Science.gov

Sample records for active site resulted

  1. Permafrost and active layer monitoring in the maritime Antarctic: Preliminary results from CALM sites on Livingston and Deception Islands

    USGS Publications Warehouse

    Ramos, M.; Vieira, G.; Blanco, J.J.; Hauck, C.; Hidalgo, M.A.; Tome, D.; Nevers, M.; Trindade, A.

    2007-01-01

    This paper describes results obtained from scientific work and experiments performed on Livingston and Deception Islands. Located in the South Shetland Archipelago, these islands have been some of the most sensitive regions over the last 50 years with respect to climate change with a Mean Annual Air Temperature (MAAT) close to -2 ºC. Three Circumpolar Active Layer Monitoring (CALM) sites were installed to record the thermal regime and the behaviour of the active layer in different places with similar climate, but with different soil composition, porosity, and water content. The study’s ultimate aim is to document the influence of climate change on permafrost degradation. Preliminary results, obtained in 2006, on maximum active-layer thickness (around 40 cm in the CALM of Deception Island), active layer temperature evolution, snow thickness, and air temperatures permit early characterization of energy exchange mechanisms between the ground and the atmosphere in the CALM-S sites.

  2. List 9 - Active CERCLIS Sites:

    EPA Pesticide Factsheets

    The List 9 displays the sequence of activities undertaken at active CERCLIS sites. An active site is one at which site assessment, removal, remedial, enforcement, cost recovery, or oversight activities are being planned or conducted.

  3. Immersion freezing of supermicron mineral dust particles: freezing results, testing different schemes for describing ice nucleation, and ice nucleation active site densities.

    PubMed

    Wheeler, M J; Mason, R H; Steunenberg, K; Wagstaff, M; Chou, C; Bertram, A K

    2015-05-14

    Ice nucleation on mineral dust particles is known to be an important process in the atmosphere. To accurately implement ice nucleation on mineral dust particles in atmospheric simulations, a suitable theory or scheme is desirable to describe laboratory freezing data in atmospheric models. In the following, we investigated ice nucleation by supermicron mineral dust particles [kaolinite and Arizona Test Dust (ATD)] in the immersion mode. The median freezing temperature for ATD was measured to be approximately -30 °C compared with approximately -36 °C for kaolinite. The freezing results were then used to test four different schemes previously used to describe ice nucleation in atmospheric models. In terms of ability to fit the data (quantified by calculating the reduced chi-squared values), the following order was found for ATD (from best to worst): active site, pdf-α, deterministic, single-α. For kaolinite, the following order was found (from best to worst): active site, deterministic, pdf-α, single-α. The variation in the predicted median freezing temperature per decade change in the cooling rate for each of the schemes was also compared with experimental results from other studies. The deterministic model predicts the median freezing temperature to be independent of cooling rate, while experimental results show a weak dependence on cooling rate. The single-α, pdf-α, and active site schemes all agree with the experimental results within roughly a factor of 2. On the basis of our results and previous results where different schemes were tested, the active site scheme is recommended for describing the freezing of ATD and kaolinite particles. We also used our ice nucleation results to determine the ice nucleation active site (INAS) density for the supermicron dust particles tested. Using the data, we show that the INAS densities of supermicron kaolinite and ATD particles studied here are smaller than the INAS densities of submicron kaolinite and ATD particles

  4. Biosparging results: How clean is the site?

    SciTech Connect

    Billings, J.F.; Griswold, J.E.; Billings, B.G.

    1995-12-31

    Biosparging, a technique similar to air sparging but with the design intent of plume discretization with low to moderate flows per sparge point and operational patience to allow for bioremediation, is producing remediation results distancing itself from air sparging in general. While some debate the efficacy of sparging, this paper discusses results at biosparging sites that are by design and operation significantly different than results from air sparging sites. The authors have participated in biosparging projects across the country for a number of years that have resulted in a range of applications with a large database of results. To provide insight into recent debate concerning the use of water quality results at sparging sites, data from permanent monitoring wells, located 50 to 200 feet beyond the direct influence of air movement, are provided. Water quality results from wells where systems have been off from weeks to more than a year also are provided, as well as confirmation borings of soil concentrations above, at, and below the water table. Additionally, results from new borings and monitoring wells are provided for systems after shutdown. Wells undergoing active sparging/agitation can provide results indicating clean water. Attention is focused on BTEX analytes.

  5. MUTATION OF THE ACTIVE SITE CARBOXY-LYSINE (K70) OF OXA-1 β-LACTAMASE RESULTS IN A DEACYLATION-DEFICIENT ENZYME†

    PubMed Central

    Schneider, Kyle D.; Bethel, Christopher R.; Distler, Anne M.; Hujer, Andrea M.; Bonomo, Robert A.; Leonard, David A.

    2009-01-01

    Class D β-lactamases hydrolyze β-lactam antibiotics by using an active site serine nucleophile to form a covalent acyl-enzyme intermediate, and subsequently employ water to deacylate the β-lactam and release product. Class D β-lactamases are carboxylated on the ε-amino group of an active site lysine, with the resulting carbamate functional group serving as a general base. We discovered that substitutions of the active site serine and lysine in OXA-1 β-lactamase, a monomeric class D enzyme, significantly disrupt catalytic turnover. Substitution of glycine for the nucleophilic serine (S67G) results in an enzyme that can still bind substrate but is unable to form a covalent acyl-enzyme intermediate. Substitution of the carboxylated lysine (K70), on the other hand, results in enzyme that can be acylated by substrate, but is impaired for deacylation. We employed the fluorescent penicillin BOCILLIN FL™ to show that three different substitutions for K70 (alanine, aspartate and glutamate) accumulate significant acyl-enzyme intermediate. Interestingly, BOCILLIN FL™ deacylation rates vary depending on the identity of the substituting residue, from t1/2 ≈ 60 min for K70A to undetectable deacylation for K70D. Tryptophan fluorescence spectroscopy was used to confirm that these results are applicable to natural (i.e. non-fluorescent) substrates. Deacylation by K70A, but not K70D or K70E, can be partially restored by the addition of short-chain carboxylic acid mimetics of the lysine carbamate. In conclusion, we establish the functional role of the carboxylated lysine in OXA-1 and highlight its specific role in acylation and deacylation. PMID:19485421

  6. 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.

  7. CHANG'E-3 Active Particle-induced X-ray Spectrometer: first detection near the landing site and preliminary analysis result

    NASA Astrophysics Data System (ADS)

    Peng, Wenxi; Cui, XingZhu; Wang, Huanyu; Guo, Dongya

    Active Particle-induced X-ray Spectrometer (APXS) onboard CHANG'E-3 Yutu rover was the first high energy resolution instrument of X-ray spectrometry sent to the lunar surface. The scientific objective of APXS is to investigate the elemental compositions along the route of the lunar rover on the Moon.Here, the first lunar soil detection near the landing site made by APXS is presented. The initial analysis indicate that the lunar regolith in this area is rich in both TiO2 and FeO, which is consistent with the remote sensing results.

  8. Conversion of citrate synthase into citryl-CoA lyase as a result of mutation of the active-site aspartic acid residue to glutamic acid.

    PubMed Central

    Man, W J; Li, Y; O'Connor, C D; Wilton, D C

    1991-01-01

    The active-site aspartic acid residue, Asp-362, of Escherichia coli citrate synthase was changed by site-directed mutagenesis to Glu-362, Asn-362 or Gly-362. Only very low catalytic activity could be detected with the Asp----Asn and Asp----Gly mutations. The Asp----Glu mutation produced an enzyme that expressed about 0.8% of the overall catalytic rate, and the hydrolysis step in the reaction, monitored as citryl-CoA hydrolysis, was inhibited to a similar extent. However, the condensation reaction, measured in the reverse direction as citryl-CoA cleavage to oxaloacetate and acetyl-CoA, was not affected by the mutation, and this citryl-CoA lyase activity was the major catalytic activity of the mutant enzyme. This high condensation activity in an enzyme in which the subsequent hydrolysis step was about 98% inhibited permitted considerable exchange of the methyl protons of acetyl-CoA during catalysis by the mutant enzyme. The Km for oxaloacetate was not significantly altered in the D362E mutant enzyme, whereas the Km for acetyl-CoA was about 5 times lower. A mechanism is proposed in which Asp-362 is involved in the hydrolysis reaction of this enzyme, and not as a base in the deprotonation of acetyl-CoA as recently suggested by others. [Karpusas, Branchaud & Remington (1990) Biochemistry 29, 2213-2219; Alter, Casazza, Zhi, Nemeth, Srere & Evans, (1990) Biochemistry 29, 7557-7563]. PMID:1684105

  9. Initial results from MARmara SuperSITE

    NASA Astrophysics Data System (ADS)

    Meral Ozel, Nurcan; Necmioglu, Ocal; Favali, Paolo; Douglas, John; Mathieu, Pierre-Philippe; Geli, Louis; Ergintav, Semih; Oguz Ozel, Asım; Tan, Onur; Gurbuz, Cemil; Erdik, Mustafa

    2014-05-01

    shaking measurements, has been prepared by INERIS to be set up on the field to be also set up as an early warning system prototype to be progressively parameterized and tested on near to real time condition. Slip rate on the Main Marmara Fault from 3D seismic data has been estimated and extremely young age of the North Anatolian Fault in the Sea of Marmara has been determined. Seismic risk study for IGDAS Natural Gas Network including pipelines and its components has been carried out with several earthquake scenarios in Marmara Sea. An automatic shut-off algorithm has been developed for the automatic shut-off of the gas flow at the IGDAS district regulators during an extreme event. All the European and international initiatives and projects that could have links with MARsite were identified as the initial step for the integration of data management practices and coordination with ongoing research infrastructures. EPOS and EMSO are considered to be crucial links that could provide sustainability of MARsite's developments beyond the project's lifetime. Concerning EMSO, Marmara is one of the nodes of the research infrastructure, in which a permanent installation at sea is being integrated with land-based networks. In the context of EPOS, MARsite will be a thematic core service. In addition, the data collection and dissemination in MARsite is carried out according to the data management principles of EMSO and EPOS. Dissemination activities reached a certain level of maturity through the relesea of Public Annual Report, quarterly newsletter, ID card and poster, social media interaction, dedicated web sites, videos and several conferences and workhops participated, such as GEO European Projects' Workshop, Supersites Coordination Workshop and GEO-X Plenary & Geneva Ministerial Summit .

  10. Normal Modes Expose Active Sites in Enzymes

    PubMed Central

    Glantz-Gashai, Yitav; Samson, Abraham O.

    2016-01-01

    Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes. PMID:28002427

  11. Aspects of annoyance due to noise of road traffic. Survey results at 10 sites

    NASA Technical Reports Server (NTRS)

    1981-01-01

    Results of surveys per highway site are given. A discussion is given of factors studied such as contribution of various noise sources, variation of noise levels at different sites, times and activities disturbed, and noise level and annoyance.

  12. Preliminary results from Submarine Ring of Fire 2012 - NE Lau: First explorations of hydrothermally active volcanoes across the supra-subduction zone and a return to the West Mata eruption site

    NASA Astrophysics Data System (ADS)

    Resing, J.; Embley, R. W.

    2012-12-01

    Several expeditions in the past few years have shown that the NE Lau basin has one of the densest concentrations of volcanically and hydrothermally active volcanoes on the planet. In 2008 two active submarine volcanic eruptions were discovered during a one week period and subsequent dives with the Jason remotely operated vehicle at one of the sites (West Mata) revealed an active boninite eruption taking place at 1200 m depth. Two dives at the other revealed evidence for recent eruption along the NE Lau Spreading Center. Several more expeditions in 2010-11 discovered additional evidence about the extent and types of hydrothermal activity in this area. Data from CTDO (conductivity, temperature, depth, optical) vertical casts, tow-yos, and towed camera deployments revealed more than 15 hydrothermal sites at water depths from ~800 to 2700 m that include sites from the magmatic arc, the "rear arc," and the back arc spreading centers. These sites range from high temperature black smoker sulfide-producing systems to those dominated by magmatic degassing. Dives by remotely operated vehicle (Quest 4000) in September 2012 will explore these sites and return samples for chemical, biological and geologic studies. One of the dives will be a return visit to West Mata volcano, the site of the deepest submarine eruption yet observed (in 2009). Recent multibeam data reveal large changes in West Mata's summit, suggesting that the nature of the eruption and the location of the erupting vents may have changed. In addition to the preliminary results from the science team, we will also discuss our use and experience with continuous live video transmission (through the High Definition video camera on the Quest 4000) back to shore via satellite and through the internet. Submarine Ring of Fire 2012 Science Team: Bradley Tebo, Bill Chadwick, Ed Baker, Ken Rubin, Susan Merle, Timothy Shank, Sharon Walker, Andra Bobbitt, Nathan Buck, David Butterfield, Eric Olson, John Lupton, Richard Arculus

  13. Validated ligand mapping of ACE active site

    NASA Astrophysics Data System (ADS)

    Kuster, Daniel J.; Marshall, Garland R.

    2005-08-01

    Crystal structures of angiotensin-converting enzyme (ACE) complexed with three inhibitors (lisinopril, captopril, enalapril) provided experimental data for testing the validity of a prior active site model predicting the bound conformation of the inhibitors. The ACE active site model - predicted over 18 years ago using a series of potent ACE inhibitors of diverse chemical structure - was recreated using published data and commercial software. Comparison between the predicted structures of the three inhibitors bound to the active site of ACE and those determined experimentally yielded root mean square deviation (RMSD) values of 0.43-0.81 Å, among the distances defining the active site map. The bound conformations of the chemically relevant atoms were accurately deduced from the geometry of ligands, applying the assumption that the geometry of the active site groups responsible for binding and catalysis of amide hydrolysis was constrained. The mapping of bound inhibitors at the ACE active site was validated for known experimental compounds, so that the constrained conformational search methodology may be applied with confidence when no experimentally determined structure of the enzyme yet exists, but potent, diverse inhibitors are available.

  14. SITE CHARACTERIZATION AND MONITORING TECHNOLOGY VERIFICATION: PROGRESS AND RESULTS

    EPA Science Inventory

    The Site Characterization and Monitoring Technology Pilot of the U.S. Environmental Protection Agency's Environmental Technology Verification Program (ETV) has been engaged in verification activities since the fall of 1994 (U.S. EPA, 1997). The purpose of the ETV is to promote th...

  15. The Global Oscillation Network Group site survey, 2: Results

    NASA Technical Reports Server (NTRS)

    Hill, Frank; Fischer, George; Forgach, Suzanne; Grier, Jennifer; Leibacher, John W.; Jones, Harrison P.; Jones, Patricia B.; Kupke, Renate; Stebbins, Robin T.; Clay, Donald W.

    1994-01-01

    The Global Oscillation Network Group (GONG) Project will place a network of instruments around the world to observe solar oscillations as continuously as possible for three years. The Project has now chosen the six network sites based on analysis of survey data from fifteen sites around the world. The chosen sites are: Big Bear Solar Observatory, California; Mauna Loa Solar Observatory, Hawaii; Learmonth Solar Observatory, Australia; Udaipur Solar Observatory, India; Observatorio del Teide, Tenerife; and Cerro Tololo Interamerican Observatory, Chile. Total solar intensity at each site yields information on local cloud cover, extinction coefficient, and transparency fluctuations. In addition, the performance of 192 reasonable networks assembled from the individual site records is compared using a statistical principal components analysis. An accompanying paper descibes the analysis methods in detail; here we present the results of both the network and individual site analyses. The selected network has a duty cycle of 93.3%, in good agreement with numerical simulations. The power spectrum of the network observing window shows a first diurnal sidelobe height of 3 x 10(exp -4) with respect to the central component, an improvement of a factor of 1300 over a single site. The background level of the network spectrum is lower by a factor of 50 compared to a single-site spectrum.

  16. Mars Science Laboratory: Mission, Landing Site, and Initial Results

    NASA Astrophysics Data System (ADS)

    Grotzinger, John; Blake, D.; Crisp, J.; Edgett, K.; Gellert, R.; Gomez-Elvira, J.; Hassler, D.; Mahaffy, P.; Malin, M.; Meyer, M.; Mitrofanov, I.; Vasavada, A.; Wiens, R.

