.

    2000-01-01

    Discusses the importance of assessment of materials on the World Wide Web that may be freely accessible to both instructors and students. Evaluates web sites that cover the periodic table in terms of content and design. (Contains 16 references.) (Author/YDS)

  17. Effects of B-site chemistry on BiFeO[subscript 3]-containing enhanced tetragonality systems

    SciTech Connect

    Stein, David M.; Davies, Peter K.

    2012-02-06

    The ternary perovskite systems PbTiO{sub 3}-BiFeO{sub 3}-Bi(Mg{sub 1/2}Ti{sub 1/2})O{sub 3} and PbTiO{sub 3}-BiFeO{sub 3}-BiScO{sub 3} were investigated to clarify the relationship between the observance of multiple dielectric transitions and B-site chemistry. Multiple dielectric transitions were observed for a range of compositions in the Bi(Mg{sub 1/2}Ti{sub 1/2})O{sub 3}-containing system. A temperature-dependent diffraction study confirmed the existence of a cubic and tetragonal co-existence region at temperatures between the two transitions. No similar dielectric behavior was observed in the PbTiO{sub 3}-BiFeO{sub 3}-BiScO{sub 3} system.

  18. Michaelis-Menten Kinetics and the Activation Energy Relate Soil Peroxidase Kinetics to the Lignin Chemistry

    NASA Astrophysics Data System (ADS)

    Triebwasser-Freese, D.; Tharayil, N.; Preston, C. M.; Gerard, P.

    2013-12-01

    Recently, it has been suggested that lignin exhibit a turnover rate of less than 6 years, suggesting that the enzymatic mechanisms mediating the decay of lignin are less understood. One factor that could be affecting the mean residence time of lignin in the soil is the catalytic efficiency of soil oxidoreductase enzymes. We characterized the spatial and seasonal transitions in the Michaelis-Menten kinetics and activation energy of the soil oxidoreductase enzyme, peroxidase, across three ecosystems of differing litter chemistries- pine, deciduous forest, and a cultivated field- and associate it to the soil lignin chemistries. To interpret the combined effect of Vmax and Km, the two parameters were integrated into one term which we defined as the catalytic efficiency. Generally, the peroxidases in pine soils exhibited the highest Vmax and Km, resulting in the lowest catalytic efficiency, followed by that in the deciduous soils. Meanwhile, the agricultural soils which exhibited the lowest Vmax and Km contained the highest catalytic efficiency of peroxidase. Through linear regression analysis of the kinetic parameters to the soil lignin chemistry, we discerned that the catalytic efficiency term best associated to the lignin monomer ratios (C/V, P/V, and SCV/V). The Activation Energy of peroxidase varied by depth, and seasons across the ecosystems. However, the Activation Energy of peroxidase did not relate to the lignin chemistry or quantity. Collectively, our results show that although the peroxidase Vmax and Km in the phenolic-poor soils are low, the degradation efficiency of peroxidases in this soils can be equivalent or exceed that of phenolic-rich soils. This study, through the characterization of Michaelis-Menten kinetics, provides a new insight into the mechanisms that could moderate the decomposition of lignin in soils.

  19. A small ribozyme with dual-site kinase activity

    PubMed Central

    Biondi, Elisa; Maxwell, Adam W.R.; Burke, Donald H.

    2012-01-01

    Phosphoryl transfer onto backbone hydroxyls is a recognized catalytic activity of nucleic acids. We find that kinase ribozyme K28 possesses an unusually complex active site that promotes (thio)phosphorylation of two residues widely separated in primary sequence. After allowing the ribozyme to radiolabel itself by phosphoryl transfer from [γ-32P]GTP, DNAzyme-mediated cleavage yielded two radiolabeled cleavage fragments, indicating phosphorylation sites within each of the two cleavage fragments. These sites were mapped by alkaline digestion and primer extension pausing. Enzymatic digestion and mutational analysis identified nucleotides important for activity and established the active structure as being a constrained pseudoknot with unusual connectivity that may juxtapose the two reactive sites. Nuclease sensitivities for nucleotides near the pseudoknot core were altered in the presence of GTPγS, indicating donor-induced folding. The 5′ target site was more strongly favored in full-length ribozyme K28 (128 nt) than in truncated RNAs (58 nt). Electrophoretic mobilities of self-thiophosphorylated products on organomercurial gels are distinct from the 5′ mono-thiophosphorylated product produced by reaction with polynucleotide kinase, potentially indicating simultaneous labeling of both sites within individual RNA strands. Our evidence supports a single, compact structure with local dynamics, rather than global rearrangement, as being responsible for dual-site phosphorylation. PMID:22618879

  20. Binding of Copper and Silver to Single-Site Variants of Peptidylglycine Monooxygenase Reveals the Structure and Chemistry of the Individual Metal Centers

    PubMed Central

    2015-01-01

    Peptidylglycine monooxygenase (PHM) catalyzes the final step in the biosynthesis of amidated peptides that serve as important signaling molecules in numerous endocrine pathways. The catalytic mechanism has attracted much attention because of a number of unique attributes, including the presence of a pair of uncoupled copper centers separated by 11 Å (termed CuH and CuM), an unusual Cu(I)SMet interaction at the oxygen binding M-site, and the postulated Cu(II)–superoxo intermediate. Understanding the mechanism requires determining the catalytic roles of the individual copper centers and how they change during catalysis, a task made more difficult by the overlapping spectral signals from each copper center in the wild-type (WT) protein. To aid in this effort, we constructed and characterized two PHM variants that bound metal at only one site. The H242A variant bound copper at the H-center, while the H107AH108A double mutant bound copper at the M-center; both mutants were devoid of catalytic activity. Oxidized Cu(II) forms showed electron paramagnetic resonance and extended X-ray absorption fine structure (EXAFS) spectra consistent with their previously determined Cu(II)His3O and Cu(II)His2O2 ligand sets for the H- and M-centers, respectively. Cu(I) forms, on the other hand, showed unique chemistry. The M-center bound two histidines and a methionine at all pHs, while the H-center was two-coordinate at neutral pH but coordinated a new methionine S ligand at low pH. Fourier transform infrared studies confirmed and extended previous assignments of CO binding and showed unambiguously that the 2092 cm–1 absorbing species observed in the WT and many variant forms is an M-site Cu(I)–CO adduct. Silver binding was also investigated. When H107AH108A and M109I (a WT analogue with both sites intact) were incubated with excess AgNO3, each variant bound a single Ag(I) ion, from which it was inferred that Ag(I) binds selectively at the M-center with little or no affinity for

  1. Biochemical Characterization of HydF, a Scaffolding Enzyme, in the Synthesis of the Hydrogenase Active Site Metal Center: Implications Towards the Evolution of Biocatalysts from Mineral-based Components on Early Earth

    NASA Astrophysics Data System (ADS)

    Duffus, B. R.; Shepard, E. M.; McGlynn, S. E.; Bueling, A. L.; Winslow, M. A.; Peters, J. W.; Broderick, J. B.

    2010-04-01

    [FeFe]-hydrogenase active site biosynthesis utilizes radical chemistry on a scaffold protein whose ancestor may have been one of the earliest examples of a protein that couples the chemistry of an Fe-S peptide nest with a nucleotide binding nest.

  2. The application of click chemistry in the synthesis of agents with anticancer activity

    PubMed Central

    Ma, Nan; Wang, Ying; Zhao, Bing-Xin; Ye, Wen-Cai; Jiang, Sheng

    2015-01-01

    The copper(I)-catalyzed 1,3-dipolar cycloaddition between alkynes and azides (click chemistry) to form 1,2,3-triazoles is the most popular reaction due to its reliability, specificity, and biocompatibility. This reaction has the potential to shorten procedures, and render more efficient lead identification and optimization procedures in medicinal chemistry, which is a powerful modular synthetic approach toward the assembly of new molecular entities and has been applied in anticancer drugs discovery increasingly. The present review focuses mainly on the applications of this reaction in the field of synthesis of agents with anticancer activity, which are divided into four groups: topoisomerase II inhibitors, histone deacetylase inhibitors, protein tyrosine kinase inhibitors, and antimicrotubule agents. PMID:25792812

  3. Adsorption of hydrogen sulfide onto activated carbon fibers: effect of pore structure and surface chemistry.

    PubMed

    Feng, Wenguo; Kwon, Seokjoon; Borguet, Eric; Vidic, Radisav

    2005-12-15

    To understand the nature of H2S adsorption onto carbon surfaces under dry and anoxic conditions, the effects of carbon pore structure and surface chemistry were studied using activated carbon fibers (ACFs) with different pore structures and surface areas. Surface pretreatments, including oxidation and heattreatment, were conducted before adsorption/desorption tests in a fixed-bed reactor. Raw ACFs with higher surface area showed greater adsorption and retention of sulfur, and heat treatment further enhanced adsorption and retention of sulfur. The retained amount of hydrogen sulfide correlated well with the amount of basic functional groups on the carbon surface, while the desorbed amount reflected the effect of pore structure. Temperature-programmed desorption (TPD) and thermal gravimetric analysis (TGA) showed that the retained sulfurous compounds were strongly bonded to the carbon surface. In addition, surface chemistry of the sorbent might determine the predominant form of adsorbate on the surface. PMID:16475362

  4. Chemistry Is in the News: Taxonomy of authentic news media-based learning activities1

    NASA Astrophysics Data System (ADS)

    Glaser, Rainer E.; Carson, Kathleen M.

    2005-09-01

    A brief history is given of approaches that aim at achieving a connectedness of the content of organic chemistry courses to real world issues. Recently, such approaches have relied more and more on online media resources, the tools of the Internet and the World Wide Web. We propose a six-level taxonomy of ‘authentic news media-based learning activities’ to provide a conceptual framework for the description and discussion of such approaches. The Chemistry Is in the News project was designed to allow students to draw explicit connections between the course content and real world issues in ways that engage the students in a full range of cognitive skills. The activities consisted in the study, creation, and peer review of news portfolios by student collaborative groups. A news portfolio consists of an authentic news article taken from the popular press with interpretive comments and questions.

  5. Dashboard applications to monitor experiment activities at sites

    NASA Astrophysics Data System (ADS)

    Andreeva, Julia; Belforte, Stefano; Boehm, Max; Casajus, Adrian; Flix, Josep; Gaidioz, Benjamin; Grigoras, Costin; Kokoszkiewicz, Lukasz; Lanciotti, Elisa; Rocha, Ricardo; Saiz, Pablo; Santinelli, Roberto; Sidorova, Irina; Sciabà, Andrea; Tsaregorodtsev, Andrei

    2010-04-01

    In the framework of a distributed computing environment, such as WLCG, monitoring has a key role in order to keep under control activities going on in sites located in different countries and involving people based in many different sites. To be able to cope with such a large scale heterogeneous infrastructure, it is necessary to have monitoring tools providing a complete and reliable view of the overall performance of the sites. Moreover, the structure of a monitoring system critically depends on the object to monitor and on the users it is addressed to. In this article we will describe two different monitoring systems both aimed to monitor activities and services provided in the WLCG framework, but designed in order to meet the requirements of different users: Site Status Board has an overall view of the services available in all the sites supporting an experiment, whereas Siteview provides a complete view of all the activities going on at a site, for all the experiments supported by the site.

  6. Architecture and active site of particulate methane monooxygenase

    PubMed Central

    Culpepper, Megen A.; Rosenzweig, Amy C.

    2012-01-01

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. Understanding pMMO function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. Crystal structures of pMMOs from three different methanotrophs reveal a trimeric architecture, consisting of three copies each of the pmoB, pmoA, and pmoC subunits. There are three distinct metal centers in each protomer of the trimer, mononuclear and dinuclear copper sites in the periplasmic regions of pmoB and a mononuclear site within the membrane that can be occupied by copper or zinc. Various models for the pMMO active site have been proposed within these structural constraints, including dicopper, tricopper, and diiron centers. Biochemical and spectroscopic data on pMMO and recombinant soluble fragments, denoted spmoB proteins, indicate that the active site involves copper and is located at the site of the dicopper center in the pmoB subunit. Initial spectroscopic evidence for O2 binding at this site has been obtained. Despite these findings, questions remain about the active site identity and nuclearity and will be the focus of future studies. PMID:22725967

  7. The Construction of Metal-Organic Framework with Active Backbones by the Utilization of Reticular Chemistry

    NASA Astrophysics Data System (ADS)

    Choi, Eunwoo

    With the principles of reticular chemistry, metal-organic frameworks with ultra-high porosity, chiral-recognition unit as a chiral stationary phase, metalloporhyrins for enhanced hydrogen adsorption and an intrinsic conductivity to form porous conductors, have been prepared. This dissertation presents how the principles of reticular chemistry were utilized to achieve in the preparations of metal-organic frameworks with a large surface area and active backbones. Through the simple isoreticular (having the same framework topology) expansion from MOF-177 composed with 1,3,5-tris(4'-carboxyphenyl-)benzene (BTB3-) as the strut; MOF-200 was prepared with 4,4',4"-(benzene-1,3,5-triyl-tris(benzene-4,1-diy1))tribenzoic acid an extension from BTB3- by a phenylene unit to yield one of the most porous MOFs with a Langmuir surface area of 10,400 m2. and the lowest density of 0.22 cm3.g-1. A successful thermal polymerization reaction at 325 °C inside of the pores of highly porous MOF, MOF-177, was performed and verified the integrity of the MOF structure even after the thermal reaction. 1,4-Diphenylbutadiyne that is known to polymerize upon heating to form a conjugated backbone was impregnated via solution-diffusion into MOF-177 and then subsequently polymerized by heat to form polymer impregnated MOF-177. Characterization was carried out using powder X-ray diffraction and volumetric sorption analyzer. MOF-1020 with a linear quaterphenyl dicarboxylate-based strut was designed to contain a chiral bisbinaphthyl crown-ether moiety for alkyl ammonium resolution was precisely placed into a Zn4O(CO2)6-based cubic MOF structure. Unfortunately, the chiral resolution was not achieved due to the sensitivity and the pore environment of MOF-1020. However, an interesting phenomenon was observed, where the loss of crystallinity occurs upon solvent removal while the crystallites remain shiny and crystalline, but it readily is restored upon re-solvation of the crystallites. This rare

  8. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site.

    PubMed

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-04-20

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2domains reveal that the (HhH)2domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  9. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

    PubMed Central

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-01-01

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  10. Soluble salts at the Phoenix Lander site, Mars: A reanalysis of the Wet Chemistry Laboratory data

    NASA Astrophysics Data System (ADS)

    Toner, J. D.; Catling, D. C.; Light, B.

    2014-07-01

    The Wet Chemistry Laboratory (WCL) on the Phoenix Mars Scout Lander analyzed soils for soluble ions and found Ca2+, Mg2+, Na+, K+, Cl-, SO42-, and ClO4-. The salts that gave rise to these ions can be inferred using aqueous equilibrium models; however, model predictions are sensitive to the initial solution composition. This is problematic because the WCL data is noisy and many different ion compositions are possible within error bounds. To better characterize ion concentrations, we reanalyzed WCL data using improvements to original analyses, including Kalman optimal smoothing and ion-pair corrections. Our results for Rosy Red are generally consistent with previous analyses, except that Ca2+ and Cl- concentrations are lower. In contrast, ion concentrations in Sorceress 1 and Sorceress 2 are significantly different from previous analyses. Using the more robust Rosy Red WCL analysis, we applied equilibrium models to determine salt compositions within the error bounds of the reduced data. Modeling with FREZCHEM predicts that WCL solutions evolve Ca-Mg-ClO4-rich compositions at low temperatures. These unusual compositions are likely influenced by limitations in the experimental data used to parameterize FREZCHEM. As an alternative method to evaluate salt assemblages, we employed a chemical divide model based on the eutectic temperatures of salts. Our chemical divide model predicts that the most probable salts in order of mass abundance are MgSO4·11H2O (meridianiite), MgCO3·nH2O, Mg(ClO4)2·6H2O, NaClO4·2H2O, KClO4, NaCl·2H2O (hydrohalite), and CaCO3 (calcite). If ClO3- is included in the chemical divide model, then NaClO3 precipitates instead of NaClO4·2H2O and Mg(ClO3)2·6H2O precipitates in addition to Mg(ClO4)2·6H2O. These salt assemblages imply that at least 1.3 wt.% H2O is bound in the soil, noting that we cannot account for water in hydrated insoluble salts or deliquescent brines. All WCL solutions within error bounds precipitate Mg(ClO4)2·6H2O and/or Mg

  11. Site-selective protein-modification chemistry for basic biology and drug development

    NASA Astrophysics Data System (ADS)

    Krall, Nikolaus; da Cruz, Filipa P.; Boutureira, Omar; Bernardes, Gonçalo J. L.

    2016-02-01

    Nature has produced intricate machinery to covalently diversify the structure of proteins after their synthesis in the ribosome. In an attempt to mimic nature, chemists have developed a large set of reactions that enable post-expression modification of proteins at pre-determined sites. These reactions are now used to selectively install particular modifications on proteins for many biological and therapeutic applications. For example, they provide an opportunity to install post-translational modifications on proteins to determine their exact biological roles. Labelling of proteins in live cells with fluorescent dyes allows protein uptake and intracellular trafficking to be tracked and also enables physiological parameters to be measured optically. Through the conjugation of potent cytotoxicants to antibodies, novel anti-cancer drugs with improved efficacy and reduced side effects may be obtained. In this Perspective, we highlight the most exciting current and future applications of chemical site-selective protein modification and consider which hurdles still need to be overcome for more widespread use.

  12. Effects of steam activation on the pore structure and surface chemistry of activated carbon derived from bamboo waste

    NASA Astrophysics Data System (ADS)

    Zhang, Yan-Juan; Xing, Zhen-Jiao; Duan, Zheng-Kang; Li, Meng; Wang, Yin

    2014-10-01

    The effects of steam activation on the pore structure evolution and surface chemistry of activated carbon (AC) obtained from bamboo waste were investigated. Nitrogen adsorption-desorption isotherms revealed that higher steam activation temperatures and/or times promoted the creation of new micropores and widened the existing micropores, consequently decreasing the surface area and total pore volume. Optimum conditions included an activation temperature of 850 °C, activation time of 120 min, and steam flush generated from deionized water of 0.2 cm3 min-1. Under these conditions, AC with a BET surface area of 1210 m2 g-1 and total pore volume of 0.542 cm-3 g-1was obtained. Changes in surface chemistry were determined through Boehm titration, pH measurement, Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS). Results revealed the presence of a large number of basic groups on the surface of the pyrolyzed char and AC. Steam activation did not affect the species of oxygen-containing groups but changed the contents of these species when compared with pyrolyzed char. Scanning electron microscopy was used to observe the surface morphology of the products. AC obtained under optimum conditions showed a monolayer adsorption capacity of 330 mg g-1 for methylene blue (MB), which demonstrates its excellent potential for MB adsorption applications.

  13. An Enzyme-Mediated Methodology for the Site-Specific Radiolabeling of Antibodies Based on Catalyst-Free Click Chemistry

    PubMed Central

    Zeglis, Brian M.; Davis, Charles B.; Aggeler, Robert; Kang, Hee Chol; Chen, Aimei; Agnew, Brian J.; Lewis, Jason S.

    2013-01-01

    An enzyme- and click chemistry-mediated methodology for the site-selective radiolabeling of antibodies on the heavy chain glycans has been developed and validated. To this end, a model system based on the prostate specific membrane antigen-targeting antibody J591, the positron-emitting radiometal 89Zr, and the chelator desferrioxamine has been employed. The methodology consists of four steps: (1) the removal of sugars on the heavy chain region of the antibody to expose terminal N-acetylglucosamine residues; (2) the incorporation of azide-modified N-acetylgalactosamine monosaccharides into the glycans of the antibody; (3) the catalyst-free click conjugation of desferrioxamine-modified dibenzocyclooctynes to the azide-bearing sugars; and (4) the radiolabeling of the chelator-modified antibody with 89Zr. The site-selective labeling methodology has proven facile, reproducible, and robust, producing 89Zr-labeled radioimmunoconjguates that display high stability and immunoreactivity in vitro (>95%) in addition to high selective tumor uptake (67.5 ± 5.0 %ID/g) and tumor-to-background contrast in athymic nude mice bearing PSMA-expressing subcutaneous LNCaP xenografts. Ultimately, this strategy could play a critical role in the development of novel well-defined and highly immunoreactive radioimmunoconjugates for both the laboratory and clinic. PMID:23688208

  14. Impact mineralogy and chemistry of the cretaceous-tertiary boundary at DSDP site 576

    NASA Technical Reports Server (NTRS)

    Bostwick, Jennifer A.; Kyte, Frank T.

    1993-01-01

    We have identified the K/T boundary in pelagic clay sediments from cores at DSDP Site 576 in the western North Pacific. Detailed geochemical and trace mineralogical analyses of this boundary section are in progress and initial results indicate similarities and differences relative to the only other clay core investigated in detail; DSDP Site 596, a locality in the western South Pacific. Peak Ir concentrations of 13 ng/g in DSDP Hole 576B are virtually identical with those observed in the South Pacific, but in the North Pacific this peak is much narrower and the integrated Ir fluence of 85 ng cm(exp -2) is 4 times lower (320 in Hole 596). Of the 34 elements measured, only Ir and Cr were found to have anomalous concentrations in K/T boundary samples. Trace mineral residues were obtained by washing away clays and sequential chemical leaches (including HF) to remove typical hydrogenous and biogenous sediment components (e.g., zeolites and radiolarian opal). We attempted to quantitatively recover the entire trace mineral assemblage for grains greater than 30 micrometers in diameter. Our mineral residues were dominated by two phases: quartz and magnesioferrite spinel. Other non-opaque mineral grains we have positively identified were trace K-feldspar, plagioclase, corundum, and muscovite. Of these only K-feldspar exhibited planar deformation features (PDF). We have not found abundant plagioclase, as in the South Pacific suggesting that this phase was either not preserved in the North Pacific, or that in the south, it has a non-impact (i.e., volcanic) source. PDF in quartz were commonly obscured by secondary overgrowths on the surfaces of quartz grains, presumably from diagenetic reprecipitation of silica dissolved from opaline radiolarian tests that are common in these sediments. However, careful examination revealed that most grains had multiple sets of PDF. Of the 133 quartz grains greater than 30 micrometers analyzed, 62 percent showed evidence of shock. The largest

  15. Environmental Role of Rime Chemistry at Selected Mountain Sites in Poland

    NASA Astrophysics Data System (ADS)

    Godek, Michał; Błaś, Marek; Sobik, Mieczysław; Polkowska, Żaneta; Cichała-Kamrowska, Katarzyna; Namieśnik, Jacek

    2012-05-01

    The results of field experiments on fog pollutant deposition enhanced by local mountain climate, completed by the dendrochronological analysis of the forest response, are presented in this paper. In spite of their low absolute altitude (1,000-1,600 m a.s.l), the Sudetes and the Silesian Beskid form a noticeable orographic barrier for the airflow of the humid Atlantic air masses. This results in the increase of cloudiness and fog frequency as well as both atmospheric precipitation and horizontal precipitation volume. Between January and December 2009 the daily samples of atmospheric precipitation and rime were collected on three selected mountain tops of similar height. The selected measurement sites were situated along a 300 km WNW-ESE profile parallel to the direction of the prevailing atmospheric circulation. High day-to-day variability of rime water volume, the total ionic content and chemical composition of the individual samples were typical of each measurement site and depended on the emission patterns, synoptic situation and the local climatic conditions influenced chiefly by terrain relief. Significantly larger rime efficiency and pollution deposition via fog were observed at the westernmost Szrenica Mt site rather than more to the southeast at Śnieżnik Mt and Skrzyczne Mt. This difference should be explained by more intense orographic deformation of predominant airflow from the western sector as well as the higher liquid water content of fog in the vicinity of Szrenica. Both temporal and spatial variability of fog deposition correlates closely with the health status of the drilled trees of Norway Spruce ( Picea Abies) in the Śnieżnik Massif. The averaged annual tree rings width near the local tree line (1,350 m a.s.l.) on the summit dome of Śnieżnik decreased by 71% between 1950 and the early 1980s. This is also the area of the highest rate of atmospheric pollutant deposition due to particularly important role of fog. At an altitude of 1,200 m a

  16. Probing the Role of Active Site Water in the Sesquiterpene Cyclization Reaction Catalyzed by Aristolochene Synthase.

    PubMed

    Chen, Mengbin; Chou, Wayne K W; Al-Lami, Naeemah; Faraldos, Juan A; Allemann, Rudolf K; Cane, David E; Christianson, David W

    2016-05-24

    Aristolochene synthase (ATAS) is a high-fidelity terpenoid cyclase that converts farnesyl diphosphate exclusively into the bicyclic hydrocarbon aristolochene. Previously determined crystal structures of ATAS complexes revealed trapped active site water molecules that could potentially interact with catalytic intermediates: water "w" hydrogen bonds with S303 and N299, water molecules "w1" and "w2" hydrogen bond with Q151, and a fourth water molecule coordinates to the Mg(2+)C ion. There is no obvious role for water in the ATAS mechanism because the enzyme exclusively generates a hydrocarbon product. Thus, these water molecules are tightly controlled so that they cannot react with carbocation intermediates. Steady-state kinetics and product distribution analyses of eight ATAS mutants designed to perturb interactions with active site water molecules (S303A, S303H, S303D, N299A, N299L, N299A/S303A, Q151H, and Q151E) indicate relatively modest effects on catalysis but significant effects on sesquiterpene product distributions. X-ray crystal structures of S303A, N299A, N299A/S303A, and Q151H mutants reveal minimal perturbation of active site solvent structure. Seven of the eight mutants generate farnesol and nerolidol, possibly resulting from addition of the Mg(2+)C-bound water molecule to the initially formed farnesyl cation, but no products are generated that would suggest enhanced reactivity of other active site water molecules. However, intermediate germacrene A tends to accumulate in these mutants. Thus, apart from the possible reactivity of Mg(2+)C-bound water, active site water molecules in ATAS are not directly involved in the chemistry of catalysis but instead contribute to the template that governs the conformation of the flexible substrate and carbocation intermediates. PMID:27172425

  17. Role of the surface chemistry of activated carbons in dye removal from aqueous solution

    NASA Astrophysics Data System (ADS)

    Zhou, Hua-lei; Zhen, Wen-juan; Zhu, Qian; Wu, Xiao-bin; Chang, Zhi-dong; Li, Wen-jun

    2015-07-01

    Commercial activated carbons were modified by a series of chemical or physical treatments using H2O2, NH3, and heating under N2 flow without notably changing their pore structures. The resultant carbons were characterized by N2 adsorption and Bohem titration and then used to remove Ponceau 4R, methyl orange and brilliant blue from aqueous solutions. Surface chemistry was found to play a significantly different role in removing these three compounds. The removal of anionic Ponceau 4R increases with increasing carbon surface basicity due to the predominant dispersive interaction mechanism. In contrast, surface chemistry has little effect on the removal of anionic methyl orange, which can be explained by two parallel mechanisms involving electrostatic and dispersive interactions due to the basic amine group in a dye molecule. The influence of surface chemistry on the removal of amphoteric brilliant blue dye can also be ignored due to a weak interaction between the carbons and dye molecules, which is resulted from strong cohesive energy from electrostatic forces inside amphoteric dye molecules.

  18. Vertical dynamics of the aquifer microbial community associated with groundwater chemistry in the artificial recharge site in Korea

    NASA Astrophysics Data System (ADS)

    Moon, Hee Sun; Hyun, Sung Pil; Kim, Boa; Shin, Doyun; Ha, Kyoochul

    2014-05-01

    Artificial groundwater recharge offers an opportunity to better manage groundwater resources by storing water in aquifers and increasing the amount of groundwater available for abstraction during high demand periods. It is important to understand the linkage of microbial ecology to groundwater chemistry to assess changes in groundwater quality caused by artificial groundwater recharge. In this study, we investigated how the structure and diversity of this subsurface microbial community correlates with and impacts upon groundwater chemistry. Groundwater samples at two different depths (10 and 33 m) were collected from three monitoring wells (MLW 1, MLW 2 and MLW 3) in the artificial groundwater recharge demonstration site in Changwon, Korea. The groundwater samples were filtered with 0.45 um membrane filters and then used for the anion and cation analysis. A 4L of each groundwater sample was immediately filtered with 0.2 um membrane filters and the filters were used for DNA extraction using Fast DNA Spin Kit for soil (MP Bio, USA). Further molecular work processes including pyrosequencing were carried out at Chunlab, Inc. (Seoul, Korea). Pyrosequencing results showed all major phyla were OD 1, OD3, and OD 11 in shallow groundwater samples while Proteobacteria (β-proteobacteria and δ-proteobacteria) and Bacterioidetes were dominant phyla in deep groundwater. The Shannon diversity index indicated that the microbial community was much more diverse in shallow groundwater than in deep groundwater. Heat map and hierarchical cluster analysis based on the relative abundance of OTUs at genus level showed a clear distinction between shallow and deep groundwater. Differences in the vertical community structure were driven by the major species such as Sufuicurvum sp., Pseudomonas sp., Acidiferrobacter sp., Gallionella sp., and Ferribacterium sp. The results show that several distinct factors such as iron and sulfate concentration control the vertical composition of microbial

  19. Structure/function correlations over binuclear non-heme iron active sites.

    PubMed

    Solomon, Edward I; Park, Kiyoung

    2016-09-01

    Binuclear non-heme iron enzymes activate O2 to perform diverse chemistries. Three different structural mechanisms of O2 binding to a coupled binuclear iron site have been identified utilizing variable-temperature, variable-field magnetic circular dichroism spectroscopy (VTVH MCD). For the μ-OH-bridged Fe(II)2 site in hemerythrin, O2 binds terminally to a five-coordinate Fe(II) center as hydroperoxide with the proton deriving from the μ-OH bridge and the second electron transferring through the resulting μ-oxo superexchange pathway from the second coordinatively saturated Fe(II) center in a proton-coupled electron transfer process. For carboxylate-only-bridged Fe(II)2 sites, O2 binding as a bridged peroxide requires both Fe(II) centers to be coordinatively unsaturated and has good frontier orbital overlap with the two orthogonal O2 π* orbitals to form peroxo-bridged Fe(III)2 intermediates. Alternatively, carboxylate-only-bridged Fe(II)2 sites with only a single open coordination position on an Fe(II) enable the one-electron formation of Fe(III)-O2 (-) or Fe(III)-NO(-) species. Finally, for the peroxo-bridged Fe(III)2 intermediates, further activation is necessary for their reactivities in one-electron reduction and electrophilic aromatic substitution, and a strategy consistent with existing spectral data is discussed. PMID:27369780

  20. Molecular Imprint of Enzyme Active Site by Camel Nanobodies

    PubMed Central

    Li, Jiang-Wei; Xia, Lijie; Su, Youhong; Liu, Hongchun; Xia, Xueqing; Lu, Qinxia; Yang, Chunjin; Reheman, Kalbinur

    2012-01-01

    Screening of inhibitory Ab1 antibodies is a critical step for producing catalytic antibodies in the anti-idiotypic approach. However, the incompatible surface of the active site of the enzyme and the antigen-binding site of heterotetrameric conventional antibodies become the limiting step. Because camelid-derived nanobodies possess the potential to preferentially bind to the active site of enzymes due to their small size and long CDR3, we have developed a novel approach to produce antibodies with alliinase activities by exploiting the molecular mimicry of camel nanobodies. By screening the camelid-derived variable region of the heavy chain cDNA phage display library with alliinase, we obtained an inhibitory nanobody VHHA4 that recognizes the active site. Further screening with VHHA4 from the same variable domain of the heavy chain of a heavy-chain antibody library led to a higher incidence of anti-idiotypic Ab2 abzymes with alliinase activities. One of the abzymes, VHHC10, showed the highest activity that can be inhibited by Ab1 VHHA4 and alliinase competitive inhibitor penicillamine and significantly suppressed the B16 tumor cell growth in the presence of alliin in vitro. The results highlight the feasibility of producing abzymes via anti-idiotypic nanobody approach. PMID:22374998

  1. Active Sites Environmental Monitoring Program: Mid-FY 1991 report

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1991-10-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1990 through March 1991. The ASEMP was established in 1989 by Solid Waste Operations and the Environmental Sciences Division to provide early detection and performance monitoring at active low-level radioactive waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. Monitoring results continue to demonstrate the no LLW is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.

  2. An active-site peptide from pepsin C

    PubMed Central

    Kay, J.; Ryle, A. P.

    1971-01-01

    Porcine pepsin C is inactivated rapidly and irreversibly by diazoacetyl-dl-norleucine methyl ester in the presence of cupric ions at pH values above 4.5. The inactivation is specific in that complete inactivation accompanies the incorporation of 1mol of inhibitor residue/mol of enzyme and evidence has been obtained to suggest that the reaction occurs with an active site residue. The site of reaction is the β-carboxyl group of an aspartic acid residue in the sequence Ile-Val-Asp-Thr. This sequence is identical with the active-site sequence in pepsin and the significance of this in terms of the different activities of the two enzymes is discussed. PMID:4942834

  3. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    PubMed

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined. PMID:27243042

  4. Aldehyde Tag Coupled with HIPS Chemistry Enables the Production of ADCs Conjugated Site-Specifically to Different Antibody Regions with Distinct in Vivo Efficacy and PK Outcomes

    PubMed Central

    2015-01-01

    It is becoming increasingly clear that site-specific conjugation offers significant advantages over conventional conjugation chemistries used to make antibody–drug conjugates (ADCs). Site-specific payload placement allows for control over both the drug-to-antibody ratio (DAR) and the conjugation site, both of which play an important role in governing the pharmacokinetics (PK), disposition, and efficacy of the ADC. In addition to the DAR and site of conjugation, linker composition also plays an important role in the properties of an ADC. We have previously reported a novel site-specific conjugation platform comprising linker payloads designed to selectively react with site-specifically engineered aldehyde tags on an antibody backbone. This chemistry results in a stable C–C bond between the antibody and the cytotoxin payload, providing a uniquely stable connection with respect to the other linker chemistries used to generate ADCs. The flexibility and versatility of the aldehyde tag conjugation platform has enabled us to undertake a systematic evaluation of the impact of conjugation site and linker composition on ADC properties. Here, we describe the production and characterization of a panel of ADCs bearing the aldehyde tag at different locations on an IgG1 backbone conjugated using Hydrazino-iso-Pictet-Spengler (HIPS) chemistry. We demonstrate that in a panel of ADCs with aldehyde tags at different locations, the site of conjugation has a dramatic impact on in vivo efficacy and pharmacokinetic behavior in rodents; this advantage translates to an improved safety profile in rats as compared to a conventional lysine conjugate. PMID:24924618

  5. Evidence for cold water circulation at DSDP site 395: Isotopes and chemistry of alteration products

    SciTech Connect

    Lawrence, J.R.; Drever, J.I.

    1981-06-10

    A variety of low temperature alteration products occurs in the 573-m-thick section of basaltic rock from Site 395. Carbonate veins, smectities (predominantly saponite), zeolites, goethite, opal, and gypsum, listed in order of decreasing abundance, are present. Values of delta/sup 18/O (SMOW) of calcite veins range from +31.8 to +34.8/sup 0//00, and delta/sup 13/C (PDB) ranges from +2.3 to +4.4/sup 0//00. Apparently the calcite veins were formed at 0--15 /sup 0/C in equilibrium with deep ocean water. Some veins may have formed during glacial periods, when delta/sup 18/O of the deep water was higher than it is presently. The deepest calcite veins were formed in the temperature range 8--15 /sup 0/C. Saponite veins associated with an intrusive dolerite sill (delta/sup 18/O = +9.8 to +24.3%/sub 0/, SMOW) are estimated to have formed in the temperature range 30--160 /sup 0/C. Very extensive circulation (i.e., large water/rock ratios) predominated during alteration of the basalts as evidenced by seawater carbon and sulfur istope ratios in calcite and gypsum and carbon, sulfur and magnesium mass balance considerations.

  6. Assessment of water chemistry, habitat, and benthic macroinvertebrates at selected stream-quality monitoring sites in Chester County, Pennsylvania, 1998-2000

    USGS Publications Warehouse

    Reif, Andrew G.

    2004-01-01

    Biological, chemical, and habitat data have been collected from a network of sites in Chester County, Pa., from 1970 to 2003 to assess stream quality. Forty sites in 6 major stream basins were sampled between 1998 and 2000. Biological data were used to determine levels of impairment in the benthic-macroinvertebrate community in Chester County streams and relate the impairment, in conjunction with chemical and habitat data, to overall stream quality. Biological data consisted of benthic-macroinvertebrate samples that were collected annually in the fall. Water-chemistry samples were collected and instream habitat was assessed in support of the biological sampling. Most sites in the network were designated as nonimpacted or slightly impacted by human activities or extreme climatic conditions on the basis of biological-metric analysis of benthic-macroinvertebrate data. Impacted sites were affected by factors, such as nutrient enrichment, erosion and sedimentation, point discharges, and droughts and floods. Streams in the Schuylkill River, Delaware River, and East Branch Brandywine Creek Basins in Chester County generally had low nutrient concentrations, except in areas affected by wastewater- treatment discharges, and stream habitat that was affected by erosion. Streams in the West Branch Brandywine, Christina, Big Elk, and Octoraro Creek Basins in Chester County generally had elevated nutrient concentrations and streambottom habitat that was affected by sediment deposition. Macroinvertebrate communities identified in samples from French Creek, Pigeon Creek (Schuylkill River Basin), and East Branch Brandywine Creek at Glenmoore consistently indicate good stream conditions and were the best conditions measured in the network. Macroinvertebrate communities identified in samples from Trout Creek (site 61), West Branch Red Clay Creek (site 55) (Christina River Basin), and Valley Creek near Atglen (site 34) (Octoraro Creek Basin) indicated fair to poor stream conditions and

  7. Particulate matter chemistry and dynamics in the Twilight Zone at VERTIGO ALOHA and K2 Sites

    SciTech Connect

    Bishop, James K.B.; Wood, T.J.

    2008-03-25

    Understanding particle dynamics in the 'Twilight Zone' is critical to prediction of the ocean's carbon cycle. As part of the VERTIGO (VERtical Transformations In the Global Ocean) project, this rarely sampled regime extending from the base of the euphotic layer to 1000 m, was characterized by double-paired day/night Multiple Unit Large Volume in-situ Filtration System (MULVFS) deployments and by {approx}100 high-frequency CTD/transmissometer/turbidity sensor profiles. VERTIGO studies lasting three weeks, contrasted oligotrophic station ALOHA (22.75{sup o}N 158{sup o}W), sampled in June-July 2004, with a biologically productive location (47{sup o}N 161{sup o}E) near station K2 in the Oyashio, occupied July-August 2005. Profiles of major and minor particulate components (C{sub org}, N, P, Ca, Si, Sr, Ba, Mn) in <1, 1-51, and >51 {micro}m size fractions, in-water optics, neutrally buoyant sediment trap (NBST) fluxes, and zooplankton data were intercompared. MULVFS total C{sub org} and C-Star particle beam attenuation coefficient (C{sub P}) were consistently related at both sites with a 27 {micro}M m{sup -1} conversion factor. 26 At K2, C{sub P} profiles further showed a multitude of transient spikes throughout the water column and spike abundance profiles closely paralleled the double peaked abundance profiles of zooplankton. Also at K2, copepods contributed {approx}40% and 10%, night and day, respectively to >51 {micro}m C{sub org} of MULVFS samples in the mixed layer, but few copepods were collected in deeper waters; however, non-swimming radiolarians were quantitatively sampled. A recent hypothesis regarding POC differences between pumps and bottles is examined in light of these results. Particulate >51 {micro}m C{sub org}, N, and P at both ALOHA and K2 showed strong attenuation with depth at both sites. Notable at ALOHA were unusually high levels of >51 {micro}m Sr (up to 4 nM) in the mixed layer, a reflection of high abundances of SrSO{sub 4} precipitating

  8. Particulate matter chemistry and dynamics in the twilight zone at VERTIGO ALOHA and K2 sites

    NASA Astrophysics Data System (ADS)

    Bishop, James K. B.; Wood, T. J.

    2008-12-01

    Understanding particle dynamics in the 'Twilight Zone' is critical to prediction of the ocean's carbon cycle. As part of the VERtical Transport In the Global Ocean (VERTIGO) project, this rarely sampled regime extending from the base of the euphotic layer to 1000 m, was characterized by double-paired day/night Multiple Unit Large Volume in-situ Filtration System (MULVFS) deployments and by ˜100 high-frequency CTD/transmissometer/turbidity sensor profiles. VERTIGO studies lasting 3 weeks, contrasted oligotrophic station ALOHA (22.75°N 158°W), sampled in June-July 2004, with a biologically productive location (47 °N 161°E) near station K2 in the Oyashio, occupied July-August 2005. Profiles of major and minor particulate components (C org, N, P, Ca, Si, Sr, Ba, Mn) in <1, 1-51, and >51 μm size fractions, in-water optics, neutrally buoyant sediment trap (NBST) fluxes, and zooplankton data were intercompared. MULVFS total C org and C-Star particle beam attenuation coefficient ( C P) were consistently related at both sites with a 27 μM m -1 conversion factor. At K2, C P profiles further showed a multitude of transient spikes throughout the water column and spike abundance profiles closely paralleled the double peaked abundance profiles of zooplankton. Also at K2, copepods contributed ˜40% and 10%, night and day, respectively to >51 μm C org of MULVFS samples in the mixed layer, but few copepods were collected in deeper waters; however, non-swimming radiolarians were quantitatively sampled. A recent hypothesis regarding POC differences between pumps and bottles is examined in light of these results. Particulate >51 μm C org, N, and P at both ALOHA and K2 showed strong attenuation with depth at both sites. Notable at ALOHA were unusually high levels of >51 μm Sr (up to 4 nM) in the mixed layer, a reflection of high abundances of SrSO 4 precipitating Acantharia. Notable at K2 were major changes in water column inventories of many particulate components to 700 m

  9. Groundwater chemistry at the Nevada Test Site: Data and preliminary interpretations

    SciTech Connect

    Chapman, J.B.; Lyles, B.F.

    1993-03-01

    The interpretation of chemical analyses of groundwater collected at and near the Nevada Test Site (NTS) has been vital in developing conceptual models of groundwater flow in the area. These conceptual models are tested using recent chemical data generated by the Desert Research Institute, as well as historic analyses from the US Geological Survey. A total of 81 wells are represented by analyses from 1957 to 1990, with generally excellent agreement between repeat samples from the same location. As identified by previous workers, three hydrochemical facies are represented by the samples: Ca-Mg-HCO{sub 3} water in carbonate rocks or alluvium derived from carbonates, Na-K-HCO{sub 3} water in volcanic rocks and alluvium derived from volcanic rocks, and a mixed fades found in many carbonate and alluvium water samples, and some volcanic waters. There is a general lack of lateral continuity in chemical characteristics along presumed flowpaths within each hydrologic unit (alluvium, carbonate, and volcanic). Though a lack of continuity between basins on the east side of the NTS was expected for water in alluvial and volcanic units due to the absence of interbasin flow, chemical differences observed within individual basins suggest a dominance of vertical over lateral flow. Groundwater in volcanic materials on the east side of Yucca and Frenchman Flats and on the west side of Pahute Mesa and Yucca Mountain has a nearly pure Na-K-HCO{sub 3} signature that reflects contact with primarily volcanic material. Groundwater in volcanic units in the middle of the NTS and on the east side of Pahute Mesa contains a higher proportion of Ca, Mg, Cl, and SO{sub 4} than the other volcanic waters and indicates the contribution of water from the upper carbonate aquifer and/or hydrothermally altered regions.

  10. Interpreting detailed brine chemistry changes during early periods of in-zone CO2 storage at Cranfield site, Mississippi, USA

    NASA Astrophysics Data System (ADS)

    Sun, A. Y.; Islam, A.; Lu, J.

    2015-12-01

    Geochemical reactions can play important role on the long-term geological storage of CO2 in sites where the target formations have reactive minerals. Although the use of batch models (experimental or theoretical) is expedient, it leaves questions about how to interpret the results from the context of field scale injection. The goal of this study is to investigate changes in fluid compositions using a detailed reactive transport model. Most published CO2 geochemical studies tend to consider only a small number of components because of expensive calculations and therefore simultaneous mobility of large number of heavy metals is not clearly known. In this study we present results of coupled multiphase, multicomponent reactive transport simulations of Cranfield site, Mississipi, USA at relatively fine scale, which are obtained using the parallel PFLOTRAN code. The geochemical system consists of 22 primary or basis species, in-situ CO2 and O2 gaseous components, and 5 minerals. The number of secondary elements is 37, representing very simple to complex mineralizations occurred simultaneously in saline formation (1.81 molality). The fluid chemical compositions were measured from production fluids and mineral composition of the formation was obtained from XRD analysis of core samples. The results show brine chemistry changes in the reservoir and shed insights on the need to monitor the mobility of heavy metals such as Mg, Ca, Al, Mn, Fe, Cu, Zn, Sr, Ba, and Cd. The study provides simultaneous potential mobile inventory of these metals in the storage formations and warns possible risk through leakage into overlying zone. From storage point of view we also aim to observe the sensitivity of aforementioned constituents. Our results show pH drop from 6.91 to 3.5 and relatively small changes in HCO3- and Fe concentrations. However aqueous Ca and Al increase by orders of magnitude. The detailed geochemical effect shows trapping efficiency increased by few percent. The brine

  11. Chemistry and mineralogy of samples from the strategic petroleum reserve Bryan Mound site

    SciTech Connect

    Bild, R. W.

    1980-08-01

    The goal of the Strategic Petroleum Reserve (SPR) program is to protect the United States from a temporary cutoff of imported crude oil by stockpiling a reserve of oil in caverns in Gulf Coast salt domes. Some suitable caverns already exist as a result of solution mining activities by commercial mining companies. Most of the caverns for the program, however, will be solution mined specifically for the SPR program. The tasks assigned to Sandia National Laboratories include conducting a geotechnical program and providing interim technical support for the leaching of the first five caverns in the Bryan Mound, Texas, salt dome. This report describes chemical, mineralogical and petrological work done at Sandia as of May 1, 1980 in support of Bryan Mound activities. Samples of Bryan Mound salt cores, sidewall samples and drill cuttings have been subjected to chemical, mineralogical and petrographic analysis. Halite (NaCl) was the major mineral in all samples with anhydrite (CaSO/sub 4/) a common accessory. Minor or trace sylvite (KCl) and quartz (SiO/sub 2/) were detected in some sidewall samples. Other minor minerals found in drill cuttings included quartz; mixed carbonates of Fe, Ca and Mg; and several iron oxides. Possibly the carbonates are reaction products with the basic drilling mud or possibly pieces of caprock which contaminated the cuttings. The iron oxides were probably produced by corrosion of the drill stem or bit. Densities of several core samples were determined and insoluble residue was counted for radioactivity.

  12. Environmental control technology survey of selected US strip mining sites. Volume 2B. Alabama. Water quality impacts and overburden chemistry of Alabama study site

    SciTech Connect

    Henricks, J D; Bogner, J E; Olsen, R D; Schubert, J P; Sobek, A A; Johnson, D O

    1980-05-01

    As part of a program to examine the ability of existing control technologies to meet federal guidelines for the quality of aqueous effluents from coal mines, an intensive study of water, coal, and overburden chemistry was conducted at a surface coal mine in Alabama from May 1976 through July 1977. Sampling sites included the pit sump, a stream downgrade from the mine, the discharge from the water treatment facility, and a small stream outside the mine drainage. Water samples were collected every two weeks by Argonne subcontractors at the Alabama Geological Survey and analysed for the following parameters: specific conductance, pH, temperature, acidity, bicarbonate, carbonate, chloride, total dissolved solids, suspended solids, sulfate, and 20 metals. Analysis of the coal and overburden shows that no potential acid problem exists at this mine. Water quality is good in both streams sampled, and high levels of dissolved elements are found only in water collected from the pit sump. The mine effluent is in compliance with Office of Surface Mining water quality standards.

  13. Rat intestinal trehalase. Studies of the active site.

    PubMed

    Chen, C C; Guo, W J; Isselbacher, K J

    1987-11-01

    Rat intestinal trehalase was solubilized, purified and reconstituted into proteoliposomes. With octyl glucoside as the solubilizing detergent, the purified protein appeared as a single band on SDS/polyacrylamide-gel electrophoresis with an apparent molecular mass of 67 kDa. Kinetic studies indicated that the active site of this enzyme can be functionally divided into two adjacent regions, namely a binding site (with pKa 4.8) and a catalytic site (with pKa 7.2). Other findings suggested that the catalytic site contains a functional thiol group, which is sensitive to inhibition by N-ethylmaleimide, Hg2+ and iodoacetate. Substrate protection and iodoacetate labelling of the thiol group demonstrated that only a protein of 67 kDa was labelled. Furthermore, sucrose and phlorizin protected the thiol group, but Tris-like inhibitors did not. Structure-inhibition analysis of Tris-like inhibitors, the pH effect of Tris inhibition and Tris protection of 1-(3-dimethylaminopropyl)-3-ethylcarbodi-imide inactivation permitted characterization and location of a separate site containing a carboxy group for Tris binding, which may also be the binding region. On the basis of these findings, a possible structure for the active site of trehalase is proposed. PMID:3426558

  14. Active Site and Remote Contributions to Catalysis in Methylthioadenosine Nucleosidases

    PubMed Central

    Thomas, Keisha; Cameron, Scott A.; Almo, Steven C.; Burgos, Emmanuel S.; Gulab, Shivali A.; Schramm, Vern L.

    2015-01-01

    5′-Methylthioadenosine/S-adenosyl-L-homocysteine nucleosidases (MTANs) catalyze the hydrolysis of 5′-methylthioadenosine to adenine and 5-methylthioribose. The amino acid sequences of the MTANs from Vibrio cholerae (VcMTAN) and Escherichia coli (EcMTAN) are 60% identical and 75% similar. Protein structure folds and kinetic properties are similar. However, binding of transition-state analogues is dominated by favorable entropy in VcMTAN and by enthalpy in EcMTAN. Catalytic sites of VcMTAN and EcMTAN in contact with reactants differ by two residues; Ala113 and Val153 in VcMTAN are Pro113 and Ile152, respectively, in EcMTAN. We mutated the VcMTAN catalytic site residues to match those of EcMTAN in anticipation of altering its properties toward EcMTAN. Inhibition of VcMTAN by transition-state analogues required filling both active sites of the homodimer. However, in the Val153Ile mutant or double mutants, transition-state analogue binding at one site caused complete inhibition. Therefore, a single amino acid, Val153, alters the catalytic site cooperativity in VcMTAN. The transition-state analogue affinity and thermodynamics in mutant VcMTAN became even more unlike those of EcMTAN, the opposite of expectations from catalytic site similarity; thus, catalytic site contacts in VcMTAN are unable to recapitulate the properties of EcMTAN. X-ray crystal structures of EcMTAN, VcMTAN, and a multiple-site mutant of VcMTAN most closely resembling EcMTAN in catalytic site contacts show no major protein conformational differences. The overall protein architectures of these closely related proteins are implicated in contributing to the catalytic site differences. PMID:25806409

  15. Resonant active sites in catalytic ammonia synthesis: A structural model

    NASA Astrophysics Data System (ADS)

    Cholach, Alexander R.; Bryliakova, Anna A.; Matveev, Andrey V.; Bulgakov, Nikolai N.

    2016-03-01

    Adsorption sites Mn consisted of n adjacent atoms M, each bound to the adsorbed species, are considered within a realistic model. The sum of bonds Σ lost by atoms in a site in comparison with the bulk atoms was used for evaluation of the local surface imperfection, while the reaction enthalpy at that site was used as a measure of activity. The comparative study of Mn sites (n = 1-5) at basal planes of Pt, Rh, Ir, Fe, Re and Ru with respect to heat of N2 dissociative adsorption QN and heat of Nad + Had → NHad reaction QNH was performed using semi-empirical calculations. Linear QN(Σ) increase and QNH(Σ) decrease allowed to specify the resonant Σ for each surface in catalytic ammonia synthesis at equilibrium Nad coverage. Optimal Σ are realizable for Ru2, Re2 and Ir4 only, whereas other centers meet steric inhibition or unreal crystal structure. Relative activity of the most active sites in proportion 5.0 × 10- 5: 4.5 × 10- 3: 1: 2.5: 3.0: 1080: 2270 for a sequence of Pt4, Rh4, Fe4(fcc), Ir4, Fe2-5(bcc), Ru2, Re2, respectively, is in agreement with relevant experimental data. Similar approach can be applied to other adsorption or catalytic processes exhibiting structure sensitivity.

  16. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1980

    1980-01-01

    Describes equipment, activities, and experiments useful in chemistry instruction, including among others, a rapid method to determine available chlorine in bleach, simple flame testing apparatus, and a simple apparatus demonstrating the technique of flash photolysis. (SK)

  17. Nuclear Chemistry.

    ERIC Educational Resources Information Center

    Chemical and Engineering News, 1979

    1979-01-01

    Provides a brief review of the latest developments in nuclear chemistry. Nuclear research today is directed toward increased activity in radiopharmaceuticals and formation of new isotopes by high-energy, heavy-ion collisions. (Author/BB)

  18. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1981

    1981-01-01

    Describes 13 activities, experiments and demonstrations, including the preparation of iron (III) chloride, simple alpha-helix model, investigating camping gas, redox reactions of some organic compounds, a liquid crystal thermometer, and the oxidation number concept in organic chemistry. (JN)

  19. [Influences of uncommon isoenzymes on determination of alkaline phosphatase activity by dry-chemistry analyzers].

    PubMed

    Tozawa, T; Hashimoto, M

    2001-04-01

    Dry-chemistry(DC) analysis may be influenced by some matrix effects for measuring uncommon isoenzyme forms. Placental and intestinal alkaline phosphatase(AP) are overestimated by the VITROS DC, compared with results obtained with the wet-chemistry(WC) method of Bretaudiere, et al. using 2-amino-2-methyl-1-propanol (AMP) buffer, however, no such discrepancy between AP results in any DC method and that with a routine WC method recommended by Japanese Society of Clinical Chemistry in that 2-ethylaminoethanol(EAE) buffer is used, has been demonstrated. The type of buffer used affects differently the rates of AP isoenzymes activities. We therefore examined whether the presence of uncommon AP isoenzyme forms in serum caused aberrant DC results for AP in comparison with a routine WC method using EAE buffer. Here, serum samples with only liver AP and bone AP(n : 32); high-molecular-mass AP(n : 11); placental AP(n : 12); intestinal AP(n : 13) and immunoglobulin (Ig) bound AP(n : 12) were analyzed for total AP activity on three different DC analyzers: VITROS 700XR, FUJIDRYCHEM 5000, SPOTCHEM 4410 and a WC analyzer: HITACHI 7350. Values obtained in all of the DCs for sera containing only liver/bone AP agreed with those with the WC method. For sera containing placental AP, the VITROS values were higher than those with the WC method, while the FUJIDRYCHEM values and the SPOTCHEM values were lower. The VITROS values and the FUJIDRYCHEM values for sera containing intestinal AP were lower than those with the WC method, while the SPOTCHEM values were higher. All of the DCs did not affect high-molecular-mass AP and Ig bound liver/bone AP types of macro AP, but underestimated Ig bound intestinal type. Ig bound intestinal AP may be sieved by DC multilayer elements. PMID:11391954

  20. Water in the Active Site of Ketosteroid Isomerase

    PubMed Central

    Hanoian, Philip; Hammes-Schiffer, Sharon

    2011-01-01

    Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two waters in the Y16S mutant, one water in the Y16F and FFF mutants, and intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of 1H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less

  1. Energy transfer at the active sites of heme proteins

    SciTech Connect

    Dlott, D.D.; Hill, J.R.

    1995-12-31

    Experiments using a picosecond pump-probe apparatus at the Picosecond Free-electron Laser Center at Stanford University, were performed to investigate the relaxation of carbon monoxide bound to the active sites of heme proteins. The significance of these experiments is two-fold: (1) they provide detailed information about molecular dynamics occurring at the active sites of proteins; and (2) they provide insight into the nature of vibrational relaxation processes in condensed matter. Molecular engineering is used to construct various molecular systems which are studied with the FEL. We have studied native proteins, mainly myoglobin obtained from different species, mutant proteins produced by genetic engineering using recombinant DNA techniques, and a variety of model systems which mimic the structures of the active sites of native proteins, which are produced using molecular synthesis. Use of these different systems permits us to investigate how specific molecular structural changes affect dynamical processes occurring at the active sites. This research provides insight into the problems of how different species needs are fulfilled by heme proteins which have greatly different functionality, which is induced by rather small structural changes.

  2. Chemical Modification of Papain and Subtilisin: An Active Site Comparison

    ERIC Educational Resources Information Center

    St-Vincent, Mireille; Dickman, Michael

    2004-01-01

    An experiment using methyle methanethiosulfonate (MMTS) and phenylmethylsulfonyl flouride (PMSF) to specifically modify the cysteine and serine residues in the active sites of papain and subtilism respectively is demonstrated. The covalent modification of these enzymes and subsequent rescue of papain shows the beginning biochemist that proteins…

  3. Changes in active site histidine hydrogen bonding trigger cryptochrome activation.

    PubMed

    Ganguly, Abir; Manahan, Craig C; Top, Deniz; Yee, Estella F; Lin, Changfan; Young, Michael W; Thiel, Walter; Crane, Brian R

    2016-09-01

    Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions. PMID:27551082

  4. Current Challenges for Modeling Enzyme Active Sites by Biomimetic Synthetic Diiron Complexes

    PubMed Central

    Friedle, Simone; Reisner, Erwin; Lippard, Stephen J.

    2010-01-01

    This tutorial review describes recent progress in modeling the active sites of carboxylate-rich non-heme diiron enzymes that activate dioxygen to carry out several key reactions in nature. The chemistry of soluble methane monooxygenase, which catalyzes the selective oxidation of methane to methanol, is of particular interest for (bio)technological applications. Novel synthetic diiron complexes that mimic structural, and, to a lesser extent, functional features of these diiron enzymes are discussed. The chemistry of the enzymes is also briefly summarized. A particular focus of this review is on models that mimic characteristics of the diiron systems that were previously not emphasized, including systems that contain (i) aqua ligands, (ii) different substrates tethered to the ligand framework, (iii) dendrimers attached to carboxylates to mimic the protein environment, (iv) two N-donors in a syn-orientation with respect to the iron-iron vector, and (v) a N-rich ligand environment capable of accessing oxygenated high-valent diiron intermediates. PMID:20485834

  5. Effect of sampling site and collection method on variations in baseline clinical pathology parameters in Fischer-344 rats. 1. Clinical chemistry.

    PubMed

    Neptun, D A; Smith, C N; Irons, R D

    1985-12-01

    An analysis of the influence of blood sampling site and collection method on clinical chemistry parameters was conducted in male Fischer-344 rats. Sampling sites compared included the right ventricle, aorta, vena cava, retroorbital sinus, and tail. Methods of collection included Vacutainer (3 ml sample), syringe (exsanguination), and capillary tube. Nineteen frequently measured clinical chemistry procedures were determined, including serum enzymes, cholesterol, and triglycerides. Significant differences were noted for almost every parameter as a function of sampling site. Samples collected from the right ventricle with a Vacutainer produced the most representative results for most but not all procedures when compared to the overall mean (for all methods). The largest differences were encountered in samples obtained from tail and retroorbital plexus. Exanguination also resulted in significant differences for some parameters when compared to smaller sample volumes obtained from the same site. It was concluded that sampling site and collection method can be a major source of variation in clinical chemistry measurements, and in selection of an appropriate method, one should consider which parameters are likely to be of major interest. PMID:4092880

  6. pH at the Air-Ice Interface: Connections to Halogen Activation Chemistry

    NASA Astrophysics Data System (ADS)

    Wren, S. N.; Abbatt, J.; Donaldson, D. J.

    2014-12-01

    Halogen activation - the conversion of relatively inert sea-salt derived halides, into reactive halogen species - has significant implications for perturbing the oxidative capacity of the boundary layer, as well as for mercury oxidation. Developing a good, mechanistic understanding of halogen activation chemistry - and particularly its pH dependence - requires knowledge of surface pH. Here we described the development and use of a surface-sensitive spectroscopic approach to investigate pH at frozen surfaces. The approach, which involves glancing-angle laser-induced fluorescence in conjunction with pH-sensitive fluorescent dyes (acridine and harmine), was used to study pH at frozen surfaces following the deposition of gas phase acids or bases. We demonstrate that frozen 'pure water' and frozen 'salt water' surfaces exhibit different responses. The responses are consistent with the presence of a chemically unique, disordered region at the frozen 'pure water' surface and the presence of liquid brine at the frozen 'salt water' surface. Significantly, we show that a frozen sea water surface is resistant to changes in pH, suggesting that some buffering capacity is maintained upon freezing. Finally the pH dependence of bromine and chlorine activation from artificial saline snow is presented. Bromine release is found to depend less strongly on pre-freezing snow pH, but the release of both species is favoured for low pre-freezing pH values. In the context of these pH and halogen activation studies, the potential importance of various frozen sea ice substrates for promoting halogen activation chemistry will be discussed.

  7. Active sites environmental monitoring program. Annual report FY 1992

    SciTech Connect

    Morrissey, C.M.; Ashwood, T.L.; Hicks, D.S.

    1994-04-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) at ORNL from October 1991 through September 1992. Solid Waste Operations and the Environmental Sciences Division established ASEMP in 1989 to provide early detection and performance monitoring at active low-level waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by Chapter 2 and 3 of US Department of Energy Order 5820.2A. The Interim Waste Management Facility (IWMF) began operation in December 1991. Monitoring results from the tumulus and IWMF disposal pads continue to indicate that no LLW is leaching from the storage vaults. Storm water falling on the IWMF active pad was collected and transported to the Process Waste Treatment Plant while operators awaited approval of the National Pollutant Discharge Elimination System (NPDES) permit. Several of the recent samples collected from the active IWMF pad had pH levels above the NPDES limit of 9.0 because of alkali leached from the concrete. The increase in gross beta activity has been slight; only 1 of the 21 samples collected contained activity above the 5.0 Bq/L action level. Automated sample-collection and flow-measurement equipment has been installed at IWMF and is being tested. The flume designed to electronically measure flow from the IWMF pads and underpads is too large to be of practical value for measuring most flows at this site. Modification of this system will be necessary. A CO{sub 2} bubbler system designed to reduce the pH of water from the pads is being tested at IWMF.

  8. The Active Site of Oligogalacturonate Lyase Provides Unique Insights into Cytoplasmic Oligogalacturonate β-Elimination*

    PubMed Central

    Abbott, D. Wade; Gilbert, Harry J.; Boraston, Alisdair B.

    2010-01-01

    Oligogalacturonate lyases (OGLs; now also classified as pectate lyase family 22) are cytoplasmic enzymes found in pectinolytic members of Enterobacteriaceae, such as the enteropathogen Yersinia enterocolitica. OGLs utilize a β-elimination mechanism to preferentially catalyze the conversion of saturated and unsaturated digalacturonate into monogalacturonate and the 4,5-unsaturated monogalacturonate-like molecule, 5-keto-4-deoxyuronate. To provide mechanistic insights into the specificity of this enzyme activity, we have characterized the OGL from Y. enterocolitica, YeOGL, on oligogalacturonides and determined its three-dimensional x-ray structure to 1.65 Å. The model contains a Mn2+ atom in the active site, which is coordinated by three histidines, one glutamine, and an acetate ion. The acetate mimics the binding of the uronate group of galactourono-configured substrates. These findings, in combination with enzyme kinetics and metal supplementation assays, provide a framework for modeling the active site architecture of OGL. This enzyme appears to contain a histidine for the abstraction of the α-proton in the −1 subsite, a residue that is highly conserved throughout the OGL family and represents a unique catalytic base among pectic active lyases. In addition, we present a hypothesis for an emerging relationship observed between the cellular distribution of pectate lyase folding and the distinct metal coordination chemistries of pectate lyases. PMID:20851883

  9. Active Learning and Cooperative Learning in the Organic Chemistry Lecture Class

    NASA Astrophysics Data System (ADS)

    Paulson, Donald R.

    1999-08-01

    Faculty in the physical sciences are one of the academic groups least receptive to the use of active learning strategies and cooperative learning in their classrooms. This is particularly so in traditional lecture classes. It is the objective of this paper to show how effective these techniques can be in improving student performance in classes. The use of active learning strategies and cooperative learning groups in my organic chemistry lecture classes has increased the overall pass rate in my classes by an astounding 20-30% over the traditional lecture mode. This has been accomplished without any reduction in "standards". The actual methods employed are presented as well as a discussion of how I came to radically change the way I teach my classes.

  10. Microtopographic and depth controls on active layer chemistry in Arctic polygonal ground

    SciTech Connect

    Newman, Brent D.; Throckmorton, Heather M.; Graham, David E.; Gu, Baohua; Hubbard, Susan S.; Liang, Liyuan; Wu, Yuxin; Heikoop, J. M.; Herndon, Elizabeth M.; Phelps, Tommy J.; Wilson, Cathy; Wullschleger, Stan D.

    2015-03-24

    Polygonal ground is a signature characteristic of Arctic lowlands, and carbon release from permafrost thaw can alter feedbacks to Arctic ecosystems and climate. This study describes the first comprehensive spatial examination of active layer biogeochemistry that extends across high- and low-centered, ice wedge polygons, their features, and with depth. Water chemistry measurements of 54 analytes were made on surface and active layer pore waters collected near Barrow, Alaska, USA. Significant differences were observed between high- and low-centered polygons suggesting that polygon types may be useful for landscape-scale geochemical classification. However, differences were found for polygon features (centers and troughs) for analytes that were not significant for polygon type, suggesting that finer-scale features affect biogeochemistry differently from polygon types. Depth variations were also significant, demonstrating important multidimensional aspects of polygonal ground biogeochemistry. These results have major implications for understanding how polygonal ground ecosystems function, and how they may respond to future change.

  11. Microtopographic and depth controls on active layer chemistry in Arctic polygonal ground

    NASA Astrophysics Data System (ADS)

    Newman, B. D.; Throckmorton, H. M.; Graham, D. E.; Gu, B.; Hubbard, S. S.; Liang, L.; Wu, Y.; Heikoop, J. M.; Herndon, E. M.; Phelps, T. J.; Wilson, C. J.; Wullschleger, S. D.

    2015-03-01

    Polygonal ground is a signature characteristic of Arctic lowlands, and carbon release from permafrost thaw can alter feedbacks to Arctic ecosystems and climate. This study describes the first comprehensive spatial examination of active layer biogeochemistry that extends across high- and low-centered, ice wedge polygons, their features, and with depth. Water chemistry measurements of 54 analytes were made on surface and active layer pore waters collected near Barrow, Alaska, USA. Significant differences were observed between high- and low-centered polygons suggesting that polygon types may be useful for landscape-scale geochemical classification. However, differences were found for polygon features (centers and troughs) for analytes that were not significant for polygon type, suggesting that finer-scale features affect biogeochemistry differently from polygon types. Depth variations were also significant, demonstrating important multidimensional aspects of polygonal ground biogeochemistry. These results have major implications for understanding how polygonal ground ecosystems function, and how they may respond to future change.

  12. Support chemistry, surface area, and preparation effects on sulfided NiMo catalyst activity

    SciTech Connect

    Gardner, T.J.; McLaughlin, L.I.; Sandoval, R.S.

    1996-06-01

    Hydrous Metal Oxides (HMOs) are chemically synthesized materials which contain a homogeneous distribution of ion exchangeable alkali cations that provide charge compensation to the metal-oxygen framework. In terms of the major types of inorganic ion exchangers defined by Clearfield, these amorphous HMO materials are similar to both hydrous oxides and layered oxide ion exchangers (e.g., alkali metal titanates). For catalyst applications, the HMO material serves as an ion exchangeable support which facilitates the uniform incorporation of catalyst precursor species. Following catalyst precursor incorporation, an activation step is required to convert the catalyst precursor to the desired active phase. Considerable process development activities at Sandia National Laboratories related to HMO materials have resulted in bulk hydrous titanium oxide (HTO)- and silica-doped hydrous titanium oxide (HTO:Si)-supported NiMo catalysts that are more active in model reactions which simulate direct coal liquefaction (e.g., pyrene hydrogenation) than commercial {gamma}-Al{sub 2}O{sub 3}-supported NiMo catalysts. However, a fundamental explanation does not exist for the enhanced activity of these novel catalyst materials; possible reasons include fundamental differences in support chemistry relative to commercial oxides, high surface area, or catalyst preparation effects (ion exchange vs. incipient wetness impregnation techniques). The goals of this paper are to identify the key factors which control sulfided NiMo catalyst activity, including those characteristics of HTO- and HTO:Si-supported NiMo catalysts which uniquely set them apart from conventional oxide supports.

  13. Pore-fluid chemistry along the main axis of an active lobe at the Congo deep-sea fan

    NASA Astrophysics Data System (ADS)

    Croguennec, C.; Ruffine, L.; Guyader, V.; Le Bruchec, J.; Ruesch, B.; Caprais, J.; Cathalot, C.; de Prunelé, A.; Germain, Y.; Bollinger, C.; Dennielou, B.; Olu, K.; Rabouille, C.

    2013-12-01

    The distal lobes of the Congo deep-sea fan constitute a unique in situ laboratory to study early diagenesis of marine sediments. They are located at water depth of about 5000 m and result from the deposition of sediment transported by turbidity currents along the channel-levee systems and submarine canyon connected to the Congo River. Thus, a huge amount of organic matter, transported from the river to the lobes, undergoes decomposition processes involving different oxidants present within the sedimentary column. This drastically changes the chemistry of the pore fluids, allowing the occurence of a succession of biogeochemical processes. The present study is part of an ongoing project which aims at better understanding the role and the fate of organic matter transported to the lobe systems, as well as its implication in the distribution of the living communities encountered there. Thus, pore fluids have been sampled from 8 Calypso cores in order to determine the concentration of dissolved elements. Five sites have been investigated: four of them are located along the main axis of a currently active lobe, the last one being located on a lobe disconnected from the chenals. The analyses of methane, major (Cl, SO4, Mg, Ca, K, Na) and minor (Sr, Ba, B, Li, Mn) elements have been carried out along with total alkalinity determination. The resulting profiles show a highly heterogeneous pore-fluid chemistry. Sulphate concentration near the seawater/sediment interface varies from 3 to 29 mM, indicating intense sulphate reduction. Surprisingly the lowest values are found at the site which is disconnected from the active lobe. The manganese cycle is well defined for all cores. The core recovered at the more distal lobe exhibits very peculiar pore-fluid profiles which are likely related to a geological event, most likely sediment slide and remobilization. References: Babonneau, N., Savoye, B., Cremer, M. & Klein, B., 2002. Morphology and architecture of the present canyon and

  14. Active-Site-Accessible, Porphyrinic Metal;#8722;Organic Framework Materials

    SciTech Connect

    Farha, Omar K.; Shultz, Abraham M.; Sarjeant, Amy A.; Nguyen, SonBinh T.; Hupp, Joseph T.

    2012-02-06

    On account of their structural similarity to cofactors found in many metallo-enzymes, metalloporphyrins are obvious potential building blocks for catalytically active, metal-organic framework (MOF) materials. While numerous porphyrin-based MOFs have already been described, versions featuring highly accessible active sites and permanent microporosity are remarkably scarce. Indeed, of the more than 70 previously reported porphyrinic MOFs, only one has been shown to be both permanently microporous and contain internally accessible active sites for chemical catalysis. Attempts to generalize the design approach used in this single successful case have failed. Reported here, however, is the synthesis of an extended family of MOFs that directly incorporate a variety of metalloporphyrins (specifically Al{sup 3+}, Zn{sup 2+}, Pd{sup 2+}, Mn{sup 3+}, and Fe{sup 3+} complexes). These robust porphyrinic materials (RPMs) feature large channels and readily accessible active sites. As an illustrative example, one of the manganese-containing RPMs is shown to be catalytically competent for the oxidation of alkenes and alkanes.

  15. Nest predation increases with parental activity: Separating nest site and parental activity effects

    USGS Publications Warehouse

    Martin, T.E.; Scott, J.; Menge, C.

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection.

  16. Nest predation increases with parental activity: separating nest site and parental activity effects.

    PubMed Central

    Martin, T E; Scott, J; Menge, C

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection. PMID:11413645

  17. Oxidation of activated carbon fibers: Effect on pore size, surface chemistry, and adsorption properties

    SciTech Connect

    Mangun, C.L.; Benak, K.R.; Daley, M.A.; Economy, J.

    1999-12-01

    Activated carbon fibers (ACFs) were oxidized using both aqueous and nonaqueous treatments. As much as 29 wt% oxygen can be incorporated onto the pore surface in the form of phenolic hydroxyl, quinine, and carboxylic acid groups. The effect of oxidation on the pore size, pore volume, and the pore surface chemistry was thoroughly examined. The average micropore size is typically affected very little by aqueous oxidation while the micropore volume and surface area decreases with such a treatment. In contrast, the micropore size and micropore volume both increase with oxidation in air. Oxidation of the fibers produces surface chemistries in the pore that provide for enhanced adsorption of basic (ammonia) and polar (acetone) molecules at ambient and nonambient temperatures. The adsorption capacity of the oxidized fibers for acetone is modestly better than the untreated ACFs while the adsorption capacity for ammonia can increase up to 30 times compared to untreated ACFs. The pore surface chemical makeup was analyzed using elemental analysis, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), and X-ray photoelectron spectroscopy (XPS).

  18. Hydrothermal activity in the Lau back-arc basin: Sulfides and water chemistry

    SciTech Connect

    Fouquet, Y.; Charlou, J.L.; Donval, J.P.; Foucher, J.P. ); von Stackelberg, U.; Wiedicke, M. ); Erzinger, J. ); Herzig, P. ); Muhe, R. ); Soakai, S. ); Whitechurch, H. )

    1991-04-01

    The submersible Nautile completed 22 dives during the Nautilau cruise (R/V Nadir, April 17-May 10, 1989) for a detailed investigation of the southern Lau basin near Tonga. The objective of the scientific team from France, Germany, and Tonga was to understand the process of sea-floor ore formation associated with hydrothermal circulation along the Valu Fa back-arc ridge behind the Tonga-Kermadec trench. The four diving areas, between lat21{degree}25'S and 22{degree}40'S in water{approximately}2000 m deep, were selected on the basis of results from cruises of the R/V Jean Charcot and R/V Sonne. The Nadir cruise provided proof of hydrothermal activity-in all for areas, over more than 100 km-as indicated by the widespread occurence of hydrothermal deposits and by heat flow, conductivity, and temperature measurements near the sea bottom. The most spectacular findings were high-temperature white and black smokers and associated fauna and ore deposits. Hydrothermal water chemistry and sulfide composition data presented here indicate that this hydrothermal field is very different from the hydrothermal fields in oceanic ridges. This difference is seen in water chemistry of the hydrothermal fluid (pH=2 and high metal content) and the chemical composition of sulfides (enrichment in Ba, As, and Pb).

  19. Identification of Ice Nucleation Active Sites on Silicate Dust Particles

    NASA Astrophysics Data System (ADS)

    Zolles, Tobias; Burkart, Julia; Häusler, Thomas; Pummer, Bernhard; Hitzenberger, Regina; Grothe, Hinrich

    2015-04-01

    Mineral dusts originating from Earth's crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts [1-3]. Nevertheless, among those structures K-feldspar showed by far the highest ice nucleation activity. In this study, the reasons for its activity and the difference in the activity of the different feldspars were investigated in closer details. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. We give a potential explanation of the increased ice nucleation activity of K-feldspar. The ice nucleating sites are very much dependent on the alkali ion present by altering the water structure and the feldspar surface. The higher activity of K-feldspar can be attributed to the presence of potassium ions on the surface and surface bilayer. The alkali-ions have different hydration shells and thus an influence on the ice nucleation activity of feldspar. Chaotropic behavior of Calcium and Sodium ions are lowering the ice nucleation potential of the other feldspars, while kosmotropic Potassium has a neutral or even positive effect. Furthermore we investigated the influence of milling onto the ice nucleation of quartz particles. The ice nucleation activity can be increased by mechanical milling, by introducing more molecular, nucleation active defects to the particle surface. This effect is larger than expected by plane surface increase. [1] Atkinson et al. The Importance of Feldspar for Ice Nucleation by Mineral Dust in Mixed-Phase Clouds. Nature 2013, 498, 355-358. [2] Yakobi-Hancock et al.. Feldspar Minerals as Efficient Deposition Ice Nuclei. Atmos. Chem. Phys. 2013, 13, 11175-11185. [3] Zolles et al. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles. J. Phys. Chem. A 2015 accepted.

  20. Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

    PubMed Central

    Mukherjee, Shinjini; Juottonen, Heli; Siivonen, Pauli; Lloret Quesada, Cosme; Tuomi, Pirjo; Pulkkinen, Pertti; Yrjälä, Kim

    2014-01-01

    Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites. PMID:25105905

  1. Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site.

    PubMed

    Mukherjee, Shinjini; Juottonen, Heli; Siivonen, Pauli; Lloret Quesada, Cosme; Tuomi, Pirjo; Pulkkinen, Pertti; Yrjälä, Kim

    2014-10-01

    Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites. PMID:25105905

  2. Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing.

    PubMed

    Kelly, L C; Colin, Y; Turpault, M-P; Uroz, S

    2016-08-01

    Understanding how minerals affect bacterial communities and their in situ activities in relation to environmental conditions are central issues in soil microbial ecology, as minerals represent essential reservoirs of inorganic nutrients for the biosphere. To determine the impact of mineral type and solution chemistry on soil bacterial communities, we compared the diversity, composition, and functional abilities of a soil bacterial community incubated in presence/absence of different mineral types (apatite, biotite, obsidian). Microcosms were prepared containing different liquid culture media devoid of particular essential nutrients, the nutrients provided only in the introduced minerals and therefore only available to the microbial community through mineral dissolution by biotic and/or abiotic processes. By combining functional screening of bacterial isolates and community analysis by bromodeoxyuridine DNA immunocapture and 16S rRNA gene pyrosequencing, we demonstrated that bacterial communities were mainly impacted by the solution chemistry at the taxonomic level and by the mineral type at the functional level. Metabolically active bacterial communities varied with solution chemistry and mineral type. Burkholderia were significantly enriched in the obsidian treatment compared to the biotite treatment and were the most effective isolates at solubilizing phosphorous or mobilizing iron, in all the treatments. A detailed analysis revealed that the 16S rRNA gene sequences of the OTUs or isolated strains assigned as Burkholderia in our study showed high homology with effective mineral-weathering bacteria previously recovered from the same experimental site. PMID:27138048

  3. Osteoinductive activity of insulin-functionalized cell culture surfaces obtained using diazonium chemistry

    NASA Astrophysics Data System (ADS)

    Mikulska, Anna; Filipowska, Joanna; Osyczka, Anna; Nowakowska, Maria; Szczubiałka, Krzysztof

    2014-12-01

    Polymeric surfaces suitable for cell culture (DR/Pec) were constructed from diazoresin (DR) and pectin (Pec) in a form of ultrathin films using the layer-by-layer (LbL) technique. The surfaces were functionalized with insulin using diazonium chemistry. Such functionalized surfaces were used to culture human mesenchymal stem cells (hMSCs) to assess their suitability for bone tissue engineering and regeneration. The activity of insulin immobilized on the surfaces (DR/Pec/Ins) was compared to that of insulin dissolved in the culture medium. Human MSC grown on insulin-immobilized DR/Pec surfaces displayed increased proliferation and higher osteogenic activity. The latter was determined by means of alkaline phosphatase (ALP) activity, which increases at early stages of osteoblasts differentiation. Insulin dissolved in the culture medium did not stimulate cell proliferation and its osteogenic activity was significantly lower. Addition of recombinant human bone morphogenetic protein 2 (rhBMP-2) to the culture medium further increased ALP activity in hMSCs indicating additive osteogenic action of immobilized insulin and rhBMP-2

  4. Osteoinductive activity of insulin-functionalized cell culture surfaces obtained using diazonium chemistry

    PubMed Central

    Mikulska, Anna; Filipowska, Joanna; Osyczka, Anna M.; Nowakowska, Maria; Szczubiałka, Krzysztof

    2015-01-01

    Polymeric surfaces suitable for cell culture (DR/Pec) were constructed from diazoresin (DR) and pectin (Pec) in a form of ultrathin films using the layer-by-layer (LbL) technique. The surfaces were functionalized with insulin using diazonium chemistry. Such functionalized surfaces were used to culture human mesenchymal stem cells (hMSCs) to assess their suitability for bone tissue engineering and regeneration. The activity of insulin immobilized on the surfaces (DR/Pec/Ins) was compared to that of insulin dissolved in the culture medium. Human MSC grown on insulin-immobilized DR/Pec surfaces displayed increased proliferation and higher osteogenic activity. The latter was determined by means of alkaline phosphatase (ALP) activity, which increases at early stages of osteoblasts differentiation. Insulin dissolved in the culture medium did not stimulate cell proliferation and its osteogenic activity was significantly lower. Addition of recombinant human bone morphogenetic protein 2 (rhBMP-2) to the culture medium further increased ALP activity in hMSCs indicating additive osteogenic action of immobilized insulin and rhBMP-2. PMID:25629028

  5. Enzymatically Active Microgels from Self-Assembling Protein Nanofibrils for Microflow Chemistry

    PubMed Central

    2015-01-01

    Amyloid fibrils represent a generic class of protein structure associated with both pathological states and with naturally occurring functional materials. This class of protein nanostructure has recently also emerged as an excellent foundation for sophisticated functional biocompatible materials including scaffolds and carriers for biologically active molecules. Protein-based materials offer the potential advantage that additional functions can be directly incorporated via gene fusion producing a single chimeric polypeptide that will both self-assemble and display the desired activity. To succeed, a chimeric protein system must self-assemble without the need for harsh triggering conditions which would damage the appended functional protein molecule. However, the micrometer to nanoscale patterning and morphological control of protein-based nanomaterials has remained challenging. This study demonstrates a general approach for overcoming these limitations through the microfluidic generation of enzymatically active microgels that are stabilized by amyloid nanofibrils. The use of scaffolds formed from biomaterials that self-assemble under mild conditions enables the formation of catalytic microgels while maintaining the integrity of the encapsulated enzyme. The enzymatically active microgel particles show robust material properties and their porous architecture allows diffusion in and out of reactants and products. In combination with microfluidic droplet trapping approaches, enzymatically active microgels illustrate the potential of self-assembling materials for enzyme immobilization and recycling, and for biological flow-chemistry. These design principles can be adopted to create countless other bioactive amyloid-based materials with diverse functions. PMID:26030507

  6. Circumstellar chemistry

    NASA Technical Reports Server (NTRS)

    Glassgold, Alfred E.; Huggins, Patrick J.

    1987-01-01

    The study of the outer envelopes of cool evolved stars has become an active area of research. The physical properties of CS envelopes are presented. Observations of many wavelengths bands are relevant. A summary of observations and a discussion of theoretical considerations concerning the chemistry are summarized. Recent theoretical considerations show that the thermal equilibrium model is of limited use for understanding the chemistry of the outer CS envelopes. The theoretical modeling of the chemistry of CS envelopes provides a quantitive test of chemical concepts which have a broader interest than the envelopes themselves.

  7. Effects of low-level radioactive-waste disposal on water chemistry in the unsaturated zone at a site near Sheffield, Illinois, 1982-84

    USGS Publications Warehouse

    Peters, C.A.; Striegl, R.G.; Mills, P.C.; Healy, R.W.

    1992-01-01

    A 1982-84 field study defined the chemistry of water collected from the unsaturated zone at a low-level radioactive-waste disposal site near Sheffield, Bureau County, Ill. Chemical data were evaluated to determine the principal, naturally occurring geochemical reactions in the unsaturated zone and to evaluate waste-induced effects on pore-water chemistry. Samples of precipitation, unsaturated-zone pore water, and saturated-zone water were analyzed for specific conductance, pH, alkalinity, major cations and anions, dissolved organic carbon, gross alpha and beta radiation, and tritium. Little change in concentration of most major constituents in the unsaturated-zone water was observed with respect to depth or distance from disposal trenches. Tritium and dissolved organic carbon concentrations were, however, dependent on proximity to trenches. The primary reactions, both on-site and off-site, were carbonate and clay dissolution, cation exchange, and the oxidation of pyrite. The major difference between on-site and off-site inorganic water chemistry resulted from the removal of the Roxana Silt and the Radnor Till Member of the Glasford Formation from on-site. Off-site, the Roxana Silt contributed substantial quantities of sodium to solution from montmorillonite dissolution and associated cation-exchange reactions. The Radnor Till Member provided exchange surfaces for magnesium. Precipitation at the site had an ionic composition of calcium zinc sulfate and an average pH of 4.6. Within 0.3 meter of the land surface, infiltrating rainwater or snowmelt changed to an ionic composition of calcium sulfate off-site and calcium bicarbonate on-site and had an average pH of 7.9; below that depth, pH averaged 7.5 and the ionic composition generally was calcium magnesium bicarbonate. Alkalinity and specific conductance differed primarily according to composition of geologic materials. Tritium concentrations ranged from 0.2 (detection limit) to 1,380 nanocuries per liter. The

  8. Effects of low-level radioactive-waste disposal on water chemistry in the unsaturated zone at a site near Sheffield, Illinois, 1982-84

    USGS Publications Warehouse

    Peters, C.A.; Striegl, R.G.; Mills, P.C.; Healy, R.W.

    1992-01-01

    A 1982-84 field study defined the chemistry of water collected from the unsaturated zone at a low-level radioactive-waste disposal site near Sheffield, Bureau County, Illinois. Chemical data were evaluated to determine the principal naturally occurring geochemical reactions in the unsaturated zone and to evaluate waste-induced effects on pore-water chemistry. Samples of precipitation, unsaturated-zone pore water, and saturated-zone water were analyzed for specific conductance, pH, alkalinity, major cations and anions, dissolved organic carbon, gross alpha and beta radiation, and tritium. Little change in concentration of most major constituents in the unsaturated-zone water was observed with respect to depth or distance from disposal trenches. Tritium and dissolved organic carbon concentrations were, however, dependent on proximity to trenches. The primary reactions, both on- site and off-site, were carbonate and clay dissolution, cation exchange, and the oxidation of pyrite. The major difference between on-site and off-site inorganic water chemistry resulted from the removal of the Roxana Silt and the Radnor Till Member of the Glasford Formation from on-site. Off-site, the Roxana Silt contributed substantial quantities of sodium to solution from montmorillonite dissolution and associated cation-exchange reactions. The Radnor Till Member provided exchange surfaces for magnesium. Precipitation at the site had an ionic composition of calcium zinc sulfate and an average pH of 4.6. Within 0.3 meter of the land surface, infiltrating rain water or snowmelt changed to an ionic canposition of calcium sulfate off-site and calcium bicarbonate on-site and had an average pH of 7.9; below that depth, pH averaged 7.5 and the ionic composition generally was calcium magnesium bicarbonate. Alkalinity and specific conductance differed primarily according to composition of geologic materials. Tritium concentrations ranged from 0.2 (detection limit) to 1,380 nanocuries per liter. The

  9. Active Sites Environmental Monitoring Program. FY 1993: Annual report

    SciTech Connect

    Morrissey, C.M.; Ashwood, T.L.; Hicks, D.S.; Marsh, J.D.

    1994-08-01

    This report continues a series of annual and semiannual reports that present the results of the Active Sites Environmental Monitoring Program (ASEMP) monitoring activities. The report details monitoring data for fiscal year (FY) 1993 and is divided into three major areas: SWSA 6 [including tumulus pads, Interim Waste Management Facility (IWMF), and other sites], the low-level Liquid-Waste Solidification Project (LWSP), and TRU-waste storage facilities in SWSA 5 N. The detailed monitoring methodology is described in the second revision of the ASEMP program plan. This report also presents a summary of the methodology used to gather data for each major area along with the results obtained during FY 1993.

  10. Active sites in char gasification: Final technical report

    SciTech Connect

    Wojtowicz, M.; Lilly, W.D.; Perkins, M.T.; Hradil, G.; Calo, J.M.; Suuberg, E.M.

    1987-09-01

    Among the key variables in the design of gasifiers and combustors is the reactivity of the chars which must be gasified or combusted. Significant loss of unburned char is unacceptable in virtually any process; the provision of sufficient residence time for complete conversion is essential. A very wide range of reactivities are observed, depending upon the nature of the char in a process. The current work focuses on furthering the understanding of gasification reactivities of chars. It has been well established that the reactivity of char to gasification generally depends upon three principal factors: (1) the concentration of ''active sites'' in the char; (2) mass transfer within the char; and (3) the type and concentration of catalytic impurities in the char. The present study primarily addresses the first factor. The subject of this research is the origin, nature, and fate of active sites in chars derived from parent hydrocarbons with coal-like structure. The nature and number of the active sites and their reactivity towards oxygen are examined in ''model'' chars derived from phenol-formaldehyde type resins. How the active sites are lost by the process of thermal annealing during heat treatment of chars are studied, and actual rate for the annealing process is derived. Since intrinsic char reactivities are of primary interest in the present study, a fair amount of attention was given to the model char synthesis and handling so that the effect of catalytic impurities and oxygen-containing functional groups in the chemical structure of the material were minimized, if not completely eliminated. The project would not be considered complete without comparing characteristic features of synthetic chars with kinetic behavior exhibited by natural chars, including coal chars.

  11. Potential sites of CFTR activation by tyrosine kinases.

    PubMed

    Billet, Arnaud; Jia, Yanlin; Jensen, Timothy J; Hou, Yue-Xian; Chang, Xiu-Bao; Riordan, John R; Hanrahan, John W

    2016-05-01

    The CFTR chloride channel is tightly regulated by phosphorylation at multiple serine residues. Recently it has been proposed that its activity is also regulated by tyrosine kinases, however the tyrosine phosphorylation sites remain to be identified. In this study we examined 2 candidate tyrosine residues near the boundary between the first nucleotide binding domain and the R domain, a region which is important for channel function but devoid of PKA consensus sequences. Mutating tyrosines at positions 625 and 627 dramatically reduced responses to Src or Pyk2 without altering the activation by PKA, suggesting they may contribute to CFTR regulation. PMID:26645934

  12. Brownian aggregation rate of colloid particles with several active sites

    SciTech Connect

    Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V.; Polshchitsin, Alexey A.; Yakovleva, Galina E.; Maltsev, Valeri P.

    2014-08-14

    We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shown to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure.

  13. Stratospheric chemistry

    SciTech Connect

    Brune, W.H. )

    1991-01-01

    Advances in stratospheric chemistry made by investigators in the United States from 1987 to 1990 are reviewed. Subject areas under consideration include photochemistry of the polar stratosphere, photochemistry of the global stratosphere, and assessments of inadvertent modification of the stratosphere by anthropogenic activity. Particular attention is given to early observations and theories, gas phase chemistry, Antarctic observations, Arctic observations, odd-oxygen, odd-hydrogen, odd-nitrogen, halogens, aerosols, modeling of stratospheric ozone, and reactive nitrogen effects.

  14. Hydrogeologic properties and ground-water chemistry of the Rattlesnake Ridge interbed at well 699-25-80 (DB-14) Hanford Site

    SciTech Connect

    Spane, F.A. Jr.; Howland, M.D.; Strait, S.R.

    1980-11-01

    Offsite migration studies were conducted to characterize the hydraulic properties and groundwater chemistry of confined aquifer systems within the Hanford Site. These studies support the recommendations in ERDA-1538 to provide input for hydrologic modeling of groundwater flow within the Hanford Site, to afford information concerning possible contamination of underlying confined aquifer systems and to make the results available to the public. This report presents analytical results and aquifer test procedures used in characterizing the Rattlesnake Ridge interbed at well 699-25-80. The overall close association in groundwater chemistries and presence of elevated nitrate levels suggest that the Rattlesnake Ridge interbed may be locally in communication with the overlying unconfined aquifer system. Other physical evidence which indicates a potential local communication with the unconfined aquifer system includes: favorable stratigraphic position; absence of the confining Elephant Mountain basalt in surrounding areas; and intersection of a recharge boundary during aquifer tests of well 699-25-80.

  15. Viscoelasticity of living materials: mechanics and chemistry of muscle as an active macromolecular system.

    PubMed

    Qian, Hong

    2008-06-01

    At the molecular and cellular level, mechanics and chemistry are two aspects of the same macromolecular system. We present a bottom-up approach to such systems based on Kramers' diffusion theory of chemical reactions, the theory of polymer dynamics, and the recently developed models for molecular motors. Using muscle as an example, we develop a viscoelastic theory of muscle in terms of an simple equation for single motor protein movement. Both A.V. Hill's contractile component and A.F. Huxley's equation of sliding-filament motion are shown to be special cases of the general viscoelastic theory of the active material. Some disparity between the mechanical and the chemical views of cross-bridges and motor proteins are noted, and a duality between force and energy in discrete states and transitions of macromolecular systems is discussed. PMID:18589499

  16. Discovery and Characterization of Non-ATP Site Inhibitors of the Mitogen Activated Protein (MAP) Kinases

    SciTech Connect

    Comess, Kenneth M.; Sun, Chaohong; Abad-Zapatero, Cele; Goedken, Eric R.; Gum, Rebecca J.; Borhani, David W.; Argiriadi, Maria; Groebe, Duncan R.; Jia, Yong; Clampit, Jill E.; Haasch, Deanna L.; Smith, Harriet T.; Wang, Sanyi; Song, Danying; Coen, Michael L.; Cloutier, Timothy E.; Tang, Hua; Cheng, Xueheng; Quinn, Christopher; Liu, Bo; Xin, Zhili; Liu, Gang; Fry, Elizabeth H.; Stoll, Vincent; Ng, Teresa I.; Banach, David; Marcotte, Doug; Burns, David J.; Calderwood, David J.; Hajduk, Philip J.

    2012-03-02

    Inhibition of protein kinases has validated therapeutic utility for cancer, with at least seven kinase inhibitor drugs on the market. Protein kinase inhibition also has significant potential for a variety of other diseases, including diabetes, pain, cognition, and chronic inflammatory and immunologic diseases. However, as the vast majority of current approaches to kinase inhibition target the highly conserved ATP-binding site, the use of kinase inhibitors in treating nononcology diseases may require great selectivity for the target kinase. As protein kinases are signal transducers that are involved in binding to a variety of other proteins, targeting alternative, less conserved sites on the protein may provide an avenue for greater selectivity. Here we report an affinity-based, high-throughput screening technique that allows nonbiased interrogation of small molecule libraries for binding to all exposed sites on a protein surface. This approach was used to screen both the c-Jun N-terminal protein kinase Jnk-1 (involved in insulin signaling) and p38{alpha} (involved in the formation of TNF{alpha} and other cytokines). In addition to canonical ATP-site ligands, compounds were identified that bind to novel allosteric sites. The nature, biological relevance, and mode of binding of these ligands were extensively characterized using two-dimensional {sup 1}H/{sup 13}C NMR spectroscopy, protein X-ray crystallography, surface plasmon resonance, and direct enzymatic activity and activation cascade assays. Jnk-1 and p38{alpha} both belong to the MAP kinase family, and the allosteric ligands for both targets bind similarly on a ledge of the protein surface exposed by the MAP insertion present in the CMGC family of protein kinases and distant from the active site. Medicinal chemistry studies resulted in an improved Jnk-1 ligand able to increase adiponectin secretion in human adipocytes and increase insulin-induced protein kinase PKB phosphorylation in human hepatocytes, in

  17. Porous structure and surface chemistry of phosphoric acid activated carbon from corncob

    NASA Astrophysics Data System (ADS)

    Sych, N. V.; Trofymenko, S. I.; Poddubnaya, O. I.; Tsyba, M. M.; Sapsay, V. I.; Klymchuk, D. O.; Puziy, A. M.

    2012-11-01

    Active carbons have been prepared from corncob using chemical activation with phosphoric acid at 400 °C using varied ratio of impregnation (RI). Porous structure of carbons was characterized by nitrogen adsorption and scanning electron microscopy. Surface chemistry was studied by IR and potentiometric titration method. It has been shown that porosity development was peaked at RI = 1.0 (SBET = 2081 m2/g, Vtot = 1.1 cm3/g), while maximum amount of acid surface groups was observed at RI = 1.25. Acid surface groups of phosphoric acid activated carbons from corncob includes phosphate and strongly acidic carboxylic (pK = 2.0-2.6), weakly acidic carboxylic (pK = 4.7-5.0), enol/lactone (pK = 6.7-7.4; 8.8-9.4) and phenol (pK = 10.1-10.7). Corncob derived carbons showed high adsorption capacity to copper, especially at low pH. Maximum adsorption of methylene blue and iodine was observed for carbon with most developed porosity (RI = 1.0).

  18. High pressure chemistry of red phosphorus by photo-activated simple molecules

    NASA Astrophysics Data System (ADS)

    Ceppatelli, M.; Fanetti, S.; Bini, R.; Caporali, M.; Peruzzini, M.

    2014-05-01

    High pressure (HP) is very effective in reducing intermolecular distances and inducing unexpected chemical reactions. In addition the photo-activation of the reactants in HP conditions can lead to very efficient and selective processes. The chemistry of phosphorus is currently based on the white molecular form. The red polymeric allotrope, despite more stable and much less toxic, has not attracted much attention so far. However, switching from the white to the red form would benefit any industrial procedure, especially from an environmental point of view. On the other side, water and ethanol are renewable, environmental friendly and largely available molecules, usable as reactants and photo-activators in HP conditions. Here we report a study on the HP photo-induced reactivity of red phosphorus with water and ethanol, showing the possibility of very efficient and selective processes, leading to molecular hydrogen and valuable phosphorus compounds. The reactions have been studied by means of FTIR and Raman spectroscopy and pressure has been generated using membrane Diamond (DAC) and Sapphire (SAC) anvil cells. HP reactivity has been activated by the two-photon absorption of near-UV wavelengths and occurred in total absence of solvents, catalysts and radical initiators, at room T and mild pressure conditions (0.2-1.5 GPa).

  19. Specific activity of polypyrrole nanoparticulate immunoreagents: comparison of surface chemistry and immobilization options.

    PubMed

    Pope, M R; Armes, S P; Tarcha, P J

    1996-01-01

    Polypyrrole-based colloids with differing surface chemistries were compared with respect to the specific activity of immobilized antibody. Monoclonal antibody to the alpha subunit of human chorionic gonadotropin (hCG) was modified by incorporation of cystamine into the Fc-carbohydrate, followed by reduction with dithiothreitol resulting in the generation of 4.5 free thiols per IgG. The reduced IgG was added to clean, unmodified and surface-modified polypyrrole colloids. Functionalized colloids included carboxylate-modified polypyrrole, poly[pyrrole-co-1-(2-carboxyethyl) pyrrole]-silica composite, and amine forms of the carboxylated colloids. The amine-functionalized colloids were subsequently treated with sulfosuccinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate to provide thiol-reactive maleimide surface groups. Following the conjugation of IgG to the colloids, bound and soluble antibody activity was quantitated using a sequentially competitive immunoassay for hCG, based on an automated commercial hCG kit. The results indicated that all forms of polypyrrole retained the equivalence of between 12 and 33 micrograms of IgG activity/mg of colloidal solids, relative to the unmodified soluble IgG. PMID:8853457

  20. Understanding the chemistry behind the antioxidant activities of butylated hydroxytoluene (BHT): a review.

    PubMed

    Yehye, Wageeh A; Rahman, Noorsaadah Abdul; Ariffin, Azhar; Abd Hamid, Sharifah Bee; Alhadi, Abeer A; Kadir, Farkaad A; Yaeghoobi, Marzieh

    2015-08-28

    Hindered phenols find a wide variety of applications across many different industry sectors. Butylated hydroxytoluene (BHT) is a most commonly used antioxidant recognized as safe for use in foods containing fats, pharmaceuticals, petroleum products, rubber and oil industries. In the past two decades, there has been growing interest in finding novel antioxidants to meet the requirements of these industries. To accelerate the antioxidant discovery process, researchers have designed and synthesized a series of BHT derivatives targeting to improve its antioxidant properties to be having a wide range of antioxidant activities markedly enhanced radical scavenging ability and other physical properties. Accordingly, some structure-activity relationships and rational design strategies for antioxidants based on BHT structure have been suggested and applied in practice. We have identified 14 very sensitive parameters, which may play a major role on the antioxidant performance of BHT. In this review, we attempt to summarize the current knowledge on this topic, which is of significance in selecting and designing novel antioxidants using a well-known antioxidant BHT as a building-block molecule. Our strategy involved investigation on understanding the chemistry behind the antioxidant activities of BHT, whether through hydrogen or electron transfer mechanism to enable promising anti-oxidant candidates to be synthesized. PMID:26150290

  1. Synthesis and amylin receptor activity of glycomimetics of pramlintide using click chemistry.

    PubMed

    Yule, Lauren R; Bower, Rebekah L; Kaur, Harveen; Kowalczyk, Renata; Hay, Debbie L; Brimble, Margaret A

    2016-06-21

    Pramlintide (Symlin®), a synthetic analogue of the neuroendocrine hormone amylin, is devoid of the tendency to form cytotoxic amyloid fibrils and is currently used in patients with type I and type II diabetes mellitus as an adjunctive therapy with insulin or insulin analogues. As part of an on-going search for a pramlintide analogue with improved pharmacokinetic properties, we herein report the synthesis of mono- and di-glycosylated analogues of pramlintide and their activity at the AMY1(a) receptor. Introduction of N-glycosylated amino acids into the pramlintide sequence afforded the native N-linked glycomimetics whilst use of Cu(i)-catalysed azide-alkyne 1,3-dipolar cycloaddition (click) chemistry delivered 1,2,3-triazole linked glycomimetics. AMY1(a) receptor activity was retained by incorporation of single or multiple GlcNAc moieties at positions 21 and 35 of native pramlintide. Importantly, no difference in AMY1(a) activity was observed between native N-linked glycomimetics and 1,2,3-triazole linked glycomimetics demonstrating that the click variants can act as surrogates for the native N-glycosides in a biological setting. PMID:27139251

  2. Site-Specific Labeling of Protein Kinase CK2: Combining Surface Display and Click Chemistry for Drug Discovery Applications.