    2012-10-01

    Scheduled to land on August 5, 2012, the Mars Science Laboratory rover, Curiosity, will conduct an investigation of modern and ancient environments. Recent mission results will be discussed. Curiosity has a lifetime of at least one Mars year ( 23 months), and drive capability of at least 20 km. The MSL science payload was specifically assembled to assess habitability and includes a gas chromatograph-mass spectrometer and gas analyzer that will search for organic carbon in rocks, regolith fines, and the atmosphere; an x-ray diffractometer that will determine mineralogical diversity; focusable cameras that can image landscapes and rock/regolith textures in natural color; an alpha-particle x-ray spectrometer for in situ determination of rock and soil chemistry; a laser-induced breakdown spectrometer to remotely sense the chemical composition of rocks and minerals; an active neutron spectrometer designed to search for water in rocks/regolith; a weather station to measure modern-day environmental variables; and a sensor designed for continuous monitoring of background solar and cosmic radiation. The 155-km diameter Gale Crater was chosen as Curiosity’s field site based on several attributes: an interior mound of ancient flat-lying strata extending almost 5 km above the elevation of the landing site; the lower few hundred meters of the mound show a progression with relative age from clay-bearing to sulfate-bearing strata, separated by an unconformity from overlying likely anhydrous strata; the landing ellipse is characterized by a mixture of alluvial fan and high thermal inertia/high albedo stratified deposits; and a number of stratigraphically/geomorphically distinct fluvial features. Gale’s regional context and strong evidence for a progression through multiple potentially habitable environments, represented by a stratigraphic record of extraordinary extent, insure preservation of a rich record of the environmental history of early Mars.

  17. The A Allele of the Single-Nucleotide Polymorphism rs630923 Creates a Binding Site for MEF2C Resulting in Reduced CXCR5 Promoter Activity in B-Cell Lymphoblastic Cell Lines.

    PubMed

    Mitkin, Nikita A; Muratova, Alisa M; Schwartz, Anton M; Kuprash, Dmitry V

    2016-01-01

    Chemokine receptor CXCR5 is highly expressed in B-cells and under normal conditions is involved in their migration to specific areas of secondary lymphoid organs. B-cells are known to play an important role in various autoimmune diseases including multiple sclerosis (MS) where areas of demyelinating lesions attract B-cells by overexpressing CXCL13, the CXCR5 ligand. In this study, we aimed to determine the functional significance of single-nucleotide polymorphism rs630923 (A/C), which is located in cxcr5 gene promoter, and its common allele is associated with increased risk of MS. Using bioinformatics and pull-down assay in B-lymphoblastic cell lines, we showed that protective minor rs630923 "A" allele created functional binding site for MEF2C transcription factor. Elevated MEF2C expression in B-cells correlated with reduced activity of cxcr5 promoter containing rs630923 "A" allele. This effect that was fully neutralized by MEF2C-directed siRNA may mechanistically explain the protective role of the rs630923 minor allele in MS. Using site-directed mutagenesis of the cxcr5 gene promoter, we were unable to find any experimental evidence for the previously proposed role of NFκB transcription factors in rs630923-mediated CXCR5 promoter regulation. Thus, our results identify MEF2C as a possible mediator of protective function of the rs630923 "A" allele in MS.

  18. Policy Impacts on Pedagogical Practice and ICT Use: An Exploration of the Results from Sites 2006

    ERIC Educational Resources Information Center

    Law, N.; Lee, M. W.; Chan, A.

    2010-01-01

    The Second Information Technology in Education Study (SITES) 2006 results reveal that principals' perceived presence of lifelong learning-related pedagogical activities in their schools had changed markedly since the same data was collected in 1998 in SITES-M1. More intriguing was the fact that the directions of the changes were quite different…

  19. 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.

  20. 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.

  1. Electrokinetic remediation of plutonium-contaminated nuclear site wastes: results from a pilot-scale on-site trial.

    PubMed

    Agnew, Kieran; Cundy, Andrew B; Hopkinson, Laurence; Croudace, Ian W; Warwick, Phillip E; Purdie, Philip

    2011-02-28

    This paper examines the field-scale application of a novel low-energy electrokinetic technique for the remediation of plutonium-contaminated nuclear site soils, using soil wastes from the Atomic Weapons Establishment (AWE) Aldermaston site, Berkshire, UK as a test medium. Soils and sediments with varying composition, contaminated with Pu through historical site operations, were electrokinetically treated at laboratory-scale with and without various soil pre-conditioning agents. Results from these bench-scale trials were used to inform a larger on-site remediation trial, using an adapted containment pack with battery power supply. 2.4 m(3) (ca. 4t onnes) of Pu-contaminated soil was treated for 60 days at a power consumption of 33 kWh/m(3), and then destructively sampled. Radiochemical data indicate mobilisation of Pu in the treated soil, and migration (probably as a negatively charged Pu-citrate complex) towards the anodic compartment of the treatment cell. Soil in the cathodic zone of the treatment unit was remediated to a level below free-release disposal thresholds (1.7 Bq/g, or <0.4 Bq/g above background activities). The data show the potential of this method as a low-cost, on-site tool for remediation of radioactively contaminated soils and wastes which can be operated remotely on working sites, with minimal disruption to site infrastructure or operations.

  2. 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

  3. 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)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.

  4. Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site.

    PubMed

    Roberts, Kenneth M; Khan, Crystal A; Hinck, Cynthia S; Fitzpatrick, Paul F

    2014-12-16

    Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein's regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The k(cat)/K(phe) value is down 10⁴ for the mutant enzyme, and the K(m) value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain.

  5. 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.

  6. Modification of a thiol at the active site of the Ascaris suum NAD-malic enzyme results in changes in the rate-determining steps for oxidative decarboxylation of L-malate

    SciTech Connect

    Gavva, S.R.; Harris, B.G.; Cook, P.F. ); Weiss, P.M. )

    1991-06-11

    A thiol group at the malate-binding site of the NAD-malic enzyme from Ascaris suum has been modified to thiocyanate. The modified enzyme generally exhibits slight increases in K{sub NAD} and K{sub i metal} and decreases in V{sub max} as the metal size increases from Mg{sup 2+} to Mn{sup 2+} to Cd{sup 2+}, indicative of crowding in the site. The K{sub malate} value increases 10- to 30-fold, suggesting that malate does not bind optimally to the modified enzyme. Deuterium isotope effects on V and V/K{sub malate} increase with all three metal ions compared to the native enzyme concomitant with a decrease in the {sup 13}C isotope effect, suggesting a switch in the rate limitation of the hydride transfer and decarboxylation steps with hydride transfer becoming more rate limiting. The {sup 13}C effect decreases only slightly when obtained with deuterated malate, suggestive of the presence of a secondary {sup 13}C effect in the hydride transfer step, similar to data obtained with non-nicotinamide-containing dinucleotide substrates for the native enzyme (see the preceding paper in this issue). The native enzyme is inactivated in a time-dependent manner by Cd{sup 2+}. This inactivation occurs whether the enzyme alone is present or whether the enzyme is turning over with Cd{sup 2+} as the divalent metal activator. Upon inactivation, only Cd{sup 2+} ions are bound at high stoichiometry to the enzyme, which eventually becomes denatured. Conversion of the active-site thiol to thiocyanate makes it more difficult to inactivate the enzyme by treatment with Cd{sup 2+}.

  7. [Structural regularities in activated cleavage sites of thrombin receptors].

    PubMed

    Mikhaĭlik, I V; Verevka, S V

    1999-01-01

    Comparison of thrombin receptors activation splitting sites sequences testifies to their similarity both in activation splitting sites of protein precursors and protein proteinase inhibitors reactive sites. In all these sites corresponded to effectory sites P2'-positions are placed by hydrophobic amino-acids only. The regularity defined conforms with previous thesis about the role of effectory S2'-site in regulation of the processes mediated by serine proteinases.

  8. 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.

  9. Extended Bioventing Testing Results at the BX Service Station Site, Patrick AFB, Florida

    DTIC Science & Technology

    2007-11-02

    Parsons Engineering Science, Inc. (Parsons ES) is pleased to submit the results of the extended bioventing testing at the BX Service Station Site at...injection bioventing , and 1 year of full-scale air injection bioventing . The purpose of this letter is to summarize site and remediation activities to...and three tables are attached. The as-built bioventing system and sampling/respiration testing locations are illustrated on Figure 1. Table 1

  10. Understanding site-specific PSHA results by hazard deaggregation into site intensities

    NASA Astrophysics Data System (ADS)

    Klügel, Jens-Uwe

    2016-04-01

    From 1998 till 2015 Swiss Nuclear Power Plants sponsored a set of comprehensive site-specific PSHA-studies (PEGASOS, PEGASOS Refinement Project) to define review level earthquakes as well as the input for their plant specific probabilistic risk assessments. The studies were performed following the US SSHAC procedures at their most elaborated level 4. Safety experts and risk analysts of Swiss Nuclear Power Plants recently have been mandated to implement the final results of the studies in their risk assessment studies. For an in depth understanding of the consequences of the hazard on practical decision making it is reasonable to compare the new studies with the original hazard assessment studies used for the development of the seismic design basis of the plants. These studies were performed in terms of intensity. For the comparison a hazard deaggregation methodology was developed that allows for the conversion of standard uniform hazard spectra (UHS) into site-intensity (factors) hazard curves. The method was applied for the nuclear power plant Goesgen using the PEGASOS hazard. The results were compared with the results of earlier hazard studies as well as with actual deterministic and probabilistic hazard studies performed independently from the PEGASOS study in terms of EMS-98 intensities. The comparison revealed that the results of the PEGASOS study led to site intensity factors comparable with the results of studies from the 1970-ies. The study may have under predicted the safety importance of historical large earthquakes like the Basel earthquake of 1356. Therefore, an important conclusion is that probabilistic hazard studies for critical infrastructures have to be accompanied by an independent physics-based study (modelling hazard assessment) that allows to perform a safety evaluation of historical earthquakes. The paper presents the deaggregation methodology and the results of its application.

  11. MAX-91: Polarimetric SAR results on Montespertoli site

    NASA Technical Reports Server (NTRS)

    Baronti, S.; Luciani, S.; Moretti, S.; Paloscia, S.; Schiavon, G.; Sigismondi, S.

    1993-01-01

    The polarimetric Synthetic Aperture Radar (SAR) is a powerful sensor for high resolution ocean and land mapping and particularly for monitoring hydrological parameters in large watersheds. There is currently much research in progress to assess the SAR operational capability as well as to estimate the accuracy achievable in the measurements of geophysical parameters with the presently available airborne and spaceborne sensors. An important goal of this research is to improve our understanding of the basic mechanisms that control the interaction of electro-magnetic waves with soil and vegetation. This can be done both by developing electromagnetic models and by analyzing statistical relations between backscattering and ground truth data. A systematic investigation, which aims at a better understanding of the information obtainable from the multi-frequency polarimetric SAR to be used in agro-hydrology, is in progress by our groups within the framework of SIR-C/X-SAR Project and has achieved a most significant milestone with the NASA/JPL Aircraft Campaign named MAC-91. Indeed this experiment allowed us to collect a large and meaningful data set including multi-temporal multi-frequency polarimetric SAR measurements and ground truth. This paper presents some significant results obtained over an agricultural flat area within the Montespertoli site, where intensive ground measurements were carried out. The results are critically discussed with special regard to the information associated with polarimetric data.

  12. Active and regulatory sites of cytosolic 5'-nucleotidase.

    PubMed

    Pesi, Rossana; Allegrini, Simone; Careddu, Maria Giovanna; Filoni, Daniela Nicole; Camici, Marcella; Tozzi, Maria Grazia

    2010-12-01

    Cytosolic 5'-nucleotidase (cN-II), which acts preferentially on 6-hydroxypurine nucleotides, is essential for the survival of several cell types. cN-II catalyses both the hydrolysis of nucleotides and transfer of their phosphate moiety to a nucleoside acceptor through formation of a covalent phospho-intermediate. Both activities are regulated by a number of phosphorylated compounds, such as diadenosine tetraphosphate (Ap₄A), ADP, ATP, 2,3-bisphosphoglycerate (BPG) and phosphate. On the basis of a partial crystal structure of cN-II, we mutated two residues located in the active site, Y55 and T56. We ascertained that the ability to catalyse the transfer of phosphate depends on the presence of a bulky residue in the active site very close to the aspartate residue that forms the covalent phospho-intermediate. The molecular model indicates two possible sites at which adenylic compounds may interact. We mutated three residues that mediate interaction in the first activation site (R144, N154, I152) and three in the second (F127, M436 and H428), and found that Ap₄A and ADP interact with the same site, but the sites for ATP and BPG remain uncertain. The structural model indicates that cN-II is a homotetrameric protein that results from interaction through a specific interface B of two identical dimers that have arisen from interaction of two identical subunits through interface A. Point mutations in the two interfaces and gel-filtration experiments indicated that the dimer is the smallest active oligomerization state. Finally, gel-filtration and light-scattering experiments demonstrated that the native enzyme exists as a tetramer, and no further oligomerization is required for enzyme activation.

  13. 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.

  14. 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

  15. Spectroscopic studies of the active site of galactose oxidase

    SciTech Connect

    Knowles, P.F.; Brown, R.D. III; Koenig, S.H.

    1995-07-19

    X-ray absorption and EPR spectroscopy have been used to probe the copper site structure in galactose oxidase at pH 4.5 and 7.0. the results suggest that there are no major differences in the structure of the tetragonal Cu(II) site at these pH values. Analysis of the extended X-ray absorption fine structure (EXAFS) indicates that four N,O scatterers are present at approximately 2 {Angstrom}; these are presumably the equatorial ligands. In addition, the EXAFS data establish that oxidative activation to produce the active-site tyrosine radical does not cause major changes in the copper coordination environment. Therefore results obtained on the one-electron reduced enzyme, containing Cu(II) but not the tyrosine radical, probably also apply to the catalytically active Cu(II)/tyrosine radical state. Solvent water exchange, inhibitor binding, and substrate binding have been probed via nuclear magnetic relaxation dispersion (NMRD) measurements. The NMRD profile of galactose oxidase is quantitatively consistent with the rapid exchange of a single, equatorial water ligand with a Cu(II)-O separation of about 2.4 {Angstrom}. Azide and cyanide displace this coordinated water. The binding of azide and the substrate dihydroxyacetone produce very similar effects on the NMRD profile of galactose oxidase, indicating that substrates also bind to the active site Cu(II) in an equatorial position.

  16. ENHANCED CONTROL OF MERCURY BY WET FLUE GAS DESULFURIZATION SYSTEMS--SITE 2 RESULTS

    SciTech Connect

    G. Blythe; S. Miller; C. Richardson; K. Searcy

    2000-02-01

    The U.S. Department of Energy and EPRI are co-funding this project to improve the control of mercury emissions from coal-fired power plants equipped with wet flue gas desulfurization (FGD) systems. The project is investigating catalytic oxidation of vapor-phase elemental mercury to a form that is more effectively captured in wet FGD systems. If successfully developed, the process could be applicable to over 90,000 MW of utility generating capacity with existing FGD systems, and to future FGD installations. Field tests are being conducted to determine whether candidate catalyst materials remain active towards mercury oxidation after extended flue gas exposure. Catalyst life will have a large impact on the cost effectiveness of this potential process. A mobile catalyst test unit is being used to test the activity of four different catalysts for a period of up to six months at each of three utility sites. Catalyst testing at the first site, which fires Texas lignite, was completed in December 1998. Testing at the second test site, which fires a Powder River Basin subbituminous coal, was completed in the fall of 1999, and testing at the third site, which fires a high-sulfur bituminous coal, will begin in early 2000. This technical note reports results from Site 2; results from Site 1 were reported in a previous technical note. At Site 2, catalysts were tested in several forms, including powders dispersed in sand bed reactors and in more commercially viable forms such as extruded beads and coated honeycomb structures. This technical note presents results from Site 2 for both the sand bed reactors and commercial catalyst forms. Site 3 results are not yet available, but should be available late in the year 2000. Field testing is being supported by laboratory tests to screen catalysts for activity at specific flue gas compositions, to investigate catalyst deactivation mechanisms and to investigate methods for regenerating spent catalysts. Laboratory results related to the

  17. 2016 Annual Inspection and Radiological Survey Results for the Piqua, Ohio, Decommissioned Reactor Site, July 2016

    SciTech Connect

    Zimmerman, Brian; Miller, Michele

    2016-07-01

    This report presents the findings of the annual inspection and radiological survey of the Piqua, Ohio, Decommissioned Reactor Site (site). The decommissioned nuclear power demonstration facility was inspected and surveyed on April 15, 2016. The site, located on the east bank of the Great Miami River in Piqua, Ohio, was in fair physical condition. There is no requirement for a follow-up inspection, partly because City of Piqua (City) personnel participated in a March 2016 meeting to address reoccurring safety concerns. Radiological survey results from 104 locations revealed no removable contamination. One direct beta activity reading in a floor drain on the 56-foot level (1674 disintegrations per minute [dpm]/100 square centimeters [cm2]) exceeded the minimum detectable activity (MDA). Beta activity has been detected in the past at this floor drain. The reading was well below the action level of 5000 dpm/100 cm2.

  18. MYST protein acetyltransferase activity requires active site lysine autoacetylation.

    PubMed

    Yuan, Hua; Rossetto, Dorine; Mellert, Hestia; Dang, Weiwei; Srinivasan, Madhusudan; Johnson, Jamel; Hodawadekar, Santosh; Ding, Emily C; Speicher, Kaye; Abshiru, Nebiyu; Perry, Rocco; Wu, Jiang; Yang, Chao; Zheng, Y George; Speicher, David W; Thibault, Pierre; Verreault, Alain; Johnson, F Bradley; Berger, Shelley L; Sternglanz, Rolf; McMahon, Steven B; Côté, Jacques; Marmorstein, Ronen

    2012-01-04

    The MYST protein lysine acetyltransferases are evolutionarily conserved throughout eukaryotes and acetylate proteins to regulate diverse biological processes including gene regulation, DNA repair, cell-cycle regulation, stem cell homeostasis and development. Here, we demonstrate that MYST protein acetyltransferase activity requires active site lysine autoacetylation. The X-ray crystal structures of yeast Esa1 (yEsa1/KAT5) bound to a bisubstrate H4K16CoA inhibitor and human MOF (hMOF/KAT8/MYST1) reveal that they are autoacetylated at a strictly conserved lysine residue in MYST proteins (yEsa1-K262 and hMOF-K274) in the enzyme active site. The structure of hMOF also shows partial occupancy of K274 in the unacetylated form, revealing that the side chain reorients to a position that engages the catalytic glutamate residue and would block cognate protein substrate binding. Consistent with the structural findings, we present mass spectrometry data and biochemical experiments to demonstrate that this lysine autoacetylation on yEsa1, hMOF and its yeast orthologue, ySas2 (KAT8) occurs in solution and is required for acetylation and protein substrate binding in vitro. We also show that this autoacetylation occurs in vivo and is required for the cellular functions of these MYST proteins. These findings provide an avenue for the autoposttranslational regulation of MYST proteins that is distinct from other acetyltransferases but draws similarities to the phosphoregulation of protein kinases.

  19. MYST protein acetyltransferase activity requires active site lysine autoacetylation

    PubMed Central

    Yuan, Hua; Rossetto, Dorine; Mellert, Hestia; Dang, Weiwei; Srinivasan, Madhusudan; Johnson, Jamel; Hodawadekar, Santosh; Ding, Emily C; Speicher, Kaye; Abshiru, Nebiyu; Perry, Rocco; Wu, Jiang; Yang, Chao; Zheng, Y George; Speicher, David W; Thibault, Pierre; Verreault, Alain; Johnson, F Bradley; Berger, Shelley L; Sternglanz, Rolf; McMahon, Steven B; Côté, Jacques; Marmorstein, Ronen

    2012-01-01

    The MYST protein lysine acetyltransferases are evolutionarily conserved throughout eukaryotes and acetylate proteins to regulate diverse biological processes including gene regulation, DNA repair, cell-cycle regulation, stem cell homeostasis and development. Here, we demonstrate that MYST protein acetyltransferase activity requires active site lysine autoacetylation. The X-ray crystal structures of yeast Esa1 (yEsa1/KAT5) bound to a bisubstrate H4K16CoA inhibitor and human MOF (hMOF/KAT8/MYST1) reveal that they are autoacetylated at a strictly conserved lysine residue in MYST proteins (yEsa1-K262 and hMOF-K274) in the enzyme active site. The structure of hMOF also shows partial occupancy of K274 in the unacetylated form, revealing that the side chain reorients to a position that engages the catalytic glutamate residue and would block cognate protein substrate binding. Consistent with the structural findings, we present mass spectrometry data and biochemical experiments to demonstrate that this lysine autoacetylation on yEsa1, hMOF and its yeast orthologue, ySas2 (KAT8) occurs in solution and is required for acetylation and protein substrate binding in vitro. We also show that this autoacetylation occurs in vivo and is required for the cellular functions of these MYST proteins. These findings provide an avenue for the autoposttranslational regulation of MYST proteins that is distinct from other acetyltransferases but draws similarities to the phosphoregulation of protein kinases. PMID:22020126

  20. Mutations in exons 10 and 11 of human glucokinase result in conformational variations in the active site of the structure contributing to poor substrate binding - explains hyperglycemia in type 2 diabetic patients.

    PubMed

    Yellapu, Nandakumar; Mahto, Manoj Kumar; Valasani, Koteswara Rao; Sarma, P V G K; Matcha, Bhaskar

    2015-01-01

    Mutations in the glucokinase (GK) gene play a critical role in the establishment of type 2 diabetes. In our earlier study, R308K mutation in GK in a clinically proven type 2 diabetic patient showed, structural and functional variations that contributed immensely to the hyperglycemic condition. In the extension of this work, a cohort of 30 patients with established type 2 diabetic condition were chosen and the exons 10 and 11 of GK were PCR-amplified and sequenced. The sequence alignment showed A379S, D400Y, E300A, E395A, E395G, H380N, I348N, L301M, M298I, M381G, M402R, R308K, R394P, R397S, and S398R mutations in 12 different patients. The structural analysis of these mutated GKs, showed a variable number of β-α-β units, hairpins, β-bulges, strands, helices, helix-helix interactions, β-turns, and γ-turns along with the RMSD variations when compared to wild-type GK. Molecular modeling studies revealed that the substrate showed variable binding orientations and could not fit into the active site of these mutated structures; moreover, it was expelled out of the conformations. Therefore, these structural variations in GK due to mutations could be one of the strongest reasons for the hyperglycemic levels in these type 2 diabetic patients.

  1. Extended Bioventing Testing Results for SWMU 55 (IRP Site FT-03), Charleston AFB, South Carolina

    DTIC Science & Technology

    2007-11-02

    This letter presents the results of the bioventing system monitoring performed by Parsons Engineering Science, Inc. (Parsons ES) during June 1998 at...approximately 4.5 years of pilot- scale system operation and 1 year of expanded-scale bioventing system operation. The purposes of this letter are to summarize...site and bioventing activities to date, present the results of the June 1998 system monitoring event, compare these results with previous pilot testing

  2. ENHANCED CONTROL OF MERCURY BY WET FLUE GAS DESULFURIZATION SYSTEMS--SITE 2 RESULTS

    SciTech Connect

    G. Blythe; S. Miller; C. Richardson; K. Searcy

    2000-06-01

    The U.S. Department of Energy and EPRI are co-funding this project to improve the control of mercury emissions from coal-fired power plants equipped with wet flue gas desulfurization (FGD) systems. The project is investigating catalytic oxidation of vapor-phase elemental mercury to a form that is more effectively captured in wet FGD systems. If successfully developed, the process could be applicable to over 90,000 MW of utility generating capacity with existing FGD systems, and to future FGD installations. Field tests are being conducted to determine whether candidate catalyst materials remain active towards mercury oxidation after extended flue gas exposure. Catalyst life will have a large impact on the cost effectiveness of this potential process. A mobile catalyst test unit is being used to test the activity of four different catalysts for a period of up to six months at each of three utility sites. Catalyst testing at the first site, which fires Texas lignite, was completed in December 1998. Testing at the second test site, which fires a Powder River Basin subbituminous coal, was completed in the fall of 1999, and testing at the third site, which fires a high-sulfur bituminous coal, will begin in 2000. This technical note reports results from Site 2; results from Site 1 were reported in a previous technical note. At Site 2, catalysts were tested in several forms, including powders dispersed in sand bed reactors and in commercial forms such as extruded beads and coated honeycomb structures. This technical note presents results from Site 2 for both the sand bed reactors and commercial catalyst forms. Field testing is being supported by laboratory tests to screen catalysts for activity at specific flue gas compositions, to investigate catalyst deactivation mechanisms and to investigate methods for regenerating spent catalysts. Laboratory results related to the Site 2 field effort are also included and discussed in this technical note. Preliminary economics, based

  3. 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.

  4. Results of employee involvement in planning and implementing the Treatwell 5-a-Day work-site study.

    PubMed

    Hunt, M K; Lederman, R; Potter, S; Stoddard, A; Sorensen, G

    2000-04-01

    When work-site health promotion programs incorporate theories of community organization, it is likely that employee ownership and participation are enhanced. This article reports quantitative indicators of involvement of Employee Advisory Board (EAB) members in the Treatwell 5-a-Day work-site study and examines relationships between EAB member time spent on project activities and work-site size, with indicators of the extent of implementation and variables associated with behavior change and work-site support. The results reported here indicate that a greater number of EAB member hours spent on program activities was associated with a greater number of events implemented. Smaller work-site size was associated with greater employee awareness of the program and greater participation in project activities as reported on the employee survey. These results suggest that the number of hours employee representatives devote to project activities might be an important consideration in planning employee involvement in work-site health promotion programming.

  5. Results of Bioventing System Monitoring at Site FC-2, Kelly Air Force Base (AFB), Texas

    DTIC Science & Technology

    2007-11-02

    This letter presents the results of the bioventing system monitoring performed by Parsons Engineering Science, Inc. (Parsons ES) during the week of...to assess the extent of remediation completed during approximately 1 year of expanded-scale bioventing system operation. The purpose of this letter...is to summarize site and bioventing activities to date, present the results of the most recent respiration testing and soil gas sampling event, and

  6. Acquisition Information Management system telecommunication site survey results

    SciTech Connect

    Hake, K.A.; Key, B.G.

    1993-09-01

    The Army acquisition community currently uses a dedicated, point-to-point secure computer network for the Army Material Plan Modernization (AMPMOD). It must transition to the DOD supplied Defense Secure Network 1 (DSNET1). This is one of the first networks of this size to begin the transition. The type and amount of computing resources available at individual sites may or may not meet the new network requirements. This task surveys these existing telecommunications resources available in the Army acquisition community. It documents existing communication equipment, computer hardware, associated software, and recommends appropriate changes.

  7. ASME N510 test results for Savannah River Site AACS filter compartments

    SciTech Connect

    Paul, J.D.; Punch, T.M.

    1995-02-01

    The K-Reactor at the Savannah River Site recently implemented design improvements for the Airborne Activity Confinement System (AACS) by procuring, installing, and testing new Air Cleaning Units, or filter compartments, to ASME AG-11, N509, and N510 requirements. Specifically, these new units provide documentable seismic resistance to a Design Basis Accident earthquake, provide 2 inch adsorber beds with 0.25 second residence time, and meet all AG-1, N509, and N510 requirements for testability and maintainability. This paper presents the results of the Site acceptance testing and discusses an issue associated with sample manifold qualification testing.

  8. Active site amino acid sequence of human factor D.

    PubMed

    Davis, A E

    1980-08-01

    Factor D was isolated from human plasma by chromatography on CM-Sephadex C50, Sephadex G-75, and hydroxylapatite. Digestion of reduced, S-carboxymethylated factor D with cyanogen bromide resulted in three peptides which were isolated by chromatography on Sephadex G-75 (superfine) equilibrated in 20% formic acid. NH2-Terminal sequences were determined by automated Edman degradation with a Beckman 890C sequencer using a 0.1 M Quadrol program. The smallest peptide (CNBr III) consisted of the NH2-terminal 14 amino acids. The other two peptides had molecular weights of 17,000 (CNBr I) and 7000 (CNBr II). Overlap of the NH2-terminal sequence of factor D with the NH2-terminal sequence of CNBr I established the order of the peptides. The NH2-terminal 53 residues of factor D are somewhat more homologous with the group-specific protease of rat intestine than with other serine proteases. The NH2-terminal sequence of CNBr II revealed the active site serine of factor D. The typical serine protease active site sequence (Gly-Asp-Ser-Gly-Gly-Pro was found at residues 12-17. The region surrounding the active site serine does not appear to be more highly homologous with any one of the other serine proteases. The structural data obtained point out the similarities between factor D and the other proteases. However, complete definition of the degree of relationship between factor D and other proteases will require determination of the remainder of the primary structure.

  9. 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.

  10. [Mechanism of arginine deiminase activity by site-directed mutagenesis].

    PubMed

    Li, Lifeng; Ni, Ye; Sun, Zhihao

    2012-04-01

    Arginine deiminase (ADI) has been studied as a potential anti-cancer agent for inhibiting arginine-auxotrophic tumors (such as melanomas and hepatocellular carcinomas) in phase III clinical trials. In this work, we studied the molecular mechanism of arginine deiminase activity by site-directed mutagenesis. Three mutation sites, A128, H404 and 1410, were introduced into wild-type ADI gene by QuikChange site-directed mutagenesis method, and four ADI mutants M1 (A128T), M2 (H404R), M3 (I410L), and M4 (A128T, H404R) were obtained. The ADI mutants were individually expressed in Escherichia coli BL21 (DE3), and the enzymatic properties of the purified mutant proteins were determined. The results show that both A128T and H404R had enhanced optimum pH, higher activity and stability of ADI under physiological condition (pH 7.4), as well as reduced K(m) value. This study provides an insight into the molecular mechanism of the ADI activity, and also the experimental evidence for the rational protein evolution in the future.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Review of analytical results from the proposed agent disposal facility site, Aberdeen Proving Ground

    SciTech Connect

    Brubaker, K.L.; Reed, L.L.; Myers, S.W.; Shepard, L.T.; Sydelko, T.G.

    1997-09-01

    Argonne National Laboratory reviewed the analytical results from 57 composite soil samples collected in the Bush River area of Aberdeen Proving Ground, Maryland. A suite of 16 analytical tests involving 11 different SW-846 methods was used to detect a wide range of organic and inorganic contaminants. One method (BTEX) was considered redundant, and two {open_quotes}single-number{close_quotes} methods (TPH and TOX) were found to lack the required specificity to yield unambiguous results, especially in a preliminary investigation. Volatile analytes detected at the site include 1, 1,2,2-tetrachloroethane, trichloroethylene, and tetrachloroethylene, all of which probably represent residual site contamination from past activities. Other volatile analytes detected include toluene, tridecane, methylene chloride, and trichlorofluoromethane. These compounds are probably not associated with site contamination but likely represent cross-contamination or, in the case of tridecane, a naturally occurring material. Semivolatile analytes detected include three different phthalates and low part-per-billion amounts of the pesticide DDT and its degradation product DDE. The pesticide could represent residual site contamination from past activities, and the phthalates are likely due, in part, to cross-contamination during sample handling. A number of high-molecular-weight hydrocarbons and hydrocarbon derivatives were detected and were probably naturally occurring compounds. 4 refs., 1 fig., 8 tabs.

  16. Controlled Orientation of Active Sites in a Nanostructured Multienzyme Complex

    PubMed Central

    Lim, Sung In; Yang, Byungseop; Jung, Younghan; Cha, Jaehyun; Cho, Jinhwan; Choi, Eun-Sil; Kim, Yong Hwan; Kwon, Inchan

    2016-01-01

    Multistep cascade reactions in nature maximize reaction efficiency by co-assembling related enzymes. Such organization facilitates the processing of intermediates by downstream enzymes. Previously, the studies on multienzyme nanocomplexes assembled on DNA scaffolds demonstrated that closer interenzyme distance enhances the overall reaction efficiency. However, it remains unknown how the active site orientation controlled at nanoscale can have an effect on multienzyme reaction. Here, we show that controlled alignment of active sites promotes the multienzyme reaction efficiency. By genetic incorporation of a non-natural amino acid and two compatible bioorthogonal chemistries, we conjugated mannitol dehydrogenase to formate dehydrogenase with the defined active site arrangement with the residue-level accuracy. The study revealed that the multienzyme complex with the active sites directed towards each other exhibits four-fold higher relative efficiency enhancement in the cascade reaction and produces 60% more D-mannitol than the other complex with active sites directed away from each other. PMID:28004799

  17. 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.

  18. An active site water network in the plasminogen activator pla from Yersinia pestis.

    PubMed

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

    2010-07-14

    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 A. 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.

  19. Experimental Results of Site Calibration and Sensitivity Measurements in OTR for UWB Systems

    NASA Astrophysics Data System (ADS)

    Viswanadham, Chandana; Rao, P. Mallikrajuna

    2016-08-01

    System calibration and parameter accuracy measurement of electronic support measures (ESM) systems is a major activity, carried out by electronic warfare (EW) engineers. These activities are very critical and needs good understanding in the field of microwaves, antennas, wave propagation, digital and communication domains. EW systems are broad band, built with state-of-the art electronic hardware, installed on different varieties of military platforms to guard country's security from time to time. EW systems operate in wide frequency ranges, typically in the order of thousands of MHz, hence these are ultra wide band (UWB) systems. Few calibration activities are carried within the system and in the test sites, to meet the accuracies of final specifications. After calibration, parameters are measured for their accuracies either in feed mode by injecting the RF signals into the front end or in radiation mode by transmitting the RF signals on to system antenna. To carry out these activities in radiation mode, a calibrated open test range (OTR) is necessary in the frequency band of interest. Thus site calibration of OTR is necessary to be carried out before taking up system calibration and parameter measurements. This paper presents the experimental results of OTR site calibration and sensitivity measurements of UWB systems in radiation mode.

  20. Volatile Organic Compound Investigation Results, 300 Area, Hanford Site, Washington

    SciTech Connect

    Peterson, Robert E.; Williams, Bruce A.; Smith, Ronald M.