    PubMed

    Nienberg, Christian; Retterath, Anika; Becher, Kira-Sophie; Saenger, Thorsten; Mootz, Henning D; Jose, Joachim

    2016-01-01

    Human CK2 is a heterotetrameric constitutively active serine/threonine protein kinase and is an emerging target in current anti-cancer drug discovery. The kinase is composed of two catalytic CK2α subunits and two regulatory CK2β subunits. In order to establish an assay to identify protein-protein-interaction inhibitors (PPI) of the CK2α/CK2β interface, a bioorthogonal click reaction was used to modify the protein kinase α-subunit with a fluorophore. By expanding the genetic code, the unnatural amino acid para azidophenylalanine (pAzF) could be incorporated into CK2α. Performing the SPAAC click reaction (Strain-Promoted Azide-Alkyne Cycloaddition) by the use of a dibenzylcyclooctyne-fluorophore (DBCO-fluorophore) led to a specifically labeled human protein kinase CK2α. This site-specific labeling does not impair the phosphorylation activity of CK2, which was evaluated by capillary electrophoresis. Furthermore a dissociation constant (KD) of 631 ± 86.2 nM was determined for the substrate αS1-casein towards CK2α. This labeling strategy was also applied to CK2β subunit on Escherichia coli, indicating the site-specific modifications of proteins on the bacterial cell surface when displayed by Autodisplay. PMID:27355959

  3. Current activities handbook: formerly utilized sites remedial action program

    SciTech Connect

    1981-02-27

    This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the activities each of the thirteen state legislatures potentially affected by the Formerly Utilized Sites Remedial Action Program. It contains a description of the state legislative procedural rules and a schedule of each legislative session; a summary of pending relevant legislation; the name and telephone number of legislative and state agency contacts; and the full text of all bills identified.

  4. Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2

    PubMed Central

    Aglietti, Robin A.; Floor, Stephen N.; McClendon, Chris L.; Jacobson, Matthew P.; Gross, John D.

    2013-01-01

    Summary Removal of the 5′ cap structure by Dcp2 is a major step in several 5′–3′ mRNA decay pathways. The activity of Dcp2 is enhanced by Dcp1 and bound coactivators, yet the details of how these interactions are linked to chemistry are poorly understood. Here we report three crystal structures of the catalytic Nudix hydrolase domain of Dcp2 that demonstrate binding of a catalytically essential metal ion, and enzyme kinetics are used to identify several key active site residues involved in acid/base chemistry of decapping. Using NMR and molecular dynamics, we find that a conserved metal binding loop on the catalytic domain undergoes conformational changes during the catalytic cycle. These findings describe key events during the chemical step of decapping, suggest local active site conformational changes are important for activity, and provide a framework to explain stimulation of catalysis by the regulatory domain of Dcp2 and associated coactivators. PMID:23911090

  5. Turbine Chemistry Modeling

    NASA Technical Reports Server (NTRS)

    Liu, Nan-Suey; Wey, Thomas

    2001-01-01

    Many of the engine exhaust species resulting in significant environmental impact exist in trace amounts. Recent research, e.g., conducted at MIT-AM, has pointed to the intra-engine environment as a possible site for important trace chemistry activity. In addition, the key processes affecting the trace species activity occurring downstream in the air passages of the turbine and exhaust nozzle are not well understood. Most recently, an effort has been initiated at NASA Glenn Research Center under the UEET Program to evaluate and further develop CFD-based technology for modeling and simulation of intra-engine trace chemical changes relevant to atmospheric effects of pollutant emissions from aircraft engines. This presentation will describe the current effort conducted at Glenn; some preliminary results relevant to the trace species chemistry in a turbine passage will also be presented to indicate the progress to date.

  6. VERTICAL MIXING AND CHEMISTRY OVER AN ARID URBAN SITE: FIRST RESULTS FROM AIRCRAFT OBSERVATIONS MADE DURING THE PHOENIX SUNRISE CAMPAIGN.

    SciTech Connect

    BERKOWITZ,C.M.; SPRINGSTON,S.R.; DORAN,J.C.; FAST,J.D.

    2002-01-13

    The role of boundary layer mixing is increasingly recognized as an important factor in determining the concentrations of ozone and other trace gases near the surface. While the concentrations at the surface can vary widely due to horizontal transport of chemical plumes, the boundary layer is also characterized by turbulence that follows a diurnal cycle in height and intensity. Surface oxidant concentrations can therefore undergo significant changes even in the absence of photochemistry. A central goal of the Phoenix 2001 Field Campaign was to study vertical mixing with the onset of convection and to quantify the effect of this mixing on chemistry within an urban boundary layer. As part of this study, a series of low altitude aircraft sampling flights were made over the Greater Phoenix area between June 16-30, 2001. The resulting observations, in conjunction with a series of surface measurements and meteorological observations, are being used to study the vertical transport and reactivity of ozone and ozone-precursors shortly after sunrise. Additional details of this campaign are given in Doran, et al. (2002). It was anticipated that turbulence over Phoenix at night would be suppressed as a result of cooling of the boundary layer over the city. By sampling shortly after sunrise, we hoped to collect measurements above the residual nocturnal stable layer and to continue sampling through the developmental period of a convectively active boundary layer. We report here on the first analysis of these observations, made from a Gulstream-1 (G-1) aircraft operated by the U.S. Department of Energy.

  7. Activity Structures and the Unfolding of Problem-Solving Actions in High-School Chemistry Classrooms

    NASA Astrophysics Data System (ADS)

    Criswell, Brett A.; Rushton, Greg T.

    2014-02-01

    In this paper, we argue for a more systematic approach for studying the relationship between classroom practices and scientific practices—an approach that will likely better support the systemic reforms being promoted in the Next Generation Science Standards in the USA and similar efforts in other countries. One component of that approach is looking at how the nature of the activity structure may influence the relative alignment between classroom and scientific practices. To that end, we build on previously published research related to the practices utilized by five high-school chemistry teachers as they enacted problem-solving activities in which students were likely to generate proposals that were not aligned with normative scientific understandings. In that prior work, our analysis had emphasized micro-level features of the talk interactions and how they related to the way students' ideas were explored; in the current paper, the analysis zooms out to consider the macro-level nature of the enactments associated with the activity structure of each lesson examined. Our data show that there were two general patterns to the activity structure across the 14 lessons scrutinized, and that each pattern had associated with it a constellation of features that impinged on the way the problem space was navigated. A key finding is that both activity structures (the expansive and the open) had features that aligned with scientific practices espoused in the Next Generation Science Standards—and both had features that were not aligned with those practices. We discuss the nature of these two structures, evidence of the relationship of each structure to key features of how the lessons unfolded, and the implications of these findings for both future research and the training of teachers.

  8. The effects of rock type and landscape position on solution chemistry of soils in the Biosphere 2 Desert Site of the Santa Catalina Mountains Critical Zone Observatory

    NASA Astrophysics Data System (ADS)

    Penprase, S. B.; Abramson, N.; LaSharr, K.; Chorover, J.

    2014-12-01

    The interaction of near surface soil water with surrounding rock and soil matter plays a crucial role in determining the chemical composition of biogeological systems. This interaction drives subsurface processes such as erosion, mineralization, and depletion. However, how and why soil pore water chemistry fluctuates based on localized conditions such as rock type and landscape position is not fully understood. This study examines the role these two factors play in altering soil water chemistry by analyzing samples collected from schist and granite field sites within the Biosphere 2 Desert Site of the Santa Catalina Mountains Critical Zone Observatory. We hypothesized that soil water from the schist site would have higher solute concentrations than the granite site because schist is a more weatherable rock and, thus, is more susceptible to chemical erosion. We also hypothesized that soil water from convergent positions would have higher solute concentrations than those from divergent positions due to a longer upgradient flow path. Each field site was situated within a Zero Order Basin (ZOB) with seven Zero Tension Lysimeters (ZTL). At the schist site, there were 3 convergent (SC 1-3) and 4 divergent (SD 1-4) ZTL positions. For the granite site, there were 4 convergent (GC 1-2, 4-5) and 3 divergent (GD 1-3) ZTLs. Samples were collected following rainstorms from July 2011-July 2013. Each solution sample was analyzed for major and trace cations, anions, pH, EC, and organic and inorganic carbon. Comparisons between SC and GC and all schist and all granite are consistent with the hypotheses for multiple elements. Results also indicate higher solute levels for SC relative to SD. Thus, our analyses suggest that rock type and landscape position influence the chemical composition of soil water at these two sites.

  9. A STUDY ON LEGIONELLA PNEUMOPHILA, WATER CHEMISTRY, AND ATMOSPHERIC CONDITIONS IN COOLING TOWERS AT THE SAVANNAH RIVER SITE

    SciTech Connect

    Smith, C.; Brigmon, R.

    2009-10-20

    Legionnaires disease is a pneumonia caused by the inhalation of the bacterium Legionella pneumophila. The majority of illnesses have been associated with cooling towers since these devices can harbor and disseminate the bacterium in the aerosolized mist generated by these systems. Historically, Savannah River Site (SRS) cooling towers have had occurrences of elevated levels of Legionella in all seasons of the year and in patterns that are difficult to predict. Since elevated Legionella in cooling tower water are a potential health concern a question has been raised as to the best control methodology. In this work we analyze available chemical, biological, and atmospheric data to determine the best method or key parameter for control. The SRS 4Q Industrial Hygiene Manual, 4Q-1203, 1 - G Cooling Tower Operation and the SRNL Legionella Sampling Program, states that 'Participation in the SRNL Legionella Sampling Program is MANDATORY for all operating cooling towers'. The resulting reports include L. pneumophila concentration information in cells/L. L. pneumophila concentrations >10{sup 7} cells/L are considered elevated and unsafe so action must be taken to reduce these densities. These remedial actions typically include increase biocide addition or 'shocking'. Sometimes additional actions are required if the problem persists including increase tower maintenance (e.g. cleaning). Evaluation of 14 SRS cooling towers, seven water quality parameters, and five Legionella serogroups over a three-plus year time frame demonstrated that cooling tower water Legionella densities varied widely though out this time period. In fact there was no one common consistent significant variable across all towers. The significant factors that did show up most frequently were related to suspended particulates, conductivity, pH, and dissolved oxygen, not chlorine or bromine as might be expected. Analyses of atmospheric data showed that there were more frequent significant elevated Legionella

  10. Identification of covalent active site inhibitors of dengue virus protease

    PubMed Central

    Koh-Stenta, Xiaoying; Joy, Joma; Wang, Si Fang; Kwek, Perlyn Zekui; Wee, John Liang Kuan; Wan, Kah Fei; Gayen, Shovanlal; Chen, Angela Shuyi; Kang, CongBao; Lee, May Ann; Poulsen, Anders; Vasudevan, Subhash G; Hill, Jeffrey; Nacro, Kassoum

    2015-01-01

    Dengue virus (DENV) protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described. PMID:26677315

  11. Teaching with the Case Study Method to Promote Active Learning in a Small Molecule Crystallography Course for Chemistry Students

    ERIC Educational Resources Information Center

    Campbell, Michael G.; Powers, Tamara M.; Zheng, Shao-Liang

    2016-01-01

    Implementing the case study method in a practical X-ray crystallography course designed for graduate or upper-level undergraduate chemistry students is described. Compared with a traditional lecture format, assigning small groups of students to examine literature case studies encourages more active engagement with the course material and…

  12. Activity Theory as a Tool to Address the Problem of Chemistry's Lack of Relevance in Secondary School Chemical Education

    ERIC Educational Resources Information Center

    Van Aalsvoort, Joke

    2004-01-01

    In a previous article, the problem of chemistry's lack of relevance in secondary chemical education was analysed using logical positivism as a tool. This article starts with the hypothesis that the problem can be addressed by means of activity theory, one of the important theories within the sociocultural school. The reason for this expectation is…

  13. Temperature and substrate chemistry as major drivers of interregional variability of leaf microbial decomposition and cellulolytic activity in headwater streams.

    PubMed

    Fenoy, Encarnación; Casas, J Jesús; Díaz-López, Manuel; Rubio, Juan; Guil-Guerrero, J Luís; Moyano-López, Francisco J

    2016-11-01

    Abiotic factors, substrate chemistry and decomposers community composition are primary drivers of leaf litter decomposition. In soil, much of the variation in litter decomposition is explained by climate and substrate chemistry, but with a significant contribution of the specialisation of decomposer communities to degrade specific substrates (home-field advantage, HFA). In streams, however, HFA effects on litter decomposition have not been explicitly tested. We evaluated responses of microbial decomposition and β-glucosidase activity to abiotic factors, substrate and decomposer assemblages, using a reciprocal litter transplant experiment: 'ecosystem type' (mountain vs lowland streams) × 'litter chemistry' (alder vs reed). Temperature, pH and ionic concentration were higher in lowland streams. Decomposition for both species was faster in lowland streams. Decomposition of reed was more accelerated in lowland compared with mountain streams than that of alder, suggesting higher temperature sensitivity of decomposition in reed. Q10 (5°C-15°C) values of β-glucosidase activity were over 2. The alkaline pH and high ionic concentration of lowland streams depleted enzyme activity. We found similar relationships of decomposition or enzyme activity with abiotic factors for both species, suggesting limited support to the HFA hypothesis. Overall, our results suggest a prime role of temperature interacting with substrate chemistry on litter decomposition. PMID:27515735

  14. The Use of Molecular Modeling as "Pseudoexperimental" Data for Teaching VSEPR as a Hands-On General Chemistry Activity

    ERIC Educational Resources Information Center

    Martin, Christopher B.; Vandehoef, Crissie; Cook, Allison

    2015-01-01

    A hands-on activity appropriate for first-semester general chemistry students is presented that combines traditional VSEPR methods of predicting molecular geometries with introductory use of molecular modeling. Students analyze a series of previously calculated output files consisting of several molecules each in various geometries. Each structure…

  15. COMPUTATIONAL CHEMISTRY METHOD FOR PREDICTING VAPOR PRESSURES AND ACTIVITY COEFFICIENTS OF POLAR ORGANIC OXYGENATES IN PM2.5

    EPA Science Inventory

    Parameterizations of interactions of polar multifunctional organic oxygenates in PM2.5 must be included in aerosol chemistry models for evaluating control strategies for reducing ambient concentrations of PM2.5 compounds. Vapor pressures and activity coefficients of these compo...

  16. Removal of Aromatic Pollutant Surrogate from Water by Recyclable Magnetite-Activated Carbon Nanocomposite: An Experiment for General Chemistry

    ERIC Educational Resources Information Center

    Furlan, Ping Y.; Melcer, Michael E.

    2014-01-01

    A general chemistry laboratory experiment using readily available chemicals is described to introduce college students to an exciting class of nanocomposite materials. In a one-step room temperature synthetic process, magnetite nanoparticles are embedded onto activated carbon matrix. The resultant nanocomposite has been shown to combine the…

  17. Tracing footprints of environmental events in tree ring chemistry using neutron activation analysis

    NASA Astrophysics Data System (ADS)

    Sahin, Dagistan

    The aim of this study is to identify environmental effects on tree-ring chemistry. It is known that industrial pollution, volcanic eruptions, dust storms, acid rain and similar events can cause substantial changes in soil chemistry. Establishing whether a particular group of trees is sensitive to these changes in soil environment and registers them in the elemental chemistry of contemporary growth rings is the over-riding goal of any Dendrochemistry research. In this study, elemental concentrations were measured in tree-ring samples of absolutely dated eleven modern forest trees, grown in the Mediterranean region, Turkey, collected and dated by the Malcolm and Carolyn Wiener Laboratory for Aegean and Near Eastern Dendrochronology laboratory at Cornell University. Correlations between measured elemental concentrations in the tree-ring samples were analyzed using statistical tests to answer two questions. Does the current concentration of a particular element depend on any other element within the tree? And, are there any elements showing correlated abnormal concentration changes across the majority of the trees? Based on the detailed analysis results, the low mobility of sodium and bromine, positive correlations between calcium, zinc and manganese, positive correlations between trace elements lanthanum, samarium, antimony, and gold within tree-rings were recognized. Moreover, zinc, lanthanum, samarium and bromine showed strong, positive correlations among the trees and were identified as possible environmental signature elements. New Dendrochemistry information found in this study would be also useful in explaining tree physiology and elemental chemistry in Pinus nigra species grown in Turkey. Elemental concentrations in tree-ring samples were measured using Neutron Activation Analysis (NAA) at the Pennsylvania State University Radiation Science and Engineering Center (RSEC). Through this study, advanced methodologies for methodological, computational and

  18. Methionine sulfoxide reductase: chemistry, substrate binding, recycling process and oxidase activity.

    PubMed

    Boschi-Muller, Sandrine; Branlant, Guy

    2014-12-01

    Three classes of methionine sulfoxide reductases are known: MsrA and MsrB which are implicated stereo-selectively in the repair of protein oxidized on their methionine residues; and fRMsr, discovered more recently, which binds and reduces selectively free L-Met-R-O. It is now well established that the chemical mechanism of the reductase step passes through formation of a sulfenic acid intermediate. The oxidized catalytic cysteine can then be recycled by either Trx when a recycling cysteine is operative or a reductant like glutathione in the absence of recycling cysteine which is the case for 30% of the MsrBs. Recently, it was shown that a subclass of MsrAs with two recycling cysteines displays an oxidase activity. This reverse activity needs the accumulation of the sulfenic acid intermediate. The present review focuses on recent insights into the catalytic mechanism of action of the Msrs based on kinetic studies, theoretical chemistry investigations and new structural data. Major attention is placed on how the sulfenic acid intermediate can be formed and the oxidized catalytic cysteine returns back to its reduced form. PMID:25108804

  19. Microtopographic and depth controls on active layer chemistry in Arctic polygonal ground

    DOE PAGESBeta

    Newman, Brent D.; Throckmorton, Heather M.; Graham, David E.; Gu, Baohua; Hubbard, Susan S.; Liang, Liyuan; Wu, Yuxin; Heikoop, J. M.; Herndon, Elizabeth M.; Phelps, Tommy J.; et al

    2015-03-24

    Polygonal ground is a signature characteristic of Arctic lowlands, and carbon release from permafrost thaw can alter feedbacks to Arctic ecosystems and climate. This study describes the first comprehensive spatial examination of active layer biogeochemistry that extends across high- and low-centered, ice wedge polygons, their features, and with depth. Water chemistry measurements of 54 analytes were made on surface and active layer pore waters collected near Barrow, Alaska, USA. Significant differences were observed between high- and low-centered polygons suggesting that polygon types may be useful for landscape-scale geochemical classification. However, differences were found for polygon features (centers and troughs) formore » analytes that were not significant for polygon type, suggesting that finer-scale features affect biogeochemistry differently from polygon types. Depth variations were also significant, demonstrating important multidimensional aspects of polygonal ground biogeochemistry. These results have major implications for understanding how polygonal ground ecosystems function, and how they may respond to future change.« less

  20. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer.

    PubMed

    Dinpajooh, Mohammadhasan; Martin, Daniel R; Matyushov, Dmitry V

    2016-01-01

    Enzymes in biology's energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work. PMID:27306204

  1. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    NASA Astrophysics Data System (ADS)

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-06-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.

  2. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    PubMed Central

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-01-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work. PMID:27306204

  3. Aerosol and precipitation chemistry measurements in a remote site in Central Amazonia: the role of biogenic contribution

    NASA Astrophysics Data System (ADS)

    Pauliquevis, T.; Lara, L. L.; Antunes, M. L.; Artaxo, P.

    2012-06-01

    In this analysis a 3.5 years data set of aerosol and precipitation chemistry, obtained in a remote site in Central Amazonia (Balbina, (1°55' S, 59°29' W, 174 m a.s.l.), about 200 km north of Manaus) is discussed. Aerosols were sampled using stacked filter units (SFU), which separate fine (d < 2.5 μm) and coarse mode (2.5 μm < d < 10.0 μm) aerosol particles. Filters were analyzed for particulate mass (PM), Equivalent Black Carbon (BCE) and elemental composition by Particle Induced X-Ray Emission (PIXE). Rainwater samples were collected using a wet-only sampler and samples were analyzed for pH and ionic composition, which was determined using ionic chromatography (IC). Natural sources dominated the aerosol mass during the wet season, when it was predominantly of natural biogenic origin mostly in the coarse mode, which comprised up to 81% of PM10. Biogenic aerosol from both primary emissions and secondary organic aerosol dominates the fine mode in the wet season, with very low concentrations (average 2.2 μg m-3). Soil dust was responsible for a minor fraction of the aerosol mass (less than 17%). Sudden increases in the concentration of elements as Al, Ti and Fe were also observed, both in fine and coarse mode (mostly during the April-may months), which we attribute to episodes of Saharan dust transport. During the dry periods, a significant contribution to the fine aerosols loading was observed, due to the large-scale transport of smoke from biomass burning in other portions of the Amazon basin. This contribution is associated with the enhancement of the concentration of S, K, Zn and BCE. Chlorine, which is commonly associated to sea salt and also to biomass burning emissions, presented higher concentration not only during the dry season but also for the April-June months, due to the establishment of more favorable meteorological conditions to the transport of Atlantic air masses to Central Amazonia. The chemical composition of rainwater was similar to those

  4. The copper active site of CBM33 polysaccharide oxygenases.

    PubMed

    Hemsworth, Glyn R; Taylor, Edward J; Kim, Robbert Q; Gregory, Rebecca C; Lewis, Sally J; Turkenburg, Johan P; Parkin, Alison; Davies, Gideon J; Walton, Paul H

    2013-04-24

    The capacity of metal-dependent fungal and bacterial polysaccharide oxygenases, termed GH61 and CBM33, respectively, to potentiate the enzymatic degradation of cellulose opens new possibilities for the conversion of recalcitrant biomass to biofuels. GH61s have already been shown to be unique metalloenzymes containing an active site with a mononuclear copper ion coordinated by two histidines, one of which is an unusual τ-N-methylated N-terminal histidine. We now report the structural and spectroscopic characterization of the corresponding copper CBM33 enzymes. CBM33 binds copper with high affinity at a mononuclear site, significantly stabilizing the enzyme. X-band EPR spectroscopy of Cu(II)-CBM33 shows a mononuclear type 2 copper site with the copper ion in a distorted axial coordination sphere, into which azide will coordinate as evidenced by the concomitant formation of a new absorption band in the UV/vis spectrum at 390 nm. The enzyme's three-dimensional structure contains copper, which has been photoreduced to Cu(I) by the incident X-rays, confirmed by X-ray absorption/fluorescence studies of both aqueous solution and intact crystals of Cu-CBM33. The single copper(I) ion is ligated in a T-shaped configuration by three nitrogen atoms from two histidine side chains and the amino terminus, similar to the endogenous copper coordination geometry found in fungal GH61. PMID:23540833

  5. The Copper Active Site of CBM33 Polysaccharide Oxygenases

    PubMed Central

    2013-01-01

    The capacity of metal-dependent fungal and bacterial polysaccharide oxygenases, termed GH61 and CBM33, respectively, to potentiate the enzymatic degradation of cellulose opens new possibilities for the conversion of recalcitrant biomass to biofuels. GH61s have already been shown to be unique metalloenzymes containing an active site with a mononuclear copper ion coordinated by two histidines, one of which is an unusual τ-N-methylated N-terminal histidine. We now report the structural and spectroscopic characterization of the corresponding copper CBM33 enzymes. CBM33 binds copper with high affinity at a mononuclear site, significantly stabilizing the enzyme. X-band EPR spectroscopy of Cu(II)-CBM33 shows a mononuclear type 2 copper site with the copper ion in a distorted axial coordination sphere, into which azide will coordinate as evidenced by the concomitant formation of a new absorption band in the UV/vis spectrum at 390 nm. The enzyme’s three-dimensional structure contains copper, which has been photoreduced to Cu(I) by the incident X-rays, confirmed by X-ray absorption/fluorescence studies of both aqueous solution and intact crystals of Cu-CBM33. The single copper(I) ion is ligated in a T-shaped configuration by three nitrogen atoms from two histidine side chains and the amino terminus, similar to the endogenous copper coordination geometry found in fungal GH61. PMID:23540833

  6. Genetically Encoded Azide Containing Amino Acid in Mammalian Cells Enables Site-Specific Antibody-Drug Conjugates Using Click Cycloaddition Chemistry.

    PubMed

    VanBrunt, Michael P; Shanebeck, Kurt; Caldwell, Zachary; Johnson, Jeffrey; Thompson, Pamela; Martin, Thomas; Dong, Huifang; Li, Gary; Xu, Hengyu; D'Hooge, Francois; Masterson, Luke; Bariola, Pauline; Tiberghien, Arnaud; Ezeadi, Ebele; Williams, David G; Hartley, John A; Howard, Philip W; Grabstein, Kenneth H; Bowen, Michael A; Marelli, Marcello

    2015-11-18

    Antibody-drug conjugates (ADC) have emerged as potent antitumor drugs that provide increased efficacy, specificity, and tolerability over chemotherapy for the treatment of cancer. ADCs generated by targeting cysteines and lysines on the antibody have shown efficacy, but these products are heterogeneous, and instability may limit their dosing. Here, a novel technology is described that enables site-specific conjugation of toxins to antibodies using chemistry to produce homogeneous, potent, and highly stable conjugates. We have developed a cell-based mammalian expression system capable of site-specific integration of a non-natural amino acid containing an azide moiety. The azide group enables click cycloaddition chemistry that generates a stable heterocyclic triazole linkage. Antibodies to Her2/neu were expressed to contain N6-((2-azidoethoxy)carbonyl)-l-lysine at four different positions. Each site allowed over 95% conjugation efficacy with the toxins auristatin F or a pyrrolobenzodiazepine (PBD) dimer to generate ADCs with a drug to antibody ratio of >1.9. The ADCs were potent and specific in in vitro cytotoxicity assays. An anti Her2/neu conjugate demonstrated stability in vivo and a PBD containing ADC showed potent efficacy in a mouse tumor xenograph model. This technology was extended to generate fully functional ADCs with four toxins per antibody. The high stability of the azide-alkyne linkage, combined with the site-specific nature of the expression system, provides a means for the generation of ADCs with optimized pharmacokinetic, biological, and biophysical properties. PMID:26332743

  7. Eliciting Metacognitive Experiences and Reflection in a Year 11 Chemistry Classroom: An Activity Theory Perspective

    ERIC Educational Resources Information Center

    Thomas, Gregory P.; McRobbie, Campbell J.

    2013-01-01

    Concerns regarding students' learning and reasoning in chemistry classrooms are well documented. Students' reasoning in chemistry should be characterized by conscious consideration of chemical phenomenon from laboratory work at macroscopic, molecular/sub-micro and symbolic levels. Further, students should develop metacognition in relation to such…

  8. An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

    SciTech Connect

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-08-13

    The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

  9. Target-classification approach applied to active UXO sites

    NASA Astrophysics Data System (ADS)

    Shubitidze, F.; Fernández, J. P.; Shamatava, Irma; Barrowes, B. E.; O'Neill, K.

    2013-06-01

    This study is designed to illustrate the discrimination performance at two UXO active sites (Oklahoma's Fort Sill and the Massachusetts Military Reservation) of a set of advanced electromagnetic induction (EMI) inversion/discrimination models which include the orthonormalized volume magnetic source (ONVMS), joint diagonalization (JD), and differential evolution (DE) approaches and whose power and flexibility greatly exceed those of the simple dipole model. The Fort Sill site is highly contaminated by a mix of the following types of munitions: 37-mm target practice tracers, 60-mm illumination mortars, 75-mm and 4.5'' projectiles, 3.5'', 2.36'', and LAAW rockets, antitank mine fuzes with and without hex nuts, practice MK2 and M67 grenades, 2.5'' ballistic windshields, M2A1-mines with/without bases, M19-14 time fuzes, and 40-mm practice grenades with/without cartridges. The site at the MMR site contains targets of yet different sizes. In this work we apply our models to EMI data collected using the MetalMapper (MM) and 2 × 2 TEMTADS sensors. The data for each anomaly are inverted to extract estimates of the extrinsic and intrinsic parameters associated with each buried target. (The latter include the total volume magnetic source or NVMS, which relates to size, shape, and material properties; the former includes location, depth, and orientation). The estimated intrinsic parameters are then used for classification performed via library matching and the use of statistical classification algorithms; this process yielded prioritized dig-lists that were submitted to the Institute for Defense Analyses (IDA) for independent scoring. The models' classification performance is illustrated and assessed based on these independent evaluations.

  10. Differential Active Site Loop Conformations Mediate Promiscuous Activities in the Lactonase SsoPox

    PubMed Central

    Elias, Mikael; Chabriere, Eric

    2013-01-01

    Enzymes are proficient catalysts that enable fast rates of Michaelis-complex formation, the chemical step and products release. These different steps may require different conformational states of the active site that have distinct binding properties. Moreover, the conformational flexibility of the active site mediates alternative, promiscuous functions. Here we focused on the lactonase SsoPox from Sulfolobus solfataricus. SsoPox is a native lactonase endowed with promiscuous phosphotriesterase activity. We identified a position in the active site loop (W263) that governs its flexibility, and thereby affects the substrate specificity of the enzyme. We isolated two different sets of substitutions at position 263 that induce two distinct conformational sampling of the active loop and characterized the structural and kinetic effects of these substitutions. These sets of mutations selectively and distinctly mediate the improvement of the promiscuous phosphotriesterase and oxo-lactonase activities of SsoPox by increasing active-site loop flexibility. These observations corroborate the idea that conformational diversity governs enzymatic promiscuity and is a key feature of protein evolvability. PMID:24086491

  11. Spectroscopic Definition of the Ferroxidase Site in M Ferritin: Comparison of Binuclear Substrate vs. Cofactor Active Sites

    PubMed Central

    Schwartz, Jennifer K.; Liu, Xiaofeng S.; Tosha, Takehiko; Theil, Elizabeth C.; Solomon, Edward I.

    2008-01-01

    Maxi ferritins, 24 subunit protein nanocages, are essential in humans, plants, bacteria, and other animals for the concentration and storage of iron as hydrated ferric oxide, while minimizing free radical generation or use by pathogens. Formation of the precursors to these ferric oxides is catalyzed at a non-heme biferrous substrate site, which has some parallels with the cofactor sites in other biferrous enzymes. A combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field MCD (VTVH MCD) has been used to probe Fe(II) binding to the substrate active site in frog M ferritin. These data determined that the active site within each subunit consists of two inequivalent five-coordinate (5C) ferrous centers that are weakly anti-ferromagnetically coupled, consistent with a μ-1,3 carboxylate bridge. The active site ligand set is unusual and likely includes a terminal water bound to each Fe(II) center. The Fe(II) ions bind to the active sites in a concerted manner, and cooperativity among the sites in each subunit is observed, potentially providing a mechanism for the control of ferritin iron loading. Differences in geometric and electronic structure – including a weak ligand field, availability of two water ligands at the biferrous substrate site, and the single carboxylate bridge in ferritin – coincide with the divergent reaction pathways observed between this substrate site and the previously studied cofactor active sites. PMID:18576633

  12. Metal active site elasticity linked to activation of homocysteine in methionine synthases

    SciTech Connect

    Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.; Matthews, Rowena G.; Smith, Janet L.; Ludwig, Martha L.

    2008-04-02

    Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

  13. Evidence for segmental mobility in the active site of pepsin

    SciTech Connect

    Pohl, J.; Strop, P.; Senn, H.; Foundling, S.; Kostka, V.

    1986-05-01

    The low hydrolytic activity (k/sub cat/ < 0.001 s/sup -1/) of chicken pepsin (CP) towards tri- and tetrapeptides is enhanced at least 100 times by modification of its single sulfhydryl group of Cys-115, with little effect on K/sub m/-values. Modification thus simulates the effect of secondary substrate binding on pepsin catalysis. The rate of Cys-115 modification is substantially decreased in the presence of some competitive inhibitors, suggesting its active site location. Experiments with CP alkylated at Cys-115 with Acrylodan as a fluorescent probe or with N-iodoacetyl-(4-fluoro)-aniline as a /sup 19/F-nmr probe suggest conformation change around Cys-115 to occur on substrate or substrate analog binding. The difference /sup 1/H-nmr spectra (500 MHz) of unmodified free and inhibitor-complexed CP reveal chemical shifts almost exclusively in the aromatic region. The effects of Cu/sup + +/ on /sup 19/F- and /sup 1/H-nmr spectra have been studied. Examination of a computer graphics model of CP based on E. parasitica pepsin-inhibitor complex X-ray coordinates suggests that Cys-115 is located near the S/sub 3//S/sub 5/ binding site. The results are interpreted in favor of segmental mobility of this region important for pepsin substrate binding and catalysis.

  14. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    PubMed

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth. PMID:26940877

  15. Eel calcitonin binding site distribution and antinociceptive activity in rats

    SciTech Connect

    Guidobono, F.; Netti, C.; Sibilia, V.; Villa, I.; Zamboni, A.; Pecile, A.

    1986-03-01

    The distribution of binding site for (/sup 125/I)-eel-calcitonin (ECT) to rat central nervous system, studied by an autoradiographic technique, showed concentrations of binding in the diencephalon, the brain stem and the spinal cord. Large accumulations of grains were seen in the hypothalamus, the amygdala, in the fasciculus medialis prosencephali, in the fasciculus longitudinalis medialis, in the ventrolateral part of the periventricular gray matter, in the lemniscus medialis and in the raphe nuclei. The density of grains in the reticular formation and in the nucleus tractus spinalis nervi trigemini was more moderate. In the spinal cord, grains were scattered throughout the dorsal horns. Binding of the ligand was displaced equally by cold ECT and by salmon CT(sCT), indicating that both peptides bind to the same receptors. Human CT was much weaker than sCT in displacing (/sup 125/I)-ECT binding. The administration of ECT into the brain ventricles of rats dose-dependently induced a significant and long-lasting enhancement of hot-plate latencies comparable with that obtained with sCT. The antinociceptive activity induced by ECT is compatible with the topographical distribution of binding sites for the peptide and is a further indication that fish CTs are active in the mammalian brain.

  16. Extension of polyphenolics by CWPO-C peroxidase mutant containing radical-robust surface active site.

    PubMed

    Pham, L T Mai; Kim, S Jin; Ahn, U Suk; Choi, J Weon; Song, B Keun; Kim, Y Hwan

    2014-01-01

    Expressed as insoluble forms in Escherichia coli, native cationic cell wall peroxidase (CWPO-C) from the poplar tree and mutant variants were successfully reactivated via refolding experiments and used to elucidate the previously presumed existence of an electron transfer (ET) pathway in the CWPO-C structure. Their catalytic properties were fully characterized through various analyses including steady-state kinetic, direct oxidation of lignin macromolecules and their respective stabilities during the polymerization reactions. The analysis results proved that the 74th residue on the CWPO-C surface plays an important role in catalyzing the macromolecules via supposed ET mechanism. By comparing the residual activities of wild-type CWPO-C and mutant 74W CWPO-C after 3 min, mutation of tyrosine 74 residue to tryptophan increased the radical resistance of peroxidase up to ten times dramatically while maintaining its capability to oxidize lignin macromolecules. Furthermore, extension of poly(catechin) as well as lignin macromolecules with CWPO-C Y74W mutant clearly showed that this radical-resistant peroxidase mutant can increase the molecular weight of various kinds of polyphenolics by using surface-located active site. The anti-oxidation activity of the synthesized poly(catechin) was confirmed by xanthine oxidase assay. The elucidation of a uniquely catalytic mechanism in CWPO-C may improve the applicability of the peroxidase/H2O2 catalyst to green polymer chemistry. PMID:24122664

  17. Site Redistribution, Partial Frozen-in Defect Chemistry, and Electrical Properties of Ba1-x(Zr,Pr)O3-δ.

    PubMed

    Antunes, Isabel; Mikhalev, Sergey; Mather, Glenn Christopher; Kharton, Vladislav Vadimovich; Figueiras, Fábio Gabriel; Alves, Adriana; Rodrigues, Joana; Correia, Maria Rosário; Frade, Jorge Ribeiro; Fagg, Duncan Paul

    2016-09-01

    Changes in nominal composition of the perovskite (ABO3) solid solution Ba1-x(Zr,Pr)O3-δ and adjusted firing conditions at very high temperatures were used to induce structural changes involving site redistribution and frozen-in point defects, as revealed by Raman and photoluminescence spectroscopies. Complementary magnetic measurements allowed quantification of the reduced content of Pr. Weak dependence of oxygen stoichiometry with temperature was obtained by coulometric titration at temperatures below 1000 °C, consistent with a somewhat complex partial frozen-in defect chemistry. Electrical conductivity measurements combined with transport number and Seebeck coefficient measurements showed prevailing electronic transport and also indicated trends expected for partial frozen-in conditions. Nominal Ba deficiency and controlled firing at very high temperatures allows adjustment of structure and partial frozen-in defect chemistry, opening the way to engineer relevant properties for high-temperature electrochemical applications. PMID:27509311

  18. Arctic chlorine activation and ozone depletion: Comparison of chemistry transport models with satellite observations.

    NASA Astrophysics Data System (ADS)

    Grooß, J.-U.; Wegner, T.; Müller, R.; Chipperfield, M. P.; Feng, W.; Santee, M. L.

    2009-04-01

    The accurate simulation of Arctic stratospheric ozone depletion has been an issue for two decades. However, there are still notable quantitative discrepancies between the models and observations. We show results from the SLIMCAT and CLaMS 3D chemistry-transport models that differ in some aspects of simulated chlorine activation and descent in the polar vortex. Consequently, the estimates of accumulated ozone depletion in the polar vortex for these two models in cold Arctic winters still largely disagree. As shown recently by Santee et al. (JGR, 2008) using MLS and ACE data, the extent of chlorine activation for the cold Arctic winter of 2004/2005 within the basic SLIMCAT model is overestimated with the likely consequence of too much simulated ozone depletion. In contrast, the CLaMS simulation for the same winter shows too little chlorine activation compared to observations, and therefore likely too little loss. For SLIMCAT the version used by Santee et al. has been updated to replace the equilibrium treatment of NAT PSCs with a Lagrangian microphysical scheme. This leads to smaller regions of NAT particles and less denitrification, in better agreement with observations. The impact of this on the modeled extent of chlorine activation will be discussed. For CLaMS we have changed the parameterization of heterogeneous reactions on liquid aerosols from Carslaw et al. to that of Shi et al. (2001), with which chlorine activation on liquid aerosol becomes more efficient. In turn, the simulated chlorine activation agrees better with the observations. The impact of these model changes on chlorine activation and ozone loss will be assessed and remaining model-observation discrepancies will be discussed in terms of different model formulations. We will also show the impact of recent lab measurements of Cl2O2 absorption cross sections by von Hobe et al. (2009) on the simulated ozone depletion. References: von Hobe, M., F. Stroh, H. Beckers, T. Benter, and H. Willner, The UV

  19. Microelectrode Studies of Interstitial Water Chemistry and Photosynthetic Activity in a Hot Spring Microbial Mat

    PubMed Central

    Revsbech, Niels P.; Ward, David M.

    1984-01-01

    Microelectrodes were used to measure oxygen, pH, and oxygenic photosynthetic activity in a hot spring microbial mat (Octopus Spring, Yellowstone National Park), where the cyanobacterium Synechococcus lividus and the filamentous bacterium Chloroflexus aurantiacus are the only known phototrophs. The data showed very high biological activities in the topmost layers of the microbial mat, resulting in extreme values for oxygen and pH. At a 1-mm depth at a 55°C site, oxygen and pH reached 900 μM and 9.4, respectively, just after solar noon, whereas anoxic conditions with a pH of 7.2 were measured before sunrise. Although diurnal changes between these extremes occurred over hours during a diurnal cycle, microbial activity was great enough to give the same response in 1 to 2 min after artificial shading. Oxygenic photosynthesis was confined to a 0.5- to 1.1-mm layer at sites with temperatures at or above about 50°C, with maximum activities in the 55 to 60°C region. The data suggest that S. lividus is the dominant primary producer of the mat. PMID:16346607

  20. Microelectrode studies of interstitial water chemistry and photosynthetic activity in a hot spring microbial mat

    SciTech Connect

    Revsbech, N.P.; Ward, D.M.

    1984-08-01

    Microelectrodes were used to measure oxygen, pH, and oxygenic photosynthetic activity in a hot spring microbial mat (Octopus Spring, Yellowstone National Park), where the cyanobacterium Synechoccus lividus and the filamentous bacteria Chloroflexus aurantiacus are the only known phototrophs. The data showed very high biological activities in the topmost layers of the microbial mat, resulting in extreme values for oxygen and pH. At a 1-mm depth at a 55 C site, oxygen and pH reached 900 micro M and 9.4, respectively, just after solar noon, whereas anoxic conditions with pH of 7.2 were measured before sunrise. Although diurnal changes between these extremes occurred over hours during a diurnal cycle microbial activity was great enough to give the same response in 1 to 2 mm after artificial shading. Oxygenic photosynthesis was confined to a 0.5- to 1.1-mm layer at sites with temperatures at or above about 50 C, with maximum activities in the 55 to 60 C region. The data suggest that S. lividus is the dominant primary producer of the mat. 30 references, 5 figures.

  1. Active Sites Environmental Monitoring Program: Program plan. Revision 1

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  2. Take-Home Challenges: Extending Discovery-Based Activities beyond the General Chemistry Classroom

    NASA Astrophysics Data System (ADS)

    Mason, P. K.; Sarquis, A. M.

    1996-04-01

    In an effort to more effectively integrate the experimental nature of chemistry into our students' experiences, we are developing and implementing discovery-based activities into both the laboratory and lecture components of general chemistry. Below we describe and provide an example of a "take-home challenge" intended to supplement the lecture component of the course. These take-home challenges involve the student in chemistry exploration outside of class and extend the context of content and experimentation into a nontraditional laboratory environment. Over 25 take-home challenges have been developed to date. Preliminary evaluation of the impact of the take-home challenges shows that students reporting themselves as receiving a B or C grade in the course find the challenges very useful in helping them gain a conceptual understanding of the phenomena addressed. Students earning an A grade report little or no impact on their learning. Prepared as one-page handouts, each take-home challenge begins with a scene-setting introduction followed by pertinent background information, a list of materials to be collected, and any appropriate safety precautions. The exploration component of the activity integrates leading questions with the procedural instructions to help guide the students through the discovery process and challenge them to stretch their understanding of the chemistry. After completing a take-home challenge activity, students submit written reports containing responses to the questions posed, observations of data collected, and their responses to the challenge. The accompanying sample take-home challenge activity is provided as a novel adaptation of the belch phenomenon that challenges students to experiment in order to explain the factors that account for the observed behavior. Persons interested in field testing the take-home challenges with their classes should contact the authors. Belch Bottle Challenge: What factors are responsible for the behavior of a

  3. The lunar regolith - Comparative studies of the Apollo and Luna sites. Chemistry of soils from Apollo 17, Luna 16, 20, and 24

    NASA Technical Reports Server (NTRS)

    Laul, J. C.; Papike, J. J.; Simon, S. B.

    1982-01-01

    The present investigation represents an extension of a comparative regolith study reported by Labotka et al. (1980) to the Apollo 17 site and to the east limb of the moon (Luna 16, 20, and 24 sites). Chemical systematics are considered, taking into account major and minor element characteristics, and large ion-lithophile patterns (K, REE, and Th). Attention is also given to chemical mixing calculations and the significance of the fine fraction. It is found that the chemistries of 1000-90, 90-20, and 20-10 micrometer size fractions are very similar to each other but quite different from the 'less than 10 micrometer' fine fractions. The 'less than 10 micrometer' fine fractions, which comprise about 5 to 20% of the bulk soils, are consistently more feldspathic and enriched in LIL-rich material relative to the coarse fractions in all soils. The KREEP type is different at each site and is largely derived locally.

  4. Active Site and Laminarin Binding in Glycoside Hydrolase Family 55*

    PubMed Central

    Bianchetti, Christopher M.; Takasuka, Taichi E.; Deutsch, Sam; Udell, Hannah S.; Yik, Eric J.; Bergeman, Lai F.; Fox, Brian G.

    2015-01-01

    The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100–10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. PMID:25752603

  5. Active site and laminarin binding in glycoside hydrolase family 55.

    PubMed

    Bianchetti, Christopher M; Takasuka, Taichi E; Deutsch, Sam; Udell, Hannah S; Yik, Eric J; Bergeman, Lai F; Fox, Brian G

    2015-05-01

    The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100-10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. PMID:25752603

  6. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426

    PubMed Central

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a “hot spot” in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity. PMID:25706379

  7. Global distribution and surface activity of macromolecules in offline simulations of marine organic chemistry

    DOE PAGESBeta

    Ogunro, Oluwaseun O.; Burrows, Susannah M.; Elliott, Scott; Frossard, Amanda A.; Hoffman, Forrest M.; Letscher, Robert T.; Moore, J. Keith; Russell, Lynn M.; Wang, Shanlin; Wingenter, Oliver W.

    2015-10-13

    Here, organic macromolecules constitute high percentage components of remote sea spray. They enter the atmosphere through adsorption onto bubbles followed by bursting at the ocean surface, and go on to influence the chemistry of the fine mode aerosol. We present a global estimate of mixed-layer organic macromolecular distributions, driven by offline marine systems model output. The approach permits estimation of oceanic concentrations and bubble film surface coverages for several classes of organic compound. Mixed layer levels are computed from the output of a global ocean biogeochemistry model by relating the macromolecules to standard biogeochemical tracers. Steady state is assumed formore » labile forms, and for longer-lived components we rely on ratios to existing transported variables. Adsorption is then represented through conventional Langmuir isotherms, with equilibria deduced from laboratory analogs. Open water concentrations locally exceed one micromolar carbon for the total of protein, polysaccharide and refractory heteropolycondensate. The shorter-lived lipids remain confined to regions of strong biological activity. Results are evaluated against available measurements for all compound types, and agreement is generally quite reasonable. Global distributions are further estimated for both fractional coverage of bubble films at the air-water interface and the two-dimensional concentration excess. Overall, we show that macromolecular mapping provides a novel tool for the comprehension of oceanic surfactant distributions. Results may prove useful in planning field experiments and assessing the potential response of surface chemical behaviors to global change.« less

  8. Global distribution and surface activity of macromolecules in offline simulations of marine organic chemistry

    SciTech Connect

    Ogunro, Oluwaseun O.; Burrows, Susannah M.; Elliott, Scott; Frossard, Amanda A.; Hoffman, Forrest M.; Letscher, Robert T.; Moore, J. Keith; Russell, Lynn M.; Wang, Shanlin; Wingenter, Oliver W.

    2015-10-13

    Here, organic macromolecules constitute high percentage components of remote sea spray. They enter the atmosphere through adsorption onto bubbles followed by bursting at the ocean surface, and go on to influence the chemistry of the fine mode aerosol. We present a global estimate of mixed-layer organic macromolecular distributions, driven by offline marine systems model output. The approach permits estimation of oceanic concentrations and bubble film surface coverages for several classes of organic compound. Mixed layer levels are computed from the output of a global ocean biogeochemistry model by relating the macromolecules to standard biogeochemical tracers. Steady state is assumed for labile forms, and for longer-lived components we rely on ratios to existing transported variables. Adsorption is then represented through conventional Langmuir isotherms, with equilibria deduced from laboratory analogs. Open water concentrations locally exceed one micromolar carbon for the total of protein, polysaccharide and refractory heteropolycondensate. The shorter-lived lipids remain confined to regions of strong biological activity. Results are evaluated against available measurements for all compound types, and agreement is generally quite reasonable. Global distributions are further estimated for both fractional coverage of bubble films at the air-water interface and the two-dimensional concentration excess. Overall, we show that macromolecular mapping provides a novel tool for the comprehension of oceanic surfactant distributions. Results may prove useful in planning field experiments and assessing the potential response of surface chemical behaviors to global change.

  9. Mentha suaveolens Ehrh. (Lamiaceae) Essential Oil and Its Main Constituent Piperitenone Oxide: Biological Activities and Chemistry.