    2008-07-07

    Unexpectedly high concentrations of volatile organic compounds (VOC) were discovered while drilling in the unconfined aquifer beneath the Hanford Site’s 300 Area during 2006. The discovery involved an interval of relatively finer-grained sediment within the unconfined aquifer, an interval that is not sampled by routine groundwater monitoring. Although VOC contamination in the unconfined aquifer has been identified and monitored, the concentrations of newly discovered contamination are much higher than encountered previously, with some new results significantly higher than the drinking water standards. The primary contaminant is trichloroethene, with lesser amounts of tetrachloroethene. Both chemicals were used extensively as degreasing agents during the fuels fabrication process. A biological degradation product of these chemicals, 1,2-dichloroethene, was also detected. To further define the nature and extent of this contamination, additional characterization drilling was undertaken during 2007. Four locations were drilled to supplement the information obtained at four locations drilled during the earlier investigation in 2006. The results of the combined drilling indicate that the newly discovered contamination is limited to a relatively finer-grained interval of Ringold Formation sediment within the unconfined aquifer. The extent of this contamination appears to be the area immediately east and south of the former South Process Pond. Samples collected from the finer-grained sediment at locations along the shoreline confirm the presence of the contamination near the groundwater/river interface. Contamination was not detected in river water that flows over the area where the river channel potentially incises the finer-grained interval of aquifer sediment. The source for this contamination is not readily apparent. A search of historical documents and the Hanford Waste Information Data System did not provide definitive clues as to waste disposal operations and

  1. Perspective: On the active site model in computational catalyst screening

    NASA Astrophysics Data System (ADS)

    Reuter, Karsten; Plaisance, Craig P.; Oberhofer, Harald; Andersen, Mie

    2017-01-01

    First-principles screening approaches exploiting energy trends in surface adsorption represent an unparalleled success story in recent computational catalysis research. Here we argue that our still limited understanding of the structure of active sites is one of the major bottlenecks towards an ever extended and reliable use of such computational screening for catalyst discovery. For low-index transition metal surfaces, the prevalently chosen high-symmetry (terrace and step) sites offered by the nominal bulk-truncated crystal lattice might be justified. For more complex surfaces and composite catalyst materials, computational screening studies will need to actively embrace a considerable uncertainty with respect to what truly are the active sites. By systematically exploring the space of possible active site motifs, such studies might eventually contribute towards a targeted design of optimized sites in future catalysts.

  2. Diffusional correlations among multiple active sites in a single enzyme.

    PubMed

    Echeverria, Carlos; Kapral, Raymond

    2014-04-07

    Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.

  3. Mutations inducing an active-site aperture in Rhizobium sp. sucrose isomerase confer hydrolytic activity.

    PubMed

    Lipski, Alexandra; Watzlawick, Hildegard; Ravaud, Stéphanie; Robert, Xavier; Rhimi, Moez; Haser, Richard; Mattes, Ralf; Aghajari, Nushin

    2013-02-01

    Sucrose isomerase is an enzyme that catalyzes the production of sucrose isomers of high biotechnological and pharmaceutical interest. Owing to the complexity of the chemical synthesis of these isomers, isomaltulose and trehalulose, enzymatic conversion remains the preferred method for obtaining these products. Depending on the microbial source, the ratio of the sucrose-isomer products varies significantly. In studies aimed at understanding and explaining the underlying molecular mechanisms of these reactions, mutations obtained using a random-mutagenesis approach displayed a major hydrolytic activity. Two of these variants, R284C and F164L, of sucrose isomerase from Rhizobium sp. were therefore crystallized and their crystal structures were determined. The three-dimensional structures of these mutants allowed the identification of the molecular determinants that favour hydrolytic activity compared with transferase activity. Substantial conformational changes resulting in an active-site opening were observed, as were changes in the pattern of water molecules bordering the active-site region.

  4. Robotics at Savannah River site: activity report

    SciTech Connect

    Byrd, J.S.

    1984-09-01

    The objectives of the Robotics Technology Group at the Savannah River Laboratory are to employ modern industrial robots and to develop unique automation and robotic systems to enhance process operations at the Savannah River site (SRP and SRL). The incentives are to improve safety, reduce personnel radiation exposure, improve product quality and productivity, and to reduce operating costs. During the past year robotic systems have been installed to fill chemical dilution vials in a SRP laboratory at 772-F and remove radioactive waste materials in the SRL Californium Production Facility at 773-A. A robotic system to lubricate an extrusion press has been developed and demonstrated in the SRL robotics laboratory and is scheduled for installation at the 321-M fuel fabrication area. A mobile robot was employed by SRP for a radiation monitoring task at a waste tank top in H-Area. Several other robots are installed in the SRL robotics laboratories and application development programs are underway. The status of these applications is presented in this report.

  5. 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.

  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. Active sites of thioredoxin reductases: why selenoproteins?

    PubMed

    Gromer, Stephan; Johansson, Linda; Bauer, Holger; Arscott, L David; Rauch, Susanne; Ballou, David P; Williams, Charles H; Schirmer, R Heiner; Arnér, Elias S J

    2003-10-28

    Selenium, an essential trace element for mammals, is incorporated into a selected class of selenoproteins as selenocysteine. All known isoenzymes of mammalian thioredoxin (Trx) reductases (TrxRs) employ selenium in the C-terminal redox center -Gly-Cys-Sec-Gly-COOH for reduction of Trx and other substrates, whereas the corresponding sequence in Drosophila melanogaster TrxR is -Ser-Cys-Cys-Ser-COOH. Surprisingly, the catalytic competence of these orthologous enzymes is similar, whereas direct Sec-to-Cys substitution of mammalian TrxR, or other selenoenzymes, yields almost inactive enzyme. TrxRs are therefore ideal for studying the biology of selenocysteine by comparative enzymology. Here we show that the serine residues flanking the C-terminal Cys residues of Drosophila TrxRs are responsible for activating the cysteines to match the catalytic efficiency of a selenocysteine-cysteine pair as in mammalian TrxR, obviating the need for selenium. This finding suggests that the occurrence of selenoenzymes, which implies that the organism is selenium-dependent, is not necessarily associated with improved enzyme efficiency. Our data suggest that the selective advantage of selenoenzymes is a broader range of substrates and a broader range of microenvironmental conditions in which enzyme activity is possible.

  8. Community Update on Site Activities, July 19, 2013

    EPA Pesticide Factsheets

    In an effort to engage and inform community members interested in the New Bedford Harbor Superfund Site cleanup, EPA will be issuing periodic topic-based fact sheets that will provide background information and updates about ongoing activities.

  9. Are nest sites actively chosen? Testing a common assumption for three non-resource limited birds

    NASA Astrophysics Data System (ADS)

    Goodenough, A. E.; Elliot, S. L.; Hart, A. G.

    2009-09-01

    Many widely-accepted ecological concepts are simplified assumptions about complex situations that remain largely untested. One example is the assumption that nest-building species choose nest sites actively when they are not resource limited. This assumption has seen little direct empirical testing: most studies on nest-site selection simply assume that sites are chosen actively (and seek explanations for such behaviour) without considering that sites may be selected randomly. We used 15 years of data from a nestbox scheme in the UK to test the assumption of active nest-site choice in three cavity-nesting bird species that differ in breeding and migratory strategy: blue tit ( Cyanistes caeruleus), great tit ( Parus major) and pied flycatcher ( Ficedula hypoleuca). Nest-site selection was non-random (implying active nest-site choice) for blue and great tits, but not for pied flycatchers. We also considered the relative importance of year-specific and site-specific factors in determining occupation of nest sites. Site-specific factors were more important than year-specific factors for the tit species, while the reverse was true for pied flycatchers. Our results show that nest-site selection, in birds at least, is not always the result of active choice, such that choice should not be assumed automatically in studies of nesting behaviour. We use this example to highlight the need to test key ecological assumptions empirically, and the importance of doing so across taxa rather than for single "model" species.

  10. Spatially-explicit bioaccumulation modeling in aquatic environments: Results from two demonstration sites.

    PubMed

    von Stackelberg, Katherine; Williams, Marc A; Clough, Jonathan; Johnson, Mark S

    2017-03-11

    Bioaccumulation models quantify the relationship between sediment and water exposure concentrations and resulting tissue levels of chemicals in aquatic organisms, and represent a key link in the suite of tools used to support decision making at contaminated sediment sites. Predicted concentrations in the aquatic food web provide exposure estimates for human health and ecological risk assessments, which, in turn, provide risk-based frameworks for evaluating potential remedial activities and other management alternatives based on the fish consumption pathway. Despite the widespread use of bioaccumulation models to support remedial decision-making, concerns remain about the predictive power of these models. A review of the available literature finds the increased mathematical complexity of typical bioaccumulation model applications is not matched by the deterministic exposure concentrations used to drive the models. We tested a spatially explicit exposure model (FishRand) at two nominally contaminated sites and compared results to estimates of bioaccumulation based on conventional, non-spatial techniques and monitoring data. Differences in predicted fish tissue concentrations across applications were evident, although these demonstration sites were only mildly contaminated and would not warrant management actions on the basis of fish consumption. Nonetheless, predicted tissue concentrations based on the spatially-explicit exposure characterization consistently outperformed conventional, non-spatial techniques across a variety of model performance metrics. These results demonstrate the improved predictive power as well as greater flexibility in evaluating the impacts of food web exposure and fish foraging behavior in a heterogeneous exposure environment. This article is protected by copyright. All rights reserved.

  11. [Results of 2 years of activity].

    PubMed

    Panigazzi, M

    2010-01-01

    Work-related injuries and occupational diseases are a scourge of modern, western societies, which, although technologically advanced, have difficulty in preventing, treating and rehabilitating victims with speed and efficiency. The current hospital neuromotor rehabilitation centres, whether public or accredited private structures, have notable difficulty in meeting the demand, which despite annual fluctuations and variable needs, does not, overall, seem to be decreasing. We present the results of an organization model developed at the "Fondazione Maugeri" Scientific Institute (Pavia, Italy), the criteria used for the activity, the technological innovations employed to determine ability, and the prospects for further development. This model is effective from a health care-rehabilitative point of view, also in the light of the new legislative scenarios, and is sustainable from an economic points of view; overall it is, therefore, efficient.

  12. 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.

  13. Sand Flux Results for Aeolian Dunes at Current and Candidate Landing Sites on Mars

    NASA Astrophysics Data System (ADS)

    Chojnacki, M.; Urso, A.; Yingling, W.

    2015-12-01

    It is now known unambiguously that wind-driven bedform activity is occurring on Mars today. It has also been demonstrated the rapid aeolian abrasion of sedimentary deposits that potentially host ancient habitable environments may provide the best mechanism for exposing samples containing relatively undegraded organics (Farley et al. 2014). Thus, current processes operating on the surface of Mars are highly relevant to our understanding of the past. Here, we discuss new sand flux results of active dune across Mars, including several current and candidate landing sites with Meridiani Planum, Gale crater, Valles Marineris, and Mawrth Vallis. For this task, we have utilized multi-temporal images acquired annually by the HiRISE camera (25 cm/pixel) along with co-located HiRISE Digital Terrain Models. Falling dunes in Coprates Chasma (Mars 2020 candidate landing site) measuring 6-10 meters in height were detected migrating on average 0.5 m per Earth year, yielding crest fluxes of 3.1 m3 m-1 yr-1 (units hereafter assumed). Barchans near the MSL rover at Gale crater have slightly lower fluxes of 1.2, while earlier work in Endeavour crater, the current site of the Opportunity Rover, showed dome dunes with fluxes as high as 13 (average of 6.8; Chojnacki et al. 2015). New results of Mawrth Vallis (Mars 2020 candidate) dunes suggest these high rates are not uncommon, as barchans there possess average fluxes of 11.5. Assuming ripple reptation rates are 1/10th that of crest fluxes, total flux (saltation plus reptation) would range 3.2 to 12.7 m3 m-1 yr-1 for all sites studied herein. Active dunes and the abrasion susceptibility (Sa) of local rocks are relevant to assess how sand fluxes modify the landscape. Using the methodology and assumptions (Sa for basalt, mean trajectory height etc.) described in Bridges et al. (2012), we estimated abrasion rates of local basaltic bedrock. For example, sand blasting at Mawrth Vallis is estimated to produce 2-8 μm/yr for flat ground and 15

  14. Tellurium in active volcanic environments: Preliminary results

    NASA Astrophysics Data System (ADS)

    Milazzo, Silvia; Calabrese, Sergio; D'Alessandro, Walter; Brusca, Lorenzo; Bellomo, Sergio; Parello, Francesco

    2014-05-01

    Tellurium is a toxic metalloid and, according to the Goldschmidt classification, a chalcophile element. In the last years its commercial importance has considerably increased because of its wide use in solar cells, thermoelectric and electronic devices of the last generation. Despite such large use, scientific knowledge about volcanogenic tellurium is very poor. Few previous authors report result of tellurium concentrations in volcanic plume, among with other trace metals. They recognize this element as volatile, concluding that volcanic gases and sulfur deposits are usually enriched with tellurium. Here, we present some results on tellurium concentrations in volcanic emissions (plume, fumaroles, ash leachates) and in environmental matrices (soils and plants) affected by volcanic emissions and/or deposition. Samples were collected at Etna and Vulcano (Italy), Turrialba (Costa Rica), Miyakejima, Aso, Asama (Japan), Mutnovsky (Kamchatka) at the crater rims by using common filtration techniques for aerosols (polytetrafluoroethylene filters). Filters were both eluted with Millipore water and acid microwave digested, and analyzed by inductively coupled plasma mass spectrometry (ICP-MS). Volcanic ashes emitted during explosive events on Etna and Copahue (Argentina) were analyzed for tellurium bulk composition and after leaching experiments to evaluate the soluble fraction of tellurium. Soils and leaves of vegetation were also sampled close to active volcanic vents (Etna, Vulcano, Nisyros, Nyiragongo, Turrialba, Gorely and Masaya) and investigated for tellurium contents. Preliminary results showed very high enrichments of tellurium in volcanic emissions comparing with other volatile elements like mercury, arsenic, thallium and bismuth. This suggests a primary transport in the volatile phase, probably in gaseous form (as also suggested by recent studies) and/or as soluble salts (halides and/or sulfates) adsorbed on the surface of particulate particles and ashes. First

  15. 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.

  16. Extended Bioventing Testing Results at Site FSA-1 (Former Tank Nos. 19 and 20), Air Force Plant 4, Texas

    DTIC Science & Technology

    2007-11-02

    Parsons Engineering Science, Inc. (Parsons ES) is pleased to submit the results of the extended bioventing testing at Site FSA-1 at Air Force Plant 4...April 1997 to assess the extent of remediation completed during approximately 1 year of full-scale air injection bioventing . The purpose of this...letter is to summarize site and bioventing activities to date, present the results of the most recent respiration testing and soil gas sampling, and make

  17. Identification of putative active site residues of ACAT enzymes.

    PubMed

    Das, Akash; Davis, Matthew A; Rudel, Lawrence L

    2008-08-01

    In this report, we sought to determine the putative active site residues of ACAT enzymes. For experimental purposes, a particular region of the C-terminal end of the ACAT protein was selected as the putative active site domain due to its high degree of sequence conservation from yeast to humans. Because ACAT enzymes have an intrinsic thioesterase activity, we hypothesized that by analogy with the thioesterase domain of fatty acid synthase, the active site of ACAT enzymes may comprise a catalytic triad of ser-his-asp (S-H-D) amino acid residues. Mutagenesis studies revealed that in ACAT1, S456, H460, and D400 were essential for activity. In ACAT2, H438 was required for enzymatic activity. However, mutation of D378 destabilized the enzyme. Surprisingly, we were unable to identify any S mutations of ACAT2 that abolished catalytic activity. Moreover, ACAT2 was insensitive to serine-modifying reagents, whereas ACAT1 was not. Further studies indicated that tyrosine residues may be important for ACAT activity. Mutational analysis showed that the tyrosine residue of the highly conserved FYXDWWN motif was important for ACAT activity. Furthermore, Y518 was necessary for ACAT1 activity, whereas the analogous residue in ACAT2, Y496, was not. The available data suggest that the amino acid requirement for ACAT activity may be different for the two ACAT isozymes.

  18. Promoter-proximal polyadenylation sites reduce transcription activity

    PubMed Central

    Andersen, Pia K.; Lykke-Andersen, Søren; Jensen, Torben Heick

    2012-01-01

    Gene expression relies on the functional communication between mRNA processing and transcription. We previously described the negative impact of a point-mutated splice donor (SD) site on transcription. Here we demonstrate that this mutation activates an upstream cryptic polyadenylation (CpA) site, which in turn causes reduced transcription. Functional depletion of U1 snRNP in the context of the wild-type SD triggers the same CpA event accompanied by decreased RNA levels. Thus, in accordance with recent findings, U1 snRNP can shield premature pA sites. The negative impact of unshielded pA sites on transcription requires promoter proximity, as demonstrated using artificial constructs and supported by a genome-wide data set. Importantly, transcription down-regulation can be recapitulated in a gene context devoid of splice sites by placing a functional bona fide pA site/transcription terminator within ∼500 base pairs of the promoter. In contrast, promoter-proximal positioning of a pA site-independent histone gene terminator supports high transcription levels. We propose that optimal communication between a pA site-dependent gene terminator and its promoter critically depends on gene length and that short RNA polymerase II-transcribed genes use specialized termination mechanisms to maintain high transcription levels. PMID:23028143

  19. 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.

  20. First Results from the Cryogenic Dark Matter Search Experiment at the Deep Site

    SciTech Connect

    Mandic, Vuk

    2004-06-01

    The Cryogenic Dark Matter Search (CDMS) experiment is designed to search for dark matter in the form of the Weakly Interacting Massive Particles (WIMPs). For this purpose, CDMS uses detectors based on crystals of Ge and Si, operated at the temperature of 20 mK, and providing a two-fold signature of an interaction: the ionization and the athermal phonon signals. The two signals, along with the passive and active shielding of the experimental setup, and with the underground experimental sites, allow very effective suppression and rejection of different types of backgrounds. This dissertation presents the commissioning and the results of the first WIMP-search run performed by the CDMS collaboration at the deep underground site at the Soudan mine in Minnesota. We develop different methods of suppressing the dominant background due to the electron-recoil events taking place at the detector surface and we apply these algorithms to the data set. These results place the world's most sensitive limits on the WIMP-nucleon spin-independent elastic-scattering cross-section. Finally, they examine the compatibility of the supersymmetric WIMP-models with the direct-detection experiments (such as CDMS) and discuss the implications of the new CDMS result on these models.

  1. BAX Activation is Initiated at a Novel Interaction Site

    PubMed Central

    Gavathiotis, Evripidis; Suzuki, Motoshi; Davis, Marguerite L.; Pitter, Kenneth; Bird, Gregory H.; Katz, Samuel G.; Tu, Ho-Chou; Kim, Hyungjin; Cheng, Emily H.-Y.; Tjandra, Nico; Walensky, Loren D.

    2008-01-01

    BAX is a pro-apoptotic protein of the BCL-2 family stationed in the cytosol until activated by a diversity of stress stimuli to induce cell death. Anti-apoptotic proteins such as BCL-2 counteract BAX-mediated cell death. Although an interaction site that confers survival functionality has been defined for anti-apoptotic proteins, an activation site has not been identified for BAX, rendering its explicit trigger mechanism unknown. We previously developed Stabilized Alpha-Helix of BCL-2 domains (SAHBs) that directly initiate BAX-mediated mitochondrial apoptosis. Here we demonstrate by NMR analysis that BIM SAHB binds BAX at an interaction site that is distinct from the canonical binding groove characterized for anti-apoptotic proteins. The specificity of the BIM SAHB-BAX interaction is highlighted by point mutagenesis that abrogates functional activity, confirming that BAX activation is initiated at this novel structural location. Thus, we have now defined a BAX interaction site for direct activation, establishing a new target for therapeutic modulation of apoptosis. PMID:18948948

  2. Characterization of the active site of ADP-ribosyl cyclase.

    PubMed

    Munshi, C; Thiel, D J; Mathews, I I; Aarhus, R; Walseth, T F; Lee, H C

    1999-10-22

    ADP-ribosyl cyclase synthesizes two Ca(2+) messengers by cyclizing NAD to produce cyclic ADP-ribose and exchanging nicotinic acid with the nicotinamide group of NADP to produce nicotinic acid adenine dinucleotide phosphate. Recombinant Aplysia cyclase was expressed in yeast and co-crystallized with a substrate, nicotinamide. x-ray crystallography showed that the nicotinamide was bound in a pocket formed in part by a conserved segment and was near the central cleft of the cyclase. Glu(98), Asn(107) and Trp(140) were within 3.5 A of the bound nicotinamide and appeared to coordinate it. Substituting Glu(98) with either Gln, Gly, Leu, or Asn reduced the cyclase activity by 16-222-fold, depending on the substitution. The mutant N107G exhibited only a 2-fold decrease in activity, while the activity of W140G was essentially eliminated. The base exchange activity of all mutants followed a similar pattern of reduction, suggesting that both reactions occur at the same active site. In addition to NAD, the wild-type cyclase also cyclizes nicotinamide guanine dinucleotide to cyclic GDP-ribose. All mutant enzymes had at least half of the GDP-ribosyl cyclase activity of the wild type, some even 2-3-fold higher, indicating that the three coordinating amino acids are responsible for positioning of the substrate but not absolutely critical for catalysis. To search for the catalytic residues, other amino acids in the binding pocket were mutagenized. E179G was totally devoid of GDP-ribosyl cyclase activity, and both its ADP-ribosyl cyclase and the base exchange activities were reduced by 10,000- and 18,000-fold, respectively. Substituting Glu(179) with either Asn, Leu, Asp, or Gln produced similar inactive enzymes, and so was the conversion of Trp(77) to Gly. However, both E179G and the double mutant E179G/W77G retained NAD-binding ability as shown by photoaffinity labeling with [(32)P]8-azido-NAD. These results indicate that both Glu(179) and Trp(77) are crucial for catalysis and

  3. Involvement of novel autophosphorylation sites in ATM activation.

    PubMed

    Kozlov, Sergei V; Graham, Mark E; Peng, Cheng; Chen, Philip; Robinson, Phillip J; Lavin, Martin F

    2006-08-09

    ATM kinase plays a central role in signaling DNA double-strand breaks to cell cycle checkpoints and to the DNA repair machinery. Although the exact mechanism of ATM activation remains unknown, efficient activation requires the Mre11 complex, autophosphorylation on S1981 and the involvement of protein phosphatases and acetylases. We report here the identification of several additional phosphorylation sites on ATM in response to DNA damage, including autophosphorylation on pS367 and pS1893. ATM autophosphorylates all these sites in vitro in response to DNA damage. Antibodies against phosphoserine 1893 revealed rapid and persistent phosphorylation at this site after in vivo activation of ATM kinase by ionizing radiation, paralleling that observed for S1981 phosphorylation. Phosphorylation was dependent on functional ATM and on the Mre11 complex. All three autophosphorylation sites are physiologically important parts of the DNA damage response, as phosphorylation site mutants (S367A, S1893A and S1981A) were each defective in ATM signaling in vivo and each failed to correct radiosensitivity, genome instability and cell cycle checkpoint defects in ataxia-telangiectasia cells. We conclude that there are at least three functionally important radiation-induced autophosphorylation events in ATM.

  4. 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.

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

    PubMed Central

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

    2015-01-01

    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 (Mw 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

  6. 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…

  7. 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.

  8. Comparison of Grab, Air, and Surface Results for Radiation Site Characterization

    NASA Astrophysics Data System (ADS)

    Glassford, Eric Keith

    2011-12-01

    energy photons from 234Th and 234mPa, the short-lived decay products of 238U, and 235U. Two sided t-tests and coefficient of variation were used to compare sampling types. The large grab samples had the lowest calculated coefficient of variation results for activity and atom percentage. The wipe samples had the highest calculated coefficient of variation of mean specific activity (dis/sec/g) for all three energies. The air filter samples had the highest coefficient of variation calculation for mean atom percentage, for both uranium isotopes examined. The data indicated that the large mass sample was the most effective at characterizing the rolling mill radioactive site conditions, since this would indicate which samples had the smallest variations compared to the mean. Additionally, measurement results of natural uranium in the samples indicate that the distribution of radioactive contamination at the sampling location is most likely non-homogeneous and that the size of the sample collected and analyzed must be sufficiently large to insure that the analytical results are truly representative of the activity present.

  9. Standardization activities for harmonization of test results.

    PubMed

    Dati, F; Brand, B

    2000-07-01

    In the last years the search for sensitive and specific markers of renal damage and/or renal function has conducted to the development of laboratory assays for measurement of urinary proteins such as albumin, beta(2)-microglobulin, alpha(1)-microglobulin, cystatin C, etc. Furthermore, there have been new applications of already known markers based on different, reformulated methods which often rely on more advanced technologies. It is evident that such developments are connected with analytical and interpretative problems for laboratory managers and clinicians. In this situation, it is essential that international societies develop comprehensive measures for the quality management of these assays and issue uniform and carefully elaborated guidelines to ensure optimal test utilization. International activities are also directed to the development of optimized and standardized methods as well as to the production and evaluation of appropriate reference materials and, finally, to the establishment of appropriate reference ranges and cut-off values for specific analytes. The main use of reference materials is in the transfer of their accurately assigned values to the calibrators of diagnostic companies for calibration of commercially available test systems. These international standardization activities and strategies will allow a harmonized approach to disease management using a more reliable laboratory testing based on quality and value.

  10. Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins

    PubMed Central

    Yamada, Kazunori D.; Nishi, Hafumi; Nakata, Junichi; Kinoshita, Kengo

    2016-01-01

    Functional sites on proteins play an important role in various molecular interactions and reactions between proteins and other molecules. Thus, mutations in functional sites can severely affect the overall phenotype. Progress of genome sequencing projects has yielded a wealth of information on single nucleotide variants (SNVs), especially those with less than 1% minor allele frequency (rare variants). To understand the functional influence of genetic variants at a protein level, we investigated the relationship between SNVs and protein functional sites in terms of minor allele frequency and the structural position of variants. As a result, we observed that SNVs were less abundant at ligand binding sites, which is consistent with a previous study on SNVs and protein interaction sites. Additionally, we found that non-rare variants tended to be located slightly apart from enzyme active sites. Examination of non-rare variants revealed that most of the mutations resulted in moderate changes of the physico-chemical properties of amino acids, suggesting the existence of functional constraints. In conclusion, this study shows that the mapping of genetic variants on protein structures could be a powerful approach to evaluate the functional impact of rare genetic variations. PMID:27924270

  11. Monocopper active site for partial methane oxidation in Cu-exchanged 8MR zeolites

    SciTech Connect

    Kulkarni, Ambarish R.; Zhao, Zhi -Jian; Siahrostami, Samira; Nørskov, Jens K.; Studt, Felix

    2016-08-17

    Direct conversion of methane to methanol using oxygen is experiencing renewed interest owing to the availability of new natural gas resources. Copper-exchanged zeolites such as mordenite and ZSM-5 have shown encouraging results, and di- and tri-copper species have been suggested as active sites. Recently, small eight-membered ring (8MR) zeolites including SSZ-13, -16, and -39 have been shown to be active for methane oxidation, but the active sites and reaction mechanisms in these 8MR zeolites are not known. In this work, we use density functional theory (DFT) calculations to systematically evaluate monocopper species as active sites for the partial methane oxidation reaction in Cu-exchanged SSZ-13. On the basis of kinetic and thermodynamic arguments, we suggest that [CuIIOH]+ species in the 8MR are responsible for the experimentally observed activity. Furthermore, our results successfully explain the available spectroscopic data and experimental observations including (i) the necessity of water for methanol extraction and (ii) the effect of Si/Al ratio on the catalyst activity. Monocopper species have not yet been suggested as an active site for the partial methane oxidation reaction, and our results suggest that [CuIIOH]+ active site may provide complementary routes for methane activation in zeolites in addition to the known [Cu–O–Cu]2+ and Cu3O3 motifs.

  12. Monocopper active site for partial methane oxidation in Cu-exchanged 8MR zeolites

    DOE PAGES

    Kulkarni, Ambarish R.; Zhao, Zhi -Jian; Siahrostami, Samira; ...

    2016-08-17

    Direct conversion of methane to methanol using oxygen is experiencing renewed interest owing to the availability of new natural gas resources. Copper-exchanged zeolites such as mordenite and ZSM-5 have shown encouraging results, and di- and tri-copper species have been suggested as active sites. Recently, small eight-membered ring (8MR) zeolites including SSZ-13, -16, and -39 have been shown to be active for methane oxidation, but the active sites and reaction mechanisms in these 8MR zeolites are not known. In this work, we use density functional theory (DFT) calculations to systematically evaluate monocopper species as active sites for the partial methane oxidationmore » reaction in Cu-exchanged SSZ-13. On the basis of kinetic and thermodynamic arguments, we suggest that [CuIIOH]+ species in the 8MR are responsible for the experimentally observed activity. Furthermore, our results successfully explain the available spectroscopic data and experimental observations including (i) the necessity of water for methanol extraction and (ii) the effect of Si/Al ratio on the catalyst activity. Monocopper species have not yet been suggested as an active site for the partial methane oxidation reaction, and our results suggest that [CuIIOH]+ active site may provide complementary routes for methane activation in zeolites in addition to the known [Cu–O–Cu]2+ and Cu3O3 motifs.« less

  13. 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

    2016-09-06

    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.

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

    PubMed Central

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

    2016-01-01

    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

  15. Identification of inhibitors against the potential ligandable sites in the active cholera toxin.

    PubMed

    Gangopadhyay, Aditi; Datta, Abhijit

    2015-04-01

    The active cholera toxin responsible for the massive loss of water and ions in cholera patients via its ADP ribosylation activity is a heterodimer of the A1 subunit of the bacterial holotoxin and the human cytosolic ARF6 (ADP Ribosylation Factor 6). The active toxin is a potential target for the design of inhibitors against cholera. In this study we identified the potential ligandable sites of the active cholera toxin which can serve as binding sites for drug-like molecules. By employing an energy-based approach to identify ligand binding sites, and comparison with the results of computational solvent mapping, we identified two potential ligandable sites in the active toxin which can be targeted during structure-based drug design against cholera. Based on the probe affinities of the identified ligandable regions, docking-based virtual screening was employed to identify probable inhibitors against these sites. Several indole-based alkaloids and phosphates showed strong interactions to the important residues of the ligandable region at the A1 active site. On the other hand, 26 top scoring hits were identified against the ligandable region at the A1 ARF6 interface which showed strong hydrogen bonding interactions, including guanidines, phosphates, Leucopterin and Aristolochic acid VIa. This study has important implications in the application of hybrid structure-based and ligand-based methods against the identified ligandable sites using the identified inhibitors as reference ligands, for drug design against the active cholera toxin.

  16. Barium ions selectively activate BK channels via the Ca2+-bowl site.

    PubMed

    Zhou, Yu; Zeng, Xu-Hui; Lingle, Christopher J

    2012-07-10

    Activation of Ca(2+)-dependent BK channels is increased via binding of micromolar Ca(2+) to two distinct high-affinity sites per BK α-subunit. One site, termed the Ca(2+) bowl, is embedded within the second RCK domain (RCK2; regulator of conductance for potassium) of each α-subunit, while oxygen-containing residues in the first RCK domain (RCK1) have been linked to a separate Ca(2+) ligation site. Although both sites are activated by Ca(2+) and Sr(2+), Cd(2+) selectively favors activation via the RCK1 site. Divalent cations of larger ionic radius than Sr(2+) are thought to be ineffective at activating BK channels. Here we show that Ba(2+), better known as a blocker of K(+) channels, activates BK channels and that this effect arises exclusively from binding at the Ca(2+)-bowl site. Compared with previous estimates for Ca(2+) bowl-mediated activation by Ca(2+), the affinity of Ba(2+) to the Ca(2+) bowl is reduced about fivefold, and coupling of binding to activation is reduced from ∼3.6 for Ca(2+) to about ∼2.8 for Ba(2+). These results support the idea that ionic radius is an important determinant of selectivity differences among different divalent cations observed for each Ca(2+)-binding site.

  17. Maintenance of plastid RNA editing activities independently of their target sites.

    PubMed

    Tillich, Michael; Poltnigg, Peter; Kushnir, Sergei; Schmitz-Linneweber, Christian

    2006-03-01

    RNA editing in plant organelles is mediated by site-specific, nuclear-encoded factors. Previous data suggested that the maintenance of these factors depends on the presence of their rapidly evolving cognate sites. The surprising ability of allotetraploid Nicotiana tabacum (tobacco) to edit a foreign site in the chloroplast ndhA messenger RNA was thought to be inherited from its diploid male ancestor, Nicotiana tomentosiformis. Here, we show that the same ndhA editing activity is also present in Nicotiana sylvestris, which is the female diploid progenitor of tobacco and which lacks the ndhA site. Hence, heterologous editing is not simply a result of tobacco's allopolyploid genome organization. Analyses of other editing sites after sexual or somatic transfer between land plants showed that heterologous editing occurs at a surprisingly high frequency. This suggests that the corresponding editing activities are conserved despite the absence of their target sites, potentially because they serve other functions in the plant cell.

  18. The active site structure and mechanism of phosphoenolpyruvate utilizing enzymes

    SciTech Connect

    Cheng, K.C.