    PubMed

    Božović, Mijat; Pirolli, Adele; Ragno, Rino

    2015-01-01

    Since herbal medicines play an important role in the treatment of a wide range of diseases, there is a growing need for their quality control and standardization. Mentha suaveolens Ehrh. (MS) is an aromatic herb with fruit and a spearmint flavor, used in the Mediterranean areas as a traditional medicine. It has an extensive range of biological activities, including cytotoxic, antimicrobial, antioxidant, anti-inflammatory, hypotensive and insecticidal properties, among others. This study aims to review the scientific findings and research reported to date on MS that prove many of the remarkable various biological actions, effects and some uses of this species as a source of bioactive natural compounds. On the other hand, piperitenone oxide (PO), the major chemical constituent of the carvone pathway MS essential oil, has been reported to exhibit numerous bioactivities in cells and animals. Thus, this integrated overview also surveys and interprets the present knowledge of chemistry and analysis of this oxygenated monoterpene, as well as its beneficial bioactivities. Areas for future research are suggested. PMID:25985361

  10. Active Upper-atmosphere Chemistry and Dynamics from Polar Circulation Reversal on Titan

    NASA Technical Reports Server (NTRS)

    Teanby, Nicholas A.; Irwin, Patrick Gerard Joseph; Nixon, Conor A.; DeKok, Remco; Vinatier, Sandrine; Coustenis, Athena; Sefton-Nash, Elliot; Calcutt, Simon B.; Flasar, Michael F.

    2012-01-01

    Saturn's moon Titan has a nitrogen atmosphere comparable to Earth's, with a surface pressure of 1.4 bar. Numerical models reproduce the tropospheric conditions very well but have trouble explaining the observed middle-atmosphere temperatures, composition and winds. The top of the middle-atmosphere circulation has been thought to lie at an altitude of 450 to 500 kilometres, where there is a layer of haze that appears to be separated from the main haze deck. This 'detached' haze was previously explained as being due to the colocation of peak haze production and the limit of dynamical transport by the circulation's upper branch. Herewe report a build-up of trace gases over the south pole approximately two years after observing the 2009 post-equinox circulation reversal, from which we conclude that middle-atmosphere circulation must extend to an altitude of at least 600 kilometres. The primary drivers of this circulation are summer-hemisphere heating of haze by absorption of solar radiation and winter-hemisphere cooling due to infrared emission by haze and trace gases; our results therefore imply that these effects are important well into the thermosphere (altitudes higher than 500 kilometres). This requires both active upper-atmosphere chemistry, consistent with the detection of high-complexity molecules and ions at altitudes greater than 950 kilometres, and an alternative explanation for the detached haze, such as a transition in haze particle growth from monomers to fractal structures.

  11. Hot-electron-mediated surface chemistry: toward electronic control of catalytic activity.

    PubMed

    Park, Jeong Young; Kim, Sun Mi; Lee, Hyosun; Nedrygailov, Ievgen I

    2015-08-18

    Energy dissipation at surfaces and interfaces is mediated by excitation of elementary processes, including phonons and electronic excitation, once external energy is deposited to the surface during exothermic chemical processes. Nonadiabatic electronic excitation in exothermic catalytic reactions results in the flow of energetic electrons with an energy of 1-3 eV when chemical energy is converted to electron flow on a short (femtosecond) time scale before atomic vibration adiabatically dissipates the energy (in picoseconds). These energetic electrons that are not in thermal equilibrium with the metal atoms are called "hot electrons". The detection of hot electron flow under atomic or molecular processes and understanding its role in chemical reactions have been major topics in surface chemistry. Recent studies have demonstrated electronic excitation produced during atomic or molecular processes on surfaces, and the influence of hot electrons on atomic and molecular processes. We outline research efforts aimed at identification of the intrinsic relation between the flow of hot electrons and catalytic reactions. We show various strategies for detection and use of hot electrons generated by the energy dissipation processes in surface chemical reactions and photon absorption. A Schottky barrier localized at the metal-oxide interface of either catalytic nanodiodes or hybrid nanocatalysts allows hot electrons to irreversibly transport through the interface. We show that the chemicurrent, composed of hot electrons excited by the surface reaction of CO oxidation or hydrogen oxidation, correlates well with the turnover rate measured separately by gas chromatography. Furthermore, we show that hot electron flows generated on a gold thin film by photon absorption (or internal photoemission) can be amplified by localized surface plasmon resonance. The influence of hot charge carriers on the chemistry at the metal-oxide interface are discussed for the cases of Au, Ag, and Pt

  12. Kinetics of Hydrogen Atom Abstraction from Substrate by an Active Site Thiyl Radical in Ribonucleotide Reductase

    PubMed Central

    2015-01-01

    Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides in all organisms. Active E. coli class Ia RNR is an α2β2 complex that undergoes reversible, long-range proton-coupled electron transfer (PCET) over a pathway of redox active amino acids (β-Y122 → [β-W48] → β-Y356 → α-Y731 → α-Y730 → α-C439) that spans ∼35 Å. To unmask PCET kinetics from rate-limiting conformational changes, we prepared a photochemical RNR containing a [ReI] photooxidant site-specifically incorporated at position 355 ([Re]-β2), adjacent to PCET pathway residue Y356 in β. [Re]-β2 was further modified by replacing Y356 with 2,3,5-trifluorotyrosine to enable photochemical generation and spectroscopic observation of chemically competent tyrosyl radical(s). Using transient absorption spectroscopy, we compare the kinetics of Y· decay in the presence of substrate and wt-α2, Y731F-α2 ,or C439S-α2, as well as with 3′-[2H]-substrate and wt-α2. We find that only in the presence of wt-α2 and the unlabeled substrate do we observe an enhanced rate of radical decay indicative of forward radical propagation. This observation reveals that cleavage of the 3′-C–H bond of substrate by the transiently formed C439· thiyl radical is rate-limiting in forward PCET through α and has allowed calculation of a lower bound for the rate constant associated with this step of (1.4 ± 0.4) × 104 s–1. Prompting radical propagation with light has enabled observation of PCET events heretofore inaccessible, revealing active site chemistry at the heart of RNR catalysis. PMID:25353063

  13. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. PMID:25902402

  14. Driving reactions: Surmounting activation barriers in solid state chemistry using hydroxide melts and RF plasmas

    NASA Astrophysics Data System (ADS)

    Friedman, Todd Lawrence

    1997-11-01

    This thesis explores several techniques for surmounting activation barriers in solid state chemistry. The two major issues addressed are the use of a solution-based molten hydroxide system to increase the rate of reactant diffusion over that in the solid state, and the use of an RF plasma to break bonds in gaseous reactants for subsequent reaction with a solid. Part I describes the use of molten alkali metal hydroxides as a low-temperature solvent system for both electrodeposition and precipitation of high valent copper oxides. Cyclic voltammetry was used to determine the effects of various reaction conditions on copper dissolved in the melts, including copper activity, temperature, and atmosphere composition. The results of this study indicate that copper oxide phases become less soluble at higher copper activities, temperatures, and pHsb2O values. Also, the Cu(II)/Cu(III) redox wave, important for the electrodeposition of cuprate phases with high copper formal oxidation states, is observed below 300sp°C in air and at 350sp°C in dry argon. NaCuOsb2 was electrodeposited under constant current conditions. Iodometric titrations and annealing studies indicate that NaCuOsb2 is oxygen deficient and tends to lose additional oxygen on heating. The hydroxide method was also successful in the deposition of thin films of superconducting EuBasb2Cusb4Osb8 on SrTiOsb3 substrates. The films were found to be superconducting with a Tsbc of 75 K in the absence of annealing. In Part II, the idea of circumventing activation energy barriers is applied to the problem of environmentally harmful perfluorocarbons (PFCs). Mass spectrometry was used to determine the PFC emissions from two semiconductor manufacturing processes: oxide etch and post-CVD chamber clean. Because of radical recombination to thermodynamically stable species, most of the PFCs used in these processes are emitted to the atmosphere. A prototype abatement device which uses an RF plasma to provide the activation energy

  15. Identification of the biologically active liquid chemistry induced by a nonthermal atmospheric pressure plasma jet.

    PubMed

    Wende, Kristian; Williams, Paul; Dalluge, Joe; Gaens, Wouter Van; Aboubakr, Hamada; Bischof, John; von Woedtke, Thomas; Goyal, Sagar M; Weltmann, Klaus-Dieter; Bogaerts, Annemie; Masur, Kai; Bruggeman, Peter J

    2015-01-01

    The mechanism of interaction of cold nonequilibrium plasma jets with mammalian cells in physiologic liquid is reported. The major biological active species produced by an argon RF plasma jet responsible for cell viability reduction are analyzed by experimental results obtained through physical, biological, and chemical diagnostics. This is complemented with chemical kinetics modeling of the plasma source to assess the dominant reactive gas phase species. Different plasma chemistries are obtained by changing the feed gas composition of the cold argon based RF plasma jet from argon, humidified argon (0.27%), to argon/oxygen (1%) and argon/air (1%) at constant power. A minimal consensus physiologic liquid was used, providing isotonic and isohydric conditions and nutrients but is devoid of scavengers or serum constituents. While argon and humidified argon plasma led to the creation of hydrogen peroxide dominated action on the mammalian cells, argon-oxygen and argon-air plasma created a very different biological action and was characterized by trace amounts of hydrogen peroxide only. In particular, for the argon-oxygen (1%), the authors observed a strong negative effect on mammalian cell proliferation and metabolism. This effect was distance dependent and showed a half life time of 30 min in a scavenger free physiologic buffer. Neither catalase and mannitol nor superoxide dismutase could rescue the cell proliferation rate. The strong distance dependency of the effect as well as the low water solubility rules out a major role for ozone and singlet oxygen but suggests a dominant role of atomic oxygen. Experimental results suggest that O reacts with chloride, yielding Cl2(-) or ClO(-). These chlorine species have a limited lifetime under physiologic conditions and therefore show a strong time dependent biological activity. The outcomes are compared with an argon MHz plasma jet (kinpen) to assess the differences between these (at least seemingly) similar plasma sources

  16. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Presents chemistry experiments, laboratory procedures, demonstrations, teaching suggestions, and classroom materials/activities. These include: game for teaching ionic formulas; method for balancing equations; description of useful redox series; computer programs (with listings) for water electrolysis simulation and for determining chemical…

  17. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Presents chemistry experiments, laboratory procedures, demonstrations, and classroom materials/activities. These include: experiments on colloids, processing of uranium ore, action of heat on carbonates; color test for phenols and aromatic amines; solvent properties of non-electrolytes; stereoscopic applications/methods; a valency balance;…

  18. Site-selective spectroscopy of the solid-state defect chemistry in erbium-doped barium titanate.

    PubMed

    Bak, John D; Wright, John C

    2005-10-01

    Erbium-doped barium titanate crystals were studied by laser-induced fluorescence spectroscopy. Thirteen spectroscopically distinct erbium ion sites were found. The relative concentrations of the different sites changed as a function of the crystal and its preparation and treatment. One major site was present in all crystals. The site distribution was changed either by growing codoped crystals with donor (La3+) and acceptor (Sc3+) ions or by changing the temperature and partial pressure of the oxygen in the annealing atmosphere. Equilibrium calculations were done to simulate the defect distributions that result from the charge compensation of the erbium ions. Comparison with the observed dependence of the site spectral intensities indicated that the erbium enters the lattice on barium sites. We assigned the dominant site to an erbium ion on a barium site that is locally compensated by a barium vacancy, whereas the other lower-intensity sites corresponded to erbium ions that are locally compensated by an electron and a more complex center of an erbium, a barium vacancy, and a hole. The spectra of one sample showed that its defects were different and were characteristic of a sample that had not equilibrated. The new sites in this sample were assigned to erbium entering the lattice on a titanium site, which was then locally compensated by an oxygen vacancy or a hole. Heating equilibrated the sample and changed the erbium to a barium site. PMID:16853368

  19. Active site models for the Cu(A) site of peptidylglycine α-hydroxylating monooxygenase and dopamine β-monooxygenase.

    PubMed

    Kunishita, Atsushi; Ertem, Mehmed Z; Okubo, Yuri; Tano, Tetsuro; Sugimoto, Hideki; Ohkubo, Kei; Fujieda, Nobutaka; Fukuzumi, Shunichi; Cramer, Christopher J; Itoh, Shinobu

    2012-09-01

    A mononuclear copper(II) superoxo species has been invoked as the key reactive intermediate in aliphatic substrate hydroxylation by copper monooxygenases such as peptidylglycine α-hydroxylating monooxygenase (PHM), dopamine β-monooxygenase (DβM), and tyramine β-monooxygenase (TβM). We have recently developed a mononuclear copper(II) end-on superoxo complex using a N-[2-(2-pyridyl)ethyl]-1,5-diazacyclooctane tridentate ligand, the structure of which is similar to the four-coordinate distorted tetrahedral geometry of the copper-dioxygen adduct found in the oxy-form of PHM (Prigge, S. T.; Eipper, B. A.; Mains, R. E.; Amzel, L. M. Science2004, 304, 864-867). In this study, structures and physicochemical properties as well as reactivity of the copper(I) and copper(II) complexes supported by a series of tridentate ligands having the same N-[2-(2-pyridyl)ethyl]-1,5-diazacyclooctane framework have been examined in detail to shed light on the chemistry dictated in the active sites of mononuclear copper monooxygenases. The ligand exhibits unique feature to stabilize the copper(I) complexes in a T-shape geometry and the copper(II) complexes in a distorted tetrahedral geometry. Low temperature oxygenation of the copper(I) complexes generated the mononuclear copper(II) end-on superoxo complexes, the structure and spin state of which have been further characterized by density functional theory (DFT) calculations. Detailed kinetic analysis on the O(2)-adduct formation reaction gave the kinetic and thermodynamic parameters providing mechanistic insights into the association and dissociation processes of O(2) to the copper complexes. The copper(II) end-on superoxo complex thus generated gradually decomposed to induce aliphatic ligand hydroxylation. Kinetic and DFT studies on the decomposition reaction have suggested that C-H bond abstraction occurs unimolecularly from the superoxo complex with subsequent rebound of the copper hydroperoxo species to generate the oxygenated

  20. Metavanadate at the active site of the phosphatase VHZ.

    PubMed

    Kuznetsov, Vyacheslav I; Alexandrova, Anastassia N; Hengge, Alvan C

    2012-09-01

    Vanadate is a potent modulator of a number of biological processes and has been shown by crystal structures and NMR spectroscopy to interact with numerous enzymes. Although these effects often occur under conditions where oligomeric forms dominate, the crystal structures and NMR data suggest that the inhibitory form is usually monomeric orthovanadate, a particularly good inhibitor of phosphatases because of its ability to form stable trigonal-bipyramidal complexes. We performed a computational analysis of a 1.14 Å structure of the phosphatase VHZ in complex with an unusual metavanadate species and compared it with two classical trigonal-bipyramidal vanadate-phosphatase complexes. The results support extensive delocalized bonding to the apical ligands in the classical structures. In contrast, in the VHZ metavanadate complex, the central, planar VO(3)(-) moiety has only one apical ligand, the nucleophilic Cys95, and a gap in electron density between V and S. A computational analysis showed that the V-S interaction is primarily ionic. A mechanism is proposed to explain the formation of metavanadate in the active site from a dimeric vanadate species that previous crystallographic evidence has shown to be able to bind to the active sites of phosphatases related to VHZ. Together, the results show that the interaction of vanadate with biological systems is not solely reliant upon the prior formation of a particular inhibitory form in solution. The catalytic properties of an enzyme may act upon the oligomeric forms primarily present in solution to generate species such as the metavanadate ion observed in the VHZ structure. PMID:22876963

  1. Manganese oxide-induced strategy to high-performance iron/nitrogen/carbon electrocatalysts with highly exposed active sites

    NASA Astrophysics Data System (ADS)

    Sun, Tao; Wu, Qiang; Zhuo, Ou; Jiang, Yufei; Bu, Yongfeng; Yang, Lijun; Wang, Xizhang; Hu, Zheng

    2016-04-01

    Iron/nitrogen/carbon (Fe/N/C) catalyst is so far the most promising non-precious metal electrocatalyst for oxygen reduction reaction (ORR) in acidic medium, whose performance depends closely on the synthesis chemistry. Herein, we report a MnOx-induced strategy to construct the Fe/N/C with highly exposed Fe-Nx active sites, which involves the uniform spreading of polyaniline on hierarchical N-doped carbon nanocages by a reactive-template polymerization, followed by the successive iron incorporation and polyaniline pyrolysis. The resulting Fe/N/C demonstrates an excellent ORR performance, including an onset potential of 0.92 V (vs. RHE), four electron selectivity, superb stability and immunity to methanol crossover. The excellent performance is well correlated with the greatly enhanced surface active sites of the catalyst stemming from the unique MnOx-induced strategy. This study provides an efficient approach for exploring the advanced ORR electrocatalysts by increasing the exposed active sites.Iron/nitrogen/carbon (Fe/N/C) catalyst is so far the most promising non-precious metal electrocatalyst for oxygen reduction reaction (ORR) in acidic medium, whose performance depends closely on the synthesis chemistry. Herein, we report a MnOx-induced strategy to construct the Fe/N/C with highly exposed Fe-Nx active sites, which involves the uniform spreading of polyaniline on hierarchical N-doped carbon nanocages by a reactive-template polymerization, followed by the successive iron incorporation and polyaniline pyrolysis. The resulting Fe/N/C demonstrates an excellent ORR performance, including an onset potential of 0.92 V (vs. RHE), four electron selectivity, superb stability and immunity to methanol crossover. The excellent performance is well correlated with the greatly enhanced surface active sites of the catalyst stemming from the unique MnOx-induced strategy. This study provides an efficient approach for exploring the advanced ORR electrocatalysts by increasing the

  2. Effect of gamma radiation on groundwater chemistry and glass leaching as related to the NNWSI repository site

    SciTech Connect

    Abrajano, T.; Bates, J.; Ebert, W.; Gerding, T.

    1986-05-01

    To address the effect of ionizing radiation on groundwater chemistry and waste form durability, NNWSI is performing an extensive set of experiments as a function of dose rate (2 x 10{sup 5}, 1 x 10{sup 4}, 1 x 10{sup 3}, and 0 rad/h). The results of the tests done at 2 x 10{sup 5} rad/h have been reported, while the 1 x 10{sup 3} and 0 rad/h tests are in progress. This paper presents an overview of the results of the tests done at 1 x 10{sup 4} rad/h and discusses the relevance of these tests to repository conditions. An interpretation of the results relating to the manner by which the glass waste form corrodes is presented elsewhere. A complete discussion of the effect of gamma radiation on groundwater chemistry and waste form durability will be presented when the series of experiments are complete.

  3. Hydride binding to the active site of [FeFe]-hydrogenase.

    PubMed

    Chernev, Petko; Lambertz, Camilla; Brünje, Annika; Leidel, Nils; Sigfridsson, Kajsa G V; Kositzki, Ramona; Hsieh, Chung-Hung; Yao, Shenglai; Schiwon, Rafael; Driess, Matthias; Limberg, Christian; Happe, Thomas; Haumann, Michael

    2014-11-17

    [FeFe]-hydrogenase from green algae (HydA1) is the most efficient hydrogen (H2) producing enzyme in nature and of prime interest for (bio)technology. Its active site is a unique six-iron center (H-cluster) composed of a cubane cluster, [4Fe4S]H, cysteine-linked to a diiron unit, [2Fe]H, which carries unusual carbon monoxide (CO) and cyanide ligands and a bridging azadithiolate group. We have probed the molecular and electronic configurations of the H-cluster in functional oxidized, reduced, and super-reduced or CO-inhibited HydA1 protein, in particular searching for intermediates with iron-hydride bonds. Site-selective X-ray absorption and emission spectroscopy were used to distinguish between low- and high-spin iron sites in the two subcomplexes of the H-cluster. The experimental methods and spectral simulations were calibrated using synthetic model complexes with ligand variations and bound hydride species. Distinct X-ray spectroscopic signatures of electronic excitation or decay transitions in [4Fe4S]H and [2Fe]H were obtained, which were quantitatively reproduced by density functional theory calculations, thereby leading to specific H-cluster model structures. We show that iron-hydride bonds are absent in the reduced state, whereas only in the super-reduced state, ligand rotation facilitates hydride binding presumably to the Fe-Fe bridging position at [2Fe]H. These results are in agreement with a catalytic cycle involving three main intermediates and at least two protonation and electron transfer steps prior to the H2 formation chemistry in [FeFe]-hydrogenases. PMID:25369169

  4. Palladium-triggered deprotection chemistry for protein activation in living cells

    NASA Astrophysics Data System (ADS)

    Li, Jie; Yu, Juntao; Zhao, Jingyi; Wang, Jie; Zheng, Siqi; Lin, Shixian; Chen, Long; Yang, Maiyun; Jia, Shang; Zhang, Xiaoyu; Chen, Peng R.

    2014-04-01

    Employing small molecules or chemical reagents to modulate the function of an intracellular protein, particularly in a gain-of-function fashion, remains a challenge. In contrast to inhibitor-based loss-of-function approaches, methods based on a gain of function enable specific signalling pathways to be activated inside a cell. Here we report a chemical rescue strategy that uses a palladium-mediated deprotection reaction to activate a protein within living cells. We identify biocompatible and efficient palladium catalysts that cleave the propargyl carbamate group of a protected lysine analogue to generate a free lysine. The lysine analogue can be genetically and site-specifically incorporated into a protein, which enables control over the reaction site. This deprotection strategy is shown to work with a range of different cell lines and proteins. We further applied this biocompatible protection group/catalyst pair for caging and subsequent release of a crucial lysine residue in a bacterial Type III effector protein within host cells, which reveals details of its virulence mechanism.

  5. Hybrid [FeFe]-hydrogenases with modified active sites show remarkable residual enzymatic activity.

    PubMed

    Siebel, Judith F; Adamska-Venkatesh, Agnieszka; Weber, Katharina; Rumpel, Sigrun; Reijerse, Edward; Lubitz, Wolfgang

    2015-02-24

    [FeFe]-hydrogenases are to date the only enzymes for which it has been demonstrated that the native inorganic binuclear cofactor of the active site Fe2(adt)(CO)3(CN)2 (adt = azadithiolate = [S-CH2-NH-CH2-S](2-)) can be synthesized on the laboratory bench and subsequently inserted into the unmaturated enzyme to yield fully functional holo-enzyme (Berggren, G. et al. (2013) Nature 499, 66-70; Esselborn, J. et al. (2013) Nat. Chem. Biol. 9, 607-610). In the current study, we exploit this procedure to introduce non-native cofactors into the enzyme. Mimics of the binuclear subcluster with a modified bridging dithiolate ligand (thiodithiolate, N-methylazadithiolate, dimethyl-azadithiolate) and three variants containing only one CN(-) ligand were inserted into the active site of the enzyme. We investigated the activity of these variants for hydrogen oxidation as well as proton reduction and their structural accommodation within the active site was analyzed using Fourier transform infrared spectroscopy. Interestingly, the monocyanide variant with the azadithiolate bridge showed ∼50% of the native enzyme activity. This would suggest that the CN(-) ligands are not essential for catalytic activity, but rather serve to anchor the binuclear subsite inside the protein pocket through hydrogen bonding. The inserted artificial cofactors with a propanedithiolate and an N-methylazadithiolate bridge as well as their monocyanide variants also showed residual activity. However, these activities were less than 1% of the native enzyme. Our findings indicate that even small changes in the dithiolate bridge of the binuclear subsite lead to a rather strong decrease of the catalytic activity. We conclude that both the Brønsted base function and the conformational flexibility of the native azadithiolate amine moiety are essential for the high catalytic activity of the native enzyme. PMID:25633077

  6. Site-specific PEGylation of lidamycin and its antitumor activity.

    PubMed

    Li, Liang; Shang, Boyang; Hu, Lei; Shao, Rongguang; Zhen, Yongsu

    2015-05-01

    In this study, N-terminal site-specific mono-PEGylation of the recombinant lidamycin apoprotein (rLDP) of lidamycin (LDM) was prepared using a polyethyleneglycol (PEG) derivative (M w 20 kDa) through a reactive terminal aldehyde group under weak acidic conditions (pH 5.5). The biochemical properties of mPEG-rLDP-AE, an enediyne-integrated conjugate, were analyzed by SDS-PAGE, RP-HPLC, SEC-HPLC and MALDI-TOF. Meanwhile, in vitro and in vivo antitumor activity of mPEG-rLDP-AE was evaluated by MTT assays and in xenograft model. The results indicated that mPEG-rLDP-AE showed significant antitumor activity both in vitro and in vivo. After PEGylation, mPEG-rLDP still retained the binding capability to the enediyne AE and presented the physicochemical characteristics similar to that of native LDP. It is of interest that the PEGylation did not diminish the antitumor efficacy of LDM, implying the possibility that this derivative may function as a payload to deliver novel tumor-targeted drugs. PMID:26579455

  7. Activity theory as a tool to address the problem of chemistry's lack of relevance in secondary school chemical education

    NASA Astrophysics Data System (ADS)

    van Aalsvoort, Joke

    In a previous article, the problem of chemistry's lack of relevance in secondary chemical education was analysed using logical positivism as a tool. This article starts with the hypothesis that the problem can be addressed by means of activity theory, one of the important theories within the sociocultural school. The reason for this expectation is that, while logical positivism creates a divide between science and society, activity theory offers a model of society in which science and society are related. With the use of this model, a new course for grade nine has been constructed. This results in a confirmation of the hypothesis, at least at a theoretical level. A comparison with the Salters' approach is made in order to demonstrate the relative merits of a mediated way of dealing with the problem of the lack of relevance of chemistry in chemical education.

  8. Allosteric site-mediated active site inhibition of PBP2a using Quercetin 3-O-rutinoside and its combination.

    PubMed

    Rani, Nidhi; Vijayakumar, Saravanan; P T V, Lakshmi; Arunachalam, Annamalai

    2016-08-01

    Recent crystallographic study revealed the involvement of allosteric site in active site inhibition of penicillin binding protein (PBP2a), where one molecule of Ceftaroline (Cef) binds to the allosteric site of PBP2a and paved way for the other molecule (Cef) to bind at the active site. Though Cef has the potency to inhibit the PBP2a, its adverse side effects are of major concern. Previous studies have reported the antibacterial property of Quercetin derivatives, a group of natural compounds. Hence, the present study aims to evaluate the effect of Quercetin 3-o-rutinoside (Rut) in allosteric site-mediated active site inhibition of PBP2a. The molecular docking studies between allosteric site and ligands (Rut, Que, and Cef) revealed a better binding efficiency (G-score) of Rut (-7.790318) and Cef (-6.194946) with respect to Que (-5.079284). Molecular dynamic (MD) simulation studies showed significant changes at the active site in the presence of ligands (Rut and Cef) at allosteric site. Four different combinations of Rut and Cef were docked and their G-scores ranged between -6.320 and -8.623. MD studies revealed the stability of the key residue (Ser403) with Rut being at both sites, compared to other complexes. Morphological analysis through electron microscopy confirmed that combination of Rut and Cefixime was able to disturb the bacterial cell membrane in a similar fashion to that of Rut and Cefixime alone. The results of this study indicate that the affinity of Rut at both sites were equally good, with further validations Rut could be considered as an alternative for inhibiting MRSA growth. PMID:26360629

  9. Active site hydrophobicity is critical to the bioluminescence activity of Vibrio harveyi luciferase.

    PubMed

    Li, Chi-Hui; Tu, Shiao-Chun

    2005-10-01

    Vibrio harveyi luciferase is an alphabeta heterodimer containing a single active site, proposed earlier to be at a cleft in the alpha subunit. In this work, six conserved phenylalanine residues at this proposed active site were subjected to site-directed mutations to investigate their possible functional roles and to delineate the makeup of luciferase active site. After initial screening of Phe --> Ala mutants, alphaF46, alphaF49, alphaF114, and alphaF117 were chosen for additional mutations to Asp, Ser, and Tyr. Comparisons of the general kinetic properties of wild-type and mutated luciferases indicated that the hydrophobic nature of alphaF46, alphaF49, alphaF114, and alphaF117 was important to luciferase V(max) and V(max)/K(m), which were reduced by 3-5 orders of magnitude for the Phe --> Asp mutants. Both alphaF46 and alphaF117 also appeared to be involved in the binding of reduced flavin substrate. Additional studies on the stability and yield of the 4a-hydroperoxyflavin intermediate II and measurements of decanal substrate oxidation by alphaF46D, alphaF49D, alphaF114D, and alphaF117D revealed that their marked reductions in the overall quantum yield (phi( degrees )) were a consequence of diminished yields of luciferase intermediates and, with the exception of alphaF114D, emission quantum yield of the excited emitter due to the replacement of the hydrophobic Phe by the anionic Asp. The locations of these four critical Phe residues in relation to other essential and/or hydrophobic residues are depicted in a refined map of the active site. Functional implications of these residues are discussed. PMID:16185065

  10. Groundwater Chemistry and Hydrogeology of the Upper Saddle Mountains Basalt-Confined Aquifer South and Southeast of the Hanford Site

    SciTech Connect

    Newcomer, Darrell R. ); Thornton, Edward C. ); Liikala, Terry L. )

    2002-11-20

    This report describes groundwater monitoring within the upper basalt-confined aquifer in areas bordering the Hanford Site to the south and southeast. The purpose of the sample was to demonstrate that constituents analyzed were within the range of background concentrations and to evaluate any potential connection between groundwater on and off the Hanford Site.

  11. Hydrothermal mineralogy and fluid inclusions chemistry to understand the roots of active geothermal systems

    NASA Astrophysics Data System (ADS)

    Chambefort, I. S.; Dilles, J. H.; Heinrich, C.

    2013-12-01

    An integrated study to link magmatic textures, magmatic mineral compositions, hydrothermal alteration zoning, hydrothermal mineral chemistry, and fluid inclusion compositions has been undertaken to link an intrusive complex and its degassing alteration halo with their surface equivalent in an active geothermal system. Ngatamariki geothermal system, New Zealand, presents a unique feature in the Taupo Volcanic Zone (TVZ). Drilling intercepted an intrusive complex with a high temperature alteration halo similarly to what is observed in magmatic-derived ore deposits. Thus it presents the perfect opportunity to study the magmatic-hydrothermal transition of the TVZ by characterizing the nature of the deep magmatic fluids link to the heat source of the world known geothermal fields. The record of magmatic-hydrothermal fluid-rock interactions preserved at Ngatamariki may be analogous of processes presently occurring at depth beneath TVZ geothermal systems. The intrusive complex consists of over 5 km3 of tonalite, diorite, basalt and aplitic dykes. Evidence of undercooling subsolidus magmatic textures such as myrmekite and skeletal overgrowth are commonly observed and often linked to volatile loss. The fluids released during the crystallization of the intrusive complex are interpreted to be at the origin of the surrounding high temperature alteration halo. Advanced argillic to potassic alteration and high temperature acidic assemblage is associated with high-temperature quartz veining at depth and vuggy silica at the paleo-surface. Major element compositions of the white micas associated with the high temperature halo show a transition from, muscovite to phengite, muscovitic illite away from the intrusion, with a transition to pyrophyllite and/ or topaz, and andalusite characteristic of more acidic conditions. Abundant high-density (up to 59 wt% NaCl eq and homogenization temperatures of 550 degree Celsius and above) coexist with low-density vapor fluid inclusions. This

  12. A proposed definition of the 'activity' of surface sites on lactose carriers for dry powder inhalation.

    PubMed

    Grasmeijer, Floris; Frijlink, Henderik W; de Boer, Anne H

    2014-06-01

    A new definition of the activity of surface sites on lactose carriers for dry powder inhalation is proposed which relates to drug detachment during dispersion. The new definition is expected to improve the understanding of 'carrier surface site activity', which stimulates the unambiguous communication about this subject and may aid in the rational design and interpretation of future formulation studies. In contrast to the currently prevailing view on carrier surface site activity, it follows from the newly proposed definition that carrier surface site activity depends on more variables than just the physicochemical properties of the carrier surface. Because the term 'active sites' is ambiguous, it is recommended to use the term 'highly active sites' instead to denote carrier surface sites with a relatively high activity. PMID:24613490

  13. Disturbance opens recruitment sites for bacterial colonization in activated sludge.

    PubMed

    Vuono, David C; Munakata-Marr, Junko; Spear, John R; Drewes, Jörg E

    2016-01-01

    Little is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: (i) the availability of resources left unconsumed by established species and (ii) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems. PMID:25727891

  14. Construction of DNA recognition sites active in Haemophilus transformation.

    PubMed Central

    Danner, D B; Smith, H O; Narang, S A

    1982-01-01

    Competent Haemophilus cells recognize and preferentially take up Haemophilus DNA during genetic transformation. This preferential uptake is correlated with the presence on incoming DNA of an 11-base-pair (bp) sequence, 5'-A-A-G-T-G-C-G-G-T-C-A-3'. To prove that this sequence is the recognition site that identifies Haemophilus DNA to the competent cell, we have now constructed a series of plasmids, each of which contains the 11-bp sequence. Using two different assay systems we have tested the ability of fragments from these plasmids to compete with cloned Haemophilus DNA fragments that naturally contain the 11-bp sequence. We find that the addition of the 11-bp sequence to a DNA fragment is necessary and sufficient for preferential uptake of that fragment. However, plasmid DNAs containing this sequence may vary as much as 48-fold in uptake activity, and this variation correlates with the A+T-richness of the DNA flanking the 11-mer. Images PMID:6285382

  15. Characterization of active site residues of nitroalkane oxidase.

    PubMed

    Valley, Michael P; Fenny, Nana S; Ali, Shah R; Fitzpatrick, Paul F

    2010-06-01

    The flavoenzyme nitroalkane oxidase catalyzes the oxidation of primary and secondary nitroalkanes to the corresponding aldehydes and ketones plus nitrite. The structure of the enzyme shows that Ser171 forms a hydrogen bond to the flavin N5, suggesting that it plays a role in catalysis. Cys397 and Tyr398 were previously identified by chemical modification as potential active site residues. To more directly probe the roles of these residues, the S171A, S171V, S171T, C397S, and Y398F enzymes have been characterized with nitroethane as substrate. The C397S and Y398 enzymes were less stable than the wild-type enzyme, and the C397S enzyme routinely contained a substoichiometric amount of FAD. Analysis of the steady-state kinetic parameters for the mutant enzymes, including deuterium isotope effects, establishes that all of the mutations result in decreases in the rate constants for removal of the substrate proton by approximately 5-fold and decreases in the rate constant for product release of approximately 2-fold. Only the S171V and S171T mutations alter the rate constant for flavin oxidation. These results establish that these residues are not involved in catalysis, but rather are required for maintaining the protein structure. PMID:20056514

  16. Detection limit for activation measurements in ultralow background sites

    NASA Astrophysics Data System (ADS)

    Trache, Livius; Chesneanu, D.; Margineanu, R.; Pantelica, A.; Ghita, D. G.; Burducea, I.; Straticiuc, M.; Tang, X. D.

    2014-09-01

    We used 12C +13C fusion at the beam energies E = 6, 7 and 8 MeV to determine the sensitivity and the limits of activation method measurements in ultralow background sites. A 13C beam of 0.5 μA from the 3 MV Tandem accelerator of the Horia Hulubei National Institute of Physics and Nuclear Engineering - IFIN HH impinged on thick graphite targets. After about 24 hrs of irradiation targets were measured in two different laboratories: one with a heavy shielded Ge detector in the institute (at the surface) and one located underground in the microBequerel laboratory, in the salt mine of Slanic-Prahova, Romania. The 1369- and 2754 keV peaks from 24Na deactivation were clearly observed in the γ-ray spectra obtained for acquisitions lasting a few hours, or a few days. Determination of the detection limit in evaluating the cross sections for the target irradiated at Ec . m = 3 MeV indicates the fact that it is possible to measure gamma spectrum in underground laboratory down to Ec . m = 2 . 6 MeV. Cleaning the spectra with beta-gamma coincidences and increasing beam intensity 20 times will take as further down. The measurements are motivated by the study of the 12 C +12 C reaction at astrophysical energies.

  17. N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

    PubMed Central

    Chen, Kai; Deng, Xin; Yu, Miao; Han, Dali; Hao, Ziyang; Liu, Jianzhao; Lu, Xingyu; Dore, Louis C; Weng, Xiaocheng; Ji, Quanjiang; Mets, Laurens; He, Chuan

    2015-01-01

    SUMMARY N6-methyldeoxyadenosine (6mA or m6A) is a DNA modification preserved in prokaryotes to eukaryotes. It is widespread in bacteria, and functions in DNA mismatch repair, chromosome segregation, and virulence regulation. In contrast, the distribution and function of 6mA in eukaryotes have been unclear. Here we present a comprehensive analysis of the 6mA landscape in the genome of Chlamydomonas using new sequencing approaches. We identified the 6mA modification in 84% of genes in Chlamydomonas. We found that 6mA mainly locates at ApT dinucleotides around transcription start sites (TSS) with a bimodal distribution, and appears to mark active genes. A periodic pattern of 6mA deposition was also observed at base resolution, which is associated with nucleosome distribution near the TSS, suggesting a possible role in nucleosome positioning. The new genome-wide mapping of 6mA and its unique distribution in the Chlamydomonas genome suggest potential regulatory roles of 6mA in gene expression in eukaryotic organisms. PMID:25936837

  18. Design, synthesis and antiviral activity of entry inhibitors that target the CD4-binding site of HIV-1

    PubMed Central

    Curreli, Francesca; Choudhury, Spreeha; Pyatkin, Ilya; Zagorodnikov, Victor P.; Bulay, Anna Khulianova; Altieri, Andrea; Kwon, Young Do; Kwong, Peter D.; Debnath, Asim K.

    2012-01-01

    The CD4 binding site on HIV-1 gp120 has been validated as a drug target to prevent HIV-1 entry to cells. Previously, we identified two small molecule inhibitors consisting of a 2,2,6,6-tetramethylpiperidine ring linked by an oxalamide to a p-halide-substituted phenyl group, which target this site, specifically, a cavity termed “Phe43 cavity”. Here we use synthetic chemistry, functional assessment and structure-based analysis to explore variants of each region of these inhibitors for improved antiviral properties. Alterations of the phenyl group and of the oxalamide linker indicated that these regions were close to optimal in the original lead compounds. Design of a series of compounds, where the tetramethylpiperidine ring was replaced with new scaffolds, lead to improved antiviral activity. These new scaffolds provide insight into the surface chemistry at the entrance of the cavity and offer additional opportunities by which to optimize further these potential-next-generation therapeutics and microbicides against HIV-1. PMID:22524483

  19. Using Low-Tech Interactions in the Chemistry Classroom to Engage Students in Active Learning

    ERIC Educational Resources Information Center

    Shaver, Michael P.

    2010-01-01

    Two complementary techniques to gauge student understanding and inspire interactive learning in the chemistry classroom are presented. Specifically, this article explores the use of student responses with their thumbs as an alternative to electronic-response systems and complementing these experiences with longer, task-based questions in an…

  20. Space Resources for Teachers: Chemistry; Including Suggestions for Classroom Activities and Laboratory Experiments.

    ERIC Educational Resources Information Center

    Lawrence, Richard M.

    This publication is composed of 10 units, each based on an area of space science and technology in which chemistry plays an important role. Each resource unit can be used independently of the others and materials can be selected from within a unit. The materials range in difficulty from the junior high level of understanding to those that will…

  1. "Chemistry Is in the News": Taxonomy of Authentic News Media-Based Learning Activities. Research Report

    ERIC Educational Resources Information Center

    Glaser, Rainer E.; Carson, Kathleen M.

    2005-01-01

    A brief history is given of approaches that aim at achieving a connectedness of the content of organic chemistry courses to real world issues. Recently, such approaches have relied more and more on online media resources, the tools of the Internet and the World Wide Web. We propose a six-level taxonomy of 'authentic news media-based learning…

  2. Island Explorations: Discovering Effects of Environmental Research-Based Lab Activities on Analytical Chemistry Students

    ERIC Educational Resources Information Center

    Tomasik, Janice Hall; LeCaptain, Dale; Murphy, Sarah; Martin, Mary; Knight, Rachel M.; Harke, Maureen A.; Burke, Ryan; Beck, Kara; Acevedo-Polakovich, I. David

    2014-01-01

    Motivating students in analytical chemistry can be challenging, in part because of the complexity and breadth of topics involved. Some methods that help encourage students and convey real-world relevancy of the material include incorporating environmental issues, research-based lab experiments, and service learning projects. In this paper, we…

  3. Infrared and Raman Spectroscopy: A Discovery-Based Activity for the General Chemistry Curriculum

    ERIC Educational Resources Information Center

    Borgsmiller, Karen L.; O'Connell, Dylan J.; Klauenberg, Kathryn M.; Wilson, Peter M.; Stromberg, Christopher J.

    2012-01-01

    A discovery-based method is described for incorporating the concepts of IR and Raman spectroscopy into the general chemistry curriculum. Students use three sets of springs to model the properties of single, double, and triple covalent bonds. Then, Gaussian 03W molecular modeling software is used to illustrate the relationship between bond…

  4. "JCE" Classroom Activity #110: Artistic Anthocyanins and Acid-Base Chemistry

    ERIC Educational Resources Information Center

    Lech, Jenna; Dounin, Vladimir

    2011-01-01

    Art and science are sometimes viewed as opposing subjects, but are united in many ways. With an increased awareness of the benefits of interdisciplinary studies in education, it is desirable to show students how different subjects impact one another. Visual arts are greatly connected to chemistry in several ways. Pigments are usually synthetically…

  5. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  6. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  7. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  8. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  9. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  10. Low temperature syntheses and reactivity of Cu2O2 active-site models.

    PubMed

    Citek, Cooper; Herres-Pawlis, Sonja; Stack, T Daniel P

    2015-08-18

    Nature's facility with dioxygen outmatches modern chemistry in the oxidation and oxygenation of materials and substrates for biosynthesis and cellular metabolism. The Earth's most abundant naturally occurring oxidant is-frankly-poorly understood and controlled, and thus underused. Copper-based enzyme metallocofactors are ubiquitous to the efficient consumption of dioxygen by all domains of life. Over the last several decades, we have joined many research groups in the study of copper- and dioxygen-dependent enzymes through close investigation of synthetically derived, small-molecule active-site analogs. Simple copper-dioxygen clusters bearing structural and spectroscopic similarity to dioxygen-activating enzymes can be probed for their fundamental geometrical, electronic, and reactive properties using the tools available to inorganic and synthetic chemistry. Our exploration of the copper-dioxygen arena has sustained product evaluation of the key dynamics and reactivity of binuclear Cu2O2 compounds. Almost exclusively operating at low temperatures, from -78 °C to solution characterization even at -125 °C, we have identified numerous compounds supported by simple and easily accessed, low molecular weight ligands-chiefly families of bidentate diamine chelates. We have found that by stripping away complexity in comparison to extended protein tertiary structures or sophisticated, multinucleating architectures, we can experimentally manipulate activated compounds and open pathways of reactivity toward exogenous substrates that both inform on and extend fundamental mechanisms of oxygenase enzymes. Our recent successes have advanced understanding of the tyrosinase enzyme, and related hemocyanin and NspF, and the copper membrane monooxygenases, specifically particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO). Tyrosinase, ubiquitously distributed throughout life, is fundamental to the copper-based oxidation of phenols and the production of chromophores

  11. Active-site mutagenesis of tetanus neurotoxin implicates TYR-375 and GLU-271 in metalloproteolytic activity.

    PubMed

    Rossetto, O; Caccin, P; Rigoni, M; Tonello, F; Bortoletto, N; Stevens, R C; Montecucco, C

    2001-08-01

    Tetanus neurotoxin (TeNT) blocks neurotransmitter release by cleaving VAMP/synaptobrevin, a membrane associated protein involved in synaptic vesicle fusion. Such activity is exerted by the N-terminal 50kDa domain of TeNT which is a zinc-dependent endopeptidase (TeNT-L-chain). Based on the three-dimensional structure of botulinum neurotoxin serotype A (BoNT/A) and serotype B (BoNT/B), two proteins closely related to TeNT, and on X-ray scattering studies of TeNT, we have designed mutations at two active site residues to probe their involvement in activity. The active site of metalloproteases is composed of a primary sphere of residues co-ordinating the zinc atom, and a secondary sphere of residues that determines proteolytic specificity and activity. Glu-261 and Glu-267 directly co-ordinates the zinc atom in BoNT/A and BoNT/B respectively and the corresponding residue of TeNT was replaced by Asp or by the non conservative residue Ala. Tyr-365 is 4.3A away from zinc in BoNT/A, and the corresponding residue of TeNT was replaced by Phe or by Ala. The purified mutants had CD, fluorescence and UV spectra closely similar to those of the wild-type molecule. The proteolytic activity of TeNT-Asp-271 (E271D) is similar to that of the native molecule, whereas that of TeNT-Phe-375 (Y375F) is lower than the control. Interestingly, the two Ala mutants are completely devoid of enzymatic activity. These results demonstrate that both Glu-271 and Tyr-375 are essential for the proteolytic activity of TeNT. PMID:11306125

  12. GAS HYDRATES AT TWO SITES OF AN ACTIVE CONTINENTAL MARGIN.

    USGS Publications Warehouse

    Kvenvolden, K.A.

    1985-01-01

    Sediment containing gas hydrates from two distant Deep Sea Drilling Project sites (565 and 568), located about 670 km apart on the landward flank of the Middle America Trench, was studied to determine the geochemical conditions that characterize the occurrence of gas hydrates. Site 565 was located in the Pacific Ocean offshore the Nicoya Peninsula of Costa Rica in 3,111 m of water. The depth of the hole at this site was 328 m, and gas hydrates were recovered from 285 and 319 m. Site 568 was located about 670 km to the northwest offshore Guatemala in 2,031 m of water. At this site the hole penetrated to 418 m, and gas hydrates were encountered at 404 m.

  13. Dynamically Achieved Active Site Precision in Enzyme Catalysis

    PubMed Central

    2015-01-01

    Conspectus The grand challenge in enzymology is to define and understand all of the parameters that contribute to enzymes’ enormous rate accelerations. The property of hydrogen tunneling in enzyme reactions has moved the focus of research away from an exclusive focus on transition state stabilization toward the importance of the motions of the heavy atoms of the protein, a role for reduced barrier width in catalysis, and the sampling of a protein conformational landscape to achieve a family of protein substates that optimize enzyme–substrate interactions and beyond. This Account focuses on a thermophilic alcohol dehydrogenase for which the chemical step of hydride transfer is rate determining across a wide range of experimental conditions. The properties of the chemical coordinate have been probed using kinetic isotope effects, indicating a transition in behavior below 30 °C that distinguishes nonoptimal from optimal C–H activation. Further, the introduction of single site mutants has the impact of either enhancing or eliminating the temperature dependent transition in catalysis. Biophysical probes, which include time dependent hydrogen/deuterium exchange and fluorescent lifetimes and Stokes shifts, have also been pursued. These studies allow the correlation of spatially resolved transitions in protein motions with catalysis. It is now possible to define a long-range network of protein motions in ht-ADH that extends from a dimer interface to the substrate binding domain across to the cofactor binding domain, over a distance of ca. 30 Å. The ongoing challenge to obtaining spatial and temporal resolution of catalysis-linked protein motions is discussed. PMID:25539048

  14. Water oxidation chemistry of a synthetic dinuclear ruthenium complex containing redox-active quinone ligands.

    PubMed

    Isobe, Hiroshi; Tanaka, Koji; Shen, Jian-Ren; Yamaguchi, Kizashi

    2014-04-21

    We investigated theoretically the catalytic mechanism of electrochemical water oxidation in aqueous solution by a dinuclear ruthenium complex containing redox-active quinone ligands, [Ru2(X)(Y)(3,6-tBu2Q)2(btpyan)](m+) [X, Y = H2O, OH, O, O2; 3,6-tBu2Q = 3,6-di-tert-butyl-1,2-benzoquinone; btpyan =1,8-bis(2,2':6',2″-terpyrid-4'-yl)anthracene] (m = 2, 3, 4) (1). The reaction involves a series of electron and proton transfers to achieve redox leveling, with intervening chemical transformations in a mesh scheme, and the entire molecular structure and motion of the catalyst 1 work together to drive the catalytic cycle for water oxidation. Two substrate water molecules can bind to 1 with simultaneous loss of one or two proton(s), which allows pH-dependent variability in the proportion of substrate-bound structures and following pathways for oxidative activation of the aqua/hydroxo ligands at low thermodynamic and kinetic costs. The resulting bis-oxo intermediates then undergo endothermic O-O radical coupling between two Ru(III)-O(•) units in an anti-coplanar conformation leading to bridged μ-peroxo or μ-superoxo intermediates. The μ-superoxo species can liberate oxygen with the necessity for the preceding binding of a water molecule, which is possible only after four-electron oxidation is completed. The magnitude of catalytic current would be limited by the inherent sluggishness of the hinge-like bending motion of the bridged μ-superoxo complex that opens up the compact, hydrophobic active site of the catalyst and thereby allows water entry under dynamic conditions. On the basis of a newly proposed mechanism, we rationalize the experimentally observed behavior of electrode kinetics with respect to potential and discuss what causes a high overpotential for water oxidation by 1. PMID:24694023

  15. Site-Specific, Intramolecular Cross-Linking of Pin1 Active Site Residues by the Lipid Electrophile 4-Oxo-2-nonenal

    PubMed Central

    2016-01-01

    Products of oxidative damage to lipids include 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-nonenal (ONE), both of which are cytotoxic electrophiles. ONE reacts more rapidly with nucleophilic amino acid side chains, resulting in covalent protein adducts, including residue–residue cross-links. Previously, we demonstrated that peptidylprolyl cis/trans isomerase A1 (Pin1) was highly susceptible to adduction by HNE and that the catalytic cysteine (Cys113) was the preferential site of modification. Here, we show that ONE also preferentially adducts Pin1 at the catalytic Cys but results in a profoundly different modification. Results from experiments using purified Pin1 incubated with ONE revealed the principal product to be a Cys-Lys pyrrole-containing cross-link between the side chains of Cys113 and Lys117. In vitro competition assays between HNE and ONE demonstrate that ONE reacts more rapidly than HNE with Cys113. Exposure of RKO cells to alkynyl-ONE (aONE) followed by copper-mediated click chemistry and streptavidin purification revealed that Pin1 is also modified by ONE in cells. Analysis of the Pin1 crystal structure reveals that Cys113 and Lys117 are oriented toward each other in the active site, facilitating formation of an ONE cross-link. PMID:25739016

  16. Shape-selective catalysts for Fischer-Tropsch chemistry : atomic layer deposition of active catalytic metals. Activity report : January 1, 2005 - September 30, 2005.