    1989-01-01

    Arginine specific reagents showed irreversible inhibition of avian liver mitochondrial phosphoenolpyruvate carboxykinase. Potent protection against modification was elicited by CO{sub 2} or CO{sub 2} in the presence of other substrates. Labeling of enzyme with (7-{sup 14}C) phenylglyoxal showed that 1 or 2 arginines are involved in CO{sub 2} binding and activation. Peptide map studies showed this active site arginine residues is located at position 289. Histidine specific reagents showed pseudo first order inhibition of avian mitochondrial phosphoenolpyruvate carboxykinase activity. The best protection against modification was elicited by IDP or IDP and Mn{sup +2}. One histidine residue is at or near the phosphoenolpyruvate binding site as demonstrated in the increased absorbance at 240 nm and proton relaxation rate studies. Circular dichroism studies reveal that enzyme structure was perturbed by diethylpyrocarbonate modification. Metal binding studies suggest that this enzyme has only one metal binding site. The putative binding sites from several GTP and phosphoenolpyruvate utilizing enzymes are observed in P-enolpyruvate carboxykinase from different species.

  19. Characterization of Active Site Residues of Nitroalkane Oxidase†

    PubMed Central

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

    2010-01-01

    The flavoenzyme nitroalkane oxidase catalyzes the oxidation of primary and secondary nitrolkanes to the corresponding aldehydes and ketones plus nitrite. The structure of the enzyme shows that Serl71 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 ~5-fold and decreases in the rate constant for product release of ~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

  20. Client satisfaction. Operations research activities and results.

    PubMed

    1998-06-01

    Operations research (OR) is a major component of the Quality Assurance Project's (QAP) strategy for improving the quality of health care delivery worldwide. QAP's Operations Research Program aims to improve the feasibility, utility, and cost-effectiveness of quality assurance strategies in developing countries. QAP and its field partners work to maximize the utility of each field study's findings. As such, the project hopes to disseminate information on all aspects of important OR projects, from the initial design to implementation and results. Over the course of the project, QAP's staff and their partners will develop studies in 16 technical areas. One key area of interest is the study of client satisfaction with health care delivery. The project currently has two major studies on client satisfaction underway in Niger and Peru. Phase one results from the Niger research and QAP and the Max Salud Institute in Peru are discussed.

  1. 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.

  2. A Processive Carbohydrate Polymerase That Mediates Bifunctional Catalysis Using a Single Active Site

    PubMed Central

    May, John F.; Levengood, Matthew R.; Splain, Rebecca A.; Brown, Christopher D.; Kiessling, Laura L.

    2012-01-01

    Even in the absence of a template, glycosyltransferases can catalyze the synthesis of carbohydrate polymers of specific sequence. The paradigm has been that one enzyme catalyzes the formation of one type of glycosidic linkage, yet certain glycosyltransferases generate polysaccharide sequences composed of two distinct linkage types. In principle, bifunctional glycosyltransferases can possess separate active sites for each catalytic activity or one active site with dual activities. We encountered the fundamental question of one or two distinct active sites in our investigation of the galactosyltransferase GlfT2. GlfT2 catalyzes the formation of mycobacterial galactan, a critical cell-wall polymer composed of galactofuranose residues connected with alternating, regioisomeric linkages. We found that GlfT2 mediates galactan polymerization using only one active site that manifests dual regioselectivity. Structural modeling of the bifunctional glycosyltransferases hyaluronan synthase and cellulose synthase suggests that these enzymes also generate multiple glycosidic linkages using a single active site. These results highlight the versatility of glycosyltransferases for generating polysaccharides of specific sequence. We postulate that a hallmark of processive elongation of a carbohydrate polymer by a bifunctional enzyme is that one active site can give rise to two separate types of glycosidic bonds. PMID:22217153

  3. 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.

  4. Face the Edges: Catalytic Active Sites of Nanomaterials

    PubMed Central

    Ni, Bing

    2015-01-01

    Edges are special sites in nanomaterials. The atoms residing on the edges have different environments compared to those in other parts of a nanomaterial and, therefore, they may have different properties. Here, recent progress in nanomaterial fields is summarized from the viewpoint of the edges. Typically, edge sites in MoS2 or metals, other than surface atoms, can perform as active centers for catalytic reactions, so the method to enhance performance lies in the optimization of the edge structures. The edges of multicomponent interfaces present even more possibilities to enhance the activities of nanomaterials. Nanoframes and ultrathin nanowires have similarities to conventional edges of nanoparticles, the application of which as catalysts can help to reduce the use of costly materials. Looking beyond this, the edge structures of graphene are also essential for their properties. In short, the edge structure can influence many properties of materials. PMID:27980960

  5. 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.

  6. Potential sites of CFTR activation by tyrosine kinases

    PubMed Central

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

    2016-01-01

    ABSTRACT 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

  7. MSK1 activity is controlled by multiple phosphorylation sites

    PubMed Central

    McCOY, Claire E.; Campbell, David G.; Deak, Maria; Bloomberg, Graham B.; Arthur, J. Simon C.

    2004-01-01

    MSK1 (mitogen- and stress-activated protein kinase) is a kinase activated in cells downstream of both the ERK1/2 (extracellular-signal-regulated kinase) and p38 MAPK (mitogen-activated protein kinase) cascades. In the present study, we show that, in addition to being phosphorylated on Thr-581 and Ser-360 by ERK1/2 or p38, MSK1 can autophosphorylate on at least six sites: Ser-212, Ser-376, Ser-381, Ser-750, Ser-752 and Ser-758. Of these sites, the N-terminal T-loop residue Ser-212 and the ‘hydrophobic motif’ Ser-376 are phosphorylated by the C-terminal kinase domain of MSK1, and their phosphorylation is essential for the catalytic activity of the N-terminal kinase domain of MSK1 and therefore for the phosphorylation of MSK1 substrates in vitro. Ser-381 is also phosphorylated by the C-terminal kinase domain, and mutation of Ser-381 decreases MSK1 activity, probably through the inhibition of Ser-376 phosphorylation. Ser-750, Ser-752 and Ser-758 are phosphorylated by the N-terminal kinase domain; however, their function is not known. The activation of MSK1 in cells therefore requires the activation of the ERK1/2 or p38 MAPK cascades and does not appear to require additional signalling inputs. This is in contrast with the closely related RSK (p90 ribosomal S6 kinase) proteins, whose activity requires phosphorylation by PDK1 (3-phosphoinositide-dependent protein kinase 1) in addition to phosphorylation by ERK1/2. PMID:15568999

  8. 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)

  9. Mantle to hydrothermal vent sites of the Southern Mariana Trough back-arc Basin: Results from the Taiga Project

    NASA Astrophysics Data System (ADS)

    Seama, N.; Okino, K.; Nogi, Y.; Sato, T.; Matsuno, T.; Yoshikawa, S.; Mochizuki, N.; Shinohara, M.

    2012-12-01

    The southern Mariana Trough back-arc basin shows an EPR type axial relief in morphology and constant low mantle Bouguer anomaly along the spreading axis (Kitada et al., 2006), suggesting abundance of magma supply, even though the full spreading rate of 40 km/Myr is categorized as slow spreading. Further, five hydrothermal vent sites exist within 5 km near the spreading axis at 13 N; two sites on the spreading axis, one site at the eastern foot of the axial high, and two sites on an off-axis knoll. We selected this area as one of three integrated target sites for the Taiga Project, and we conducted series of JAMSTEC research cruises for four different types of geophysical surveys, together with dive observation and samplings by the submersible Shinkai6500. The geophysical surveys consists of 1) a marine magnetotelluric (MT) survey of a 130 km length transect across the spreading axis using 10 ocean bottom electro-magnetometers, 2) a 15 km scale seismic reflection/refraction survey and seismicity observation using 9 ocean bottom seismometers (OBS), 3) near-bottom acoustic and magnetic mapping around all the hydrothermal sites using the AUV Urashima, and 4) a magnetometric resistivity (MMR) survey around the on-axis hydrothermal sites. Two-dimensional electrical resistivity structure of the upper mantle from the MT analysis shows highly asymmetry, which may be affected by hydration driven by water release from the subducting slab; that may result in abundant magma supply to support EPR type axial morphology. Three months OBS observation shows that the seismicity near the hydrothermal vent sites is very low, suggesting that hydrothermal activities are not related to tectonic stress. Moreover, the morphology of the mound and knoll near the three off-axis hydrothermal sites shows undeformed features without any faults, suggesting that their formation is closely related to an off-axis magma upwelling system rather than fault systems. The two on-axis hydrothermal sites

  10. 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.

  11. Number and locations of agonist binding sites required to activate homomeric Cys-loop receptors.

    PubMed

    Rayes, Diego; De Rosa, María José; Sine, Steven M; Bouzat, Cecilia

    2009-05-06

    Homo-pentameric Cys-loop receptors contain five identical agonist binding sites, each formed at a subunit interface. To determine the number and locations of binding sites required to generate a stable active state, we constructed a receptor subunit with a mutation that disables the agonist binding site and a reporter mutation that alters unitary conductance and coexpressed mutant and nonmutant subunits. Although receptors with a range of different subunit compositions are produced, patch-clamp recordings reveal that the amplitude of each single-channel opening event reports the number and, for certain subunit combinations, the locations of subunits with intact binding sites. We find that receptors with three binding sites at nonconsecutive subunit interfaces exhibit maximal mean channel open time, receptors with binding sites at three consecutive or two nonconsecutive interfaces exhibit intermediate open time, and receptors with binding sites at two consecutive or one interface exhibit brief open time. Macroscopic recordings after rapid application of agonist reveal that channel activation slows and the extent of desensitization decreases as the number of binding sites per receptor decreases. The overall results provide a framework for defining mechanisms of activation and drug modulation for homo-pentameric Cys-loop receptors.

  12. 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

  13. Analytical results from an environmental investigation of six sites on Kirtland Air Force Base, New Mexico, 1993-94

    USGS Publications Warehouse

    Wilcox, Ralph

    1995-01-01

    The six sites investigated include silver recovery units; a buried caustic drain line; a neutralization pit; an evaporation/infiltration pond; the Manzano fire training area; and a waste oil underground storage tank. Environmental samples of soil, pond sediment, soil gas, and water and gas in floor drains were collected and analyzed. Field quality-control samples were also collected and analyzed in association with the environmental samples. The six sites were investigated because past or current activities could have resulted in contamination of soil, pond sediment, or water and sediment in drains.

  14. 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.

  15. Vitamin K epoxide reductase: homology, active site and catalytic mechanism.

    PubMed

    Goodstadt, Leo; Ponting, Chris P

    2004-06-01

    Vitamin K epoxide reductase (VKOR) recycles reduced vitamin K, which is used subsequently as a co-factor in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. VKORC1, a subunit of the VKOR complex, has recently been shown to possess this activity. Here, we show that VKORC1 is a member of a large family of predicted enzymes that are present in vertebrates, Drosophila, plants, bacteria and archaea. Four cysteine residues and one residue, which is either serine or threonine, are identified as likely active-site residues. In some plant and bacterial homologues the VKORC1 homologous domain is fused with domains of the thioredoxin family of oxidoreductases. These might reduce disulfide bonds of VKORC1-like enzymes as a prerequisite for their catalytic activities.

  16. Modification of the ATP inhibitory site of the Ascaris suum phosphofructokinase results in the stabilization of an inactive T state

    SciTech Connect

    Rao, G.S.J.; Cook, P.F.; Harris, B.G. )

    1991-10-15

    Treatment of the Ascaris suum phosphofructokinase (PFK) with 2{prime},3{prime}-dialdehyde ATP (oATP) results in an enzyme form that is inactive. The conformational integrity of the active site, however, is preserved, suggesting that oATP modification locks the PFK into an inactive T state that cannot be activated. A rapid, irreversible first-order inactivation of the PFK is observed in the presence of oATP. The rate of inactivation is saturable and gives a K{sub oATP} of 1.07 {plus minus} 0.27 mM. Complete protection against inactivation is afforded by high concentrations of ATP. This desensitized enzyme incorporates only 0.2-0.3 mol of ({sup 3}H)oATP/subunit, suggesting that in te native enzyme inactivation perhaps results from the modification of the ATP inhibitory site rather than the catalytic site. Modification of an active-site thiol by 4,4{prime}-dithiodipyridine is prevented yb ATP before and after oATP treatment. Finally, gel filtration HPLC studies show that the oATP-modified enzyme retains its tetrameric state and neither the tryptophan fluorescence nor the circular dichroic spectra of the modified enzyme are affected by fructose 2,6-bisphosphate, suggesting that the enzyme is locked into a tetrameric inactive T state.

  17. Structural mechanism of RuBisCO activation by carbamylation of the active site lysine.

    PubMed

    Stec, Boguslaw

    2012-11-13

    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 CO(2). We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O(2) and CO(2) bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO(2) defines an elusive, preactivation complex that contains a metal cation Mg(2+) surrounded by three H(2)O/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.

  18. 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

  19. 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.

  20. 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.

  1. Gamma exposure rates due to neutron activation of soil: site of Hood detonation, Operation Plumbbob

    SciTech Connect

    Auxier, J.A.; Ohnesorge, W.F.

    1980-06-01

    This paper is the result of some recent discussions of exposure rates within the first few hours of the Hood detonation of the Plumbbob series due to neutron activation of soil. We estimated the exposure rates from 1/2 to 3 h after the detonation from ground zero to 1000 yards from ground zero. The area was assumed to be uncontaminated by fallout. Soil samples from the area of the Nevada Test Site at which the Hood device was detonated were sent to ORNL by Dr. John Malik of Los Alamos and by Mr. Gordon Jacks of the Nevada Test Site. These samples were irradiated at the DOSAR facility and the resulting activity analyzed. Calculations of exposure rates were then made based on the analyzed activity and the measured thermal neutron fluences at DOSAR and at the Hood Site.

  2. Identification of Phosphorylation Sites Altering Pollen Soluble Inorganic Pyrophosphatase Activity.

    PubMed

    Eaves, Deborah J; Haque, Tamanna; Tudor, Richard L; Barron, Yoshimi; Zampronio, Cleidiane G; Cotton, Nicholas P J; de Graaf, Barend H J; White, Scott A; Cooper, Helen J; Franklin, F Christopher H; Harper, Jeffery F; Franklin-Tong, Vernonica E

    2017-03-01

    Protein phosphorylation regulates numerous cellular processes. Identifying the substrates and protein kinases involved is vital to understand how these important posttranslational modifications modulate biological function in eukaryotic cells. Pyrophosphatases catalyze the hydrolysis of inorganic phosphate (PPi) to inorganic phosphate Pi, driving biosynthetic reactions; they are essential for low cytosolic inorganic phosphate. It was suggested recently that posttranslational regulation of Family I soluble inorganic pyrophosphatases (sPPases) may affect their activity. We previously demonstrated that two pollen-expressed sPPases, Pr-p26.1a and Pr-p26.1b, from the flowering plant Papaver rhoeas were inhibited by phosphorylation. Despite the potential significance, there is a paucity of data on sPPase phosphorylation and regulation. Here, we used liquid chromatographic tandem mass spectrometry to map phosphorylation sites to the otherwise divergent amino-terminal extensions on these pollen sPPases. Despite the absence of reports in the literature on mapping phosphorylation sites on sPPases, a database survey of various proteomes identified a number of examples, suggesting that phosphorylation may be a more widely used mechanism to regulate these enzymes. Phosphomimetic mutants of Pr-p26.1a/b significantly and differentially reduced PPase activities by up to 2.5-fold at pH 6.8 and 52% in the presence of Ca(2+) and hydrogen peroxide over unmodified proteins. This indicates that phosphoregulation of key sites can inhibit the catalytic responsiveness of these proteins in concert with key intracellular events. As sPPases are essential for many metabolic pathways in eukaryotic cells, our findings identify the phosphorylation of sPPases as a potential master regulatory mechanism that could be used to attenuate metabolism.

  3. First Principles Computational Study of the Active Site of Arginase

    SciTech Connect

    Ivanov, Ivaylo; Klien, Micheal

    2004-01-14

    Ab initio density functional theory (DFT) methods were used to investigate the structural features of the active site of the binuclear enzyme rat liver arginase. Special emphasis was placed on the crucial role of the second shell ligand interactions. These interactions were systematically studied by performing calculations on models of varying size. It was determined that a water molecule, and not hydroxide, is the bridging exogenous ligand. The carboxylate ligands facilitate the close approach of the Mn (II) ions by attenuating the metal-metal electrostatic repulsion. Of the two metals, MnA was shown to carry a larger positive charge. Analysis of the electronic properties of the active site revealed that orbitals involving the terminal Asp234 residue, as well as the flexible -1,1 bridging Asp232, lie at high energies, suggesting weaker coordination. This is reflected in certain structural variability present in our models and is also consistent with recent experimental findings. Finally, implications of our findings for the biological function of the enzyme are delineated.

  4. Chemical Analysis of the Moon at the Surveyor VII Landing Site: Preliminary Results.

    PubMed

    Turkevich, A L; Franzgrote, E J; Patterson, J H

    1968-10-04

    The alpha-scattering experiment aboard Surveyor VII has provided a chemical analysis of the moon in the area of the crater Tycho. The preliminary results indicate a chemical composition similar to that already found at two mare sites, but with a lower concentration of elements of the iron group (titanium through copper).

  5. Ecosystem Model Performance at Wetlands: Results from the North American Carbon Program Site Synthesis

    NASA Astrophysics Data System (ADS)

    Sulman, B. N.; Desai, A. R.; Schroeder, N. M.; NACP Site Synthesis Participants

    2011-12-01

    Northern peatlands contain a significant fraction of the global carbon pool, and their responses to hydrological change are likely to be important factors in future carbon cycle-climate feedbacks. Global-scale carbon cycle modeling studies typically use general ecosystem models with coarse spatial resolution, often without peatland-specific processes. Here, seven ecosystem models were used to simulate CO2 fluxes at three field sites in Canada and the northern United States, including two nutrient-rich fens and one nutrient-poor, sphagnum-dominated bog, from 2002-2006. Flux residuals (simulated - observed) were positively correlated with measured water table for both gross ecosystem productivity (GEP) and ecosystem respiration (ER) at the two fen sites for all models, and were positively correlated with water table at the bog site for the majority of models. Modeled diurnal cycles at fen sites agreed well with eddy covariance measurements overall. Eddy covariance GEP and ER were higher during dry periods than during wet periods, while model results predicted either the opposite relationship or no significant difference. At the bog site, eddy covariance GEP had no significant dependence on water table, while models predicted higher GEP during wet periods. All models significantly over-estimated GEP at the bog site, and all but one over-estimated ER at the bog site. Carbon cycle models in peatland-rich regions could be improved by incorporating better models or measurements of hydrology and by inhibiting GEP and ER rates under saturated conditions. Bogs and fens likely require distinct treatments in ecosystem models due to differences in nutrients, peat properties, and plant communities.

  6. Geodetic results from ISAGEX data. [for obtaining center of mass coordinates for geodetic camera sites

    NASA Technical Reports Server (NTRS)

    Marsh, J. G.; Douglas, B. C.; Walls, D. M.

    1974-01-01

    Laser and camera data taken during the International Satellite Geodesy Experiment (ISAGEX) were used in dynamical solutions to obtain center-of-mass coordinates for the Astro-Soviet camera sites at Helwan, Egypt, and Oulan Bator, Mongolia, as well as the East European camera sites at Potsdam, German Democratic Republic, and Ondrejov, Czechoslovakia. The results are accurate to about 20m in each coordinate. The orbit of PEOLE (i=15) was also determined from ISAGEX data. Mean Kepler elements suitable for geodynamic investigations are presented.

  7. Combined remediation technologies: results from field trials at chlorinated solvent impacted sites

    NASA Astrophysics Data System (ADS)

    O'Carroll, D. M.; Chowdhury, A. I.; Lomheim, L.; Boparai, H. K.; Weber, K.; Austrins, L. M.; Edwards, E.; Sleep, B.; de Boer, C. V.; Garcia, A. N.

    2015-12-01

    Non-aqueous phase liquids (NAPLs) are one class of waste liquids often generated from waste mixtures in industrial processes containing surfactants, chlorinated hydrocarbons and other compounds. Chlorinated solvents, a particularly persistent NAPL contaminant, frequently contaminate water sources for decades and are one of the more common contaminants at brownfield and industrialized sites. Although considerable advances in our understanding of the phenomena governing NAPL remediation have been made, and a number of innovative remediation technologies have been developed, existing technologies are rarely able to achieve clean up goals in contaminated aquifers at the completion of remedial activities. The development and pilot scale testing of new and innovative remediation technologies is, therefore, crucial to achieve clean up goals at contaminated sites. Our research group is currently investigating a number of innovative remediation technologies, either individually or as combined remedies. This includes the applicability of nanometals and ISCO (e.g., persulfate) for contaminated site remediation. These technologies can be combined with technologies to enhance amendment delivery (e.g., electrokinetics) or create conditions favorable for enhanced biotic contaminant degradation. This presentation will discuss outcomes from a number of field trials conducted at chlorinated solvent impacted sites by our group with a particular focus on combined remediation technologies.

  8. C-H Activation on Co,O Sites: Isolated Surface Sites versus Molecular Analogs.

    PubMed

    Estes, Deven P; Siddiqi, Georges; Allouche, Florian; Kovtunov, Kirill V; Safonova, Olga V; Trigub, Alexander L; Koptyug, Igor V; Copéret, Christophe

    2016-11-16

    The activation and conversion of hydrocarbons is one of the most important challenges in chemistry. Transition-metal ions (V, Cr, Fe, Co, etc.) isolated on silica surfaces are known to catalyze such processes. The mechanisms of these processes are currently unknown but are thought to involve C-H activation as the rate-determining step. Here, we synthesize well-defined Co(II) ions on a silica surface using a metal siloxide precursor followed by thermal treatment under vacuum at 500 °C. We show that these isolated Co(II) sites are catalysts for a number of hydrocarbon conversion reactions, such as the dehydrogenation of propane, the hydrogenation of propene, and the trimerization of terminal alkynes. We then investigate the mechanisms of these processes using kinetics, kinetic isotope effects, isotopic labeling experiments, parahydrogen induced polarization (PHIP) NMR, and comparison with a molecular analog. The data are consistent with all of these reactions occurring by a common mechanism, involving heterolytic C-H or H-H activation via a 1,2 addition across a Co-O bond.

  9. 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

  10. Lamellipodial actin mechanically links myosin activity with adhesion site formation

    PubMed Central

    Giannone, Gregory; Dubin-Thaler, Benjamin; Rossier, Olivier; Cai, Yunfei; Chaga, Oleg; Jiang, Guoying; Beaver, William; Döbereiner, Hans-Günther; Freund, Yoav; Borisy, Gary; Sheetz, Michael P.

    2013-01-01

    Summary Cell motility proceeds by cycles of edge protrusion, adhesion and retraction. Whether these functions are coordinated by biochemical or biomechanical processes is unknown. We find that myosin II pulls the rear of the lamellipodial actin network, causing upward bending, edge retraction and initiation of new adhesion sites. The network then separates from the edge and condenses over the myosin. Protrusion resumes as lamellipodial actin regenerates from the front and extends rearward until it reaches newly assembled myosin, initiating the next cycle. Upward bending, observed by evanescence and electron microscopy, results in ruffle formation when adhesion strength is low. Correlative fluorescence and electron microscopy shows that the regenerating lamellipodium forms a cohesive, separable layer of actin above the lamellum. Thus, actin polymerization periodically builds a mechanical link, the lamellipodium, connecting myosin motors with the initiation of adhesion sites, suggesting that the major functions driving motility are coordinated by a biomechanical process. PMID:17289574

  11. Evaluation of the likelihood of DNAPL presence at NPL sites: National results. Final report

    SciTech Connect

    Not Available

    1993-09-01

    The document presents the results of a survey undertaken by the U.S. Environmental Protection Agency's (EPA's) Office of Emergency and Remedial Response (Superfund). The survey was designed to estimate the proportion of National Priorities List (NPL) sites where Dense Nonaqueous Phase Liquids (DNAPLs) may be present. Earlier studies by OERR suggested that DNAPLs may be more common at hazardous waste sites than previously thought, and may act as a continuing source of contamination thus reducing the ability of pump-and-treat systems to attain cleanup goals within expected timeframes (Evaluation of Ground Water Extraction Remedies, Phase II, EPA 9355.4-05). The study represents the first systematic nation-wide review of NPL sites designed to estimate the extent of subsurface DNAPL contamination.

  12. 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.

  13. Docking and molecular dynamics studies at trypanothione reductase and glutathione reductase active sites.

    PubMed

    Iribarne, Federico; Paulino, Margot; Aguilera, Sara; Murphy, Miguel; Tapia, Orlando

    2002-05-01

    A theoretical docking study on the active sites of trypanothione reductase (TR) and glutathione reductase (GR) with the corresponding natural substrates, trypanothione disulfide (T[S]2) and glutathione disulfide (GSSG), is reported. Molecular dynamics simulations were carried out in order to check the robustness of the docking results. The energetic results are in agreement with previous experimental findings and show the crossed complexes have lower stabilization energies than the natural ones. To test DOCK3.5, four nitro furanic compounds, previously designed as potentially active anti-chagasic molecules, were docked at the GR and TR active sites with the DOCK3.5 procedure. A good correlation was found between differential inhibitory activity and relative interaction energy (affinity). The results provide a validation test for the use of DOCK3.5 in connection with the design of anti-chagasic drugs.

  14. 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

  15. Preliminary results from comparisons of redundant tiltmeters at three sites in central california

    USGS Publications Warehouse

    Mortensen, C.E.; Johnston, M.J.S.

    1979-01-01

    The U.S. Geological Survey has been operating a network of shallow-borehole tiltmeters in central California since June 1973. At six sites redundant instruments have been installed as a check on data coherency. These include the Sage Ranch, Tres Pinos, New Idria, Aromas, Bear Valley and San Juan Bautista tiltmeter sites. Preliminary results from the comparison of redundant data from the Aromas, Bear Valley and San Juan Bautista sites for periods of eight, three and seven months respectively, suggest that short period tilt signals in the range 5 min < T < 3-5 h and ranging in amplitude from 5 ?? 10-8 to 10-6 rad, but not including step offsets, show excellent agreement on closely spaced instruments. Agreement is not as good in this period range for instruments at San Juan Bautista with a separation of 200 m. Signals of interest observed in this period range include coseismic tilts, teleseisms and tilts associated with creep events. Tilt signals in the period range 3-5 h < T < 2- 5 weeks are not always coherent at all three of the redundant tilt sites studied. Tilt signals in this period range have amplitudes up to 5 ?? 10-6 rad and wavelengths down to at least the instrument separation at the closely spaced sites (~several meters). Regarding longerterm coherency, the instruments at San Juan Bautista with 200-m spacing, agree within 0.5 ??rad for the N-S component and 0.7 jurad for the E-W component for a period of two months. The closely spaced redundant instruments at Aromas agree within 2 ??rad for the N-S component and 1 ??rad for the E-W component for the eight-month period of operation. Data from the three sites have been checked for effects of temperature, atmospheric pressure and rainfall. The latter appears to be critically site dependent. The worst case tilts for 1 inch of rainfall can be more than 1 jurad with a duration of a few days to a week. Typical rain-induced tilts are less than 0.3 ??rad for 1 inch of rain. The two instruments at the Sage Ranch

  16. The 3.6m Indo-Belgian Devasthal Optical Telescope: performance results on site

    NASA Astrophysics Data System (ADS)

    Ninane, Nathalie; Bastin, Christian; Flebus, Carlo; Kumar, Brijesh

    2016-07-01

    AMOS SA has been awarded of the contract for the design, manufacturing, assembly, tests and on site installation (Devasthal, Nainital in central Himalayan region) of the 3.6 m Indo-Belgian Devasthal Optical Telescope (IDOT). The telescope has Ritchey-Chrétien optical configuration with one axial and two side Cassegrain ports. The meniscus primary mirror is active and it is supported by pneumatic actuators. The azimuth axis system is equipped with hydrostatic bearing. After successful factory acceptance at AMOS SA, the telescope has been dismounted, packed, transported, and remounted on site. This paper provides the final performances (i.e. image quality, pointing and tracking) measured during sky tests at Devasthal Observatory.

  17. 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.

  18. 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.

  19. Substrate shuttling between active sites of uroporphyrinogen decarboxylase is not required to generate coproporphyrinogen

    PubMed Central

    Phillips, John D.; Warby, Christy A.; Whitby, Frank G.; Kushner, James P.; Hill, Christopher P.

    2009-01-01

    Summary Uroporphyrinogen Decarboxylase (URO-D; EC 4.1.1.37), the fifth enzyme of the heme biosynthetic pathway, is required for the production of heme, vitamin B12, siroheme, and chlorophyll precursors. URO-D catalyzes the sequential decarboxylation of the four acetate side chains on the pyrrole groups of uroporphyrinogen to produce coproporphyrinogen. URO-D is a stable homodimer with the active site clefts of the two subunits adjacent to each other. It has been hypothesized that the two catalytic centers interact functionally, perhaps by shuttling of reaction intermediates between subunits. We tested this hypothesis by construction of a single chain protein (scURO-D) in which the two subunits were connected by a flexible linker. The crystal structure of this protein was shown to be superimposible with wild-type activity and have comparable catalytic activity. Mutations that impaired one or the other of the two active sites of scURO-D resulted in approximately half of wild-type activity. The distribution of reaction intermediates was the same for mutant and wild-type sequences, and was unaltered in a competition experiment using the I and III isomer substrates. These observations indicate that communication between active sites is not required for enzyme function, and suggest that the dimeric structure of URO-D is required to achieve conformational stability and create a large active site cleft. PMID:19362562

  20. Substrate Shuttling Between Active Sites of Uroporphyrinogen Decarboxylase in Not Required to Generate Coproporphyrinogen

    SciTech Connect

    Phillips, J.; Warby, C; Whitby, F; Kushner, J; Hill, C

    2009-01-01

    Uroporphyrinogen decarboxylase (URO-D; EC 4.1.1.37), the fifth enzyme of the heme biosynthetic pathway, is required for the production of heme, vitamin B12, siroheme, and chlorophyll precursors. URO-D catalyzes the sequential decarboxylation of four acetate side chains in the pyrrole groups of uroporphyrinogen to produce coproporphyrinogen. URO-D is a stable homodimer, with the active-site clefts of the two subunits adjacent to each other. It has been hypothesized that the two catalytic centers interact functionally, perhaps by shuttling of reaction intermediates between subunits. We tested this hypothesis by construction of a single-chain protein (single-chain URO-D) in which the two subunits were connected by a flexible linker. The crystal structure of this protein was shown to be superimposable with wild-type activity and to have comparable catalytic activity. Mutations that impaired one or the other of the two active sites of single-chain URO-D resulted in approximately half of wild-type activity. The distributions of reaction intermediates were the same for mutant and wild-type sequences and were unaltered in a competition experiment using I and III isomer substrates. These observations indicate that communication between active sites is not required for enzyme function and suggest that the dimeric structure of URO-D is required to achieve conformational stability and to create a large active-site cleft.

  1. Evolution of anatase surface active sites probed by in situ sum-frequency phonon spectroscopy.

    PubMed

    Cao, Yue; Chen, Shiyou; Li, Yadong; Gao, Yi; Yang, Deheng; Shen, Yuen Ron; Liu, Wei-Tao

    2016-09-01

    Surface active sites of crystals often govern their relevant surface chemistry, yet to monitor them in situ in real atmosphere remains a challenge. Using surface-specific sum-frequency spectroscopy, we identified the surface phonon mode associated with the active sites of undercoordinated titanium ions and conjoint oxygen vacancies, and used it to monitor them on anatase (TiO2) (101) under ambient conditions. In conjunction with theory, we determined related surface structure around the active sites and tracked the evolution of oxygen vacancies under ultraviolet irradiation. We further found that unlike in vacuum, the surface oxygen vacancies, which dominate the surface reactivity, are strongly regulated by ambient gas molecules, including methanol and water, as well as weakly associated species, such as nitrogen and hydrogen. The result revealed a rich interplay between prevailing ambient species and surface reactivity, which can be omnipresent in environmental and catalytic applications of titanium dioxides.

  2. Evolution of anatase surface active sites probed by in situ sum-frequency phonon spectroscopy

    PubMed Central

    Cao, Yue; Chen, Shiyou; Li, Yadong; Gao, Yi; Yang, Deheng; Shen, Yuen Ron; Liu, Wei-Tao

    2016-01-01

    Surface active sites of crystals often govern their relevant surface chemistry, yet to monitor them in situ in real atmosphere remains a challenge. Using surface-specific sum-frequency spectroscopy, we identified the surface phonon mode associated with the active sites of undercoordinated titanium ions and conjoint oxygen vacancies, and used it to monitor them on anatase (TiO2) (101) under ambient conditions. In conjunction with theory, we determined related surface structure around the active sites and tracked the evolution of oxygen vacancies under ultraviolet irradiation. We further found that unlike in vacuum, the surface oxygen vacancies, which dominate the surface reactivity, are strongly regulated by ambient gas molecules, including methanol and water, as well as weakly associated species, such as nitrogen and hydrogen. The result revealed a rich interplay between prevailing ambient species and surface reactivity, which can be omnipresent in environmental and catalytic applications of titanium dioxides. PMID:27704049

  3. An active site mutation increases the polymerase activity of the guinea pig-lethal Marburg virus.

    PubMed

    Koehler, Alexander; Kolesnikova, Larissa; Becker, Stephan

    2016-10-01

    Marburg virus (MARV) causes severe, often fatal, disease in humans and transient illness in rodents. Sequential passaging of MARV in guinea pigs resulted in selection of a lethal virus containing 4 aa changes. A D184N mutation in VP40 (VP40D184N), which leads to a species-specific gain of viral fitness, and three mutations in the active site of viral RNA-dependent RNA polymerase L, which were investigated in the present study for functional significance in human and guinea pig cells. The transcription/replication activity of L mutants was strongly enhanced by a substitution at position 741 (S741C), and inhibited by other substitutions (D758A and A759D) in both species. The polymerase activity of L carrying the S741C substitution was eightfold higher in guinea pig cells than in human cells upon co-expression with VP40D184N, suggesting that the additive effect of the two mutations provides MARV a replicative advantage in the new host.