    SciTech Connect

    Cronauer, D. C.

    2011-04-15

    Argonne National Laboratory is carrying out a research program to create, prepare, and evaluate catalysts to promote Fischer-Tropsch (FT) chemistry - specifically, the reaction of hydrogen with carbon monoxide to form long-chain hydrocarbons. In addition to needing high activity, it is desirable that the catalysts have high selectivity and stability with respect to both mechanical strength and aging properties. The broad goal is to produce diesel fraction components and avoiding excess yields of both light hydrocarbons and heavy waxes. Originally the goal was to prepare shape-selective catalysts that would limit the formation of long-chain products and yet retain the active metal sites in a protected 'cage.' Such catalysts were prepared with silica-containing fractal cages. The activity was essentially the same as that of catalysts without the cages. We are currently awaiting follow-up experiments to determine the attrition strength of these catalysts. A second experimental stage was undertaken to prepare and evaluate active FT catalysts formed by atomic-layer deposition [ALD] of active components on supported membranes and particulate supports. The concept was that of depositing active metals (i.e. ruthenium, iron or cobalt) upon membranes with well defined flow channels of small diameter and length such that the catalytic activity and product molecular weight distribution could be controlled. In order to rapidly evaluate the catalytic membranes, the ALD coating processes were performed in an 'exploratory mode' in which ALD procedures from the literature appropriate for coating flat surfaces were applied to the high surface area membranes. Consequently, the Fe and Ru loadings in the membranes were likely to be smaller than those expected for complete monolayer coverage. In addition, there was likely to be significant variation in the Fe and Ru loading among the membranes due to difficulties in nucleating these materials on the aluminum oxide surfaces. The first

  17. Liaison activities with the Institute of Physcial Chemistry of the Russian Academy of Sciences: Midyear report

    SciTech Connect

    Delegard, C.H.

    1996-05-29

    The task `IPC/RAS Liaison and Tank Waste Testing` is a program being conducted in fiscal year (FY) 1996 with the support of the U.S. Department of Energy (DOE) Office of Science and Technology, EM-53 Efficient Separations and Processing (ESP) Crosscutting Program, under the technical task plan (TTP) RLA6C342. The principal investigator is Cal Delegard of the Westinghouse Hanford Company. The task involves a technical liaison with the Institute of Physical Chemistry of the Russian Academy of Sciences (IPC/RAS) and their DOE-supported investigations into the fundamental and applied chemistry of the transuranium elements (primarily neptunium, plutonium, and americium) and technetium in @ine media. The task has three purposes: 1. Providing technical information and technical direction to the IPC/RAS. 2. Disseminating IPC/RAS data and information to the DOE technical community. 3. Verifying IPC/RAS results through laboratory testing and comparison with published data.

  18. Robotics and Automation Activities at the Savannah River Site: A Site Report for SUBWOG 39F

    SciTech Connect

    Teese, G.D.

    1995-09-28

    The Savannah River Site has successfully used robots, teleoperators, and remote video to reduce exposure to ionizing radiation, improve worker safety, and improve the quality of operations. Previous reports have described the use of mobile teleoperators in coping with a high level liquid waste spill, the removal of highly contaminated equipment, and the inspection of nuclear reactor vessels. This report will cover recent applications at the Savannah River, as well as systems which SRS has delivered to other DOE site customers.

  19. Chemistry of runoff and shallow ground water at the Cattlemans Detention basin site, South Lake Tahoe, California, August 2000-November 2001

    USGS Publications Warehouse

    Prudic, David E.; Sager, Sienna J.; Wood, James L.; Henkelman, Katherine K.; Caskey, Rachel M.

    2005-01-01

    A study at the Cattlemans detention basin site began in November 2000. The site is adjacent to Cold Creek in South Lake Tahoe, California. The purpose of the study is to evaluate the effects of the detention basin on ground-water discharge and changes in nutrient loads to Cold Creek, a tributary to Trout Creek and Lake Tahoe. The study is being done in cooperation with the Tahoe Engineering Division of the El Dorado County Department of Transportation. This report summarizes data collected prior to and during construction of the detention basin and includes: (1) nutrient and total suspended solid concentrations of urban runoff; (2) distribution of unconsolidated deposits; (3) direction of ground-water flow; and (4) chemistry of shallow ground water and Cold Creek. Unconsolidated deposits in the area of the detention basin were categorized into three classes: fill material consisting of a red-brown loamy sand with some gravel and an occasional cobble that was placed on top of the meadow; meadow deposits consisting of gray silt and sand with stringers of coarse sand and fine gravel; and a deeper brown to yellow-brown sand and gravel with lenses of silt and sand. Prior to construction of the detention basin, ground water flowed west-northwest across the area of the detention basin toward Cold Creek. The direction of ground-water flow did not change during construction of the detention basin. Median concentrations of dissolved iron and chloride were 500 and 30 times higher, respectively, in ground water from the meadow deposits than dissolved concentrations in Cold Creek. Median concentration of sulfate in ground water from the meadow deposits was 0.4 milligrams per liter and dissolved oxygen was below the detection level of 0.3 milligrams per liter. The relatively high concentrations of iron and the lack of sulfate in the shallow ground water likely are caused by chemical reactions and biological microbial oxidation of organic matter in the unconsolidated deposits

  20. Chemistry of zerumbone. 2. Regulation of ring bond cleavage and unique antibacterial activities of zerumbone derivatives.

    PubMed

    Kitayama, T; Yamamoto, K; Utsumi, R; Takatani, M; Hill, R K; Kawai, Y; Sawada, S; Okamoto, T

    2001-10-01

    Further investigation of the chemistry of the eleven-membered cyclic sesquiterpene, zerumbone, the major component of the wild ginger, Zingiber zerumbet Smith, has revealed a new selective epoxidation process, a further example of a novel Favorskii-initiated double ring contraction, and a regiospecific fragmentation of zerumbone dibromide derivatives. Several zerumbone derivatives were found to be selective inhibitors of the growth of gram-positive bacteria. PMID:11758909

  1. Unexpected reactivity of 2-fluorolinalyl diphosphate in the active site of crystalline 2-methylisoborneol synthase

    PubMed Central

    Köksal, Mustafa; Chou, Wayne K. W.; Cane, David E.; Christianson, David W.

    2013-01-01

    The crystal structure of 2-methylisoborneol synthase (MIBS) from Streptomyces coelicolor A3(2) has been determined in its unliganded state and in complex with 2 Mg2+ ions and cis-2-fluorogeranyl diphosphate at 1.85 Å and 2.00 Å resolution, respectively. Under normal circumstances, MIBS catalyzes the cyclization of the naturally-occurring, non-canonical 11-carbon isoprenoid substrate, 2-methylgeranyl diphosphate, which first undergoes an ionization-isomerization-ionization sequence through the tertiary diphosphate intermediate 2-methyllinalyl diphosphate to enable subsequent cyclization chemistry. MIBS does not exhibit catalytic activity with 2-fluorogeranyl diphosphate, and we recently reported the crystal structure of MIBS complexed with this unreactive substrate analogue [Köksal, M., Chou, W. K. W., Cane, D. E., Christianson, D. W. (2012) Biochemistry 51, 3011–3020]. However, cocrystallization of MIBS with the fluorinated analogue of the tertiary allylic diphosphate intermediate, 2-fluorolinalyl diphosphate, reveals unexpected reactivity for the intermediate analogue and yields the crystal structure of the complex with the primary allylic diphosphate, 2-fluoroneryl diphosphate. Comparison with the structure of the unliganded enzyme reveals that the crystalline enzyme active site remains partially open, presumably due to the binding of only 2 Mg2+ ions. Assays in solution indicate that MIBS catalyzes the generation of (1R)-(+)-camphor from the substrate 2-fluorolinalyl diphosphate, suggesting that both 2-fluorolinalyl diphosphate and 2-methyllinalyl diphosphate follow the identical cyclization mechanism leading to 2-substituted isoborneol products; however, the initially generated 2-fluoroisoborneol cyclization product is unstable and undergoes elimination of hydrogen fluoride to yield (1R)-(+)-camphor. PMID:23844678

  2. Improving upon Nature: Active site remodeling produces highly efficient aldolase activity towards hydrophobic electrophilic substrates

    PubMed Central

    Cheriyan, Manoj; Toone, Eric J.; Fierke, Carol A.

    2012-01-01

    Substrate specificity of enzymes is frequently narrow and constrained by multiple interactions, limiting the use of natural enzymes in biocatalytic applications. Aldolases have important synthetic applications, but the usefulness of these enzymes is hampered by their narrow reactivity profile with unnatural substrates. To explore the determinants of substrate selectivity and alter the specificity of E. coli 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, we employed structure-based mutagenesis coupled with library screening of mutant enzymes localized to the bacterial periplasm. We identified two active site mutations (T161S/S184L) that work additively to enhance the substrate specificity of this aldolase to include catalysis of retro-aldol cleavage of (4S)-2-keto-4-hydroxy-4-(2′-pyridyl)butyrate (S-KHPB). These mutations improve the value of kcat/KMS-KHPB by >450-fold, resulting in a catalytic efficiency that is comparable to that of the wild-type enzyme with the natural substrate while retaining high stereoselectivity. Moreover, the value of kcatS-KHPB for this mutant enzyme, a parameter critical for biocatalytic applications, is 3-fold higher than the maximum value achieved by the natural aldolase with any substrate. This mutant also possesses high catalytic efficiency for the retro-aldol cleavage of the natural substrate, KDPG, and a >50-fold improved activity for cleavage of 2-keto-4-hydroxy-octonoate (KHO), a non-functionalized hydrophobic analog. These data suggest a substrate binding mode that illuminates the origin of facial selectivity in aldol addition reactions catalyzed by KDPG and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolases. Furthermore, targeting mutations to the active site provides marked improvement in substrate selectivity, demonstrating that structure-guided active site mutagenesis combined with selection techniques can efficiently identify proteins with characteristics that compare favorably to naturally occurring enzymes. PMID

  3. Changes in permeability and fluid chemistry of the Topopah Spring Member of the Paintbrush tuff (Nevada Test Site) when held in a temperature gradient: summary of results

    SciTech Connect

    Moore, D.E.; Morrow, C.A.; Byerlee, J.D.

    1984-06-01

    The permeability and groundwater chemistry results for the Topopah Spring Member are reported and compared with the results from the previous work on Bullfrog. Permeability measurements made on samples of the Topopah Spring Member of the Paintbrush Tuff at room-temperature and in a temperature gradient show that the initially high (3-65 {mu}da) permeabilities are little affected by heating to at least 150{sup 0}C. These permeability relationships are favvorable for the disposal of nuclear waste in this stuff in an unsaturated zone at the Nevada Test Site. The fluids discharged from the samples of tuff during the experiments are dilute, nearly neutral solutions that differ only slightly from the starting groundwater composition. 8 references, 10 figures, 5 tables.

  4. Atomically-thin two-dimensional sheets for understanding active sites in catalysis.

    PubMed

    Sun, Yongfu; Gao, Shan; Lei, Fengcai; Xie, Yi

    2015-02-01

    Catalysis can speed up chemical reactions and it usually occurs on the low coordinated steps, edges, terraces, kinks and corner atoms that are often called "active sites". However, the atomic level interplay between active sites and catalytic activity is still an open question, owing to the large difference between idealized models and real catalysts. This stimulates us to pursue a suitable material model for studying the active sites-catalytic activity relationship, in which the atomically-thin two-dimensional sheets could serve as an ideal model, owing to their relatively simple type of active site and the ultrahigh fraction of active sites that are comparable to the overall atoms. In this tutorial review, we focus on the recent progress in disclosing the factors that affect the activity of reactive sites, including characterization of atomic coordination number, structural defects and disorder in ultrathin two-dimensional sheets by X-ray absorption fine structure spectroscopy, positron annihilation spectroscopy, electron spin resonance and high resolution transmission electron microscopy. Also, we overview their applications in CO catalytic oxidation, photocatalytic water splitting, electrocatalytic oxygen and hydrogen evolution reactions, and hence highlight the atomic level interplay among coordination number, structural defects/disorder, active sites and catalytic activity in the two-dimensional sheets with atomic thickness. Finally, we also present the major challenges and opportunities regarding the role of active sites in catalysis. We believe that this review provides critical insights for understanding the catalysis and hence helps to develop new catalysts with high catalytic activity. PMID:25382246

  5. The active sites of supported silver particle catalysts in formaldehyde oxidation.

    PubMed

    Chen, Yaxin; Huang, Zhiwei; Zhou, Meijuan; Hu, Pingping; Du, Chengtian; Kong, Lingdong; Chen, Jianmin; Tang, Xingfu

    2016-08-01

    Surface silver atoms with upshifted d-orbitals are identified as the catalytically active sites in formaldehyde oxidation by correlating their activity with the number of surface silver atoms, and the degree of the d-orbital upshift governs the catalytic performance of the active sites. PMID:27406403

  6. Inorganic ground-water chemistry at an experimental New Albany Shale (Devonian-Mississippian) in situ gasification site

    USGS Publications Warehouse

    Branam, T.D.; Comer, J.B.; Shaffer, N.R.; Ennis, M.V.; Carpenter, S.H.

    1991-01-01

    Experimental in situ gasification of New Albany Shale (Devonian-Mississippian) has been conducted in Clark County. Analyses of ground water sampled from a production well and nine nearby monitoring wells 3 months after a brief in situ gasification period revealed changes in water chemistry associated with the gasification procedure. Dissolved iron, calcium and sulphate in ground water from the production well and wells as much as 2 m away were significantly higher than in ground water from wells over 9 m away. Dissolved components in the more distant wells are in the range of those in regional ground water. Thermal decomposition of pyrite during the gasification process generated the elevated levels of iron and sulphate in solution. High concentrations of calcium indicate buffering by dissolution of carbonate minerals. While iron quickly precipitates, calcium and sulphate remain in the ground water. Trends in the concentration of sulphate show that altered ground water migrated mostly in a south-westerly direction from the production well along natural joints in the New Albany Shale. ?? 1991.

  7. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations

    PubMed Central

    Steinkellner, Georg; Gruber, Christian C.; Pavkov-Keller, Tea; Binter, Alexandra; Steiner, Kerstin; Winkler, Christoph; Łyskowski, Andrzej; Schwamberger, Orsolya; Oberer, Monika; Schwab, Helmut; Faber, Kurt; Macheroux, Peter; Gruber, Karl

    2014-01-01

    The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites (‘catalophores’). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C–C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts. PMID:24954722

  8. Spatial, Hysteretic, and Adaptive Host-Guest Chemistry in a Metal-Organic Framework with Open Watson-Crick Sites.

    PubMed

    Cai, Hong; Li, Mian; Lin, Xiao-Rong; Chen, Wei; Chen, Guang-Hui; Huang, Xiao-Chun; Li, Dan

    2015-09-01

    Biological and artificial molecules and assemblies capable of supramolecular recognition, especially those with nucleobase pairing, usually rely on autonomous or collective binding to function. Advanced site-specific recognition takes advantage of cooperative spatial effects, as in local folding in protein-DNA binding. Herein, we report a new nucleobase-tagged metal-organic framework (MOF), namely ZnBTCA (BTC=benzene-1,3,5-tricarboxyl, A=adenine), in which the exposed Watson-Crick faces of adenine residues are immobilized periodically on the interior crystalline surface. Systematic control experiments demonstrated the cooperation of the open Watson-Crick sites and spatial effects within the nanopores, and thermodynamic and kinetic studies revealed a hysteretic host-guest interaction attributed to mild chemisorption. We further exploited this behavior for adenine-thymine binding within the constrained pores, and a globally adaptive response of the MOF host was observed. PMID:26178173

  9. Site-specific labeling of RNA by combining genetic alphabet expansion transcription and copper-free click chemistry.

    PubMed

    Someya, Tatsuhiko; Ando, Ami; Kimoto, Michiko; Hirao, Ichiro

    2015-08-18

    Site-specific labeling of long-chain RNAs with desired molecular probes is an imperative technique to facilitate studies of functional RNA molecules. By genetic alphabet expansion using an artificial third base pair, called an unnatural base pair, we present a post-transcriptional modification method for RNA transcripts containing an incorporated azide-linked unnatural base at specific positions, using a copper-free click reaction. The unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) functions in transcription. Thus, we chemically synthesized a triphosphate substrate of 4-(4-azidopentyl)-pyrrole-2-carbaldehyde (N3-PaTP), which can be site-specifically introduced into RNA, opposite Ds in templates by T7 transcription. The N3-Pa incorporated in the transcripts was modified with dibenzocyclooctyne (DIBO) derivatives. We demonstrated the transcription of 17-, 76- and 260-mer RNA molecules and their site-specific labeling with Alexa 488, Alexa 594 and biotin. This method will be useful for preparing RNA molecules labeled with any functional groups of interest, toward in vivo experiments. PMID:26130718

  10. Gas-phase alkyl amines in urban air; comparison with a boreal forest site and importance for local atmospheric chemistry

    NASA Astrophysics Data System (ADS)

    Hellén, H.; Kieloaho, A.-J.; Hakola, H.

    2014-09-01

    Low-molecular-weight aliphatic amines were measured in the ambient urban background air at the SMEAR III station (Station for Measuring Forest Ecosystem-Atmosphere Relations III) in Helsinki, Finland, from May until late August 2011. The alkyl amines measured were dimethylamine (DMA), ethylamine (EA), trimethylamine (TMA), propylamine (PA), diethylamine (DEA), butylamine (BA) and triethylamine (TEA). Of these amines, DMA + EA and TMA + PA were the most abundant, with average concentrations of 24 and 8 ppt. The ranges of weekly mean concentrations of DMA + EA and TMA + PA were

    site (SMEAR II), indicating the presence at the latter site of some additional sources. Amine lifetimes are short, varying from 2.3 h to 7.6 h against hydroxyl (OH) radicals. The amine concentrations were scaled against OH reactivity and compared with the OH reactivities of aromatic hydrocarbons and terpenes. The results showed that amines strongly influenced the total OH reactivity, especially at the boreal forest site in May, September and October, showing contributions almost as high as those of monoterpenes.

  11. Impact-shocked rocks--insights into Archean and extraterrestrial microbial habitats (and sites for prebiotic chemistry?)

    NASA Technical Reports Server (NTRS)

    Cockell, C. S.

    2004-01-01

    Impact-shocked gneiss shocked to greater than 10 GPa in the Haughton impact structure in the Canadian High Arctic has an approximately 25-times greater pore surface area than unshocked rocks. These pore spaces provide microhabitats for a diversity of heterotrophic microorganisms and in the near-surface environment of the rocks, where light levels are sufficient, cyanobacteria. Shocked rocks provide a moisture retaining, UV protected microenvironment. During the Archean, when impact fluxes were more than two orders of magnitude higher than today, the shocked-rock habitat was one of the most common terrestrial habitats and might have provided a UV-shielded refugium for primitive life. These potential habitats are in high abundance on Mars where impact crater habitats could have existed over geologic time periods of billions of years, suggesting that impact-shocked rocks are important sites to search for biomolecules in extraterrestrial life detection strategies. In addition to being favourable sites for life, during the prebiotic period of planetary history impact-shocked rocks might have acted as a site for the concentration of reactants for prebiotic syntheses. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

  12. Groundwater chemistry and isotope signatures of potential CCS sites in Korea - A baseline study for leakage detection

    NASA Astrophysics Data System (ADS)

    Choi, H.; Jeong, T.; Woo, N. C.

    2013-12-01

    This research aimed at drawing a baseline of groundwater chemistry and its stable isotope signatures of hydrogen, oxygen and carbon from the deep groundwater above the CO2 sequestration layer, in which physico-chemical conditions are conceived as temperature over 40 degree Celcius and high total dissolved solids. Samples were collected from hot springs (at surface and from seep wells) and high-carbonate springs. Based on water compositions, three groups were identified as saline, alkali-carbonate and soda spring types. Saline type hot springs at the west coastline area contain -14.5‰ δ13C of CO2. Before and after rainfall events, δ13C value of samples shows no change. Hot springs at Suanbo region, located at the center are of the Korean Peninsular, were collected from deep wells of 750 m in depth, and they show the alkali-carbonate type water having δ13C values (-11.3~-10.9‰) and ECs (364~431μS/cm). Both saline and alkali-carbonate type waters show no significant change in composition, indicating that recharge by precipitation has no effect on these groundwater. All the high-carbonate springs were collected at ground surface, and enriched with Ca, Mg and HCO3., probably caused by the dissolution of CO2, and high EC values of 1,016 μS/cm. Soda springs located in Chungcheongbuk-do region have -6.8~-6.7‰ δ13C of CO2, indicating that the source of CO2 could be the upper mantle affected by the carbonate minerals in the Quaternary sedimentary bedrock. On the contrary, carbonate waters in the Gangwon-do region have -3.9~-3.7‰ δ13C of CO2, clearly indicating the source of CO2 being the upper mantle (Gerlach and Taylor, 1990). More detailed chemical and isotopic signatures of the sampled waters will be discussed in presentation.

  13. Structural mechanism of RuBisCO activation by carbamylation of the active site lysine

    PubMed Central

    Stec, Boguslaw

    2012-01-01

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO2. We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O2 and CO2 bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO2 defines an elusive, preactivation complex that contains a metal cation Mg2+ surrounded by three H2O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming. PMID:23112176

  14. The design of a bipodal bis(pentafluorophenoxy)aluminate supported on silica as an activator for ethylene polymerization using surface organometallic chemistry.

    PubMed

    Sauter, Dominique W; Popoff, Nicolas; Bashir, Muhammad Ahsan; Szeto, Kai C; Gauvin, Régis M; Delevoye, Laurent; Taoufik, Mostafa; Boisson, Christophe

    2016-04-01

    A new class of well-defined activating supports for olefin polymerization was obtained via the surface organometallic chemistry approach. High activities in slurry polymerization of ethylene along with industrial-grade physical properties of the resulting polyethylene were obtained when these activators were combined with metallocene complexes in the presence of triisobutylaluminium. PMID:26899986

  15. [Effect of macro-creatine kinase in serum on dry chemistry methods results for total creatine kinase activity].

    PubMed

    Tozawa, T; Hashimoto, M

    1999-02-01

    Most enzymes in serum that are measured in clinical laboratories can occur in macro-molecular forms in a significantly number of patients. Within dry chemistry (DC) multilayer film, physical barriers may prevent contact macro-molecular enzyme forms with the active reagent ingredients. Here, serum samples with macro-creatine kinase (macro-CK) type 1: CK-immunoglobulin complex or type 2: oligomer mitochondrial CK (CKm) were analyzed for total CK activity on three different DC analyzers: VITROS 700XR, FUJIDRYCHEM 5000, SPOTCHEM SP4410 and a classic wet chemistry (WC) analyzer: HITACHI 7350. Macro-CKs were detected and identified by electrophoresis on cellulose acetate. Serum with high amounts of oligomer CKm gave CK values by all of DC methods significantly lower than that by the WC method (p < 0.05). Oligomer CKm gradually converts into monomer forms in serum after storage. With increase in day after storage at 4 degrees C, there was a gradual shift in which percent of total CK activity for oligomer CKm decreased while the ratio of total CK activity, DC method/WC method increased. The principle of analytical method for CK activity determination is commonly to all of the DC methods, the WC method and the electrophoretic analysis. These suggest that oligomer CKm is sieved by DC multilayer film elements. In contrast, each of DC method produced highly corrected CK activities for sample containing CK-immunoglobulin complex. This difference in the effects of macro-CKs may depend upon physicochemical characteristics of analytical DC elements. PMID:10097631

  16. 78 FR 33908 - Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-05

    ... identified Wind Energy Area (WEA) on the OCS offshore Rhode Island (RI) and Massachusetts (MA). The revised... from leasing, site characterization, and site assessment in and around the Call Area (76 FR 51391). The... Bureau of Ocean Energy Management Commercial Wind Lease Issuance and Site Assessment Activities on...

  17. 77 FR 39508 - Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-03

    ... specific project proposals on those leases) in an identified Wind Energy Area (WEA) on the OCS offshore..., site characterization, and site assessment in and around the Call Area (76 FR 51391). The Call Area is... Bureau of Ocean Energy Management Commercial Wind Lease Issuance and Site Assessment Activities on...

  18. Active Layer and Moisture Measurements for Intensive Site 0 and 1, Barrow, Alaska

    DOE Data Explorer

    John Peterson

    2015-04-17

    These are measurements of Active Layer Thickness collected along several lines beginning in September, 2011 to the present. The data were collected at several time periods along the Site0 L2 Line, the Site1 AB Line, and an ERT Monitoring Line near Area A in Site1.

  19. Nuclear Site Security in the Event of Terrorist Activity

    SciTech Connect

    Thomson, M.L.; Sims, J.

    2008-07-01

    This paper, presented as a poster, identifies why ballistic protection should now be considered at nuclear sites to counter terrorist threats. A proven and flexible form of multi purpose protection is described in detail with identification of trial results that show its suitability for this role. (authors)

  20. Preliminary siting activities for new waste handling facilities at the Idaho National Engineering Laboratory

    SciTech Connect

    Taylor, D.D.; Hoskinson, R.L.; Kingsford, C.O.; Ball, L.W.

    1994-09-01

    The Idaho Waste Processing Facility, the Mixed and Low-Level Waste Treatment Facility, and the Mixed and Low-Level Waste Disposal Facility are new waste treatment, storage, and disposal facilities that have been proposed at the Idaho National Engineering Laboratory (INEL). A prime consideration in planning for such facilities is the selection of a site. Since spring of 1992, waste management personnel at the INEL have been involved in activities directed to this end. These activities have resulted in the (a) identification of generic siting criteria, considered applicable to either treatment or disposal facilities for the purpose of preliminary site evaluations and comparisons, (b) selection of six candidate locations for siting,and (c) site-specific characterization of candidate sites relative to selected siting criteria. This report describes the information gathered in the above three categories for the six candidate sites. However, a single, preferred site has not yet been identified. Such a determination requires an overall, composite ranking of the candidate sites, which accounts for the fact that the sites under consideration have different advantages and disadvantages, that no single site is superior to all the others in all the siting criteria, and that the criteria should be assigned different weighing factors depending on whether a site is to host a treatment or a disposal facility. Stakeholder input should now be solicited to help guide the final selection. This input will include (a) siting issues not already identified in the siting, work to date, and (b) relative importances of the individual siting criteria. Final site selection will not be completed until stakeholder input (from the State of Idaho, regulatory agencies, the public, etc.) in the above areas has been obtained and a strategy has been developed to make a composite ranking of all candidate sites that accounts for all the siting criteria.

  1. Hydrothermal activity in the Lau back-arc basin:Sulfides and water chemistry

    NASA Astrophysics Data System (ADS)

    Fouquet, Yves; von Stackelberg, Ulrich; Charlou, Jean Luc; Donval, Jean Pierre; Foucher, Jean Paul; Erzinger, Jorg; Herzig, Peter; Mühe, Richard; Wiedicke, Michael; Soakai, Sione; Whitechurch, Hubert

    1991-04-01

    The submersible Nautile completed 22 dives during the Nautilau cruise (R/V Nadir, April 17-May 10, 1989) for a detailed investigation of the southern Lau basin near Tonga. The objective of the scientific team from France, Germany, and Tonga was to understand the process of sea-floor ore formation associated with hydrothermal circulation along the Valu Fa back-arc ridge behind the Tonga- Kermadec trench. The four diving areas, between lat 21°25‧S and 22°40‧S in water ˜2000 m deep, were selected on the basis of results from cruises of the R/V JeanCharcot and R/V Sonne. The Nadir cruise provided proof of hydrothermal activity—in all four areas, over more than 100 km—as indicated by the widespread occurrence of hydrothermal deposits and by heat flow, conductivity, and temperature measurements near the sea bottom. The most spectacular findings were high-temperature white and black smokers and associated fauna and ore deposits. Hydrothermal water chemistry and sulfide composition data presented here indicate that this hydrothermal field is very different from the hydrothermal fields in oceanic ridges. This difference is seen in the water chemistry of the hydrothermal fluid (pH = 2 and high metal content) and the chemical composition of sulfides (enrichment in Ba, As, and Pb).

  2. Liaison activities with the institute of physical chemistry, Russian academy of sciences: FY 1996

    SciTech Connect

    Delegard, C.H.

    1996-09-23

    The task ``IPC/RAS Liaison and Tank Waste Testing`` is a program being conducted in fiscal year (FY) 1996 with the support of the U.S. Department of Energy (DOE) Office of Science and Technology, EM-53 Efficient Separations and Processing (ESP) Crosscutting Program, under the technical task plan RLA6C342. The principal investigator is Cal Delegard of the Westinghouse Hanford Company. The task involves a technical liaison with the Institute of Physical Chemistry of the Russian Academy of Sciences (IPC/RAS) and their DOE-supported investigations into the fundamental and applied chemistry of the transuranium elements (primarily neptunium, plutonium, and americium) and technetium in alkaline media. The task has three purposes: 1. Providing technical information and technical direction to the IPC/RAS. 2. Disseminating IPC/RAS data and information to the DOE technical community. 3. Verifying IPC/RAS results through laboratory testing and comparison with published data. This report fulfills the milestone ``Provide End-of-Year Report to Focus Area,`` due September 30, 1996.

  3. Blogs and Social Network Sites as Activity Systems: Exploring Adult Informal Learning Process through Activity Theory Framework

    ERIC Educational Resources Information Center

    Heo, Gyeong Mi; Lee, Romee

    2013-01-01

    This paper uses an Activity Theory framework to explore adult user activities and informal learning processes as reflected in their blogs and social network sites (SNS). Using the assumption that a web-based space is an activity system in which learning occurs, typical features of the components were investigated and each activity system then…

  4. Corrosion Control during Closure Activities at the Savannah River Site - 13514

    SciTech Connect

    Wiersma, Bruce J.; Subramanian, Karthik H.; Martin, Keisha B.

    2013-07-01

    Liquid radioactive wastes from the Savannah River Site (SRS) separation process are stored in large underground carbon steel tanks. Until the waste is removed from storage, transferred, and processed, the materials and structures of the tanks must maintain a confinement function by providing a barrier to the environment and by maintaining acceptable structural stability during normal service and design basis events (e.g., earthquake conditions). A corrosion control program is in place to ensure that degradation of the steel does not impact the structural and leak integrity functions of these waste tanks. The SRS is currently retrieving waste from older waste tanks and processing the waste through the vitrification for long term stabilization. The retrieval processes prepare the tanks for ultimate closure (i.e., grouting) by removing sludge by mechanical and/or sluicing methods, dissolving salt cake by adding water, and chemical cleaning of the residual sludge with oxalic acid. Each of these retrieval methods will result in waste chemistry that does not meet the requirements of the current corrosion control program. Given the short-term exposure and limited remaining service life for the tanks in which retrievals are being performed, an assessment of the need for corrosion controls in these tanks was performed. The assessment reviewed the corrosion rates in the more aggressive environments and the postulated loads on the structure during the closure activities. The assessment concluded that the current corrosion control program may be suspended for a short period of time while final retrieval of the waste is performed. (authors)

  5. Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

    SciTech Connect

    Miao, Yinglong; Baudry, Jerome Y

    2011-01-01

    Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site.

  6. Effects of lead shot ingestion on delta-aminolevulinic acid dehydratase activity, hemoglobin concentration, and serum chemistry in bald eagles

    USGS Publications Warehouse

    Hoffman, D.J.; Pattee, O.H.; Wiemeyer, Stanley N.; Mulhern, B.

    1981-01-01

    Lead shot ingestion by bald eagles (Haliaeetus leucocephalus) is considered to be widespread and has been implicated in the death of eagles in nature. It was recently demonstrated under experimental conditions that ingestion of as few as 10 lead shot resulted in death within 12 to 20 days. In the present study hematological responses to lead toxicity including red blood cell ALAD activity, hemoglobin concentration and 23 different blood serum chemistries were examined in five captive bald eagles that were unsuitable for rehabilitation and release. Eagles were dosed by force-feeding with 10 lead shot; they were redosed if regurgitation occurred. Red blood cell ALAD activity was inhibited by nearly 80% within 24 hours when mean blood lead concentration had increased to 0.8 parts per million (ppm). By the end of 1 week there was a significant decrease (20-25%) in hematocrit and hemoglobin, and the mean blood lead concentration was over 3 ppm. Within as little as 1-2 weeks after dosing, significant elevations in serum creatinine and serum alanine aminotransferase occurred, as well as a significant decrease in the ratio of serum aspartic aminotransferase to serum alanine aminotransferase. The mean blood lead concentration was over 5 ppm by the end of 2 weeks. These changes in serum chemistry may be indicative of kidney and liver alterations.

  7. Effects of probiotic supplementation over 5 months on routine haematology and clinical chemistry measures in healthy active adults.

    PubMed

    Cox, A J; West, N P; Horn, P L; Lehtinen, M J; Koerbin, G; Pyne, D B; Lahtinen, S J; Fricker, P A; Cripps, A W

    2014-11-01

    Use of probiotic-containing foods and probiotic supplements is increasing; however, few studies document safety and tolerability in conjunction with defined clinical end points. This paper reports the effects of 150 days of supplementation with either a single- (Bifidobacterium animalis subsp. lactis Bl-04) or a double-strain (Lactobacillus acidophilus NCFM and Bifidobacterium animalis subsp. lactis Bi-07) probiotic on routine haematology and clinical chemistry measures in healthy active adults. Pre- to post-intervention changes in laboratory measures were determined and compared between supplement and placebo groups. Overall there were few differences in routine haematology and clinical chemistry measures between supplement and placebo groups post-intervention. Exceptions included plasma calcium (P=0.03) and urea (P=0.015); however, observed changes were small and within assay-specific laboratory reference ranges. These data provide evidence supporting the use of these probiotic supplements over a period of 5 months in healthy active adults without obvious safety or tolerability issues. PMID:25052229

  8. Relationship Between Precipitation Chemistry and Meteorological Parameters at a Urban Site in the North of Queretaro State

    NASA Astrophysics Data System (ADS)

    García Martínez, R.; Hernández, G.; Solis, S.; Torres, M. D.; Padilla, H.; Báez, A.

    2010-12-01

    A total of 50 wet precipitation samples were collected per event at the Juriquilla site from mid-May 2009 to the end of May 2010. The Juriquilla sampling site was located on the roof of the Geoscience Building, Universidad Nacional Autónoma de México, at the Juriquilla Campus in the city of Querétaro located at 20°41'58"N and 100°27'28" W, at 1920 meters above sea level (masl). Sampling was done in passive collectors that consisted of a high density polyethylene funnel connected to a 2-liter polyethylene bottle, supported by a rod 1.5 m above the roof. One of the collectors was used to take samples for trace metals. The analysis was done in soluble and insoluble fractions. Al, Ag, As, Cd, Cr, Cu, Hg, Mn, Ni, Pb, V and Zn were analyzed by atomic absorption spectroscopy with a graphite furnace accessory. The other collector was used to measure pH and major ions (SO4-2, Cl-, NO3-, Ca2+, Mg2+, Na+, K+ and NH4+) in the soluble fractions, because it was assumed that these ions are completely soluble in rainwater. The major ions SO4-2, Cl-, and NO3-, were analyzed by a Varian Model 2010 ion chromatograph; Ca2+, Mg2+, Na+ and K+ were determined by flame atomic absorption spectrometry and NH4+ by a UV spectrophotometer. In this study, synoptic maps were used to analyze the transport of air masses before rainfall, enabling back trajectories to be used to estimate the source region of pollutants. To understand the variety of synoptic weather conditions, data were associated with the corresponding air mass back trajectories calculated by the NOAA HYSPLIT model (Hybrid Single-Particle Lagrangian Integrated Trajectory Model). Back trajectory models have very simple advection schemes to calculate the previous position of an air parcel by using estimated wind speed and direction for the time period prior to arrival at the selected site. In this study, the origin of the air mass for an event was evaluated by a three-day back-trajectory before arrival to Queretaro. Mass back

  9. Active Site Structure and Peroxidase Activity of Oxidatively Modified Cytochrome c Species in Complexes with Cardiolipin.

    PubMed

    Capdevila, Daiana A; Oviedo Rouco, Santiago; Tomasina, Florencia; Tortora, Verónica; Demicheli, Verónica; Radi, Rafael; Murgida, Daniel H

    2015-12-29

    We report a resonance Raman and UV-vis characterization of the active site structure of oxidatively modified forms of cytochrome c (Cyt-c) free in solution and in complexes with cardiolipin (CL). The studied post-translational modifications of Cyt-c include methionine sulfoxidation and tyrosine nitration, which lead to altered heme axial ligation and increased peroxidase activity with respect to those of the wild-type protein. In spite of the structural and activity differences between the protein variants free in solution, binding to CL liposomes induces in all cases the formation of a spectroscopically identical bis-His axial coordination conformer that more efficiently promotes lipid peroxidation. The spectroscopic results indicate that the bis-His form is in equilibrium with small amounts of high-spin species, thus suggesting a labile distal His ligand as the basis for the CL-induced increase in enzymatic activity observed for all protein variants. For Cyt-c nitrated at Tyr74 and sulfoxidized at Met80, the measured apparent binding affinities for CL are ∼4 times larger than for wild-type Cyt-c. On the basis of these results, we propose that these post-translational modifications may amplify the pro-apoptotic signal of Cyt-c under oxidative stress conditions at CL concentrations lower than for the unmodified protein. PMID:26620444

  10. Characteristic Tandem Mass Spectral Features Under Various Collision Chemistries for Site-Specific Identification of Protein S-Glutathionylation

    NASA Astrophysics Data System (ADS)

    Chou, Chi-Chi; Chiang, Bing-Yu; Lin, Jason Ching-Yao; Pan, Kuan-Ting; Lin, Chun-Hung; Khoo, Kay-Hooi

    2015-01-01

    Protein S-glutathionylation is a reversible post-translational modification widely implicated in redox regulated biological functions. Conventional biochemical methods, however, often do not allow such a mixed disulfide modification to be reliably identified on specific cysteine residues or be distinguished from other related oxidized forms. To develop more efficient mass spectrometry (MS)-based analytical strategies for this purpose, we first investigated the MS/MS fragmentation pattern of S-glutathionylated peptides under various dissociation modes, including collision-induced dissociation (CID), higher-energy C-trap dissociation (HCD), and electron transfer dissociation (ETD), using synthetic peptides derived from protein tyrosine phosphatase as models. Our results indicate that a MALDI-based high energy CID MS/MS on a TOF/TOF affords the most distinctive spectral features that would facilitate rapid and unambiguous identification of site-specific S-glutathionylation. For more complex proteomic samples best tackled by LC-MS/MS approach, we demonstrate that HCD performed on an LTQ-Orbitrap hybrid instrument fairs better than trap-based CID and ETD in allowing more protein site-specific S-glutathionylation to be confidently identified by direct database searching of the generated MS/MS dataset using Mascot. Overall, HCD afforded more peptide sequence-informative fragment ions retaining the glutathionyl modification with less neutral losses of side chains to compromise scoring. In conjunction with our recently developed chemo-enzymatic tagging strategy, our nanoLC-HCD-MS/MS approach is sufficiently sensitive to identify endogenous S-glutathionylated peptides prepared from non-stressed cells. It is anticipated that future applications to global scale analysis of protein S-glutathionylation will benefit further from current advances in both speed and mass accuracy afforded by HCD MS/MS mode on the Orbitrap series.

  11. Combined Quantum Chemistry and Photoelectron Spectroscopy Study of the Electronic Structure and Reduction Potentials of Rubredoxin Redox Site Analogues

    SciTech Connect

    Niu, Shuqiang; Wang, Xue B.; Nichols, J. A.; Wang, Lai S.; Ichiye, Toshiko

    2003-04-24

    Iron-sulfur proteins are an important class of electron carriers in a wide variety of biological reactions. Determining the intrinsic contribution of the metal site to the redox potential is crucial in understanding how the protein environment influences the overall redox properties of the Fe-S proteins. Here we combine density functional theory and coupled cluster methods with photodetachment spectroscopy to study the electronic structures and gas-phase redox potentials of the [Fe(SCH3)(4)](2-/-/0) and [Fe(SCH3)(3)](-/0) analogues of the rubredoxin redox site. The calculations show that oxidations of [Fe(SCH3)(4)](2-) and [Fe(SCH3)(4)](-) involve mainly the Fe 3d and S 3p orbitals, respectively. The calculated adiabatic and vertical detachment energies are in good agreement with the experiment for [Fe(SCH3)(3)](-) and [Fe(SCH3)(4)](-). The current results further confirm the "inverted level scheme" for the high-spin [1Fe] systems. The redox couple, [Fe(SCH3)(4)](- /2), which is the one found in rubredoxin, but cannot be accessed experimentally in the gas phase, was investigated using a thermodynamic cycle that relates it to the [Fe(SCH3)(3)](-/0) couple and the ligand association reaction, [Fe(SCH3)(3)](0/-) + SCH3- --> [Fe(SCH3)(4)](-/2-). The calculated reduction energy of [Fe(SCH3)(4)](-) (1.7 eV) compares well with the value (1.6 eV) estimated from the calculated bond energies and the experimental detachment energy of [Fe(SCH3)(3)](-). Thus, this thermodynamic cycle method can be used to estimate metal-ligand bonding energies and determine intrinsic reduction potentials from photodetachment experiments when the reduced forms are not stable in the gas phase.

  12. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles

    PubMed Central

    2015-01-01

    Mineral dusts originating from Earth’s crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts. Here we investigated in closer detail the reasons for its activity and the difference in the activity of the different feldspars. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. K-feldspar showed by far the highest ice nucleation activity. Finally, we give a potential explanation of this effect, finding alkali-metal ions having different hydration shells and thus an influence on the ice nucleation activity of feldspar surfaces. PMID:25584435

  13. Early Site Permit Demonstration Program: Recommendations for communication activities and public participation in the Early Site Permit Demonstration Program

    SciTech Connect

    Not Available

    1993-01-27

    On October 24, 1992, President Bush signed into law the National Energy Policy Act of 1992. The bill is a sweeping, comprehensive overhaul of the Nation`s energy laws, the first in more than a decade. Among other provisions, the National Energy Policy Act reforms the licensing process for new nuclear power plants by adopting a new approach developed by the US Nuclear Regulatory Commission (NRC) in 1989, and upheld in court in 1992. The NRC 10 CFR Part 52 rule is a three-step process that guarantees public participation at each step. The steps are: early site permit approval; standard design certifications; and, combined construction/operating licenses for nuclear power reactors. Licensing reform increases an organization`s ability to respond to future baseload electricity generation needs with less financial risk for ratepayers and the organization. Costly delays can be avoided because design, safety and siting issues will be resolved before a company starts to build a plant. Specifically, early site permit approval allows for site suitability and acceptability issues to be addressed prior to an organization`s commitment to build a plant. Responsibility for site-specific activities, including communications and public participation, rests with those organizations selected to try out early site approval. This plan has been prepared to assist those companies (referred to as sponsoring organizations) in planning their communications and public involvement programs. It provides research findings, information and recommendations to be used by organizations as a resource and starting point in developing their own plans.

  14. Ultrafast ligand binding dynamics in the active site of native bacterial nitric oxide reductase.

    PubMed

    Kapetanaki, Sofia M; Field, Sarah J; Hughes, Ross J L; Watmough, Nicholas J; Liebl, Ursula; Vos, Marten H

    2008-01-01

    The active site of nitric oxide reductase from Paracoccus denitrificans contains heme and non-heme iron and is evolutionarily related to heme-copper oxidases. The CO and NO dynamics in the active site were investigated using ultrafast transient absorption spectroscopy. We find that, upon photodissociation from the active site heme, 20% of the CO rebinds in 170 ps, suggesting that not all the CO transiently binds to the non-heme iron. The remaining 80% does not rebind within 4 ns and likely migrates out of the active site without transient binding to the non-heme iron. Rebinding of NO to ferrous heme takes place in approximately 13 ps. Our results reveal that heme-ligand recombination in this enzyme is considerably faster than in heme-copper oxidases and are consistent with a more confined configuration of the active site. PMID:18420024

  15. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination

    PubMed Central

    Rowley, Paul A.; Kachroo, Aashiq H.; Ma, Chien-Hui; Maciaszek, Anna D.; Guga, Piotr; Jayaram, Makkuni

    2015-01-01

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5′ to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions. PMID:25999343

  16. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination.

    PubMed

    Rowley, Paul A; Kachroo, Aashiq H; Ma, Chien-Hui; Maciaszek, Anna D; Guga, Piotr; Jayaram, Makkuni

    2015-07-13

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions. PMID:25999343

  17. Active and Widespread Halogen Chemistry in the Tropical and Subtropical Free Troposphere

    NASA Technical Reports Server (NTRS)

    Wang, Siyuan; Schmidt, Johan A.; Baidar, Sunil; Coburn, Sean; Dix, Barbara; Koenig, Theodore K.; Apel, Eric; Bowdalo, Dene; Campos, Teresa; Eloranta, Ed; Evans, Mathew J.; Digangi, Joshua P.; Zondlo, Mark A.; Gao, Ru-shan; Haggerty, Julie A.; Hall, Samuel R.; Hornbrook, Rebecca S.; Jacob, Daniel; Morley, Bruce; Pierce, Bradley; Reeves, Mike; Romashkin, Pavel; Ter Schure, Arnout; Volkamer, Rainer

    2015-01-01

    Halogens in the troposphere are increasingly recognized as playing an important role for atmospheric chemistry, and possibly climate. Bromine and iodine react catalytically to destroy ozone (O3), oxidize mercury, and modify oxidative capacity that is relevant for the lifetime of greenhouse gases. Most of the tropospheric O3 and methane (CH4) loss occurs at tropical latitudes. Here we report simultaneous measurements of vertical profiles of bromine oxide (BrO) and iodine oxide (IO) in the tropical and subtropical free troposphere (10degN to 40degS), and show that these halogens are responsible for 34% of the column-integrated loss of tropospheric O3. The observed BrO concentrations increase strongly with altitude (approx.3.4 pptv at 13.5 km), and are 2-4 times higher than predicted in the tropical free troposphere. BrO resembles model predictions more closely in stratospheric air. The largest model low bias is observed in the lower tropical transition layer (TTL) over the tropical eastern Pacific Ocean, and may reflect a missing inorganic bromine source supplying an additional 2.5-6.4 pptv total inorganic bromine (Bry), or model overestimated Bry wet scavenging. Our results highlight the importance of heterogeneous chemistry on ice clouds, and imply an additional Bry source from the debromination of sea salt residue in the lower TTL. The observed levels of bromine oxidize mercury up to 3.5 times faster than models predict, possibly increasing mercury deposition to the ocean. The halogen-catalyzed loss of tropospheric O3 needs to be considered when estimating past and future ozone radiative effects.

  18. Surface chemistry of Au/TiO2: Thermally and photolytically activated reactions

    NASA Astrophysics Data System (ADS)

    Panayotov, Dimitar A.; Morris, John R.

    2016-03-01

    The fascinating particle size dependence to the physical, photophysical, and chemical properties of gold has motivated thousands of studies focused on exploring the ability of supported gold nanoparticles to catalyze chemical transformations. In particular, titanium dioxide-supported gold (Au/TiO2) nanoparticles may provide the right combination of electronic structure, structural dynamics, and stability to affect catalysis in important practical applications from environmental remediation to selective hydrogenation to carbon monoxide oxidation. Harnessing the full potential of Au/TiO2 will require a detailed atomic-scale understanding of the thermal and photolytic processes that accompany chemical conversion. This review describes some of the unique properties exhibited by particulate gold before delving into how those properties affect chemistry on titania supports. Particular attention is given first to thermally driven reactions on single crystal system. This review then addresses nanoparticulate samples in an effort begin to bridge the so-called materials gap. Building on the foundation provided by the large body of work in the field of thermal catalysis, the review describes new research into light-driven catalysis on Au/TiO2. Importantly, the reader should bear in mind throughout this review that thermal chemistry and thermal effects typically accompany photochemistry. Distinguishing between thermally-driven stages of a reaction and photo-induced steps remains a significant challenge, but one that experimentalists and theorists are beginning to decipher with new approaches. Finally, a summary of several state-of-the-art studies describes how they are illuminating new frontiers in the quest to exploit Au/TiO2 as an efficient catalyst and low-energy photocatalyst.

  19. Active and widespread halogen chemistry in the tropical and subtropical free troposphere.

    PubMed

    Wang, Siyuan; Schmidt, Johan A; Baidar, Sunil; Coburn, Sean; Dix, Barbara; Koenig, Theodore K; Apel, Eric; Bowdalo, Dene; Campos, Teresa L; Eloranta, Ed; Evans, Mathew J; DiGangi, Joshua P; Zondlo, Mark A; Gao, Ru-Shan; Haggerty, Julie A; Hall, Samuel R; Hornbrook, Rebecca S; Jacob, Daniel; Morley, Bruce; Pierce, Bradley; Reeves, Mike; Romashkin, Pavel; Ter Schure, Arnout; Volkamer, Rainer

    2015-07-28

    Halogens in the troposphere are increasingly recognized as playing an important role for atmospheric chemistry, and possibly climate. Bromine and iodine react catalytically to destroy ozone (O3), oxidize mercury, and modify oxidative capacity that is relevant for the lifetime of greenhouse gases. Most of the tropospheric O3 and methane (CH4) loss occurs at tropical latitudes. Here we report simultaneous measurements of vertical profiles of bromine oxide (BrO) and iodine oxide (IO) in the tropical and subtropical free troposphere (10 °N to 40 °S), and show that these halogens are responsible for 34% of the column-integrated loss of tropospheric O3. The observed BrO concentrations increase strongly with altitude (∼ 3.4 pptv at 13.5 km), and are 2-4 times higher than predicted in the tropical free troposphere. BrO resembles model predictions more closely in stratospheric air. The largest model low bias is observed in the lower tropical transition layer (TTL) over the tropical eastern Pacific Ocean, and may reflect a missing inorganic bromine source supplying an additional 2.5-6.4 pptv total inorganic bromine (Bry), or model overestimated Bry wet scavenging. Our results highlight the importance of heterogeneous chemistry on ice clouds, and imply an additional Bry source from the debromination of sea salt residue in the lower TTL. The observed levels of bromine oxidize mercury up to 3.5 times faster than models predict, possibly increasing mercury deposition to the ocean. The halogen-catalyzed loss of tropospheric O3 needs to be considered when estimating past and future ozone radiative effects. PMID:26124148

  20. Active and widespread halogen chemistry in the tropical and subtropical free troposphere

    PubMed Central

    Wang, Siyuan; Schmidt, Johan A.; Baidar, Sunil; Coburn, Sean; Dix, Barbara; Koenig, Theodore K.; Apel, Eric; Bowdalo, Dene; Campos, Teresa L.; Eloranta, Ed; Evans, Mathew J.; DiGangi, Joshua P.; Zondlo, Mark A.; Gao, Ru-Shan; Haggerty, Julie A.; Hall, Samuel R.; Hornbrook, Rebecca S.; Jacob, Daniel; Morley, Bruce; Pierce, Bradley; Reeves, Mike; Romashkin, Pavel; ter Schure, Arnout; Volkamer, Rainer

    2015-01-01

    Halogens in the troposphere are increasingly recognized as playing an important role for atmospheric chemistry, and possibly climate. Bromine and iodine react catalytically to destroy ozone (O3), oxidize mercury, and modify oxidative capacity that is relevant for the lifetime of greenhouse gases. Most of the tropospheric O3 and methane (CH4) loss occurs at tropical latitudes. Here we report simultaneous measurements of vertical profiles of bromine oxide (BrO) and iodine oxide (IO) in the tropical and subtropical free troposphere (10°N to 40°S), and show that these halogens are responsible for 34% of the column-integrated loss of tropospheric O3. The observed BrO concentrations increase strongly with altitude (∼3.4 pptv at 13.5 km), and are 2–4 times higher than predicted in the tropical free troposphere. BrO resembles model predictions more closely in stratospheric air. The largest model low bias is observed in the lower tropical transition layer (TTL) over the tropical eastern Pacific Ocean, and may reflect a missing inorganic bromine source supplying an additional 2.5–6.4 pptv total inorganic bromine (Bry), or model overestimated Bry wet scavenging. Our results highlight the importance of heterogeneous chemistry on ice clouds, and imply an additional Bry source from the debromination of sea salt residue in the lower TTL. The observed levels of bromine oxidize mercury up to 3.5 times faster than models predict, possibly increasing mercury deposition to the ocean. The halogen-catalyzed loss of tropospheric O3 needs to be considered when estimating past and future ozone radiative effects. PMID:26124148

  1. Chemistry of Dry Deposition on Building Materials at an Urban Site on Indo Gangetic Plain in India

    NASA Astrophysics Data System (ADS)

    Kumar, R.; Srivastava, S. S.; Kumari, K. M.

    2008-05-01

    Dry deposition is an important pathway for removal of pollutants from the atmosphere to earth surfaces. Agra is famous for historical monuments and cultural heritage worldwide. Increase in atmospheric contamination has caused extinction threats to building materials. The main pollutants of concern are S and N species. This paper deals with deposition of F-, Cl-, SO42-, NO3-, SO2, HNO3, NH3, Na+, K+, Ca2+, Mg2+ and NH4+ on marbles and red stones at Agra a site in Indo-Gangetic Plain. Dry deposition was higher on white marble than red stone. X-ray study reveals that higher deposition on marble is probably due to chemical characteristics of surfaces. Direct measurements study are cumbersome and tedious so an alternate method of parameterization based on meteorological parameters for calculation of dry deposition of S and N compounds to building materials are simulated and computer programme was developed to make it more convenient, fast and useful. The deposition velocity of SO2, HNO3, SO42- and NO3- obtained by current parameterization method are in the reported range. Dry deposition fluxes obtained by the current parameterization method and direct measurements are in the range.

  2. Single-Site Zeolite-Anchored Organoiridium Carbonyl Complexes: Characterization of Structure and Reactivity by Spectroscopy and Computational Chemistry

    DOE PAGESBeta

    Martinez-Macias, Claudia; Chen, Mingyang; Dixon, David A.; Gates, Bruce C.

    2015-07-03

    We formed a family of HY zeolite-supported cationic organoiridium carbonyl complexes by reaction of Ir(CO)2(acac) (acac=acetylacetonate) to form supported Ir(CO)2 complexes, which were treated at 298K and 1atm with flowing gas-phase reactants, including C2H4, H2, (CO)-C-12, (CO)-C-13, and D2O. Mass spectrometry was used to identify effluent gases, and infrared and X-ray absorption spectroscopies were used to characterize the supported species, with the results bolstered by DFT calculations. The support is crystalline and presents a nearly uniform array of bonding sites for the iridium species, so these were characterized by a high degree of uniformity, which allowed a precise determination ofmore » the species involved in the replacement, for example, of one CO ligand of each Ir(CO)2 complex with ethylene. The supported species include the following: Ir(CO)2, Ir(CO)(C2H4)2, Ir(CO)(C2H4), Ir(CO)(C2H5), and (tentatively) Ir(CO)(H). The data determine a reaction network involving all of these species.« less

  3. Single-Site Zeolite-Anchored Organoiridium Carbonyl Complexes: Characterization of Structure and Reactivity by Spectroscopy and Computational Chemistry

    SciTech Connect

    Martinez-Macias, Claudia; Chen, Mingyang; Dixon, David A.; Gates, Bruce C.

    2015-07-03

    We formed a family of HY zeolite-supported cationic organoiridium carbonyl complexes by reaction of Ir(CO)2(acac) (acac=acetylacetonate) to form supported Ir(CO)2 complexes, which were treated at 298K and 1atm with flowing gas-phase reactants, including C2H4, H2, (CO)-C-12, (CO)-C-13, and D2O. Mass spectrometry was used to identify effluent gases, and infrared and X-ray absorption spectroscopies were used to characterize the supported species, with the results bolstered by DFT calculations. The support is crystalline and presents a nearly uniform array of bonding sites for the iridium species, so these were characterized by a high degree of uniformity, which allowed a precise determination of the species involved in the replacement, for example, of one CO ligand of each Ir(CO)2 complex with ethylene. The supported species include the following: Ir(CO)2, Ir(CO)(C2H4)2, Ir(CO)(C2H4), Ir(CO)(C2H5), and (tentatively) Ir(CO)(H). The data determine a reaction network involving all of these species.

  4. The Chemistry of Fragrances: A Group Exercise for Chemistry Students.

    ERIC Educational Resources Information Center

    Duprey, Roger; Sell, Charles S.; Lowe, Nigel D.

    2003-01-01

    Presents Fragrance Structured Learning Packages (SLPs), group activities designed to help students recognize the value of applying chemistry in a real-world setting. Developed by the Department of Chemistry at the University of York. (Author/KHR)

  5. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts.

    PubMed

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-01-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and (57)Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity. PMID:26486465

  6. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts

    NASA Astrophysics Data System (ADS)

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I.; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-10-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and 57Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity.

  7. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts

    PubMed Central

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I.; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-01-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and 57Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity. PMID:26486465

  8. Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

    PubMed

    Miner, Kyle D; Kurtz, Donald M

    2016-02-16

    HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites. PMID:26786892

  9. Molecular Basis for Enzymatic Sulfite Oxidation -- HOW THREE CONSERVED ACTIVE SITE RESIDUES SHAPE ENZYME ACTIVITY

    SciTech Connect

    Bailey, Susan; Rapson, Trevor; Johnson-Winters, Kayunta; Astashkin, Andrei; Enemark, John; Kappler, Ulrike

    2008-11-10

    Sulfite dehydrogenases (SDHs) catalyze the oxidation and detoxification of sulfite to sulfate, a reaction critical to all forms of life. Sulfite-oxidizing enzymes contain three conserved active site amino acids (Arg-55, His-57, and Tyr-236) that are crucial for catalytic competency. Here we have studied the kinetic and structural effects of two novel and one previously reported substitution (R55M, H57A, Y236F) in these residues on SDH catalysis. Both Arg-55 and His-57 were found to have key roles in substrate binding. An R55M substitution increased Km(sulfite)(app) by 2-3 orders of magnitude, whereas His-57 was required for maintaining a high substrate affinity at low pH when the imidazole ring is fully protonated. This effect may be mediated by interactions of His-57 with Arg-55 that stabilize the position of the Arg-55 side chain or, alternatively, may reflect changes in the protonation state of sulfite. Unlike what is seen for SDHWT and SDHY236F, the catalytic turnover rates of SDHR55M and SDHH57A are relatively insensitive to pH (~;;60 and 200 s-1, respectively). On the structural level, striking kinetic effects appeared to correlate with disorder (in SDHH57A and SDHY236F) or absence of Arg-55 (SDHR55M), suggesting that Arg-55 and the hydrogen bonding interactions it engages in are crucial for substrate binding and catalysis. The structure of SDHR55M has sulfate bound at the active site, a fact that coincides with a significant increase in the inhibitory effect of sulfate in SDHR55M. Thus, Arg-55 also appears to be involved in enabling discrimination between the substrate and product in SDH.

  10. Assessment of activation products in the Savannah River Site environment

    SciTech Connect

    Carlton, W.H.; Denham, M.

    1996-07-01

    This document assesses the impact of radioactive activation products released from SRS facilities since the first reactor became operational late in 1953. The isotopes reported here are those whose release resulted in the highest dose to people living near SRS: {sup 32}P, {sup 51}Cr, {sup 60}C, and {sup 65}Zn. Release pathways, emission control features, and annual releases to the aqueous and atmospheric environments are discussed. No single incident has resulted in a major acute release of activation products to the environment. The releases were the result of normal operations of the reactors and separations facilities. Releases declined over the years as better controls were established and production was reduced. The overall radiological impact of SRS activation product atmospheric releases from 1954 through 1994 on the offsite maximally exposed individual can be characterized by a total dose of 0.76 mrem. During the same period, such an individual received a total dose of 14,400 mrem from non-SRS sources of ionizing radiation present in the environment. SRS activation product aqueous releases between 1954 and 1994 resulted in a total dose of 54 mrem to the offsite maximally exposed individual. The impact of SRS activation product releases on offsite populations also has been evaluated.

  11. Fructose Promotes Uptake and Activity of Oligonucleotides With Different Chemistries in a Context-dependent Manner in mdx Mice.

    PubMed

    Cao, Limin; Han, Gang; Lin, Caorui; Gu, Ben; Gao, Xianjun; Moulton, Hong M; Seow, Yiqi; Yin, HaiFang

    2016-01-01

    Antisense oligonucleotide (AO)-mediated exon-skipping therapeutics shows great promise in correcting frame-disrupting mutations in the DMD gene for Duchenne muscular dystrophy. However, insufficient systemic delivery limits clinical adoption. Previously, we showed that a glucose/fructose mixture augmented AO delivery to muscle in mdx mice. Here, we evaluated if fructose alone could enhance the activities of AOs with different chemistries in mdx mice. The results demonstrated that fructose improved the potency of AOs tested with the greatest effect on phosphorodiamidate morpholino oligomer (PMO), resulted in a 4.25-fold increase in the number of dystrophin-positive fibres, compared to PMO in saline in mdx mice. Systemic injection of lissamine-labeled PMO with fructose at 25 mg/kg led to increased uptake and elevated dystrophin expression in peripheral muscles, compared to PMO in saline, suggesting that fructose potentiates PMO by enhancing uptake. Repeated intravenous administration of PMO in fructose at 50 mg/kg/week for 3 weeks and 50 mg/kg/month for 5 months restored up to 20% of wild-type dystrophin levels in skeletal muscles with improved functions without detectable toxicity, compared to untreated mdx controls. Collectively, we show that fructose can potentiate AOs of different chemistries in vivo although the effect diminished over repeated administration. PMID:27351681

  12. The Lighter Side of Chemistry.

    ERIC Educational Resources Information Center

    Lamb, William G.

    1984-01-01

    Discusses the rationale for using photochemistry to merge descriptive chemistry and molecular orbital theory in first-year chemistry courses. Includes procedures and safety information for various activities, demonstrations, and experiments involving photochemical reactions. (DH)

  13. Geologic, water-chemistry, and hydrologic data from multiple-well monitoring sites and selected water-supply wells in the Santa Clara Valley, California, 1999-2003

    USGS Publications Warehouse

    Newhouse, M.W.; Hanson, R.T.; Wentworth, C.M.; Everett, Rhett; Williams, C.F.; Tinsley, J.C.; Noce, T.E.; Carkin, B.A.

    2004-01-01

    To better identify the three-dimensional geohydrologic framework of the Santa Clara Valley, lithologic, geologic, geophysical, geomechanical, hydraulic, and water-chemistry data were collected from eight ground-water multiple-well monitoring sites constructed in Santa Clara County, California, as part of a series of cooperative studies between the U.S. Geological Survey and the Santa Clara Valley Water District. The data are being used to update and improve the three-dimensional geohydrologic framework of the basin and to address issues related to water supply, water chemistry, sequence stratigraphy, geology, and geological hazards. This report represents a compilation of data collected from 1999 to 2003, including location and design of the monitoring sites, cone penetrometer borings, geologic logs, lithologic logs, geophysical logs, core analysis, water-chemistry analysis, ground-water-level measurements, and hydraulic and geomechanical properties from wells and core samples. Exploratory cone penetrometer borings taken in the upper 17 to 130 feet at six of the monitoring sites identified the base of Holocene as no deeper than 75 feet in the central confined area and no deeper than 35 feet in the southern unconfined areas of the valley. Generalized lithologic characterization from the monitoring sites indicates about four to six different aquifer units separated by relatively fine-grained units occur within the alluvial deposits shallower than 860 feet deep. Analysis of geophysical logs indicates that coarse-grained units varied in thickness between 10 and 25 feet in the southeastern unconfined area of the valley and between 50 and 200 feet in the south-central and southwestern areas of the valley. Deviations from temperature-gradient logs indicate that the majority of horizontal ground-water flow occurs above a depth of 775 feet in the south central and above 510 feet in the southeastern areas of the valley. Bulk physical properties from more than 1,150 feet of

  14. Adsorption of a Textile Dye on Commercial Activated Carbon: A Simple Experiment to Explore the Role of Surface Chemistry and Ionic Strength

    ERIC Educational Resources Information Center

    Martins, Angela; Nunes, Nelson

    2015-01-01

    In this study, an adsorption experiment is proposed using commercial activated carbon as adsorbent and a textile azo dye, Mordant Blue-9, as adsorbate. The surface chemistry of the activated carbon is changed through a simple oxidation treatment and the ionic strength of the dye solution is also modified, simulating distinct conditions of water…

  15. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand.

    PubMed

    Parashar, Abhinav; Venkatachalam, Avanthika; Gideon, Daniel Andrew; Manoj, Kelath Murali

    2014-12-12

    The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins' active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes. PMID:25449264

  16. Active site proton delivery and the lyase activity of human CYP17A1

    SciTech Connect

    Khatri, Yogan; Gregory, Michael C.; Grinkova, Yelena V.; Denisov, Ilia G.; Sligar, Stephen G.

    2014-01-03

    equivalents and protons are funneled into non-productive pathways. This is similar to previous work with other P450 catalyzed hydroxylation. However, catalysis of carbon–carbon bond scission by the T306A mutant was largely unimpeded by disruption of the CYP17A1 acid-alcohol pair. The unique response of CYP17A1 lyase activity to mutation of Thr306 is consistent with a reactive intermediate formed independently of proton delivery in the active site, and supports involvement of a nucleophilic peroxo-anion rather than the traditional Compound I in catalysis.

  17. Characterization of an Active Thermal Erosion Site, Caribou Creek, Alaska

    NASA Astrophysics Data System (ADS)

    Busey, R.; Bolton, W. R.; Cherry, J. E.; Hinzman, L. D.

    2013-12-01

    The goal of this project is to estimate volume loss of soil over time from this site, provide parameterizations on erodibility of ice rich permafrost and serve as a baseline for future landscape evolution simulations. Located in the zone of discontinuous permafrost, the interior region of Alaska (USA) is home to a large quantity of warm, unstable permafrost that is both high in ice content and has soil temperatures near the freezing point. Much of this permafrost maintains a frozen state despite the general warming air temperature trend in the region due to the presence of a thick insulating organic mat and a dense root network in the upper sub-surface of the soil column. At a rapidly evolving thermo-erosion site, located within the Caribou-Poker Creeks Research Watershed (part of the Bonanza Creek LTER) near Chatanika, Alaska (N65.140, W147.570), the protective organic layer and associated plants were disturbed by an adjacent traditional use trail and the shifting of a groundwater spring. These triggers have led to rapid geomorphological change on the landscape as the soil thaws and sediment is transported into the creek at the valley bottom. Since 2006 (approximately the time of initiation), the thermal erosion has grown to 170 meters length, 3 meters max depth, and 15 meters maximum width. This research combines several data sets: DGPS survey, imagery from an extremely low altitude pole-based remote sensing (3 to 5 meters above ground level), and imagery from an Unmanned Aerial System (UAS) at about 60m altitude.

  18. Marine Biology Field Trip Sites. Ocean Related Curriculum Activities.

    ERIC Educational Resources Information Center

    Pauls, John

    The ocean affects all of our lives. Therefore, awareness of and information about the interconnections between humans and oceans are prerequisites to making sound decisions for the future. Project ORCA (Ocean Related Curriculum Activities) has developed interdisciplinary curriculum materials designed to meet the needs of students and teachers…

  19. Carbonate Chemistry Dynamics in an Area of Active Gas Seepage: the Hudson Canyon, US Atlantic Margin

    NASA Astrophysics Data System (ADS)

    Garcia-Tigreros Kodovska, F.; Kessler, J. D.; Leonte, M.; Chepigin, A.; Kellermann, M. Y.; Arrington, E. C.; Valentine, D. L.

    2015-12-01

    The fate of oceanic methane and its impact on the global climate has been of particular interest to the global community. The potential for vast amounts of methane to be emitted from the seafloor into the atmosphere due to gas hydrate decomposition has been under scientific evaluation. However, despite the great extent of these geological reservoirs, much of the methane released from the seafloor in deep ocean environments does not reach the atmosphere. Once dissolved in ocean water, the emitted methane can be microbially converted to either carbon dioxide or assimilated to biomass. Here, we will present results from a research cruise to the Hudson Canyon, northern US Atlantic Margin, where we investigated changes in ocean water carbonate chemistry induced by the oxidation of methane released from gas seeps. We will be presenting high precision pH data as well as methane and DIC concentrations, natural stable isotopes, and methane oxidation rates collected inside and adjacent to the Hudson Canyon in the summer of 2014.

  20. Rosetta/VIRTIS investigation of the chemistry and activity of comet 67P/Churyumov-Gerasimenko

    NASA Astrophysics Data System (ADS)

    Bockelee-Morvan, Dominique; Drossart, Pierre; Piccioni, Giuseppe; Migliorini, Alessandra; Erard, Stéphane; Capaccioni, Fabrizio; Filacchione, Gianrico; Fougere, Nicolas; Leyrat, Cedric; Crovisier, Jacques; Capaccioni, Fabrizio

    2016-07-01

    The composition of cometary ices inside cometary nuclei provides clues to the chemistry of the protoplanetary disk where they formed, 4.6 Gyr ago. These ices sublimate when the body approches the Sun, so that the coma molecular species give insights on the nucleus surface and sub-surface composition. So far, most investigations of the coma chemical composition were performed from telescopic observations from the ground or space plateforms. Since August 2014, the ESA/Rosetta spacecraft has been investigating the nucleus and inner coma of 67P/Churyumov-Gerasimenko. This talk will present an overview of the results obtained by the Visual and Infrared Thermal Imaging Spectrometer (VIRTIS) instrument onboard Rosetta, focussing on observations of molecular species. VIRTIS is composed of two channels. The VIRTIS-M channel is a spectro-imager covering the 0.27-5.1 microns range, which allowed us to map the spatial distribution of H2O and CO2 (Migliorini et al. 2016, A&A in press). VIRTIS-H is a high-spectral resolution spectrometer covering the 2-5 microns range. Spectra obtained with VIRTIS-H show signatures of H2O, CO2 (both fundamental and hot bands), 13CO2, CH4 and other C-H bearing species (Bockelee-Morvan et al. A&A, 583, A6,2015). VIRTIS is a key instrument to investigate regional, diurnal and seasonal variations of the comet outgassing.

  1. Prebiotic chemistry and atmospheric warming of early Earth by an active young Sun

    NASA Astrophysics Data System (ADS)

    Airapetian, V. S.; Glocer, A.; Gronoff, G.; Hébrard, E.; Danchi, W.

    2016-06-01

    Nitrogen is a critical ingredient of complex biological molecules. Molecular nitrogen, however, which was outgassed into the Earth’s early atmosphere, is relatively chemically inert and nitrogen fixation into more chemically reactive compounds requires high temperatures. Possible mechanisms of nitrogen fixation include lightning, atmospheric shock heating by meteorites, and solar ultraviolet radiation. Here we show that nitrogen fixation in the early terrestrial atmosphere can be explained by frequent and powerful coronal mass ejection events from the young Sun--so-called superflares. Using magnetohydrodynamic simulations constrained by Kepler Space Telescope observations, we find that successive superflare ejections produce shocks that accelerate energetic particles, which would have compressed the early Earth’s magnetosphere. The resulting extended polar cap openings provide pathways for energetic particles to penetrate into the atmosphere and, according to our atmospheric chemistry simulations, initiate reactions converting molecular nitrogen, carbon dioxide and methane to the potent greenhouse gas nitrous oxide as well as hydrogen cyanide, an essential compound for life. Furthermore, the destruction of N2, CO2 and CH4 suggests that these greenhouse gases cannot explain the stability of liquid water on the early Earth. Instead, we propose that the efficient formation of nitrous oxide could explain a warm early Earth.

  2. Testing CMAQ chemistry sensitivities in base case and emissions control runs at SEARCH and SOS99 surface sites in the southeastern US

    NASA Astrophysics Data System (ADS)

    Arnold, J. R.; Dennis, Robin L.

    CMAQ was run to simulate urban and regional tropospheric conditions in the southeastern US over 14 days in July 1999 at 32, 8 and 2 km grid spacings. Runs were made with either of two older mechanisms, Carbon Bond IV (CB4) and the Regional Acid Deposition Model, version 2 (RADM2), and with the more recent and complete California Statewide Air Pollution Research Center, version 1999 mechanism (SAPRC99) in a sensitivity matrix with a full emissions base case and separate 50% control scenarios for emissions of nitrogen oxides (NO X) and volatile organic compounds (VOC). Results from the base case were compared to observations at the Southeastern Aerosol Research and Characterization Study (SEARCH) site at Jefferson Street in Atlanta, GA (JST) and the Southern Oxidant Study (SOS) Cornelia Fort Airpark (CFA) site downwind of Nashville, TN. In the base case, SAPRC99 predicted more ozone (O 3) than CB4 or RADM2 almost every hour and especially for afternoon maxima at both JST and CFA. Performance of the 8 km models at JST was better than that of the 32 km ones for all chemistries, reducing the 1 h peak bias by as much as 30 percentage points; at CFA only the RADM2 8 km model improved. The 2 km solutions did not show improved performance over the 8 km ones at either site, with normalized 1 h bias in the peak O 3 ranging from 21% at CFA to 43% at JST. In the emissions control cases, SAPRC99 was generally more responsive than CB4 and RADM2 to NO X and VOC controls, excepting hours at JST with predicted increased O 3 from NO X control. Differential sensitivity to chemical mechanism varied by more than ±10% for NO X control at JST and CFA, and in a similar range for VOC control at JST. VOC control at the more strongly NO X- limited urban CFA site produced a differential sensitivity response of <5%. However, even when differential sensitivities in control cases were small, neither their sign nor their magnitude could be reliably determined from model performance in the full

  3. Reduction of urease activity by interaction with the flap covering the active site.

    PubMed

    Macomber, Lee; Minkara, Mona S; Hausinger, Robert P; Merz, Kenneth M

    2015-02-23

    With the increasing appreciation for the human microbiome coupled with the global rise of antibiotic resistant organisms, it is imperative that new methods be developed to specifically target pathogens. To that end, a novel computational approach was devised to identify compounds that reduce the activity of urease, a medically important enzyme of Helicobacter pylori, Proteus mirabilis, and many other microorganisms. Urease contains a flexible loop that covers its active site; Glide was used to identify small molecules predicted to lock this loop in an open conformation. These compounds were screened against the model urease from Klebsiella aerogenes, and the natural products epigallocatechin and quercetin were shown to inhibit at low and high micromolar concentrations, respectively. These molecules exhibit a strong time-dependent inactivation of urease that was not due to their oxygen sensitivity. Rather, these compounds appear to inactivate urease by reacting with a specific Cys residue located on the flexible loop. Substitution of this cysteine by alanine in the C319A variant increased the urease resistance to both epigallocatechin and quercetin, as predicted by the computational studies. Protein dynamics are integral to the function of many enzymes; thus, identification of compounds that lock an enzyme into a single conformation presents a useful approach to define potential inhibitors. PMID:25594724

  4. Reduction of Urease Activity by Interaction with the Flap Covering the Active Site

    PubMed Central

    Macomber, Lee; Minkara, Mona S.; Hausinger, Robert P.; Merz, Kenneth M.

    2015-01-01

    With the increasing appreciation for the human microbiome coupled with the global rise of antibiotic resistant organisms, it is imperative that new methods be developed to specifically target pathogens. To that end, a novel computational approach was devised to identify compounds that reduce the activity of urease, a medically important enzyme of Helicobacter pylori, Proteus mirabilis, and many other microorganisms. Urease contains a flexible loop that covers its active site; Glide was used to identify small molecules predicted to lock this loop in an open conformation. These compounds were screened against the model urease from Klebsiella aerogenes and the natural products epigallocatechin and quercetin were shown to inhibit at low and high micromolar concentrations, respectively. These molecules exhibit a strong time-dependent inactivation of urease that was not due to their oxygen sensitivity. Rather, these compounds appear to inactivate urease by reacting with a specific Cys residue located on the flexible loop. Substitution of this cysteine by alanine in the C319A variant increased the urease resistance to both epigallocatechin and quercetin, as predicted by the computational studies. Protein dynamics are integral to the function of many enzymes; thus, identification of compounds that lock an enzyme into a single conformation presents a useful approach to define potential inhibitors. PMID:25594724

  5. Encroachment of Human Activity on Sea Turtle Nesting Sites

    NASA Astrophysics Data System (ADS)

    Ziskin, D.; Aubrecht, C.; Elvidge, C.; Tuttle, B.; Baugh, K.; Ghosh, T.

    2008-12-01

    The encroachment of anthropogenic lighting on sea turtle nesting sites poses a serious threat to the survival of these animals [Nicholas, 2001]. This danger is quantified by combining two established data sets. The first is the Nighttime Lights data produced by the NOAA National Geophysical Data Center [Elvidge et al., 1997]. The second is the Marine Turtle Database produced by the World Conservation Monitoring Centre (WCMC). The technique used to quantify the threat of encroachment is an adaptation of the method described in Aubrecht et al. [2008], which analyzes the stress on coral reef systems by proximity to nighttime lights near the shore. Nighttime lights near beaches have both a direct impact on turtle reproductive success since they disorient hatchlings when they mistake land-based lights for the sky-lit surf [Lorne and Salmon, 2007] and the lights are also a proxy for other anthropogenic threats. The identification of turtle nesting sites with high rates of encroachment will hopefully steer conservation efforts to mitigate their effects [Witherington, 1999]. Aubrecht, C, CD Elvidge, T Longcore, C Rich, J Safran, A Strong, M Eakin, KE Baugh, BT Tuttle, AT Howard, EH Erwin, 2008, A global inventory of coral reef stressors based on satellite observed nighttime lights, Geocarto International, London, England: Taylor and Francis. In press. Elvidge, CD, KE Baugh, EA Kihn, HW Kroehl, ER Davis, 1997, Mapping City Lights with Nighttime Data from the DMSP Operational Linescan System, Photogrammatic Engineering and Remote Sensing, 63:6, pp. 727-734. Lorne, JK, M Salmon, 2007, Effects of exposure to artificial lighting on orientation of hatchling sea turtles on the beach and in the ocean, Endangered Species Research, Vol. 3: 23-30. Nicholas, M, 2001, Light Pollution and Marine Turtle Hatchlings: The Straw that Breaks the Camel's Back?, George Wright Forum, 18:4, p77-82. Witherington, BE, 1999, Reducing Threats To Nesting Habitat, Research and Management Techniques for

  6. Thirty years through vanadium chemistry.

    PubMed

    Costa Pessoa, J

    2015-06-01

    The relevance of vanadium in biological systems is known for many years and vanadium-based catalysts have important industrial applications, however, till the beginning of the 80s research on vanadium chemistry and biochemistry did not receive much attention from the scientific community. The understanding of the broad bioinorganic implications resulting from the similarities between phosphate and vanadate(V) and the discovery of vanadium dependent enzymes gave rise to an enormous increase in interest in the chemistry and biological relevance of vanadium. Thereupon the last 30years corresponded to a period of enormous research effort in these fields, as well as in medicinal applications of vanadium and in the development of catalysts for use in fine-chemical synthesis, some of these inspired by enzymatic active sites. Since the 80s my group in collaboration with others made contributions, described throughout this text, namely in the understanding of the speciation of vanadium compounds in aqueous solution and in biological fluids, and to the transport of vanadium compounds in blood plasma and their uptake by cells. Several new types of vanadium compounds were also synthesized and characterized, with applications either as prospective therapeutic drugs or as homogeneous or heterogenized catalysts for the production of fine chemicals. The developments made are described also considering the international context of the evolution of the knowledge in the chemistry and bioinorganic chemistry of vanadium compounds during the last 30years. This article was compiled based on the Vanadis Award presentation at the 9th International Vanadium Symposium. PMID:25843361

  7. Small Molecule Active Site Directed Tools for Studying Human Caspases.

    PubMed

    Poreba, Marcin; Szalek, Aleksandra; Kasperkiewicz, Paulina; Rut, Wioletta; Salvesen, Guy S; Drag, Marcin

    2015-11-25

    Caspases are proteases of clan CD and were described for the first time more than two decades ago. They play critical roles in the control of regulated cell death pathways including apoptosis and inflammation. Due to their involvement in the development of various diseases like cancer, neurodegenerative diseases, or autoimmune disorders, caspases have been intensively investigated as potential drug targets, both in academic and industrial laboratories. This review presents a thorough, deep, and systematic assessment of all technologies developed over the years for the investigation of caspase activity and specificity using substrates and inhibitors, as well as activity based probes, which in recent years have attracted considerable interest due to their usefulness in the investigation of biological functions of this family of enzymes. PMID:26551511

  8. Activation of brown adipose tissue mitochondrial GDP binding sites

    SciTech Connect

    Swick, A.G.

    1987-01-01

    The primary function of brown adipose tissue (BAT) is heat production. This ability is attributed to the existence of a unique inner mitochondrial membrane protein termed the uncoupling protein or thermogenin. This protein is permeable to H+ and thus allows respiration (and therefore thermogenesis) to proceed at a rapid rate, independent of ADP phosphorylation. Proton conductance can be inhibited by the binding of purine nucleotides to the uncoupling protein. The binding of (/sup 3/H)-GDP to BAT mitochondria is frequently used as a measure of BAT thermogenic activity. Rats fed a diet that was low but adequate in protein exhibited a decrease in feed efficiency. In addition, BAT thermogenesis was activated as indicated by an elevation in the level of GDP binding to BAT mitochondria. This phenomena occurred in older rats and persisted over time.

  9. More Chemistry in a Soda Bottle: A Conservation of Mass Activity

    NASA Astrophysics Data System (ADS)

    Duffy, Daniel Q.; Shaw, Stephanie A.; Bare, William O.; Goldsby, Kenneth A.

    1995-08-01

    A simple activity designed to illustrate conservation of mass is reported. The activity uses a two-liter soda bottle to contain the products of a gas-evolving reaction. While any number of gas-evolving reactions could be used in this activity, a specific procedure for vinegar and baking soda is given since these materials present nominal hazards and are readily available to K-12 teachers.

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

    SciTech Connect

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

    1995-02-01

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

  11. Water quality, organic chemistry of sediment, and biological conditions of streams near an abandoned wood-preserving plant site at Jackson, Tennessee

    USGS Publications Warehouse

    Bradfield, A.D.; Flexner, N.M.; Webster, D.A.

    1993-01-01

    An investigation of water quality, organic sediment chemistry, and biological conditions of streams near an abandoned wood-preserving plant site at Jackson, Tennessee, was conducted during December 1990. The study was designed to assess the extent of possible contamination of water and biota in the streams from creosote-related discharge originating at this Superfund site. Central Creek, adjacent to the plant, had degraded water quality and biological conditions. Water samples from the most downstream station on Central Creek contained 30 micrograms per liter of pentachlorophenol, which exceeds the State's criterion maximum concentrations of 9 micrograms per liter for fish and aquatic life. Bottom-sediment samples from stations on Central Creek contained concentrations of acenaphthene, napthalene, and phenanthrene ranging from 1,400 to 2,500 micrograms per kilogram. Chronic or acute toxicity resulted during laboratory experiments using test organisms exposed to creosote-related contaminants. Sediment elutriate samples from Central Creek caused slightly to highly toxic effects on Ceriodaphnia dubia. Pimephales promelas, and Photobacterium phosphoreum. Fish-tissue samples from this station contained concentrations of naphthalene. dibenzofuran, fluorene, and phenanthrene ranging from 1.5 to 3.9 micrograms per kilogram Blue-green algae at this station represented about 79 percent of the organisms counted, whereas diatoms accounted for only 11 percent. Benthic invertebrate and fish samples from Central Creek had low diversity and density. Sediment samples from a station on the South Fork Forked Deer River downstream from its confluence with Central Creek contained concentrations of acenaphthene, anthracene, chrysene, fluoranthene, fluorene, pyrere, and phenanthrene ranging from 2,800 to 69,000 micrograms per kilogram. Sediment elutriate samples using water as elutriate from this station contained concentrations of extractable organic compounds ranging from an estimated

  12. Redox-active on-surface polymerization of single-site divalent cations from pure metals by a ketone-functionalized phenanthroline

    SciTech Connect

    Skomski, Daniel; Tempas, Christopher D.; Bukowski, Gregory S.; Smith, Kevin A.; Tait, Steven L.

    2015-03-14

    Metallic iron, chromium, or platinum mixing with a ketone-functionalized phenanthroline ligand on a single crystal gold surface demonstrates redox activity to a well-defined oxidation state and assembly into thermally stable, one dimensional, polymeric chains. The diverging ligand geometry incorporates redox-active sub-units and bi-dentate binding sites. The gold surface provides a stable adsorption environment and directs growth of the polymeric chains, but is inert with regard to the redox chemistry. These systems are characterized by scanning tunnelling microscopy, non-contact atomic force microscopy, and X-ray photoelectron spectroscopy under ultra-high vacuum conditions. The relative propensity of the metals to interact with the ketone group is examined, and it is found that Fe and Cr more readily complex the ligand than Pt. The formation and stabilization of well-defined transition metal single-sites at surfaces may open new routes to achieve higher selectivity in heterogeneous catalysts.

  13. Redox-active on-surface polymerization of single-site divalent cations from pure metals by a ketone-functionalized phenanthroline

    NASA Astrophysics Data System (ADS)

    Skomski, Daniel; Tempas, Christopher D.; Bukowski, Gregory S.; Smith, Kevin A.; Tait, Steven L.

    2015-03-01

    Metallic iron, chromium, or platinum mixing with a ketone-functionalized phenanthroline ligand on a single crystal gold surface demonstrates redox activity to a well-defined oxidation state and assembly into thermally stable, one dimensional, polymeric chains. The diverging ligand geometry incorporates redox-active sub-units and bi-dentate binding sites. The gold surface provides a stable adsorption environment and directs growth of the polymeric chains, but is inert with regard to the redox chemistry. These systems are characterized by scanning tunnelling microscopy, non-contact atomic force microscopy, and X-ray photoelectron spectroscopy under ultra-high vacuum conditions. The relative propensity of the metals to interact with the ketone group is examined, and it is found that Fe and Cr more readily complex the ligand than Pt. The formation and stabilization of well-defined transition metal single-sites at surfaces may open new routes to achieve higher selectivity in heterogeneous catalysts.

  14. Wave activity in the tropical tropopause layer in seven reanalysis and four chemistry climate model data sets

    NASA Astrophysics Data System (ADS)

    Fujiwara, M.; Suzuki, J.; Gettelman, A.; Hegglin, M. I.; Akiyoshi, H.; Shibata, K.

    2012-06-01

    Sub-seasonal variability including equatorial waves significantly influence the dehydration and transport processes in the tropical tropopause layer (TTL). This study investigates the wave activity in the TTL in 7 reanalysis data sets (RAs; NCEP1, NCEP2, ERA40, ERA-Interim, JRA25, MERRA, and CFSR) and 4 chemistry climate models (CCMs; CCSRNIES, CMAM, MRI, and WACCM) using the zonal wave number-frequency spectral analysis method with equatorially symmetric-antisymmetric decomposition. Analyses are made for temperature and horizontal winds at 100 hPa in the RAs and CCMs and for outgoing longwave radiation (OLR), which is a proxy for convective activity that generates tropopause-level disturbances, in satellite data and the CCMs. Particular focus is placed on equatorial Kelvin waves, mixed Rossby-gravity (MRG) waves, and the Madden-Julian Oscillation (MJO). The wave activity is defined as the variance, i.e., the power spectral density integrated in a particular zonal wave number-frequency region. It is found that the TTL wave activities show significant difference among the RAs, ranging from ˜0.7 (for NCEP1 and NCEP2) to ˜1.4 (for ERA-Interim, MERRA, and CFSR) with respect to the averages from the RAs. The TTL activities in the CCMs lie generally within the range of those in the RAs, with a few exceptions. However, the spectral features in OLR for all the CCMs are very different from those in the observations, and the OLR wave activities are too low for CCSRNIES, CMAM, and MRI. It is concluded that the broad range of wave activity found in the different RAs decreases our confidence in their validity and in particular their value for validation of CCM performance in the TTL, thereby limiting our quantitative understanding of the dehydration and transport processes in the TTL.

  15. Efficient Catalytic Ozonation over Reduced Graphene Oxide for p-Hydroxylbenzoic Acid (PHBA) Destruction: Active Site and Mechanism.

    PubMed

    Wang, Yuxian; Xie, Yongbing; Sun, Hongqi; Xiao, Jiadong; Cao, Hongbin; Wang, Shaobin

    2016-04-20

    Nanocarbons have been demonstrated as promising environmentally benign catalysts for advanced oxidation processes (AOPs) upgrading metal-based materials. In this study, reduced graphene oxide (rGO) with a low level of structural defects was synthesized via a scalable method for catalytic ozonation of p-hydroxylbenzoic acid (PHBA). Metal-free rGO materials were found to exhibit a superior activity in activating ozone for catalytic oxidation of organic phenolics. The electron-rich carbonyl groups were identified as the active sites for the catalytic reaction. Electron spin resonance (ESR) and radical competition tests revealed that superoxide radical ((•)O2(-)) and singlet oxygen ((1)O2) were the reactive oxygen species (ROS) for PHBA degradation. The intermediates and the degradation pathways were illustrated from mass spectroscopy. It was interesting to observe that addition of NaCl could enhance both ozonation and catalytic ozonation efficiencies and make ·O2(-) as the dominant ROS. Stability of the catalysts was also evaluated by the successive tests. Loss of specific surface area and changes in the surface chemistry were suggested to be responsible for catalyst deactivation. PMID:27007603

  16. School Pharmacist/School Environmental Hygienic Activities at School Site.

    PubMed

    Muramatsu, Akiyoshi

    2016-01-01

    The "School Health and Safety Act" was enforced in April 2009 in Japan, and "school environmental health standards" were established by the Minister of Education, Culture, Sports, Science and Technology. In Article 24 of the Enforcement Regulations, the duties of the school pharmacist have been clarified; school pharmacists have charged with promoting health activities in schools and carrying out complete and regular checks based on the "school environmental health standards" in order to protect the health of students and staff. In supported of this, the school pharmacist group of Japan Pharmaceutical Association has created and distributed digital video discs (DVDs) on "check methods of school environmental health standards" as support material. We use the DVD to ensure the basic issues that school pharmacists deal with, such as objectives, criteria, and methods for each item to be checked, advice, and post-measures. We conduct various workshops and classes, and set up Q&A committees so that inquiries from members are answered with the help of such activities. In addition, school pharmacists try to improve the knowledge of the school staff on environmental hygiene during their in-service training. They also conduct "drug abuse prevention classes" at school and seek to improve knowledge and recognition of drugs, including "dangerous drugs". PMID:27252053

  17. An Accessory Agonist Binding Site Promotes Activation of α4β2* Nicotinic Acetylcholine Receptors*

    PubMed Central

    Wang, Jingyi; Kuryatov, Alexander; Sriram, Aarati; Jin, Zhuang; Kamenecka, Theodore M.; Kenny, Paul J.; Lindstrom, Jon

    2015-01-01

    Neuronal nicotinic acetylcholine receptors containing α4, β2, and sometimes other subunits (α4β2* nAChRs) regulate addictive and other behavioral effects of nicotine. These nAChRs exist in several stoichiometries, typically with two high affinity acetylcholine (ACh) binding sites at the interface of α4 and β2 subunits and a fifth accessory subunit. A third low affinity ACh binding site is formed when this accessory subunit is α4 but not if it is β2. Agonists selective for the accessory ACh site, such as 3-[3-(3-pyridyl)-1,2,4-oxadiazol-5-yl]benzonitrile (NS9283), cannot alone activate a nAChR but can facilitate more efficient activation in combination with agonists at the canonical α4β2 sites. We therefore suggest categorizing agonists according to their site selectivity. NS9283 binds to the accessory ACh binding site; thus it is termed an accessory site-selective agonist. We expressed (α4β2)2 concatamers in Xenopus oocytes with free accessory subunits to obtain defined nAChR stoichiometries and α4/accessory subunit interfaces. We show that α2, α3, α4, and α6 accessory subunits can form binding sites for ACh and NS9283 at interfaces with α4 subunits, but β2 and β4 accessory subunits cannot. To permit selective blockage of the accessory site, α4 threonine 126 located on the minus side of α4 that contributes to the accessory site, but not the α4β2 sites, was mutated to cysteine. Alkylation of this cysteine with a thioreactive reagent blocked activity of ACh and NS9283 at the accessory site. Accessory agonist binding sites are promising drug targets. PMID:25869137

  18. Isolated metal active site concentration and stability control catalytic CO2 reduction selectivity.

    PubMed

    Matsubu, John C; Yang, Vanessa N; Christopher, Phillip

    2015-03-01

    CO2 reduction by H2 on heterogeneous catalysts is an important class of reactions that has been studied for decades. However, atomic scale details of structure-function relationships are still poorly understood. Particularly, it has been suggested that metal particle size plays a unique role in controlling the stability of CO2 hydrogenation catalysts and the distribution of active sites, which dictates reactivity and selectivity. These studies often have not considered the possible role of isolated metal active sites in the observed dependences. Here, we utilize probe molecule diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) with known site-specific extinction coefficients to quantify the fraction of Rh sites residing as atomically dispersed isolated sites (Rhiso), as well as Rh sites on the surface of Rh nanoparticles (RhNP) for a series of TiO2 supported Rh catalysts. Strong correlations were observed between the catalytic reverse water gas shift turn over frequency (TOF) and the fraction of Rhiso sites and between catalytic methanation TOF and the fraction of RhNP sites. Furthermore, it was observed that reaction condition-induced disintegration of Rh nanoparticles, forming Rhiso active sites, controls the changing reactivity with time on stream. This work demonstrates that isolated atoms and nanoparticles of the same metal on the same support can exhibit uniquely different catalytic selectivity in competing parallel reaction pathways and that disintegration of nanoparticles under reaction conditions can play a significant role in controlling stability. PMID:25671686

  19. The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme

    NASA Astrophysics Data System (ADS)

    Qi, Jian-Xun; Jiang, Fan

    2011-05-01

    The crystallographic temperature factors (B factor) of individual atoms contain important information about the thermal motion of the atoms in a macromolecule. Previously the theory of flexibility of active site has been established based on the observation that the enzyme activity is sensitive to low concentration denaturing agents. It has been found that the loss of enzyme activity occurs well before the disruption of the three-dimensional structural scaffold of the enzyme. To test the theory of conformational flexibility of enzyme active site, crystal structures were perturbed by soaking in low concentration guanidine hydrochloride solutions. It was found that many lysozyme crystals tested could still diffract until the concentration of guanidine hydrochloride reached 3 M. It was also found that the B factors averaged over individually collected data sets were more accurate. Thus it suggested that accurate measurement of crystal temperature factors could be achieved for medium-high or even medium resolution crystals by averaging over multiple data sets. Furthermore, we found that the correctly predicted active sites included not only the more flexible residues, but also some more rigid residues. Both the flexible and the rigid residues in the active site played an important role in forming the active site residue network, covering the majority of the substrate binding residues. Therefore, this experimental prediction method may be useful for characterizing the binding site and the function of a protein, such as drug targeting.

  20. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Thirteen ideas are presented that may be of use to chemistry teachers. Topics covered include vitamin C, industrial chemistry, electrical conductivity, electrolysis, alkali metals, vibration modes infra-red, dynamic equilibrium, and some new demonstrations in gaseous combinations. (PS)

  1. ENVIRONMENTAL CHEMISTRY

    EPA Science Inventory

    Environmental chemistry is applied to estimating the exposure of ecosystems and humans to various chemical environmental stressors. Among the stressors of concern are mercury, pesticides, and arsenic. Advanced analytical chemistry techniques are used to measure these stressors ...

  2. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-11-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  3. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-01-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

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

    EPA Science Inventory

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

  5. Chemistry, antioxidant, antibacterial and antifungal activities of volatile oils and their components.

    PubMed

    De Martino, Laura; De Feo, Vincenzo; Fratianni, Florinda; Nazzaro, Filomena

    2009-12-01

    The present paper reports the chemical composition, antioxidant and antibacterial activities of several essential oils and their components. Analysis showed that three oils (Carum carvi L., Verbena officinalis L. and Majorana hortensis L.) contained predominantly oxygenated monoterpenes, while others studied (Pimpinella anisum L., Foeniculum vulgare Mill.) mainly contained anethole. C. carvi, V. officinalis and M. hortensis oils exhibited the most potent antioxidant activity, due their contents of carvacrol, anethole and estragol. Antibacterial action was assessed against a range of pathogenic and useful bacteria and fungi of agro-food interest. V. officinalis and C. carvi oils proved the most effective, in particular against Bacillus cereus and Pseudomonas aeruginosa. Carvacrol proved most active against Escherichia coli, and completely inhibited the growth of Penicillium citrinum. The oils proved inactive towards some Lactobacilli strains, whereas single components showed an appreciable activity. These results may be important for use of the essential oils as natural preservatives for food products. PMID:20120118

  6. 1993 annual report of hazardous waste activities for the Oak Ridge K-25 site

    SciTech Connect

    Not Available

    1994-02-01

    This report is a detailed listing of all of the Hazardous Waste activities occurring at Martin Marietta`s K-25 site. Contained herein are hazardous waste notification forms, waste stream reports, generator fee forms and various TSDR reports.

  7. Chemical modification studies on arginine kinase: essential cysteine and arginine residues at the active site.

    PubMed

    Zhu, Wen-Jing; Li, Miao; Wang, Xiao-Yun

    2007-12-01

    Chemical modification was used to elucidate the essential amino acids in the catalytic activity of arginine kinase (AK) from Migratoria manilensis. Among six cysteine (Cys) residues only one Cys residue was determined to be essential in the active site by Tsou's method. Furthermore, the AK modified by DTNB can be fully reactivated by dithiothreitol (DTT) in a monophasic kinetic course. At the same time, this reactivation can be slowed down in the presence of ATP, suggesting that the essential Cys is located near the ATP binding site. The ionizing groups at the AK active site were studied and the standard dissociation enthalpy (DeltaH degrees ) was 12.38kcal/mol, showing that the dissociation group may be the guanidino of arginine (Arg). Using the specific chemical modifier phenylglyoxal (PG) demonstrated that only one Arg, located near the ATP binding site, is essential for the activity of AK. PMID:17765964

  8. 78 FR 8190 - Commercial Wind Leasing and Site Assessment Activities on the Atlantic Outer Continental Shelf...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-05

    ...BOEM is reopening the comment period announced in the Notice of Intent to Prepare an Environmental Assessment (EA) for Commercial Wind Leasing and Site Assessment Activities on the OCS Offshore North...

  9. Implementation and Evaluation of Web-Based Learning Activities on Bonding and the Structure of Matter for 10-th Grade Chemistry

    NASA Astrophysics Data System (ADS)

    Frailich, Marcel

    This study deals with the development, implementation, and evaluation of web-based activities associated with the topic of chemical bonding , as taught in 10th grade chemistry. A website was developed entitled: "Chemistry and the Chemical Industry in the Service of Mankind", its URL is: http://stwww.weizmann.ac.il/g-chem/learnchem (Kesner, Frailich, & Hofstein, 2003). The main goal of this study was to assess the educational effectiveness of website activities dealing with the chemical bonding concept. These activities include visualization tools, as well as topics relevant to daily life and industrial applications. The study investigated the effectiveness of a web-based learning environment regarding the understanding of chemical bonding concepts, students' perceptions of the classroom learning environment, their attitudes regarding the relevance of learning chemistry to everyday life, and their interest in chemistry studies. As mentioned before, in the present study we focused on activities (from the website), all of which deal with chemical bonding concept. The following are the reasons for the decision to focus on this topic: (1) Chemical bonding is a key concept that is taught in 10th grade chemistry in high school. It provides the basis for many other chemistry topics that are taught later, and (2) Chemical bonding is a difficult for students using existing tools (e. g., static models in books, ball-and- stick models), which are insufficient to demonstrate the abstract nature phenomena associated with this topic. The four activities developed for this study are (1) models of the atomic structure, (2) metals -- structure and properties, (3) ionic substances in everyday life and in industry, and (4) molecular substances -- structure, properties, and uses. The study analyzed both quantitative and qualitative research. The quantitative tools of the study included: A Semantic Differential questionnaire and a Chemistry Classroom Web-Based Learning Environment

  10. Anisotropic Covalency Contributions to Superexchange Pathways in Type One Copper Active Sites

    PubMed Central

    2015-01-01

    Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites. PMID:25310460

  11. The Three Mycobacterium tuberculosis Antigen 85 Isoforms Have Unique Substrates and Activities Determined by Non-active Site Regions*

    PubMed Central

    Backus, Keriann M.; Dolan, Michael A.; Barry, Conor S.; Joe, Maju; McPhie, Peter; Boshoff, Helena I. M.; Lowary, Todd L.; Davis, Benjamin G.; Barry, Clifton E.

    2014-01-01

    The three isoforms of antigen 85 (A, B, and C) are the most abundant secreted mycobacterial proteins and catalyze transesterification reactions that synthesize mycolated arabinogalactan, trehalose monomycolate (TMM), and trehalose dimycolate (TDM), important constituents of the outermost layer of the cellular envelope of Mycobacterium tuberculosis. These three enzymes are nearly identical at the active site and have therefore been postulated to exist to evade host immunity. Distal to the active site is a second putative carbohydrate-binding site of lower homology. Mutagenesis of the three isoforms at this second site affected both substrate selectivity and overall catalytic activity in vitro. Using synthetic and natural substrates, we show that these three enzymes exhibit unique selectivity; antigen 85A more efficiently mycolates TMM to form TDM, whereas C (and to a lesser extent B) has a higher rate of activity using free trehalose to form TMM. This difference in substrate selectivity extends to the hexasaccharide fragment of cell wall arabinan. Mutation of secondary site residues from the most active isoform (C) into those present in A or B partially interconverts this substrate selectivity. These experiments in combination with molecular dynamics simulations reveal that differences in the N-terminal helix α9, the adjacent Pro216–Phe228 loop, and helix α5 are the likely cause of changes in activity and substrate selectivity. These differences explain the existence of three isoforms and will allow for future work in developing inhibitors. PMID:25028517

  12. Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase

    PubMed Central

    Seibold, Steve A.; Singh, Badri Nath; Zhang, Chunfen; Kireeva, Maria; Domecq, Céline; Bouchard, Annie; Nazione, Anthony M.; Feig, Michael; Cukier, Robert I.; Coulombe, Benoit; Kashlev, Mikhail; Hampsey, Michael; Burton, Zachary F.

    2010-01-01

    Molecular dynamics simulation of Thermus thermophilus (Tt) RNA polymerase (RNAP) in a catalytic conformation demonstrates that the active site dNMP-NTP base pair must be substantially dehydrated to support full active site closing and optimum conditions for phosphodiester bond synthesis. In silico mutant β R428A RNAP, which was designed based on substitutions at the homologous position (Rpb2 R512) of Saccharomyces cerevisiae (Sc) RNAP II, was used as a reference structure to compare to Tt RNAP in simulations. Long range conformational coupling linking a dynamic segment of the bridge α-helix, the extended fork loop, the active site, and the trigger loop-trigger helix is apparent and adversely affected in β R428A RNAP. Furthermore, bridge helix bending is detected in the catalytic structure, indicating that bridge helix dynamics may regulate phosphodiester bond synthesis as well as translocation. An active site “latch” assembly that includes a key trigger helix residue Tt β’ H1242 and highly conserved active site residues β E445 and R557 appears to help regulate active site hydration/dehydration. The potential relevance of these observations in understanding RNAP and DNAP induced fit and fidelity is discussed. PMID:20478425

  13. International Global Atmospheric Chemistry Programme global emissions inventory activity: Sulfur emissions from volcanoes, current status

    SciTech Connect

    Benkovitz, C.M.

    1995-07-01

    Sulfur emissions from volcanoes are located in areas of volcanic activity, are extremely variable in time, and can be released anywhere from ground level to the stratosphere. Previous estimates of global sulfur emissions from all sources by various authors have included estimates for emissions from volcanic activity. In general, these global estimates of sulfur emissions from volcanoes are given as global totals for an ``average`` year. A project has been initiated at Brookhaven National Laboratory to compile inventories of sulfur emissions from volcanoes. In order to complement the GEIA inventories of anthropogenic sulfur emissions, which represent conditions circa specific years, sulfur emissions from volcanoes are being estimated for the years 1985 and 1990.

  14. Active sites for NO reduction over Fe-ZSM-5 catalysts.

    PubMed

    Schwidder, M; Santhosh Kumar, M; Brückner, A; Grünert, W

    2005-02-14

    A study of Fe-ZSM-5 catalysts with variable amounts of isolated, oligomeric and heavily aggregated Fe3+ oxo sites (as evidenced by UV-Vis and EPR spectroscopic data) and their catalytic properties in the selective catalytic reduction of NO by isobutane or by NH3 is presented, which allows development of a unified concept of the active Fe sites in these reactions, according to which isolated Fe sites catalyse both SCR reactions while oligomeric sites, though also involved in the selective reduction path, limit the catalyst performance by causing the total oxidation of the reductant. PMID:15685345

  15. Site-directed mutagenesis and high-resolution NMR spectroscopy of the active site of porphobilinogen deaminase

    SciTech Connect

    Scott, A.I.; Roessner, C.A.; Stolowich, N.J.; Karuso, P.; Williams, H.J.; Grant, S.K.; Gonzalez, M.D.; Hoshino, T. )

    1988-10-18

    The active site of porphobilinogen (PBG){sup 1} deaminase from Escherichia coli has been found to contain an unusual dipyrromethane derived from four molecules of 5-aminolevulinic acid (ALA) covalently linked to Cys-242, one of the two cysteine residues conserved in E. coli and human deaminase. By use of a hemA{sup {minus}} strain of E. coli the enzyme was enriched from (5-{sup 13}C)ALA and examined by {sup 1}H-detected multiple quantum coherence spectroscopy, which revealed all of the salient features of a dipyrromethane composed of two PBG units linked heat to tail and terminating in a CH{sub 2}-S bond to a cysteine residue. Site-specific mutagenesis of Cys-99 and Cys-242, respectively, has shown that substitution of Ser for Cys-99 does not affect the enzymatic activity, whereas substitution of Ser for Cys-242 removes essentially all of the catalytic activity as measured by the conversion of the substrate PBG to uro'gen I. The NMR spectrum of the covalent complex of deaminase with the suicide inhibitor 2-bromo-(2,11-{sup 13}C{sub 2})PBG reveals that the aminomethyl terminus of the inhibitor reacts with the enzyme's cofactor at the {alpha}-free pyrrole. NMR spectroscopy of the ES{sub 2} complex confirmed a PBG-derived head-to-tail dipyrromethane attached to the {alpha}-free pyrrole position of the enzyme. A mechanistic rationale for deaminase is presented.

  16. Using the Activity Model of Inquiry to Enhance General Chemistry Students' Understanding of Nature of Science

    ERIC Educational Resources Information Center

    Marchlewicz, Sara C.; Wink, Donald J.

    2011-01-01

    Nature of science refers to the processes of scientific activity and the social and cultural premises involved in the creation of scientific knowledge. Having an informed view of nature of science is important in the development of scientifically literate citizens. However, students often come to the classroom with misconceptions about nature of…

  17. Learning by Doing: The Objectification of Knowledge across Semiotic Modalities in Middle School Chemistry Lab Activities

    ERIC Educational Resources Information Center

    Wright, Laura J.

    2008-01-01

    This analysis follows students' action and interaction with a single scientific phenomenon (bubbling/gas) over the course of a curriculum unit in a middle school science classroom to examine how and what they learn when doing laboratory activities. Taking a situated approach to interaction, I place the process of objectification in its multimodal…

  18. Variability in tannin content, chemistry and activity in a diverse group of tannin containing sorghum cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tannins are large polyphenolic polymers and are known to bind proteins, limiting their digestibility. Tannins are also known for having excellent antioxidant potential. To examine the precise impact of tannin content and composition on the biological activities (protein binding, protein digestibil...

  19. Internationalisation of the Chemistry Curriculum: Two Problem-Based Learning Activities for Undergraduate Chemists

    ERIC Educational Resources Information Center

    Overton, Tina L.; Bradley, John S.

    2010-01-01

    In this paper we describe the development and evaluation of two activities for delivery in first year B.Sc. and M.Chem. degree courses, in which we introduced an international context representing either a linguistic or a cultural modification to the previously developed case studies. The case studies focus on an industrial and an environmental…

  20. Index to NASA tech briefs, 1973. [technology transfer of research and development activities chemistry

    NASA Technical Reports Server (NTRS)

    1974-01-01

    Short announcements of technology derived from the research and development activities of NASA or the U.S. Atomic Energy Commission are issued to encourage commercial application. Emphasis is placed on information considered likely to be transferrable across industrial, regional, or disciplinary lines. Abstracts and indexes are given.

  1. TRICHLOROETHYLENE ADSORPTION BY ACTIVATED CARBON PRELOADED WITH HUMIC SUBSTANCES: EFFECTS OF SOLUTION CHEMISTRY. (R828157)

    EPA Science Inventory

    Abstract

    Trichloroethylene (TCE) adsorption by activated carbon previously loaded ("preloaded") with humic substances was found to decrease with increasing concentrations of monovalent ions (NaCl), calcium (until solubility was exceeded), or dissolved oxygen in...

  2. The Chemistry of Self-Heating Food Products: An Activity for Classroom Engagement

    ERIC Educational Resources Information Center

    Oliver-Hoyo, Maria T.; Pinto, Gabriel; Llorens-Molina, Juan Antonio

    2009-01-01

    Two commercial self-heating food products have been used to apply chemical concepts such as stoichiometry, enthalpies of reactions and solutions, and heat transfer in a classroom activity. These products are the self-heating beverages sold in Europe and the Meals, Ready to Eat or MREs used primarily by the military in the United States. The main…

  3. A Proposal for Teaching Undergraduate Chemistry Students Carbohydrate Biochemistry by Problem-Based Learning Activities

    ERIC Educational Resources Information Center

    Figueira, Angela C. M.; Rocha, Joao B. T.

    2014-01-01

    This article presents a problem-based learning (PBL) approach to teaching elementary biochemistry to undergraduate students. The activity was based on "the foods we eat." It was used to engage students' curiosity and to initiate learning about a subject that could be used by the future teachers in the high school. The experimental…

  4. Chemistry with a Peel.

    ERIC Educational Resources Information Center

    Borer, Londa; Larsen, Eric

    1997-01-01

    Presents experiments that introduce natural product chemistry into high school classrooms. In the laboratory activities, students isolate and analyze the oil in orange peels. Students also perform a steam distillation and learn about terpenes. (DDR)

  5. CLUSTER CHEMISTRY

    SciTech Connect

    Muetterties, Earl L.

    1980-05-01

    Metal cluster chemistry is one of the most rapidly developing areas of inorganic and organometallic chemistry. Prior to 1960 only a few metal clusters were well characterized. However, shortly after the early development of boron cluster chemistry, the field of metal cluster chemistry began to grow at a very rapid rate and a structural and a qualitative theoretical understanding of clusters came quickly. Analyzed here is the chemistry and the general significance of clusters with particular emphasis on the cluster research within my group. The importance of coordinately unsaturated, very reactive metal clusters is the major subject of discussion.

  6. Forensic Chemistry

    NASA Astrophysics Data System (ADS)

    Bell, Suzanne

    2009-07-01

    Forensic chemistry is unique among chemical sciences in that its research, practice, and presentation must meet the needs of both the scientific and the legal communities. As such, forensic chemistry research is applied and derivative by nature and design, and it emphasizes metrology (the science of measurement) and validation. Forensic chemistry has moved away from its analytical roots and is incorporating a broader spectrum of chemical sciences. Existing forensic practices are being revisited as the purview of forensic chemistry extends outward from drug analysis and toxicology into such diverse areas as combustion chemistry, materials science, and pattern evidence.

  7. Identification of active-site residues in protease 3C of hepatitis A virus by site-directed mutagenesis.

    PubMed Central

    Gosert, R; Dollenmaier, G; Weitz, M

    1997-01-01

    Picornavirus 3C proteases (3Cpro) are cysteine proteases related by amino acid sequence to trypsin-like serine proteases. Comparisons of 3Cpro of hepatitis A virus (HAV) to those of other picornaviruses have resulted in prediction of active-site residues: histidine at position 44 (H44), aspartic acid (D98), and cysteine (C172). To test whether these residues are key members of a putative catalytic triad, oligonucleotide-directed mutagenesis was targeted to 3Cpro in the context of natural polypeptide precursor P3. Autocatalytic processing of the polyprotein containing wild-type or variant 3Cpro was tested by in vivo expression of vaccinia virus-HAV chimeras in an animal cell-T7 hybrid system and by in vitro translation of corresponding RNAs. Comparison with proteins present in HAV-infected cells showed that both expression systems mimicked authentic polyprotein processing. Individual substitutions of H44 by tyrosine and of C172 by glycine or serine resulted in complete loss of the virus-specific proteolytic cascade. In contrast, a P3 polyprotein in which D98 was substituted by asparagine underwent only slightly delayed processing, while an additional substitution of valine (V47) by glycine within putative protein 3A caused a more pronounced loss of processing. Therefore, apparently H44 and C172 are active-site constituents whereas D98 is not. The results, furthermore, suggest that substitution of amino acid residues distant from polyprotein cleavage sites may reduce proteolytic activity, presumably by altering substrate conformation. PMID:9060667

  8. Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site

    PubMed Central

    Grossman, Moran; Born, Benjamin; Heyden, Matthias; Tworowski, Dmitry; Fields, Gregg B; Sagi, Irit; Havenith, Martina

    2012-01-01

    Solvent dynamics can play a major role in enzyme activity, but obtaining an accurate, quantitative picture of solvent activity during catalysis is quite challenging. Here, we combine terahertz spectroscopy and X-ray absorption analyses to measure changes in the coupled water-protein motions during peptide hydrolysis by a zinc-dependent human metalloprotease. These changes were tightly correlated with rearrangements at the active site during the formation of productive enzyme-substrate intermediates and were different from those in an enzyme–inhibitor complex. Molecular dynamics simulations showed a steep gradient of fast-to-slow coupled protein-water motions around the protein, active site and substrate. Our results show that water retardation occurs before formation of the functional Michaelis complex. We propose that the observed gradient of coupled protein-water motions may assist enzyme-substrate interactions through water-polarizing mechanisms that are remotely mediated by the catalytic metal ion and the enzyme active site. PMID:21926991

  9. Correlated structural kinetics and retarded solvent dynamics at the metalloprotease active site

    SciTech Connect

    Grossman, Moran; Born, Benjamin; Heyden, Matthias; Tworowski, Dmitry; Fields, Gregg B.; Sagi, Irit; Havenith, Martina

    2011-09-18

    Solvent dynamics can play a major role in enzyme activity, but obtaining an accurate, quantitative picture of solvent activity during catalysis is quite challenging. Here, we combine terahertz spectroscopy and X-ray absorption analyses to measure changes in the coupled water-protein motions during peptide hydrolysis by a zinc-dependent human metalloprotease. These changes were tightly correlated with rearrangements at the active site during the formation of productive enzyme-substrate intermediates and were different from those in an enzyme–inhibitor complex. Molecular dynamics simulations showed a steep gradient of fast-to-slow coupled protein-water motions around the protein, active site and substrate. Our results show that water retardation occurs before formation of the functional Michaelis complex. We propose that the observed gradient of coupled protein-water motions may assist enzyme-substrate interactions through water-polarizing mechanisms that are remotely mediated by the catalytic metal ion and the enzyme active site.

  10. HIV integration site distributions in resting and activated CD4+ T cells infected in culture

    PubMed Central

    Brady, Troy; Agosto, Luis M.; Malani, Nirav; Berry, Charles C.; O'Doherty, Una; Bushman, Frederic

    2010-01-01

    Objective The goal of this study was to investigate whether the location of HIV integration differs in resting versus activated T cells, a feature that could contribute to the formation of latent viral reservoirs via effects on integration targeting. Design Primary resting or activated CD4+ T cells were infected with purified X4-tropic HIV in the presence and absence of nucleoside triphosphates and genomic locations of integrated provirus determined. Methods We sequenced and analyzed a total of 2661 HIV integration sites using linker-mediated PCR and 454 sequencing. Integration site data sets were then compared to each other and to computationally generated random distributions. Results HIV integration was favored in active transcription units in both cell types, but integration sites from activated cells were found more often in genomic regions that were dense in genes, dense in CpG islands, and enriched in G/C bases. Integration sites from activated cells were also more strongly correlated with histone methylation patterns associated with active genes. Conclusion These data indicate that integration site distributions show modest but significant differences between resting and activated CD4+ T cells, and that integration in resting cells occurs more often in regions that may be suboptimal for proviral gene expression. PMID:19550285

  11. Site-specific antibody-liposome conjugation through copper-free click chemistry: a molecular biology approach for targeted photodynamic therapy (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Obaid, Girgis; Wang, Yucheng; Kuriakose, Jerrin; Broekgaarden, Mans; Alkhateeb, Ahmed; Bulin, Anne-Laure; Hui, James; Tsourkas, Andrew; Hasan, Tayyaba

    2016-03-01

    Nanocarriers, such as liposomes, have the ability to potentiate photodynamic therapy (PDT) treatment regimens by the encapsulation of high payloads of photosensitizers and enhance their passive delivery to tumors through the enhanced permeability and retention effect. By conjugating targeting moieties to the surface of the liposomal nanoconstructs, cellular selectivity is imparted on them and PDT-based therapies can be performed with significantly higher dose tolerances, as off-target toxicity is simultaneously reduced.1 However, the maximal benefits of conventional targeted nanocarriers, including liposomes, are hindered by practical limitations including chemical instability, non-selective conjugation chemistry, poor control over ligand orientation, and loss of ligand functionality following conjugation, amongst others.2 We have developed a robust, physically and chemically stable liposomal nanoplatform containing benzoporphyrin derivative photosensitizer molecules within the phospholipid bilayer and an optimized surface density of strained cyclooctyne moieties for `click' conjugation to azido-functionalized antibodies.3 The clinical chimeric anti-EGFR antibody Cetuximab is site-specifically photocrosslinked to a recombinant bioengineered that recognizes the antibody's Fc region, containing a terminal azide.4 The copper-free click conjugation of the bioengineered Cetuximab derivative to the optimized photosensitizing liposome provides exceptional control over the antibody's optimal orientation for cellular antigen binding. Importantly, the reaction occurs rapidly under physiological conditions, bioorthogonally (selectively in the presence of other biomolecules) and without the need for toxic copper catalysis.3 Such state-of-the-art conjugation strategies push the boundaries of targeted photodynamic therapy beyond the limitations of traditional chemical coupling techniques to produce more robust and effective targeted therapeutics with applications beyond

  12. Heavy air pollution episodes in Beijing during January 2013: inorganic ion chemistry and source analysis using Highly Time-Resolved Measurements in an urban site

    NASA Astrophysics Data System (ADS)

    Han, B.; Zhang, R.; Yang, W.; Bai, Z.; Ma, Z.; Zhang, W.

    2015-04-01

    Heavy air pollution episodes occurred in Beijing in January 2013 attracted intensively attention around the whole world. During this period, the authors conducted highly time-resolved measurements of water soluble ions associated with PM2.5 at an urban site, and attempted to distinguish the ion chemistry and potential sources. In this study, hourly mean concentrations of Cl-, NO3-, SO42-, Na+, NH4+, K+, Mg2+ and Ca2+ were measured during the air pollution episode in January 2013, and the ions were found to exist mainly in the form of (NH4)2SO4, NH4NO3, NaCl and KCl in aerosol particles by correlation and linear analysis. SO42- and NO3- were observed peak concentrations in 10-15, 18-20, 21-24, and 26-30 January during this monitoring campaign. The percentage of SO42- and NH4+ in total ions concentrations exhibited an increasing trend with the enhancement of PM2.5 concentration, indicating high concentrations of SO42- and NH4+ had played important roles in the formation of air pollution episodes. Ratio of [NO3-]/[SO42-] was calculated, finding the sources of SO42- would contribute more to the formation of PM2.5 than mobile sources. Diurnal variations of SO42-, NO3-, NH4+ were examined, and all of them exhibited similar pattern with high concentration in night and relative low level at daytime. Emission from coal combustion, remote transportation at night or impact of meteorological was likely to be responsible for the high level of SO42-, NH4+ andNO3-. Potential sources were identified by applying PMF. Secondary nitrate, secondary sulfate, coal combustion and biomass burning, as well as fugitive dust were considered as the major contributors to total ions.

  13. Heavy haze episodes in Beijing during January 2013: Inorganic ion chemistry and source analysis using highly time-resolved measurements from an urban site.

    PubMed

    Han, Bin; Zhang, Rui; Yang, Wen; Bai, Zhipeng; Ma, Zhiqiang; Zhang, Wenjie

    2016-02-15

    The heavy air pollution that occurred in Beijing in January of 2013 attracted intense attention around the world. During this period, we conducted highly time-resolved measurements of inorganic ions associated with PM2.5 at an urban site of Beijing, and investigated ion chemistry and potential sources. Hourly concentrations of Cl(-), NO3(-), SO4(2-), Na(+), NH4(+), K(+), Mg(2+), and Ca(2+) were measured. Peak concentrations of SO4(2-) and NO3(-) were observed on the 10th-15th, 21st-24th, and the 26th-30th during this monitoring campaign. The percentages of SO4(2-) and NH4(+) in total ion concentration increased with the enhancement of PM2.5 concentrations, indicating that high concentrations of SO4(2-) and NH4(+) may play important roles in the formation of haze episodes. The ratio of [NO3(-)]/[SO4(2-)] was calculated, revealing that the sources of SO4(2-) would contribute more to the formation of PM2.5 than mobile sources. Diurnal variations of SO4(2-), NO3(-), NH4(+) (SNA) exhibited a similar pattern, with high concentrations at night and low levels during the day, revealing that meteorological conditions, such as mixing layer height, relative humidity, were likely to be responsible for high levels of SNA at night. The roles of meteorological conditions were further discussed in the formation of secondary inorganic ions. Relative humidity and temperature played key roles and exhibited positive correlations with secondary inorganic ions. An aerosol inorganics simulation model showed that SNA existed mainly in the aqueous phase during the sampling period. Furthermore, potential sources were identified by applying positive matrix factorization model. Secondary nitrate, secondary sulfate, coal combustion and biomass burning, as well as fugitive dust, were considered to be major contributors to total ions. PMID:26657378

  14. Hydrothermal activity in the Lau back arc basin: Plumes and hot fluids chemistry

    SciTech Connect

    Charlou, J.L.; Donval, J.P.; Caprais, M.P.; Fouquet, Y. ); Erzinger, J. ); Von Stackelberg, U. )

    1990-06-01

    During the French-German cruise Nautile(April-May 1989), 22 dives have been completed to understand the processes of seafloor arc formation associated with hydrothermal circulation along the volcanic Valu FA ridge. The CTD recordings, obtained in real time inside the Nautile, show the narrow relation between the geological structure and the temperature anomalies. The anomalies' amplitude and intensity permit the precise localization of hot hydrothermal discharges (Vai Lili site), diffuse (Hine Hina field) and nonperceptible inputs. Buoyant plumes producing entrainment and vertical transport up to 200 m above the seafloor are clearly identified with high CH{sub 4} (up to 4.4 {mu}l/L) and Mn (up to 90 {mu}mol/Kg) concentrations. For the first time, black smokers (240{degree} to 334{degree}C) were collected in a back arc environment. The samples (more than 90% pure hydrothermal fluid) have end member pH (1.8), among the lowest ever measured in oceanic hydrothermal fluids. The calculated end-member concentrations are enriched for Cl(0.65-0.75 mol/kg), Na (0.52-0.58 mol/Kg), Ca (30 mmol/Kg), K (55-67 mmol/Kg), Sr (123 {mu}mol/Kg), Rb (72-92 {mu}mol/kg), Li (690 {mu}mol/Kg). Compared with other hydrothermal waters, Si is slightly depleted (12-14 mmol/Kg), Fe (1.12.5 mmol/Kg), Mn (5.8-6.9 mmol/Kg), Cu (16-43 {mu}mol/Kg), Zn (1.2- 3 mmol/Kg) concentrations are high. The Vai Lili site fluid concentrations in B (twice seawater), Ba (up to 40 {mu}mol/Kg), Zn (up to 3 mmol/Kg), Pb (up to 7 {mu}mol/kg). As (up to 11 {mu}mol/Kg) as well as the molar Cs/Rb and Fe/Mn ratios of respectively 0.024 and 0.2 are unexpected.

  15. Getting Reactions to Chemistry.

    ERIC Educational Resources Information Center

    Smith, Walter S.

    1983-01-01

    "COMETS on Careers" describes science-related careers, introduces activities illustrating a science concept being studied, and encourages use of professional persons as activity leaders. Several COMETS chemistry activities are described. These activities, which can be performed in school or at home, focus on colloids, acid/base indicators, and…

  16. The chemistry and biological activity of herbs used in Flor-Essence herbal tonic and Essiac.

    PubMed

    Tamayo, C; Richardson, M A; Diamond, S; Skoda, I

    2000-02-01

    The herbal mixtures, Essiac and Flor-Essence, are sold as nutritional supplements and used by patients to treat chronic conditions, particularly cancer. Evidence of anticancer activity for the herbal teas is limited to anecdotal reports recorded for some 40 years in Canada. Individual case reports suggest that the tea improves quality of life, alleviates pain, and in some cases, impacts cancer progression among cancer patients. Experimental studies with individual herbs have shown evidence of biological activity including antioxidant, antioestrogenic, immunostimulant, antitumour, and antiocholeretic actions. However, research that demonstrates these positive effects in the experimental setting has not been translated to the clinical arena. Currently, no clinical studies of Essiac or Flor-essence are published, but a clinical study is being planned at the British Columbia Cancer Agency by the University of Texas-Center for Alternative Medicine (UT-CAM) and Tzu-Chi Institute for Complementary and Alternative Medicine. PMID:10641040

  17. Secondary metabolites of plants from the genus chloranthus: chemistry and biological activities.

    PubMed

    Wang, An-Ran; Song, Hong-Chuan; An, Hong-Mei; Huang, Qian; Luo, Xie; Dong, Jin-Yan

    2015-04-01

    Chloranthus, a genus of the family Chloranthaceae, which is mainly distributed in eastern and southern Asia, has been used in Chinese folk medicine due to its antitumor, antifungal, and anti-inflammatory activities. This review compiles the research on isolation, structure elucidation, structural diversity, and bioactivities of Chloranthus secondary metabolites reported between 2007 and 2013. The metabolites listed encompass 82 sesquiterpenoids, 50 dimeric sesquiterpenoids, 15 diterpenoids, one coumarin, and five other compounds. Among them, dimeric sesquiterpenoids, the characteristic components of plants from the genus Chloranthus, have attracted considerable attention due to their complex structures and significant biological features, e.g., antitumor, antibacterial, antifungal, anti-inflammatory, and hepatoprotective activities, and potent and selective inhibition of the delayed rectifier (IK) K(+) current and tyrosinase. PMID:25879494

  18. Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site

    SciTech Connect

    Carra,J.; McHugh, C.; Mulligan, S.; Machiesky, L.; Soares, A.; Millard, C.

    2007-01-01

    We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the geometric relationship of arginine-tryptophan pairs, which often have significant roles in protein function. Using the unusual characteristics of the RTA system, we measured the still controversial thermodynamic changes of site-specific urea binding to a protein, results that are relevant to understanding the physical mechanisms of protein denaturation.

  19. Assessment of the site of ventricular activation by Fourier analysis of gated blood-pool studies

    SciTech Connect

    Links, J.M.; Raichlen, J.S.; Wagner, H.N. Jr.; Reid, P.R.

    1985-01-01

    The authors studied the use of first-harmonic Fourier analysis of gated blood-pool images to assess the site of ventricular activation in a group of 12 patients undergoing electrophysiologic pacing studies. They acquired gated blood-pool studies during pacing at up to four sites at each of two different rates. A total of 50 studies were made. At a pacing rate of 100 beats/min, when the pacing electrode was the right-ventricular outflow tract, 7/8; at the anterolateral left-ventricular wall, 4/4. When the Fourier activation site was at the right-ventricular apex, 9/9 times the pacing electrode was there; at the right-ventricular outflow tract, 7/10; in the left ventricle, 4/4. Fourier analysis of gated blood-pool studies can help identify the site of ventricular activation but is not sufficiently accurate to fully replace endocardial mapping.

  20. Nanostructured manganese oxides as highly active water oxidation catalysts: a boost from manganese precursor chemistry.

    PubMed

    Menezes, Prashanth W; Indra, Arindam; Littlewood, Patrick; Schwarze, Michael; Göbel, Caren; Schomäcker, Reinhard; Driess, Matthias

    2014-08-01

    We present a facile synthesis of bioinspired manganese oxides for chemical and photocatalytic water oxidation, starting from a reliable and versatile manganese(II) oxalate single-source precursor (SSP) accessible through an inverse micellar molecular approach. Strikingly, thermal decomposition of the latter precursor in various environments (air, nitrogen, and vacuum) led to the three different mineral phases of bixbyite (Mn2 O3 ), hausmannite (Mn3 O4 ), and manganosite (MnO). Initial chemical water oxidation experiments using ceric ammonium nitrate (CAN) gave the maximum catalytic activity for Mn2 O3 and MnO whereas Mn3 O4 had a limited activity. The substantial increase in the catalytic activity of MnO in chemical water oxidation was demonstrated by the fact that a phase transformation occurs at the surface from nanocrystalline MnO into an amorphous MnOx (1activities of water oxidation catalysts has been proposed by determining the amount of accessible manganese centers. PMID:25044528

  1. Human Frataxin Activates Fe–S Cluster Biosynthesis by Facilitating Sulfur Transfer Chemistry

    PubMed Central

    2015-01-01

    Iron–sulfur clusters are ubiquitous protein cofactors with critical cellular functions. The mitochondrial Fe–S assembly complex, which consists of the cysteine desulfurase NFS1 and its accessory protein (ISD11), the Fe–S assembly protein (ISCU2), and frataxin (FXN), converts substrates l-cysteine, ferrous iron, and electrons into Fe–S clusters. The physiological function of FXN has received a tremendous amount of attention since the discovery that its loss is directly linked to the neurodegenerative disease Friedreich’s ataxia. Previous in vitro results revealed a role for human FXN in activating the cysteine desulfurase and Fe–S cluster biosynthesis activities of the Fe–S assembly complex. Here we present radiolabeling experiments that indicate FXN accelerates the accumulation of sulfur on ISCU2 and that the resulting persulfide species is viable in the subsequent synthesis of Fe–S clusters. Additional mutagenesis, enzyme kinetic, UV–visible, and circular dichroism spectroscopic studies suggest conserved ISCU2 residue C104 is critical for FXN activation, whereas C35, C61, and C104 are all essential for Fe–S cluster formation on the assembly complex. These results cannot be fully explained by the hypothesis that FXN functions as an iron donor for Fe–S cluster biosynthesis, and further support an allosteric regulator role for FXN. Together, these results lead to an activation model in which FXN accelerates persulfide formation on NFS1 and favors a helix-to-coil interconversion on ISCU2 that facilitates the transfer of sulfur from NFS1 to ISCU2 as an initial step in Fe–S cluster biosynthesis. PMID:24971490

  2. Cupric-Superoxo Mediated Inter-Molecular C-H Activation Chemistry

    PubMed Central

    Peterson, Ryan L.; Himes, Richard A.; Kotani, Hiroaki; Suenobu, Tomoyoshi; Tian, Li; Siegler, Maxime A.; Solomon, Edward I.; Fukuzumi, Shunichi; Karlin, Kenneth D.

    2011-01-01

    A new cupric-superoxo complex [LCuII(O2•−)]+, which possesses particularly strong O–O and Cu–O bonding, is capable of intermolecular C-H activation of the NADH analogue 1-benzyl-1,4-dihydronicotinamide (BNAH). Kinetic studies indicate a first-order dependence on both the Cu-complex and BNAH with a deuterium kinetic isotope effect (KIE) of 12.1, similar to that observed for certain copper monooxygenases. PMID:21265534

  3. Nanorods of cryptomelane via soft chemistry method and their catalytic activity

    NASA Astrophysics Data System (ADS)

    Grigorieva, Anastasia V.; Melnik, Denis M.; Goodilin, Eugene A.; Anufrieva, Tatyana A.; Derlyukova, Lyudmila E.; Tretyakov, Yuri D.

    2012-07-01

    α-MnO2 nanorods were obtained by a fast redox transformation of aqueous solution of potassium permanganate. The formation mechanism of 1D nanocrystals proceeds via a first pH- and temperature sensitive stage followed by cation/anion control of the nanorod growth. A high surface area and nanostructuring allowed to achieve superb catalytic activity in a CO oxidation process compared to a conventionally prepared manganese dioxide.

  4. Chemistry of ash-leachates: a reliable monitoring tool for volcanic activity

    NASA Astrophysics Data System (ADS)

    Armienta, M. A.; De la Cruz-Reyna, S.; Soler, A.; Ceniceros, N.; Cruz, O.; Aguayo, A.

    2012-04-01

    Real-time volcanic hazard assessment requires the integrated interpretation of data obtained with different monitoring methods, particularly when people may be at risk. One of the methods rendering earliest precursory variations reflecting the internal state of a volcano is the geochemical analysis of gases, ground or lake waters related to volcanic systems, and volcanic ash. At Popocatépetl volcano, Central México, chemical fluctuations of the soluble cover of volcanic ash particles has proved to reflect diverse characteristics of the eruption types. Chloride, sulfate and fluoride concentrations of ash leachates have been consistently measured within the current eruptive episode beginning in December 1994. Particularly, main anions presented diverse relative concentrations in periods of dome extrusions, contrasting with hydrothermal activity or quiescence. Multivariate statistical analysis revealed that higher proportions of fluoride in the leachates corresponded to new dome emplacements and relatively higher sulfate concentrations to hydrothermal ashes, although these results may be ambiguous at times. However, different sulfur isotopic ratios were measured in sulfate from ashes erupted during periods dominated by hydrothermal activity to those emitted during dome emplacement. Additionally, ascent of fresh magma was reflected on high fluoride concentrations jointly with low 34S-SO4 isotopic values. It is thus recommended to maintain persistent analyses of ash-leachates from on-going eruptions as a monitoring tool at active volcanoes.

  5. Sunlight-driven copper-catalyst activation applied to photolatent click chemistry.

    PubMed

    Beniazza, Rédouane; Lambert, Romain; Harmand, Lydie; Molton, Florian; Duboc, Carole; Denisov, Sergey; Jonusauskas, Gedeminas; McClenaghan, Nathan D; Lastécouères, Dominique; Vincent, Jean-Marc

    2014-10-01

    The synthesis, full characterization, photoreduction properties, and catalytic activity for the copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reaction of a copper(II)-DMEDA (N,N'-dimethylethylendiamine) complex is reported. Spectroscopic studies (UV/Vis, EPR) demonstrated that under daylight illumination highly effective copper(II) to copper(I) reduction occurs in this complex. These findings are in agreement with a high photoreduction quantum yield value of 0.22 in MeOH, and a value approaching unity as determined in THF. The reduction process, which can also be conducted by irradiation at 365 nm by using a standard TLC (thin layer chromatography) lamp, is ascribed to a highly efficient photoinduced electron transfer (PET) process mediated by the benzophenone photosensitizer present in the carboxylate counterion. Having deaerated the reaction mixture, the photogenerated copper(I) species proved to be highly active for the CuAAC reaction, demonstrated by reactions conducted with low catalyst loading (0.5 mol %) on a range of clickable protected and non-protected mono- and disaccharides. Once initiated, the reaction can be stopped at any time on introducing air into the reaction medium. Deoxygenation followed by irradiation restores the activity, making the copper(II)-DMEDA complex a switchable catalyst of practical value. PMID:25171758

  6. Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions

    SciTech Connect

    Crichlow, G.; Lubetsky, J; Leng, L; Bucala, R; Lolis, E

    2009-01-01

    Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.

  7. Active Site Inhibitors Protect Protein Kinase C from Dephosphorylation and Stabilize Its Mature Form*

    PubMed Central

    Gould, Christine M.; Antal, Corina E.; Reyes, Gloria; Kunkel, Maya T.; Adams, Ryan A.; Ziyar, Ahdad; Riveros, Tania; Newton, Alexandra C.

    2011-01-01

    Conformational changes acutely control protein kinase C (PKC). We have previously shown that the autoinhibitory pseudosubstrate must be removed from the active site in order for 1) PKC to be phosphorylated by its upstream kinase phosphoinositide-dependent kinase 1 (PDK-1), 2) the mature enzyme to bind and phosphorylate substrates, and 3) the mature enzyme to be dephosphorylated by phosphatases. Here we show an additional level of conformational control; binding of active site inhibitors locks PKC in a conformation in which the priming phosphorylation sites are resistant to dephosphorylation. Using homogeneously pure PKC, we show that the active site inhibitor Gö 6983 prevents the dephosphorylation by pure protein phosphatase 1 (PP1) or the hydrophobic motif phosphatase, pleckstrin homology domain leucine-rich repeat protein phosphatase (PHLPP). Consistent with results using pure proteins, treatment of cells with the competitive inhibitors Gö 6983 or bisindolylmaleimide I, but not the uncompetitive inhibitor bisindolylmaleimide IV, prevents the dephosphorylation and down-regulation of PKC induced by phorbol esters. Pulse-chase analyses reveal that active site inhibitors do not affect the net rate of priming phosphorylations of PKC; rather, they inhibit the dephosphorylation triggered by phorbol esters. These data provide a molecular explanation for the recent studies showing that active site inhibitors stabilize the phosphorylation state of protein kinases B/Akt and C. PMID:21715334

  8. A dual site study of PM 2.5 and PM 10 aerosol chemistry in the larger region of Vienna, Austria

    NASA Astrophysics Data System (ADS)

    Puxbaum, H.; Gomiscek, B.; Kalina, M.; Bauer, H.; Salam, A.; Stopper, S.; Preining, O.; Hauck, H.

    The measurements of PM 2.5 and PM 10 at two sites—an urban site in Vienna (AUPHEP-1) and a rural site considered local background (AUPHEP-2)—indicated only low aerosol generation activity in the city on an annual basis. Defining the term "urban impact" as the difference between observations at the urban and the local background site we find an annually averaged urban impact for PM 2.5 of 3.4 μg m -3 and for PM C of 3.3 μg m -3 (the coarse fraction PM C=PM 10-PM 2.5). The relative increase of the particulate matter (PM) concentration at the urban site compared to the background site (AUPHEP-2) is annually averaged only 19% for PM 2.5, but 60% for PM C. The chemical main constituents of the PM 2.5 urban impact are black carbon (BC), organic carbon (OC), and sulfate; the main constituents of the PM C urban impact are OC and indicators for mineralic aerosol (Fe, Ca, Mg, Na, K). The BC/TC ratio of the PM 2.5 urban impact is typical as for combustion sources, e.g. automotive traffic, oil or coal combustion. Urban coarse OC is considered to originate from non-pyrogenic sources. From the trace metals investigated (As, Cd, Co, Cu, Cr, Mn, Ni, Pb, V, Zn) only Cd, Ni, Pb, and Zn exhibited a slight cold season enrichment in the urban airshed. From the weak signal of a seasonality of oil or coal combustion indicators we conclude that local domestic heating sources are using "clean fuels".

  9. Changing the Chairs: Impact of Workshop Activities in Assisting Chemistry Department Chairs in Achieving Racial and Ethnic Diversity

    ERIC Educational Resources Information Center

    Greene, Jessica; Lewis, Priscilla A.; Richmond, Geraldine L.; Stockard, Jean

    2011-01-01

    To address the low levels of underrepresented minority (URM) faculty in top-ranked chemistry departments, the National Science Foundation, the U.S. Department of Energy, and the National Institutes of Health jointly sponsored a workshop for academic chemistry leaders in September 2007. The goal of the two-and-a-half-day workshop was to create an…

  10. Molecular simulation of receptors of physiologically active compounds for purposes of medical chemistry

    NASA Astrophysics Data System (ADS)

    Baskin, Igor I.; Palyulin, Vladimir A.; Zefirov, Nikolai S.

    2009-06-01

    The general strategy of the molecular simulation of biological receptors and their interaction with ligands is considered. The procedures for construction of 3D protein models, molecular docking, evaluation of model quality, determination of the free energy of protein binding with ligands are discussed. The methods of molecular design of new medicaments based on molecular models of biological targets: virtual screening and de novo design, are presented. Examples of the above-listed approaches for the simulation of a number of pharmacologically significant receptors, analysis of receptor-ligand interactions and design of new biologically active organic compounds are given.

  11. Geochemical evaluation of the land use and human activities at a Medieval harbor site, Masuda city, Shimane Prefecture, Japan

    NASA Astrophysics Data System (ADS)

    Dalai, Banzragch; Ishiga, Hiroaki

    2014-05-01

    Large-scale harbor and settlement sites from the latter half of the eleventh through sixteenth centuries have recently been discovered in the northern part of Masuda City, Shimane Prefecture, Japan. The sites were constructed at the river mouth delta of the Takatsu and Masuda rivers, facing the Sea of Japan. In former time, the mouths of the two rivers are thought to have formed a shallow lagoon connecting with the Sea of Japan. The harbor was thus well located for ships sailing along the sea coast, especially for conducting trade with the China mainland and the Korean peninsula. Archaeological investigations have identified over 800 construction pits, blacksmith hearths, harbor structures and numerous fragments of ceramic porcelain originating both from within Japan and from Asia (China, Korea, Vietnam and Thailand). It seems that the maritime trade network operated from this Medieval harbor site by the Masuda Clan was on an East Asian scale. Consequently, the harbor site can be expected to have received a considerable amount of ancient anthropogenic matter. Concentrations of 22 elements in 66 soil samples from the Nakazu Higashihara site were determined by X-ray fluorescence spectroscopy, in order to identify the land use and human impacts on soil chemistry at the harbor site. The results show that significant differences in geochemical compositional exist between the northern and southern parts of the site due to differences in lithology and land use practice. The south area was a production area of this harbor site. Three different activity areas were recognized within this area (fire pit and charcoal area, building pillars, and a blacksmith furnace area), based on geochemical and archaeological information. Cluster analysis shows a strong relationship exists between As, Pb, Cu, Br, TS, MnO and P2O5 in the fire pit and charcoal area. These charcoal materials were likely derived from fuel used in firing and heating. Close relationships occur between Cr, Sr, Sc

  12. Active-site motions and polarity enhance catalytic turnover of hydrated subtilisin dissolved in organic solvents.

    PubMed

    Hudson, Elton P; Eppler, Ross K; Beaudoin, Julianne M; Dordick, Jonathan S; Reimer, Jeffrey A; Clark, Douglas S

    2009-04-01

    The enzyme subtilisin Carlsberg was surfactant-solubilized into two organic solvents, isooctane and tetrahydrofuran, and hydrated through stepwise changes in the thermodynamic water activity, a(w). The apparent turnover number k(cat)(app) in these systems ranged from 0.2 to 80 s(-1) and increased 11-fold in isooctane and up to 50-fold in tetrahydrofuran with increasing a(w). (19)F NMR relaxation experiments employing an active-site inhibitor were used to assess the dependence of active-site motions on a(w). The rates of NMR-derived fast (k > 10(7) s(-1)) and slow (k < 10(4) s(-1)) active-site motions increased in both solvents upon hydration, but only the slow motions correlated with k(cat). The (19)F chemical shift was a sensitive probe of the local electronic environment and provided an empirical measure of the active-site dielectric constant epsilon(as), which increased with hydration to epsilon(as) approximately 13 in each solvent. In both solvents, the transition state free energy data and epsilon(as) followed Kirkwood's model for the continuum solvation of a dipole, indicating that water also enhanced catalysis by altering the active-site's electronic environment and increasing its polarity to better stabilize the transition state. These results reveal that favorable dynamic and electrostatic effects both contribute to accelerated catalysis by solubilized subtilisin Carlsberg upon hydration in organic solvents. PMID:19317505

  13. Enhanced Enzyme Kinetic Stability by Increasing Rigidity within the Active Site*

    PubMed Central

    Xie, Yuan; An, Jiao; Yang, Guangyu; Wu, Geng; Zhang, Yong; Cui, Li; Feng, Yan

    2014-01-01

    Enzyme stability is an important issue for protein engineers. Understanding how rigidity in the active site affects protein kinetic stability will provide new insight into enzyme stabilization. In this study, we demonstrated enhanced kinetic stability of Candida antarctica lipase B (CalB) by mutating the structurally flexible residues within the active site. Six residues within 10 Å of the catalytic Ser105 residue with a high B factor were selected for iterative saturation mutagenesis. After screening 2200 colonies, we obtained the D223G/L278M mutant, which exhibited a 13-fold increase in half-life at 48 °C and a 12 °C higher T5015, the temperature at which enzyme activity is reduced to 50% after a 15-min heat treatment. Further characterization showed that global unfolding resistance against both thermal and chemical denaturation also improved. Analysis of the crystal structures of wild-type CalB and the D223G/L278M mutant revealed that the latter formed an extra main chain hydrogen bond network with seven structurally coupled residues within the flexible α10 helix that are primarily involved in forming the active site. Further investigation of the relative B factor profile and molecular dynamics simulation confirmed that the enhanced rigidity decreased fluctuation of the active site residues at high temperature. These results indicate that enhancing the rigidity of the flexible segment within the active site may provide an efficient method for improving enzyme kinetic stability. PMID:24448805

  14. Orthogonal chemistry for the synthesis of thiocoraline-triostin hybrids. Exploring their structure-activity relationship.

    PubMed

    Tulla-Puche, Judit; Auriemma, Sara; Falciani, Chiara; Albericio, Fernando

    2013-07-11

    The natural compounds triostin and thiocoraline are potent antitumor agents that act as DNA bisintercalators. From a pharmaceutical point of view, these compounds are highly attractive although they present a low pharmacokinetic profile, in part due to their low solubility. Synthetically, they represent a tour de force because no robust strategies have been developed to access a broad range of these bicyclic (depsi)peptides in a straightforward manner. Here we describe solid-phase strategies to synthesize new bisintercalators, such as thiocoraline-triostin hybrids, as well as analogues bearing soluble tags. Orthogonal protection schemes (up to five from: Fmoc, Boc Alloc, pNZ, o-NBS, and Troc), together with the right concourse of the coupling reagents (HOSu, HOBt, HOAt, Oxyma, EDC, DIPCDI, PyAOP, PyBOP, HATU, COMU), were crucial to establish the synthetic plan. In vitro studies and structure-activity relationships have been shown trends in the structure-activity relationship that will facilitate the design of new bisintercalators. PMID:23746132

  15. Recent advances in the study of (-)clausenamide: chemistry, biological activities and mechanism of action.

    PubMed

    Chu, Shi-Feng; Zhang, Jun-Tian

    2014-12-01

    Clausenamide (clau) is one of seven novel compounds isolated from Clausena lansium (Lour) skeels. Clau is unusual in that it contains 4 chiral centers yielding 8 pairs of enantiomers. After identification of the configuration of these enantiomers, the synthesis of 16 enantiomers, including optically active clau and (+) and (-)clau was carried out. During this study, many stereochemical and synthetic difficulties were solved and the Baldwin principle was updated. Production scale is now sufficient to meet the needs of clinical practice. In a pharmacological study numerous models and indicators showed that (-)clau is the active enantiomer, while (+)clau is inactive and elicits greater toxicity than (-)clau. The principal pharmacological effects of (-)clau are to increase cognition, demonstrated in ten models of memory impairment, as well as to inhibit β-amyloid (Aβ) toxicity, blocking neurofibrillary tangle formation by inhibiting the phosphorylation of tau protein. This anti-dementia effect is characterized by increased synaptic plasticity both in efficacy and in structure and provides new support for the theory that synaptic loss is the main cause of dementia. (-)Clau is considered to be a promising drug candidate for treatment of Alzheimer׳s disease and other neurodegenerative disorders. PMID:26579412

  16. Atmospheric Chemistry Measurements in Schools and Outreach Activities with Low-cost Air Quality Sensors

    NASA Astrophysics Data System (ADS)

    Fleming, Z.; Monks, P. S.; McKenzie, K.

    2014-12-01

    The increasing range of low cost air quality sensors entering the market-place or being developed in-house in the last couple of years has led to many possibilities for using these instruments for public outreach activities or citizen science projects. A range of instruments sent out into local schools for the children to interpret and analyse the data and put the air quality in their area into context. A teaching package with tutorials has been developed to bring the data to life and link in with curriculum.The instruments have also been positioned around the city of Leicester in the UK to help understand the spatial variations in air quality and to assess the impact of retro-fitting buses on a busy bus route. The data is easily accessible online on a near real time basis and the various instruments can be compared with others around the country or the world from classrooms around the world.We will give an overview of the instrumentation with a comparison with commercial and cutting edge research instrumentation, the type of activities that were carried out and the public outreach forums where the data can be used.

  17. Effects of resource activities upon repository siting and waste containment with reference to bedded salt

    SciTech Connect

    Ashby, J.; Rowe, J.

    1980-02-01

    The primary consideration for the suitability of a nuclear waste repository site is the overall ability of the repository to safely contain radioactive waste. This report is a discussion of the past, present, and future effects of resource activities on waste containment. Past and present resource activities which provide release pathways (i.e., leaky boreholes, adjacent mines) will receive initial evaluation during the early stages of any repository site study. However, other resource activities which may have subtle effects on containment (e.g., long-term pumping causing increased groundwater gradients, invasion of saline water causing lower retardation) and all potential future resource activities must also be considered during the site evaluation process. Resource activities will affect both the siting and the designing of repositories. Ideally, sites should be located in areas of low resource activity and low potential for future activity, and repository design should seek to eliminate or minimize the adverse effects of any resource activity. Buffer zones should be created to provide areas in which resource activities that might adversely affect containment can be restricted or curtailed. This could mean removing large areas of land from resource development. The impact of these frozen assets should be assessed in terms of their economic value and of their effect upon resource reserves. This step could require a major effort in data acquisition and analysis followed by extensive numerical modeling of regional fluid flow and mass transport. Numerical models should be used to assess the effects of resource activity upon containment and should include the cumulative effects of different resource activities. Analysis by other methods is probably not possible except for relatively simple cases.

  18. A caspase active site probe reveals high fractional inhibition needed to block DNA fragmentation.

    PubMed

    Méthot, Nathalie; Vaillancourt, John P; Huang, JingQi; Colucci, John; Han, Yongxin; Ménard, Stéphane; Zamboni, Robert; Toulmond, Sylvie; Nicholson, Donald W; Roy, Sophie

    2004-07-01

    Apoptotic markers consist of either caspase substrate cleavage products or phenotypic changes that manifest themselves as a consequence of caspase-mediated substrate cleavage. We have shown recently that pharmacological inhibitors of caspase activity prevent the appearance of two such apoptotic manifestations, alphaII-spectrin cleavage and DNA fragmentation, but that blockade of the latter required a significantly higher concentration of inhibitor. We investigated this phenomenon through the use of a novel radiolabeled caspase inhibitor, [(125)I]M808, which acts as a caspase active site probe. [(125)I]M808 bound to active caspases irreversibly and with high sensitivity in apoptotic cell extracts, in tissue extracts from several commonly used animal models of cellular injury, and in living cells. Moreover, [(125)I]M808 detected active caspases in septic mice when injected intravenously. Using this caspase probe, an active site occupancy assay was developed and used to measure the fractional inhibition required to block apoptosis-induced DNA fragmentation. In thymocytes, occupancy of up to 40% of caspase active sites had no effect on DNA fragmentation, whereas inhibition of half of the DNA cleaving activity required between 65 and 75% of active site occupancy. These results suggest that a high and persistent fractional inhibition will be required for successful caspase inhibition-based therapies. PMID:15067000

  19. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes.

    PubMed

    Cockburn, Darrell; Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

  20. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes

    PubMed Central

    Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

  1. Computational approaches to the determination of active site structures and reaction mechanisms in heterogeneous catalysts.

    PubMed

    Catlow, C R A; French, S A; Sokol, A A; Thomas, J M

    2005-04-15

    We apply quantum chemical methods to the study of active site structures and reaction mechanisms in mesoporous silica and metal oxide catalysts. Our approach is based on the use of both molecular cluster and embedded cluster (QM/MM) techniques, where the active site and molecular complex are described using density functional theory (DFT) and the embedding matrix simulated by shell model potentials. We consider three case studies: alkene epoxidation over the microporous TS-1 catalyst; methanol synthesis on ZnO and Cu/ZnO and C-H bond activation over Li-doped MgO. PMID:15901543

  2. Denaturation studies of active-site labeled papain using electron paramagnetic resonance and fluorescence spectroscopy.

    PubMed Central

    Ping, Z A; Butterfiel, D A

    1991-01-01

    A spin-labeled p-chloromercuribenzoate (SL-PMB) and a fluorescence probe, 6-acryloyl-2-dimethylaminonaphthalene (Acrylodan), both of which bind to the single SH group located in the active site of papain, were used to investigate the interaction of papain (EC 3.4.22.2) with two protein denaturants. It was found that the active site of papain was highly stable in urea solution, but underwent a large conformational change in guanidine hydrochloride solution. Electron paramagnetic resonance and fluorescence results were in agreement and both paralleled enzymatic activity of papain with respect to both the variation in pH and denaturation. These results strongly suggest that SL-PMB and Acrylodan labels can be used to characterize the physical state of the active site of the enzyme. PMID:1657229

  3. Failure of origin activation in response to fork stalling leads to chromosomal instability at fragile sites.

    PubMed

    Ozeri-Galai, Efrat; Lebofsky, Ronald; Rahat, Ayelet; Bester, Assaf C; Bensimon, Aaron; Kerem, Batsheva

    2011-07-01

    Perturbed DNA replication in early stages of cancer development induces chromosomal instability preferentially at fragile sites. However, the molecular basis for this instability is unknown. Here, we show that even under normal growth conditions, replication fork progression along the fragile site, FRA16C, is slow and forks frequently stall at AT-rich sequences, leading to activation of additional origins to enable replication completion. Under mild replication stress, the frequency of stalling at AT-rich sequences is further increased. Strikingly, unlike in the entire genome, in the FRA16C region additional origins are not activated, suggesting that all potential origins are already activated under normal conditions. Thus, the basis for FRA16C fragility is replication fork stalling at AT-rich sequences and inability to activate additional origins under replication stress. Our results provide a mechanism explaining the replication stress sensitivity of fragile sites and thus, the basis for genomic instability during early stages of cancer development. PMID:21726815

  4. Active-site mobility revealed by the crystal structure of arylmalonate decarboxylase from Bordetella bronchiseptica.

    PubMed

    Kuettner, E Bartholomeus; Keim, Antje; Kircher, Markus; Rosmus, Susann; Sträter, Norbert

    2008-03-21

    Arylmalonate decarboxylase (AMDase) from Bordetella bronchiseptica catalyzes the enantioselective decarboxylation of arylmethylmalonates without the need for an organic cofactor or metal ion. The decarboxylation reaction is of interest for the synthesis of fine chemicals. As basis for an analysis of the catalytic mechanism of AMDase and for a rational enzyme design, we determined the X-ray structure of the enzyme up to 1.9 A resolution. Like the distantly related aspartate or glutamate racemases, AMDase has an aspartate transcarbamoylase fold consisting of two alpha/beta domains related by a pseudo dyad. However, the domain orientation of AMDase differs by about 30 degrees from that of the glutamate racemases, and also significant differences in active-site structures are observed. In the crystals, four independent subunits showing different conformations of active-site loops are present. This finding is likely to reflect the active-site mobility necessary for catalytic activity. PMID:18258259

  5. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand

    SciTech Connect

    Parashar, Abhinav; Venkatachalam, Avanthika; Gideon, Daniel Andrew; Manoj, Kelath Murali

    2014-12-12

    Highlights: • Cyanide (CN) is a well-studied toxic principle, known to inhibit heme-enzymes. • Inhibition is supposed to result from CN binding at the active site as a ligand. • Diverse heme enzymes’ CN inhibition profiles challenge prevailing mechanism. • Poor binding efficiency of CN at low enzyme concentrations and ligand pressures. • CN-based diffusible radicals cause ‘non-productive electron transfers’ (inhibition). - Abstract: The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins’ active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes.

  6. Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor

    PubMed Central

    Spatzal, Thomas; Perez, Kathryn A; Howard, James B; Rees, Douglas C

    2015-01-01

    Dinitrogen reduction in the biological nitrogen cycle is catalyzed by nitrogenase, a two-component metalloenzyme. Understanding of the transformation of the inert resting state of the active site FeMo-cofactor into an activated state capable of reducing dinitrogen remains elusive. Here we report the catalysis dependent, site-selective incorporation of selenium into the FeMo-cofactor from selenocyanate as a newly identified substrate and inhibitor. The 1.60 Å resolution structure reveals selenium occupying the S2B site of FeMo-cofactor in the Azotobacter vinelandii MoFe-protein, a position that was recently identified as the CO-binding site. The Se2B-labeled enzyme retains substrate reduction activity and marks the starting point for a crystallographic pulse-chase experiment of the active site during turnover. Through a series of crystal structures obtained at resolutions of 1.32–1.66 Å, including the CO-inhibited form of Av1-Se2B, the exchangeability of all three belt-sulfur sites is demonstrated, providing direct insights into unforeseen rearrangements of the metal center during catalysis. DOI: http://dx.doi.org/10.7554/eLife.11620.001 PMID:26673079

  7. Evidence for linkages between ecoenzyme activity and soil organic matter chemistry following encroachment of leguminous woody plant into grasslands.

    NASA Astrophysics Data System (ADS)

    Filley, Timothy; Stott, Diane; Boutton, Thomas; Creamer, Courtney; Olk, Dan

    2010-05-01

    The encroachment of woody plants into grasslands is a worldwide phenomenon. In the Rio Grande Plains of southern Texas, subtropical thorn woodlands dominated by the N-fixing tree Prosopis glandulosa have largely replaced native grasslands as a result of fire suppression and extensive cattle grazing. This land cover change has resulted in the increase of belowground stocks of C, N, and P, changes to the amount and chemical nature of soil-stabilized plant biopolymers, and the composition and activity of soil microbes. Given that extracellular enzymes produced by plants and microbes are the principal means by which complex compounds are degraded and that the production of such enzymes is triggered or suppressed by changes in substrate and nutrient availability we sought to relate how these fundamental changes in this ecosystem are reflected in the activity of soil stabilized ecoenzymes and soil organic matter (SOM) chemistry in this system. We investigated a chronosequence of woody encroachment (14-86 yrs) into a C4-dominant grassland. We related the potential activities of five extracellular enzymes (arylamidase, acid phosphatase, β-glucosidase, β-glucosaminidase (NAGase, polyphenoloxidase (PPO)) and a general marker for hydrolytic activity, fluorescein diacetate (FDA) to the molecular composition and concentration of total hydrolysable amino acids and amino sugars, sugars, as well as CuO extractable lignin and substituted fatty acid to. When normalized to dry weight soil all chemical components increase in concentration with cluster age and all clusters have greater concentrations than background grasslands. All enzymes activities exhibit higher potential activity in woody clusters than grasslands but only NAGase and FDA increase with cluster age when normalized to dry weight of soil. Conversely, when normalized to SOC only lignin phenols, hydroxyl proline, and glucose from cellulose are positively correlated with cluster age indicating a selective accrual with

  8. Rapid Bioorthogonal Chemistry Turn-on through Enzymatic or Long Wavelength Photocatalytic Activation of Tetrazine Ligation.

    PubMed

    Zhang, Han; Trout, William S; Liu, Shuang; Andrade, Gabriel A; Hudson, Devin A; Scinto, Samuel L; Dicker, Kevin T; Li, Yi; Lazouski, Nikifar; Rosenthal, Joel; Thorpe, Colin; Jia, Xinqiao; Fox, Joseph M

    2016-05-11

    Rapid bioorthogonal reactivity can be induced by controllable, catalytic stimuli using air as the oxidant. Methylene blue (4 μM) irradiated with red light (660 nm) catalyzes the rapid oxidation of a dihydrotetrazine to a tetrazine thereby turning on reactivity toward trans-cyclooctene dienophiles. Alternately, the aerial oxidation of dihydrotetrazines can be efficiently catalyzed by nanomolar levels of horseradish peroxidase under peroxide-free conditions. Selection of dihydrotetrazine/tetrazine pairs of sufficient kinetic stability in aerobic aqueous solutions is key to the success of these approaches. In this work, polymer fibers carrying latent dihydrotetrazines were catalytically activated and covalently modified by trans-cyclooctene conjugates of small molecules, peptides, and proteins. In addition to visualization with fluorophores, fibers conjugated to a cell adhesive peptide exhibited a dramatically increased ability to mediate contact guidance of cells. PMID:27078610

  9. Chemistry of the Nudibranch Aldisa andersoni: Structure and Biological Activity of Phorbazole Metabolites

    PubMed Central

    Nuzzo, Genoveffa; Ciavatta, Maria Letizia; Kiss, Robert; Mathieu, Véronique; Leclercqz, Helene; Manzo, Emiliano; Villani, Guido; Mollo, Ernesto; Lefranc, Florence; D’Souza, Lisette; Gavagnin, Margherita; Cimino, Guido

    2012-01-01

    The first chemical study of the Indo-Pacific dorid nudibranch Aldisa andersoni resulted in the isolation of five chlorinated phenyl-pyrrolyloxazoles belonging to the phorbazole series. Two new molecules, 9-chloro-phorbazole D and N1-methyl-phorbazole A, co-occurring with known phorbazoles A, B and D, have been characterized. Phorbazoles were found to be present mainly in the external part of the mollusc. The structures of the new compounds were determined by interpretation of spectroscopic data, mainly NMR and mass spectrometry and by comparison with the literature data. Evaluation of feeding-deterrence activity as well as in vitro growth inhibitory properties in human cancer cells was also carried out. PMID:23015775

  10. Layered Double Hydroxide Nanoclusters: Aqueous, Concentrated, Stable, and Catalytically Active Colloids toward Green Chemistry.

    PubMed

    Tokudome, Yasuaki; Morimoto, Tsuyoshi; Tarutani, Naoki; Vaz, Pedro D; Nunes, Carla D; Prevot, Vanessa; Stenning, Gavin B G; Takahashi, Masahide

    2016-05-24

    Increasing attention has been dedicated to the development of nanomaterials rendering green and sustainable processes, which occur in benign aqueous reaction media. Herein, we demonstrate the synthesis of another family of green nanomaterials, layered double hydroxide (LDH) nanoclusters, which are concentrated (98.7 g/L in aqueous solvent), stably dispersed (transparent sol for >2 weeks), and catalytically active colloids of nano LDHs (isotropic shape with the size of 7.8 nm as determined by small-angle X-ray scattering). LDH nanoclusters are available as colloidal building blocks to give access to meso- and macroporous LDH materials. Proof-of-concept applications revealed that the LDH nanocluster works as a solid basic catalyst and is separable from solvents of catalytic reactions, confirming the nature of nanocatalysts. The present work closely investigates the unique physical and chemical features of this colloid, the formation mechanism, and the ability to act as basic nanocatalysts in benign aqueous reaction systems. PMID:27124717

  11. A review of chemistry and biological activities of the genus Aerva--a desert plant.

    PubMed

    Chawla, Payal; Chawla, Amit; Vasudeva, Neeru; Sharma, Surendra Kumar

    2012-01-01

    There are approximately 28 species of Aerva genus, but only a few species are medicinal of which A. persica, A. lanata and A. javanica are of great value. A number of flavonol glycosides (e.g., aervanone, kaempferol-3-galactoside, isorhamnetin-3-O-β-D-glucoside) have been reported from Aerva persica as major phytoconstituents and the minor constituents are β-cyanins (glycine betaine and trigonelline), sterols and carbohydrates. This plant is used as medicinal herb in several traditional systems of medicine all over the world, like diuretic, demulcent, purgative, emetic and tinder. Aerva plants are used to cure ulcer, lithiasis, dropsical affections, eye affection, toothache, headache, in disorders of abdomen and inflammation of internal organs. Roots and flowers are reported to possess hypoglycemic, antioxidant, anthelmintic, analgesic, antimalarial, antivenin activities and medicinal properties against rheumatism and kidney troubles. PMID:22568031

  12. Moderator Chemistry Program

    SciTech Connect

    Dewitt, L.V.; Gibbs, A.; Lambert, D.P.; Bohrer, S.R.; Fanning, R.L.; Houston, M.W.; Stinson, S.L.; Deible, R.W.; Abdel-Khalik, S.I.

    1990-11-01

    Over the past fifteen months, the Systems Chemistry Group of the Reactor Engineering Department has undertaken a comprehensive study of the Department`s moderator chemistry program at Savannah River Site (SRS). An internal review was developed to formalize and document this program. Objectives were as outlined in a mission statement and action plan. In addition to the mission statement and action plan, nine separate task reports have been issued during the course of this study. Each of these task reports is included in this document as a chapter. This document is an organized compilation of the individual reports issued by the Systems Chemistry Group in assessment of SRS moderator chemistry to determine if there were significant gaps in the program as ft existed in October, 1989. While these reviews found no significant gaps in that mode of operation, or any items that adversely affected safety, items were identified that could be improved. Many of the items have already been dear with or are in the process of completion under this Moderator Chemistry Program and other Reactor Restart programs. A complete list of the items of improvement found under this assessment is found in Chapter 9, along with a proposed time table for correcting remaining items that can be improved for the chemistry program of SRS reactors. An additional external review of the moderator chemistry processes, recommendations, and responses to/from the Reactor Corrosion Mitigation Committee is included as Appendix to this compilation.

  13. Moderator Chemistry Program

    SciTech Connect

    Dewitt, L.V.; Gibbs, A.; Lambert, D.P.; Bohrer, S.R.; Fanning, R.L.; Houston, M.W.; Stinson, S.L.; Deible, R.W.; Abdel-Khalik, S.I.

    1990-11-01

    Over the past fifteen months, the Systems Chemistry Group of the Reactor Engineering Department has undertaken a comprehensive study of the Department's moderator chemistry program at Savannah River Site (SRS). An internal review was developed to formalize and document this program. Objectives were as outlined in a mission statement and action plan. In addition to the mission statement and action plan, nine separate task reports have been issued during the course of this study. Each of these task reports is included in this document as a chapter. This document is an organized compilation of the individual reports issued by the Systems Chemistry Group in assessment of SRS moderator chemistry to determine if there were significant gaps in the program as ft existed in October, 1989. While these reviews found no significant gaps in that mode of operation, or any items that adversely affected safety, items were identified that could be improved. Many of the items have already been dear with or are in the process of completion under this Moderator Chemistry Program and other Reactor Restart programs. A complete list of the items of improvement found under this assessment is found in Chapter 9, along with a proposed time table for correcting remaining items that can be improved for the chemistry program of SRS reactors. An additional external review of the moderator chemistry processes, recommendations, and responses to/from the Reactor Corrosion Mitigation Committee is included as Appendix to this compilation.

  14. Insight into the mechanism of phosphoenolpyruvate mutase catalysis derived from site-directed mutagenesis studies of active site residues.

    PubMed

    Jia, Y; Lu, Z; Huang, K; Herzberg, O; Dunaway-Mariano, D

    1999-10-26

    PEP mutase catalyzes the conversion of phosphoenolpyruvate (PEP) to phosphonopyruvate in biosynthetic pathways leading to phosphonate secondary metabolites. A recent X-ray structure [Huang, K., Li, Z., Jia, Y., Dunaway-Mariano, D., and Herzberg, O. (1999) Structure (in press)] of the Mytilus edulis enzyme complexed with the Mg(II) cofactor and oxalate inhibitor reveals an alpha/beta-barrel backbone-fold housing an active site in which Mg(II) is bound by the two carboxylate groups of the oxalate ligand and the side chain of D85 and, via bridging water molecules, by the side chains of D58, D85, D87, and E114. The oxalate ligand, in turn, interacts with the side chains of R159, W44, and S46 and the backbone amide NHs of G47 and L48. Modeling studies identified two feasible PEP binding modes: model A in which PEP replaces oxalate with its carboxylate group interacting with R159 and its phosphoryl group positioned close to D58 and Mg(II) shifting slightly from its original position in the crystal structure, and model B in which PEP replaces oxalate with its phosphoryl group interacting with R159 and Mg(II) retaining its original position. Site-directed mutagenesis studies of the key mutase active site residues (R159, D58, D85, D87, and E114) were carried out in order to evaluate the catalytic roles predicted by the two models. The observed retention of low catalytic activity in the mutants R159A, D85A, D87A, and E114A, coupled with the absence of detectable catalytic activity in D58A, was interpreted as evidence for model A in which D58 functions in nucleophilic catalysis (phosphoryl transfer), R159 functions in PEP carboxylate group binding, and the carboxylates of D85, D87 and E114 function in Mg(II) binding. These results also provide evidence against model B in which R159 serves to mediate the phosphoryl transfer. A catalytic motif, which could serve both the phosphoryl transfer and the C-C cleavage enzymes of the PEP mutase superfamily, is proposed. PMID:10571990

  15. Localization of the binding site of tissue-type plasminogen activator to fibrin.

    PubMed Central

    Ichinose, A; Takio, K; Fujikawa, K

    1986-01-01

    Functionally active A and B chains were separated from a two-chain form of recombinant tissue-type plasminogen activator after mild reduction and alkylation. The A chain was found to be responsible for the binding to lysine-Sepharose or fibrin and the B chain contained the catalytic activity of tissue-type plasminogen activator. An extensive reduction of two-chain tissue-type plasminogen activator, however, destroyed both the binding and catalytic activities. A thermolytic fragment, Fr. 1, of tissue-type plasminogen activator that contained a growth factor and two kringle segments retained its lysine binding activity. Additional thermolytic cleavages in the kringle-2 segment of Fr. 1 caused a total loss of the binding activity. These results indicated that the binding site of tissue-type plasminogen activator to fibrin was located in the kringle-2 segment. Images PMID:3088041

  16. Crystal structure of an avian influenza polymerase PA[subscript N] reveals an endonuclease active site

    SciTech Connect

    Yuan, Puwei; Bartlam, Mark; Lou, Zhiyong; Chen, Shoudeng; Zhou, Jie; He, Xiaojing; Lv, Zongyang; Ge, Ruowen; Li, Xuemei; Deng, Tao; Fodor, Ervin; Rao, Zihe; Liu, Yingfang

    2009-11-10

    The heterotrimeric influenza virus polymerase, containing the PA, PB1 and PB2 proteins, catalyses viral RNA replication and transcription in the nucleus of infected cells. PB1 holds the polymerase active site and reportedly harbours endonuclease activity, whereas PB2 is responsible for cap binding. The PA amino terminus is understood to be the major functional part of the PA protein and has been implicated in several roles, including endonuclease and protease activities as well as viral RNA/complementary RNA promoter binding. Here we report the 2.2 angstrom (A) crystal structure of the N-terminal 197 residues of PA, termed PA(N), from an avian influenza H5N1 virus. The PA(N) structure has an alpha/beta architecture and reveals a bound magnesium ion coordinated by a motif similar to the (P)DX(N)(D/E)XK motif characteristic of many endonucleases. Structural comparisons and mutagenesis analysis of the motif identified in PA(N) provide further evidence that PA(N) holds an endonuclease active site. Furthermore, functional analysis with in vivo ribonucleoprotein reconstitution and direct in vitro endonuclease assays strongly suggest that PA(N) holds the endonuclease active site and has critical roles in endonuclease activity of the influenza virus polymerase, rather than PB1. The high conservation of this endonuclease active site among influenza strains indicates that PA(N) is an important target for the design of new anti-influenza therapeutics.

  17. In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes.

    PubMed

    Prasad, Nirmal K; Vindal, Vaibhav; Narayana, Siva Lakshmi; Ramakrishna, V; Kunal, Swaraj Priyaranjan; Srinivas, M

    2012-05-01

    Laccases belong to multicopper oxidases, a widespread class of enzymes implicated in many oxidative functions in various industrial oxidative processes like production of fine chemicals to bioremediation of contaminated soil and water. In order to understand the mechanisms of substrate binding and interaction between substrates and Pycnoporus cinnabarinus laccase, a homology model was generated. The resulted model was further validated and used for docking studies with toxic industrial dyes- acid blue 74, reactive black 5 and reactive blue 19. Interactions of chemical mediators with the laccase was also examined. The docking analysis showed that the active site always cannot accommodate the dye molecules, due to constricted nature of the active site pocket and steric hindrance of the residues whereas mediators are relatively small and can easily be accommodated into the active site pocket, which, thereafter leads to the productive binding. The binding properties of these compounds along with identification of critical active site residues can be used for further site-directed mutagenesis experiments in order to identify their role in activity and substrate specificity, ultimately leading to improved mutants for degradation of these toxic compounds. PMID:21877154

  18. Sites of Regulated Phosphorylation that Control K-Cl Cotransporter Activity

    PubMed Central

    Rinehart, Jesse; Maksimova, Yelena D.; Tanis, Jessica E.; Stone, Kathryn L.; Hodson, Caleb A.; Zhang, Junhui; Risinger, Mary; Pan, Weijun; Wu, Dianqing; Colangelo, Christopher M.; Forbush, Biff; Joiner, Clinton H.; Gulcicek, Erol E.; Gallagher, Patrick G.; Lifton, Richard P.

    2010-01-01

    Summary Modulation of intracellular chloride concentration ([Cl−]i) plays a fundamental role in cell volume regulation and neuronal response to GABA. Cl− exit via K-Cl cotransporters (KCCs) is a major determinant of [Cl−]I; however, mechanisms governing KCC activities are poorly understood. We identified two sites in KCC3 that are rapidly dephosphorylated in hypotonic conditions in cultured cells and human red blood cells in parallel with increased transport activity. Alanine substitutions at these sites result in constitutively active cotransport. These sites are highly phosphorylated in plasma membrane KCC3 in isotonic conditions, suggesting that dephosphorylation increases KCC3's intrinsic transport activity. Reduction of WNK1 expression via RNA interference reduces phosphorylation at these sites. Homologous sites are phosphorylated in all human KCCs. KCC2 is partially phosphorylated in neonatal mouse brain and dephosphorylated in parallel with KCC2 activation. These findings provide insight into regulation of [Cl−]i and have implications for control of cell volume and neuronal function. PMID:19665974

  19. Antarctic stratospheric chemistry of chlorine nitrate, hydrogen chloride, and ice - Release of active chlorine

    NASA Technical Reports Server (NTRS)

    Molina, Mario J.; Tso, Tai-Ly; Molina, Luisa T.; Wang, Frank C.-Y.

    1987-01-01

    The reaction rate between atmospheric hydrogen chloride (HCl) and chlorine nitrate (ClONO2) is greatly enhanced in the presence of ice particles; HCl dissolves readily into ice, and the collisional reaction probability for ClONO2 on the surface of ice with HCl in the mole fraction range from about 0.003 to 0.010 is in the range from about 0.05 to 0.1 for temperatures near 200 K. Chlorine is released into the gas phase on a time scale of at most a few milliseconds, whereas nitric acid (HNO3), the other product, remains in the condensed phase. This reaction could play an important role in explaining the observed depletion of ozone over Antarctica; it releases photolytically active chlorine from its most abundant reservoir species, and it promotes the formation of HNO3 and thus removes nitrogen dioxide from the gas phase. Hence it establishes the necessary conditions for the efficient catalytic destruction of ozone by halogenated free radicals.

  20. Antarctic Stratospheric Chemistry of Chlorine Nitrate, Hydrogen Chloride, and Ice: Release of Active Chlorine

    NASA Astrophysics Data System (ADS)

    Molina, Mario J.; Tso, Tai-Ly; Molina, Luisa T.; Wang, Frank C.-Y.

    1987-11-01

    The reaction rate between atmospheric hydrogen chloride (HCl) and chlorine nitrate (ClONO2) is greatly enhanced in the presence of ice particles; HCl dissolves readily into ice, and the collisional reaction probability for ClONO2 on the surface of ice with HCl in the mole fraction range from ~ 0.003 to 0.010 is in the range from ~ 0.05 to 0.1 for temperatures near 200 K. Chlorine (Cl2) is released into the gas phase on a time scale of at most a few milliseconds, whereas nitric acid (HNO3), the other product, remains in the condensed phase. This reaction could play an important role in explaining the observed depletion of ozone over Antarctica; it releases photolytically active chlorine from its most abundant reservoir species, and it promotes the formation of HNO3 and thus removes nitrogen dioxide (NO2) from the gas phase. Hence it establishes the necessary conditions for the efficient catalytic destruction of ozone by halogenated free radicals. In the absence of HCl, ClONO2 also reacts irreversibly with ice with a collision efficiency of ~ 0.02 at 200 K; the product hypochlorous acid (HOCl) is released to the gas phase on a time scale of minutes.

  1. Active sites of ligand-protected Au25 nanoparticle catalysts for CO2 electroreduction to CO

    NASA Astrophysics Data System (ADS)

    Alfonso, Dominic R.; Kauffman, Douglas; Matranga, Christopher

    2016-05-01

    Recent experimental studies have reported the electrochemical reduction of carbon dioxide (CO2) into CO at atomically precise negatively charged Au25- nanoclusters. The studies showed CO2 conversion at remarkably low overpotentials, but the exact mechanisms and nature of the active sites remain unclear. We used first-principles density functional theory and continuum solvation models to examine the role of the cluster during electrochemical CO2 reduction and analyze the free energies of proposed intermediate species. Contrary to previous assumptions, our results show that the fully ligand protected cluster is not an active CO2 reduction catalyst because formation of the crucial carboxyl intermediate required very high electrochemical potentials. Instead, our calculations suggest that the reduction process likely occurs on a dethiolated gold site, and adsorbed carboxyl intermediate formation was significantly stabilized at dethiolated gold sites. These findings point to the crucial role of exposed metal sites during electrochemical CO2 reduction at gold nanocluster catalysts.

  2. Active sites of ligand-protected Au25 nanoparticle catalysts for CO2 electroreduction to CO.

    PubMed

    Alfonso, Dominic R; Kauffman, Douglas; Matranga, Christopher

    2016-05-14

    Recent experimental studies have reported the electrochemical reduction of carbon dioxide (CO2) into CO at atomically precise negatively charged Au25 (-) nanoclusters. The studies showed CO2 conversion at remarkably low overpotentials, but the exact mechanisms and nature of the active sites remain unclear. We used first-principles density functional theory and continuum solvation models to examine the role of the cluster during electrochemical CO2 reduction and analyze the free energies of proposed intermediate species. Contrary to previous assumptions, our results show that the fully ligand protected cluster is not an active CO2 reduction catalyst because formation of the crucial carboxyl intermediate required very high electrochemical potentials. Instead, our calculations suggest that the reduction process likely occurs on a dethiolated gold site, and adsorbed carboxyl intermediate formation was significantly stabilized at dethiolated gold sites. These findings point to the crucial role of exposed metal sites during electrochemical CO2 reduction at gold nanocluster catalysts. PMID:27179498

  3. Green chemistry focus on optimization of silver nanoparticles using response surface methodology (RSM) and mosquitocidal activity: Anopheles stephensi (Diptera: Culicidae).

    PubMed

    Ondari Nyakundi, Erick; Padmanabhan, M Nalini

    2015-10-01

    There is an exigent necessity for development of environmental friendly bio-control agent(s) for elimination of mosquito due to increased resistance resurgence against synthetic control agents. Mosquito control strategy will lay a strong foundation to malaria exclusion or it can be curbed to certain level especially in the developing nations. In this study, silver nanoparticles were synthesized by green chemistry approach using Tridax procumbens leaf extract as a reducing agent. The reaction medium involved in the synthesis process was optimized by statistical experimental design using response surface methodology to obtain better yield, uniform size, shape and stability. Further, these synthesized nanoparticles were confirmed through UV-Visible, FT-IR spectroscopy, PSA and SEM Subsequently, the bioefficacy of these particles were investigated on Anopheles stephensi for larvicidal and pupicidal activity. Interestingly, time period of 90 min, temperature of 76±2 °C, pH 7.2±2, 2 mM silver nitrate (AgNO3), 3mM PEG and 2mM PVP showed excellent parameters for bioprocess design for large scale production of stabilized nanoparticles. A concentration of 5 ppm of PVP stabilized nanoparticles exhibited 100% mortality. Thus, the obtained results clearly suggest that silver nanoparticles stabilized by PEG and PVP may have important function as stabilizers, dispersants as well as larvicides for mosquito control. PMID:26010566

  4. Photography by Cameras Integrated in Smartphones as a Tool for Analytical Chemistry Represented by an Butyrylcholinesterase Activity Assay

    PubMed Central

    Pohanka, Miroslav

    2015-01-01

    Smartphones are popular devices frequently equipped with sensitive sensors and great computational ability. Despite the widespread availability of smartphones, practical uses in analytical chemistry are limited, though some papers have proposed promising applications. In the present paper, a smartphone is used as a tool for the determination of cholinesterasemia i.e., the determination of a biochemical marker butyrylcholinesterase (BChE). The work should demonstrate suitability of a smartphone-integrated camera for analytical purposes. Paper strips soaked with indoxylacetate were used for the determination of BChE activity, while the standard Ellman’s assay was used as a reference measurement. In the smartphone-based assay, BChE converted indoxylacetate to indigo blue and coloration was photographed using the phone’s integrated camera. A RGB color model was analyzed and color values for the individual color channels were determined. The assay was verified using plasma samples and samples containing pure BChE, and validated using Ellmans’s assay. The smartphone assay was proved to be reliable and applicable for routine diagnoses where BChE serves as a marker (liver function tests; some poisonings, etc.). It can be concluded that the assay is expected to be of practical applicability because of the results’ relevance. PMID:26110404

  5. Effects of pretreatment on the surface chemistry and pore size properties of nitrogen functionalized and alkylated granular activated carbon

    NASA Astrophysics Data System (ADS)

    Chen, Jiajun; Zhai, Yunbo; Chen, Hongmei; Li, Caiting; Zeng, Guangming; Pang, Daoxiong; Lu, Pei

    2012-12-01

    In this paper, granular activated carbon (GAC) from coconut shell was pretreated by HNO3, H2O2 and urea-formaldehyde resin, respectively. Then the obtained materials were functionalized in the same way for nitrogen group, and then alkylated. Effects of pretreatment on the surface chemistry and pore size of modified GACs were studied. Surface area and micropore volume of modified GAC which pretreated by HNO3 were 723.88 m2/g and 0.229 cm3/g, respectively, while virgin GAC were 742.34 m2/g and 0.276 cm3/g. Surface area and micropore volume decrease of the modified GACs which pretreated by the others two methods were more drastically. The types of groups presented were analyzed by electrophoresis, Fourier transform infrared spectroscopy (FTIR), and X-ray photoelectron spectroscopy (XPS). Nsbnd CH3 group and Cdbnd N group were detected on the surfaces of these three kinds of modified GACs. Results of XPS showed that the nitrogen functions of modified GAC which pretreated by H2O2 was 4.07%, it was more than that of the others two pretreatment methods. However, the modified GAC which pretreated by urea-formaldehyde resin was fixed more pyridine structure, which structure percentage was 45.88%, in addition, there were more basic groups or charge on the surface than the others.

  6. Photography by Cameras Integrated in Smartphones as a Tool for Analytical Chemistry Represented by an Butyrylcholinesterase Activity Assay.

    PubMed

    Pohanka, Miroslav

    2015-01-01

    Smartphones are popular devices frequently equipped with sensitive sensors and great computational ability. Despite the widespread availability of smartphones, practical uses in analytical chemistry are limited, though some papers have proposed promising applications. In the present paper, a smartphone is used as a tool for the determination of cholinesterasemia i.e., the determination of a biochemical marker butyrylcholinesterase (BChE). The work should demonstrate suitability of a smartphone-integrated camera for analytical purposes. Paper strips soaked with indoxylacetate were used for the determination of BChE activity, while the standard Ellman's assay was used as a reference measurement. In the smartphone-based assay, BChE converted indoxylacetate to indigo blue and coloration was photographed using the phone's integrated camera. A RGB color model was analyzed and color values for the individual color channels were determined. The assay was verified using plasma samples and samples containing pure BChE, and validated using Ellmans's assay. The smartphone assay was proved to be reliable and applicable for routine diagnoses where BChE serves as a marker (liver function tests; some poisonings, etc.). It can be concluded that the assay is expected to be of practical applicability because of the results' relevance. PMID:26110404

  7. Effects of biosolids and compost amendment on chemistry of soils contaminated with copper from mining activities.

    PubMed

    Sidhu, Virinder; Sarkar, Dibyendu; Datta, Rupali

    2016-03-01

    Several million metric tons of mining wastes, called stamp sands, were generated in the Upper Peninsula of Michigan during extensive copper (Cu) mining activities in the past. These materials, containing large amounts of Cu, were discharged into various offshoots of Lake Superior. Due to evidences of Cu toxicity on aquatic organisms, in due course, the materials were dredged and dumped on lake shores, thus converting these areas into vast, fallow lands. Erosion of these Cu-contaminated stamp sands back to the lakes is severely affecting aquatic life. A lack of uniform vegetation cover on stamp sands is facilitating this erosion. Understanding the fact that unless the stamp sands are fertilized to the point of sustaining vegetation growth, the problem with erosion and water quality degradation will continue, amending the stamp sands with locally available biosolids and composts, was considered. The purpose of the reported study was to assess potential effects of such organic fertilizer amendments on soil quality. As the first step of a combined laboratory and greenhouse study, a 2-month-long incubation experiment was performed to investigate the effects of biosolids and compost addition on the soil nutrient profile of stamp sands and organic matter content. Results showed that both biosolids and compost amendments resulted in significant increase in nitrogen and phosphorus concentrations and organic matter contents of stamp sands. Sequential extraction data demonstrated that Cu was mostly present as bound forms in stamp sands, and there was no significant increase in the plant available fraction of Cu because of fertilizer application. PMID:26894907

  8. Sampling and major element chemistry of the recent (A.D. 1631-1944) Vesuvius activity

    USGS Publications Warehouse

    Belkin, H.E.; Kilburn, C.R.J.; de Vivo, B.

    1993-01-01

    Detailed sampling of the Vesuvius lavas erupted in the period A.D. 1631-1944 provides a suite of samples for comprehensive chemical analyses and related studies. Major elements (Si, Ti, Al, Fetotal, Mn, Mg, Ca, Na, K and P), volatile species (Cl, F, S, H2O+, H2O- and CO2), and ferrous iron (Fe2+) were determined for one hundred and forty-nine lavas and five tephra from the A.D. 1631-1944 Vesuvius activity. The lavas represent a relatively homogeneous suite with respect to SiO2, TiO2, FeOtotal, MnO and P2O5, but show systematic variations among MgO, K2O, Na2O, Al2O3 and CaO. The average SiO2 content is 48.0 wt.% and the rocks are classified as tephriphonolites according to their content of alkalis. All of the lavas are silica-undersaturated and are nepheline, leucite, and olivine normative. There is no systematic variation in major-element composition with time, over the period A.D. 1631-1944. The inter-eruption and intra-eruption compositional differences are the same magnitude. The lavas are highly porphyritic with clinopyroxene and leucite as the major phases. Fractionation effects are not reflected in the silica content of the lavas. The variability of MgO, K2O, Na2O, and CaO can be modelled as a relative depletion or accumulation of clinopyroxene. ?? 1993.

  9. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Twelve new chemistry expermiments are described. Broad areas covered include atomic structure, solubility, gaseous diffusion, endothermic reactions, alcohols, equilibrium, atomic volumes, and some improvised apparatus. (PS)

  10. Technetium chemistry

    SciTech Connect

    Burns, C.; Bryan, J.; Cotton, F.; Ott, K.; Kubas, G.; Haefner, S.; Barrera, J.; Hall, K.; Burrell, A.

    1996-04-01

    Technetium chemistry is a young and developing field. Despite the limited knowledge of its chemistry, technetium is the workhorse for nuclear medicine. Technetium is also a significant environmental concern because it is formed as a byproduct of nuclear weapons production and fission-power generators. Development of new technetium radio-pharmaceuticals and effective environmental control depends strongly upon knowledge of basic technetium chemistry. The authors performed research into the basic coordination and organometallic chemistry of technetium and used this knowledge to address nuclear medicine and environmental applications. This is the final report of a three-year Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL).

  11. Bi-site activation occurs with the native and nucleotide-depleted mitochondrial F1-ATPase.

    PubMed Central

    Milgrom, Y M; Murataliev, M B; Boyer, P D

    1998-01-01

    Experiments are reported on the uni-site catalysis and the transition from uni-site to multi-site catalysis with bovine heart mitochondrial F1-ATPase. The very slow uni-site ATP hydrolysis is shown to occur without tightly bound nucleotides present and with or without Pi in the buffer. Measurements of the transition to higher rates and the amount of bound ATP committed to hydrolysis as the ATP concentration is increased at different fixed enzyme concentrations give evidence that the filling of a second site can initiate near maximal turnover rates. They provide rate constant information, and show that an apparent Km for a second site of about 2 microM and Vmax of 10 s-1, as suggested by others, is not operative. Careful initial velocity measurements also eliminate other suggested Km values and are consistent with bi-site activation to near maximal hydrolysis rates, with a Km of about 130 microM and Vmax of about 700 s-1. However, the results do not eliminate the possibility of additional 'hidden' Km values with similar Vmax:Km ratios. Recent data on competition between TNP-ATP and ATP revealed a third catalytic site for ATP in the millimolar concentration range. This result, and those reported in the present paper, allow the conclusion that the mitochondrial F1-ATPase can attain near maximal activity in bi-site catalysis. Our data also add to the evidence that a recent claim, that the mitochondrial F1-ATPase does not show catalytic site cooperativity, is invalid. PMID:9480927

  12. Instructional strategies for online high school chemistry: Impact on student learning, success on labs, and active engagement

    NASA Astrophysics Data System (ADS)

    McInerney, Jody R.

    A quasi-experimental mixed methods action research study was conducted at a K-12 virtual charter school with 103 high school chemistry students to investigate the relationship between participation in online synchronous lessons, student understanding of chemistry concepts and success on laboratory assignments. The study examined the impact of different instructional strategies on student success on chemistry labs as defined by lab completion rates, lab performance and concept understanding. The data show students who participated in the synchronous lessons were more successful in labs than those who did not. Different instructional strategies yielded different levels of student engagement and information gathered about student learning during synchronous lessons.

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

    SciTech Connect

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

    2015-06-04

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

  14. Modified Active Site Coordination in a Clinical Mutant of Sulfite Oxidase

    SciTech Connect

    Doonan, C.J.; Wilson, H.L.; Rajagopalan, K.V.; Garrett, R.M.; Bennett, B.; Prince, R.C.; George, G.N.

    2009-06-02

    The molybdenum site of the Arginine 160 {yields} Glutamine clinical mutant of the physiologically vital enzyme sulfite oxidase has been investigated by a combination of X-ray absorption spectroscopy and density functional theory calculations. We conclude that the mutant enzyme has a six-coordinate pseudo-octahedral active site with coordination of Glutamine O{sup {epsilon}} to molybdenum. This contrasts with the wild-type enzyme which is five-coordinate with approximately square-based pyramidal geometry. This difference in the structure of the molybdenum site explains many of the properties of the mutant enzyme which have previously been reported.

  15. Mutations Closer to the Active Site Improve the Promiscuous Aldolase Activity of 4-Oxalocrotonate Tautomerase More Effectively than Distant Mutations.

    PubMed

    Rahimi, Mehran; van der Meer, Jan-Ytzen; Geertsema, Edzard M; Poddar, Harshwardhan; Baas, Bert-Jan; Poelarends, Gerrit J

    2016-07-01

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which catalyzes enol-keto tautomerization as part of a degradative pathway for aromatic hydrocarbons, promiscuously catalyzes various carbon-carbon bond-forming reactions. These include the aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde. Here, we demonstrate that 4-OT can be engineered into a more efficient aldolase for this condensation reaction, with a >5000-fold improvement in catalytic efficiency (kcat /Km ) and a >10(7) -fold change in reaction specificity, by exploring small libraries in which only "hotspots" are varied. The hotspots were identified by systematic mutagenesis (covering each residue), followed by a screen for single mutations that give a strong improvement in the desired aldolase activity. All beneficial mutations were near the active site of 4-OT, thus underpinning the notion that new catalytic activities of a promiscuous enzyme are more effectively enhanced by mutations close to the active site. PMID:27238293

  16. Systematic mutagenesis of the active site omega loop of TEM-1 beta-lactamase.

    PubMed Central

    Petrosino, J F; Palzkill, T

    1996-01-01

    Beta-Lactamase is a bacterial protein that provides resistance against beta-lactam antibiotics. TEM-1 beta-lactamase is the most prevalent plasmid-mediated beta-lactamase in gram-negative bacteria. Normally, this enzyme has high levels of hydrolytic activity for penicillins, but mutant beta-lactamases have evolved with activity toward a variety of beta-lactam antibiotics. It has been shown that active site substitutions are responsible for changes in the substrate specificity. Since mutant beta-lactamases pose a serious threat to antimicrobial therapy, the mechanisms by which mutations can alter the substrate specificity of TEM-1 beta-lactamase are of interest. Previously, screens of random libraries encompassing 31 of 55 active site amino acid positions enabled the identification of the residues responsible for maintaining the substrate specificity of TEM-1 beta-lactamase. In addition to substitutions found in clinical isolates, many other specificity-altering mutations were also identified. Interestingly, many nonspecific substitutions in the N-terminal half of the active site omega loop were found to increase ceftazidime hydrolytic activity and decrease ampicillin hydrolytic activity. To complete the active sight study, eight additional random libraries were constructed and screened for specificity-altering mutations. All additional substitutions found to alter the substrate specificity were located in the C-terminal half of the active site loop. These mutants, much like the N-terminal omega loop mutants, appear to be less stable than the wild-type enzyme. Further analysis of a 165-YYG-167 triple mutant, selected for high levels of ceftazidime hydrolytic activity, provides an example of the correlation which exists between enzyme instability and increased ceftazidime hydrolytic activity in the ceftazidime-selected omega loop mutants. PMID:8606154

  17. Active-site motions and polarity enhance catalytic turnover of hydrated subtilisin dissolved in organic solvents

    PubMed Central

    Hudson, Elton P; Eppler, Ross K; Beaudoin, Julianne M; Dordick, Jonathan S; Reimer, Jeffrey A; Clark, Douglas S

    2009-01-01

    The enzyme subtilisin Carlsberg was surfactant-solubilized into two organic solvents, isooctane and tetrahydrofuran, and hydrated through stepwise changes in the thermodynamic water activity, aw. The apparent turnover number kcatapp in these systems ranged from 0.2 to 80 s−1 and increased 11-fold in isooctane and up to 50-fold in tetrahydrofuran with increasing aw. 19F-NMR relaxation experiments employing an active-site inhibitor were used to assess the dependence of active-site motions on aw. The rates of NMR-derived fast (k > 107 s−1) and slow (k < 104 s−1) active-site motions increased in both solvents upon hydration, but only the slow motions correlated with kcat. The 19F chemical shift was a sensitive probe of the local electronic environment and provided an empirical measure of the active-site dielectric constant εas, which increased with hydration to εas ≈ 13 in each solvent. In both solvents the transition state free energy data and εas followed Kirkwood’s model for the continuum solvation of a dipole, indicating that water also enhanced catalysis by altering the active-site’s electronic environment and increasing its polarity to better stabilize the transition state. These results reveal that favorable dynamic and electrostatic effects both contribute to accelerated catalysis by solubilized subtilisin Carlsberg upon hydration in organic solvents. PMID:19317505

  18. Acylpeptide hydrolase: inhibitors and some active site residues of the human enzyme.

    PubMed

    Scaloni, A; Jones, W M; Barra, D; Pospischil, M; Sassa, S; Popowicz, A; Manning, L R; Schneewind, O; Manning, J M

    1992-02-25

    Acylpeptide hydrolase may be involved in N-terminal deacetylation of nascent polypeptide chains and of bioactive peptides. The activity of this enzyme from human erythrocytes is sensitive to anions such as chloride, nitrate, and fluoride. Furthermore, blocked amino acids act as competitive inhibitors of the enzyme. Acetyl leucine chloromethyl ketone has been employed to identify one active site residue as His-707. Diisopropylfluorophosphate has been used to identify a second active site residue as Ser-587. Chemical modification studies with a water-soluble carbodiimide implicate a carboxyl group in catalytic activity. These results and the sequence around these active site residues, especially near Ser-587, suggest that acylpeptide hydrolase contains a catalytic triad. The presence of a cysteine residue in the vicinity of the active site is suggested by the inactivation of the enzyme by sulfhydryl-modifying agents and also by a low amount of modification by the peptide chloromethyl ketone inhibitor. Ebelactone A, an inhibitor of the formyl aminopeptidase, the bacterial counterpart of eukaryotic acylpeptide hydrolase, was found to be an effective inhibitor of this enzyme. These findings suggest that acylpeptidase hydrolase is a member of a family of enzymes with extremely diverse functions. PMID:1740429

  19. Improving the neutral phytase activity from Bacillus amyloliquefaciens DSM 1061 by site-directed mutagenesis.

    PubMed

    Xu, Wei; Shao, Rong; Wang, Zupeng; Yan, Xiuhua

    2015-03-01

    Neutral phytase is used as a feed additive for degradation of anti-nutritional phytate in aquatic feed industry. Site-directed mutagenesis of Bacillus amyloliquefaciens DSM 1061 phytase was performed with an aim to increase its activity. Mutation residues were chosen based on multiple sequence alignments and structure analysis of neutral phytsaes from different microorganisms. The mutation sites on surface (D148E, S197E and N156E) and around the active site (D52E) of phytase were selected. Analysis of the phytase variants showed that the specific activities of mutants D148E and S197E remarkably increased by about 35 and 13% over a temperature range of 40-75 °C at pH 7.0, respectively. The k cat of mutants D148E and S197E were 1.50 and 1.25 times than that of the wild-type phytase, respectively. Both D148E and S197E showed much higher thermostability than that of the wild-type phytase. However, mutants N156E and D52E led to significant loss of specific activity of the enzyme. Structural analysis revealed that these mutations may affect conformation of the active site of phytase. The present mutant phytases D148E and S197E with increased activities and thermostabilities have application potential as additives in aquaculture feed. PMID:25613522

  20. Biotinylated granulocyte/macrophage colony-stimulating factor analogues: effect of linkage chemistry on activity and binding.

    PubMed

    Angelotti, T P; Clarke, M F; Longino, M A; Emerson, S G

    1991-01-01

    Biotinylated granulocyte/macrophage colony-stimulating factor (GM-CSF) analogues with different linkage chemistries and levels of conjugated biotin were synthesized by reacting recombinant human GM-CSF with sulfosuccinimidyl 6-biotinamidohexanoate or biotin hydrazide/1-[3-(dimethylamino)-propyl]-3-ethylcarbodiimide. These chemically reactive forms of biotin produced derivatives biotinylated at amine or carboxyl groups, respectively. Amine-derivatized analogues of 1.2 and 3.8 mol of biotin/mol of protein (N1-bGM-CSF and N4-bGM-CSF) and a carboxyl-modified analogue of 4.6 mol of biotin/mol of protein (C5-bGM-CSF) were synthesized. These analogues were compared to determine the effect of biotinylation on biological activity and GM-CSF receptor binding characteristics. The biotinylated proteins migrated with the same molecular weight as the native, unmodified protein as determined by SDS-PAGE and could be detected by Western blotting with alkaline phosphatase conjugated streptavidin, thus demonstrating the biotin linkage. All three analogues retained full agonist activity relative to the native protein (EC50 = 10-15 pM) when assayed for the stimulation of human bone marrow progenitor cell growth. Cell surface GM-CSF receptor binding was characterized by the binding of the analogues to human neutrophils, with detection by fluorescein-conjugated avidin and fluorescence-activated cell sorting. The N-bGM-CSFs demonstrated GM-CSF receptor specific binding that was displaceable by excess underivatized protein, with the detected fluorescence signal decreasing with increasing biotin to protein molar ratio. In contrast, C5-bGM-CSF binding above background fluorescence could not be detected using this system, suggesting that this derivative could bind to and activate the receptor, but not simultaneously bind fluorescein-conjugated avidin. The amine-derivatized biotinylated GM-CSF analogues retained biological activity, could specifically label cell surface receptors, and may be