  4. Testing the applicability of rapid on-site enzymatic activity detection for surface water monitoring

    NASA Astrophysics Data System (ADS)

    Stadler, Philipp; Vogl, Wolfgang; Juri, Koschelnik; Markus, Epp; Maximilian, Lackner; Markus, Oismüller; Monika, Kumpan; Peter, Strauss; Regina, Sommer; Gabriela, Ryzinska-Paier; Farnleitner Andreas, H.; Matthias, Zessner

    2015-04-01

    On-site detection of enzymatic activities has been suggested as a rapid surrogate for microbiological pollution monitoring of water resources (e.g. using glucuronidases, galactosidases, esterases). Due to the possible short measuring intervals enzymatic methods have high potential as near-real time water quality monitoring tools. This presentation describes results from a long termed field test. For twelve months, two ColiMinder devices (Vienna Water Monitoring, Austria) for on-site determination of enzymatic activity were tested for stream water monitoring at the experimental catchment HOAL (Hydrological Open Air Laboratory, Center for Water Resource Systems, Vienna University of Technology). The devices were overall able to follow and reflect the diverse hydrological and microbiological conditions of the monitored stream during the test period. Continuous data in high temporal resolution captured the course of enzymatic activity in stream water during diverse rainfall events. The method also proofed sensitive enough to determine diurnal fluctuations of enzymatic activity in stream water during dry periods. The method was able to capture a seasonal trend of enzymatic activity in stream water that matches the results gained from Colilert18 analysis for E. coli and coliform bacteria of monthly grab samples. Furthermore the comparison of ColiMinder data with measurements gained at the same test site with devices using the same method but having different construction design (BACTcontrol, microLAN) showed consistent measuring results. Comparative analysis showed significant differences between measured enzymatic activity (modified fishman units and pmol/min/100ml) and cultivation based analyses (most probable number, colony forming unit). Methods of enzymatic activity measures are capable to detect ideally the enzymatic activity caused by all active target bacteria members, including VBNC (viable but nonculturable) while cultivation based methods cannot detect VBNC

  5. Mapping Microbial Populations Relative to Sites of Ongoing Serpentinization: Results from the Tablelands Ophiolite Complex, Canada

    NASA Astrophysics Data System (ADS)

    Schrenk, M. O.; Brazelton, W. J.; Woodruff, Q.; Szponar, N.; Morrill, P. L.

    2010-12-01

    assemblages consisting of diverse taxa at neutral pH background sites. Terrestrial serpentinite-hosted microbial ecosystems with their accessibility, their low phylogenetic diversity, and limited range of energetic resources provide an excellent opportunity to explore the interplay between geochemical energy and life and to elucidate the native serpentinite subsurface biosphere. From the perspective of Mars exploration, studies of serpentinite ecosystems provide the opportunity to pinpoint the organisms and physiological adaptations specifically associated with serpentinization and to directly measure their geochemical impacts. Both of these results will inform modeling and life detection efforts of the Martian subsurface environment.

  6. The Mars Science Laboratory Mission: Early Results from Gale Crater Landing Site

    NASA Astrophysics Data System (ADS)

    Flatow, I.; Grotzinger, J. P.; Blake, D.; Crisp, J. A.; Edgett, K. S.; Gellert, R.; Gomez-Elvira, J.; Hassler, D. M.; Mahaffy, P. R.; Malin, M. C.; Meyer, M. A.; Mitrofanov, I.; Vasavada, A. R.; Wiens, R. C.

    2012-12-01

    The Mars Science Laboratory rover, Curiosity, landed at Gale Crater on August 5th (PDT) and initiated an investigation of modern and ancient environments. The 155-km diameter Gale Crater was chosen as Curiosity's field site based on several attributes: the interior Mount Sharp preserves a succession of flat-lying strata extending almost 5 km above the elevation of the landing site; the lower few hundred meters of the mound show a progression with relative age from clay-bearing to sulfate-bearing strata, separated by an unconformity from overlying likely anhydrous strata; the landing ellipse is characterized by a mixture of alluvial fan and high thermal inertia/high albedo stratified deposits; and a number of stratigraphically/geomorphically distinct fluvial features. Gale's regional context and strong evidence for a progression through multiple potentially habitable environments, represented by a stratigraphic record of extraordinary extent, ensure preservation of a rich record of the environmental history of early Mars. Curiosity has an expected lifetime of at least one Mars year (~23 months), and drive capability of at least 20 km. The MSL science payload was specifically assembled to assess habitability and includes a gas chromatograph-mass spectrometer and gas analyzer that will search for organic carbon in rocks, regolith fines, and the atmosphere (SAM); an x-ray diffractometer that will determine mineralogical diversity (CheMin); focusable cameras that can image landscapes and rock/regolith textures in natural color (MAHLI, Mastcam); an alpha-particle x-ray spectrometer for in situ determination of rock and soil chemistry (APXS); a laser-induced breakdown spectrometer to remotely sense the chemical composition of rocks and minerals (ChemCam); an active/passive neutron spectrometer designed to search for water in rocks/regolith (DAN); a weather station to measure modern-day environmental variables (REMS); and a sensor designed for continuous monitoring of

  7. Wobble Pairs of the HDV Ribozyme Play Specific Roles in Stabilization of Active Site Dynamics

    PubMed Central

    Sripathi, Kamali N.; Banáš, Pavel; Reblova, Kamila; Šponer, Jiři; Otyepka, Michal

    2015-01-01

    The hepatitis delta virus (HDV) is the only known human pathogen whose genome contains a catalytic RNA motif (ribozyme). The overall architecture of the HDV ribozyme is that of a double-nested pseudoknot, with two GU pairs flanking the active site. Although extensive studies have shown that mutation of either wobble results in decreased catalytic activity, little work has focused on linking these mutations to specific structural effects on catalytic fitness. Here we use molecular dynamics simulations based on an activated structure to probe the active site dynamics as a result of wobble pair mutations. In both wild-type and mutant ribozymes, the in-line fitness of the active site (as a measure of catalytic proficiency) strongly depends on the presence of a C75(N3H3+)N1(O5′) hydrogen bond, which positions C75 as the general acid for the reaction. Our mutational analyses show that each GU wobble supports catalytically fit conformations in distinct ways; the reverse G25U20 wobble promotes high in-line fitness, high occupancy of the C75(N3H3+)G1(O5′) general-acid hydrogen bond and stabilization of the G1U37 wobble, while the G1U37 wobble acts more locally by stabilizing high in-line fitness and the C75(N3H3+)G1(O5′) hydrogen bond. We also find that stable type I A-minor and P1.1 hydrogen bonding above and below the active site, respectively, prevent local structural disorder from spreading and disrupting global conformation. Taken together, our results define specific, often redundant architectural roles for several structural motifs of the HDV ribozyme active site, expanding the known roles of these motifs within all HDV-like ribozymes and other structured RNAs. PMID:25631765

  8. Results of the characterization of an in situ coal gasification site in the state of Washington

    SciTech Connect

    Bartel, L. C.; Dobecki, T. L.; Stone, R.

    1980-01-01

    Sandia Laboratories, Lawrence Livermore Laboratory, and the Laramie Energy Technology Center participated in a Department of Energy funded program to select and characterize a potential underground coal gasification test site in the State of Washington. A site in the Centralia-Chehalis coal district, satisfying certain criteria, was selected for characterization. The characterization procedures included surface and borehole techniques and hydrology tests. Geologic structure and coal seam structure and continuity were determined using surface geophysical prospecting (seismic and electromagnetic surveys) and borehole geophysical (logging and cross-borehole, inseam seismic) techniques. A complete suite of geophysical logs was taken in eight exploratory boreholes to determine lithology and properties of the coal and surrounding strata. Coal cores taken from four different exploratory boreholes were analyzed to determine coal quality. Results of the characterization show that the coal seam of interest is approximately 47 ft thick at a depth of 570 to 600 ft at the site. The seam is characterized by high ash content, relatively low overall heating value, and a low permeability. The site appears suitable for conducting an underground coal gasification test.

  9. Results of External Technical Reviews of Site Modeling Efforts That Support System Plans

    SciTech Connect

    Shultz, John R.; Regalbuto, Monica; Pereira, Candido; Brown, Kevin G.; DePaoli, David W; Smith, Sahid C.

    2011-01-01

    An External Technical Review (ETR) team evaluated the system-level modeling and simulation tools in support of Savannah River Site and Office of River Protection liquid waste processing and disposal systems. The reviews focused on the following primary areas: software and modeling tools, capability to model needed facilities and operations, rate at which predictions are performed, and need for additional tools. The Liquid Waste Disposition Systems at these sites are highly integrated operations that involve safely storing liquid waste in underground storage tanks; removing, treating, and disposing low-activity fraction on-site; vitrifying high-level waste; and storing the vitrified waste until permanent disposition at a Federal Repository. The purpose of the ETR team was to evaluate the current process simulation tools that support the planning basis for life cycle liquid waste disposition system plans. These plans establish a base for processing the constituents of liquid waste systems to the end of the program mission. Observations and recommendations were made for each of the review areas. In general, tools appear to provide reasonable estimates for their intended purposes; however, additional functionality and new tools are needed, as well as greater flexibility and improved performance in producing estimates for planning purposes.

  10. Radiological survey results for the Peek Street site properties, Schenectady, New York

    SciTech Connect

    Foley, R.D.; Cottrell, W.D.; Carrier, R.F.

    1992-08-01

    The Peek Street Industrial Facility, located at 425 Peek Street, Schenectady, New York, was operated by the General Electric Company for the Atomic Energy Commission (AEC) between 1947 and 1955. A variety of operations using radioactive materials were conducted at the site, but the main activities were to design an intermediate breeder reactor and to develop a chemical process for the recovery of uranium and plutonium from spent reactor fuel. Nonradioactive beryllium metal was machined on the site for breeder reactor application. The 4.5-acre site was decommissioned and released in October 1955. A radiological survey was conducted by Oak Ridge National Laboratory in November 1989. The survey included scan and grid point measurements of direct radiation levels outdoors on the five properties and inside the factory building, and radionuclide analysis of samples collected from each property. Radionuclide concentrations were determined in outdoor surface and subsurface soil samples from each property and in dust, debris, and structural materials from inside the factory building. Auger holes were logged to assess location and extent of possible subsurface residual soil radioactivity. Radionuclide concentrations were deter-mined in both indoor and outdoor water samples and in selected samples of vegetation. The presence of fixed and transferable surface residual radioactivity was investigated inside the factory building and on discarded materials outdoors on the property. High-volume air samples as well as additional selected indoor and outdoor soil samples were analyzed to determine levels of elemental beryllium.

  11. New active site oriented glyoxyl-agarose derivatives of Escherichia coli penicillin G acylase

    PubMed Central

    Cecchini, Davide A; Serra, Immacolata; Ubiali, Daniela; Terreni, Marco; Albertini, Alessandra M

    2007-01-01

    Background Immobilized Penicillin G Acylase (PGA) derivatives are biocatalysts that are industrially used for the hydrolysis of Penicillin G by fermentation and for the kinetically controlled synthesis of semi-synthetic β-lactam antibiotics. One of the most used supports for immobilization is glyoxyl-activated agarose, which binds the protein by reacting through its superficial Lys residues. Since in E. coli PGA Lys are also present near the active site, an immobilization that occurs through these residues may negatively affect the performance of the biocatalyst due to the difficult diffusion of the substrate into the active site. A preferential orientation of the enzyme with the active site far from the support surface would be desirable to avoid this problem. Results Here we report how it is possible to induce a preferential orientation of the protein during the binding process on aldehyde activated supports. A superficial region of PGA, which is located on the opposite side of the active site, is enriched in its Lys content. The binding of the enzyme onto the support is consequently forced through the Lys rich region, thus leaving the active site fully accessible to the substrate. Different mutants with an increasing number of Lys have been designed and, when active, immobilized onto glyoxyl agarose. The synthetic performances of these new catalysts were compared with those of the immobilized wild-type (wt) PGA. Our results show that, while the synthetic performance of the wt PGA sensitively decreases after immobilization, the Lys enriched mutants have similar performances to the free enzyme even after immobilization. We also report the observations made with other mutants which were unable to undergo a successful maturation process for the production of active enzymes or which resulted toxic for the host cell. Conclusion The desired orientation of immobilized PGA with the active site freely accessible can be obtained by increasing the density of Lys residues

  12. Natural Attenuation of Chlorinated Solvents Performance and Cost Results from Multiple Air Force Demonstration Sites

    DTIC Science & Technology

    1999-10-01

    degree and rate of intrinsic bioremediation of CAHs is highly site specific, and is dependent upon the prevailing bio- and geochemistries of groundwater ...3.2 GEOCHEMISTRY AND BIODEGRADATION Contaminant biodegradation causes geochemical changes in the groundwater system as a result of native or... hydrologically diverse groundwater systems. Water Resources Research, 31:359-371. Clement, T.P. 1997. A modular computer code for simulating

  13. Evaluation of Discrimination Technologies and Classification Results Live Site Demonstration: Former Waikoloa Maneuver Area

    DTIC Science & Technology

    2015-06-01

    jagged volcanic rock, and most of it could not be safely traversed by the extendable reach forklift used to transport the sensor. Three separate...result of the variable background response produced by the iron-rich volcanic rock at the site. Two were identified as metal that did not match any...to prevent any excess movement of the seed items. Table 5-1 lists the seed items emplaced for the project. Table 5-1: WMA Demonstration Seed

  14. 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.

  15. Structure and nuclearity of active sites in Fe-zeolites: comparison with iron sites in enzymes and homogeneous catalysts.

    PubMed

    Zecchina, Adriano; Rivallan, Mickaël; Berlier, Gloria; Lamberti, Carlo; Ricchiardi, Gabriele

    2007-07-21

    Fe-ZSM-5 and Fe-silicalite zeolites efficiently catalyse several oxidation reactions which find close analogues in the oxidation reactions catalyzed by homogeneous and enzymatic compounds. The iron centres are highly dispersed in the crystalline matrix and on highly diluted samples, mononuclear and dinuclear structures are expected to become predominant. The crystalline and robust character of the MFI framework has allowed to hypothesize that the catalytic sites are located in well defined crystallographic positions. For this reason these catalysts have been considered as the closest and best defined heterogeneous counterparts of heme and non heme iron complexes and of Fenton type Fe(2+) homogeneous counterparts. On this basis, an analogy with the methane monooxygenase has been advanced several times. In this review we have examined the abundant literature on the subject and summarized the most widely accepted views on the structure, nuclearity and catalytic activity of the iron species. By comparing the results obtained with the various characterization techniques, we conclude that Fe-ZSM-5 and Fe-silicalite are not the ideal samples conceived before and that many types of species are present, some active and some other silent from adsorptive and catalytic point of view. The relative concentration of these species changes with thermal treatments, preparation procedures and loading. Only at lowest loadings the catalytically active species become the dominant fraction of the iron species. On the basis of the spectroscopic titration of the active sites by using NO as a probe, we conclude that the active species on very diluted samples are isolated and highly coordinatively unsaturated Fe(2+) grafted to the crystalline matrix. Indication of the constant presence of a smaller fraction of Fe(2+) presumably located on small clusters is also obtained. The nitrosyl species formed upon dosing NO from the gas phase on activated Fe-ZSM-5 and Fe-silicalite, have been analyzed

  16. Results of mobile gamma scanning activities in Tonawanda, New York

    SciTech Connect

    Cottrell, W.D.; Witt, D.A.; Rodriguez, R.E.; Carrier, R.F.

    1990-12-01

    During the 1940s, the Linde Air Products Division of Union Carbide operated a plant in Tonawanda, New York, for the Manhattan Engineer District (MED) and the Atomic Energy Commission (AEC). Uranium production and some nickel processing were conducted at the site. It is the policy of the US Department of Energy (DOE) to verify that radiological conditions at such sites or facilities comply with current DOE guidelines. Guidelines for release and use of such sites have become more stringent as research has provided more information since previous cleanups. The Formerly Utilized Sites Remedial Action Program (FUSRAP) was established as part of that effort to confirm the closeout status of facilities under contract to agencies preceding DOE during early nuclear energy development. Under the FUSRAP program, the Linde site itself has been previously investigated to determine the extent of on-site radiological contamination. As a precaution to insure that no residual radioactive materials were transported off-site, the Department of Energy requested that ORNL survey the area in the vicinity of the Linde Plant, the waste water treatment facility on Tower Road, the Sheridan Park Fire Station (District 4), and the Tonawanda Landfill to assess whether any residual radioactive material could be detected. The survey was conducted the week of April 3, 1990. Results of analysis of soil samples from the Tonawanda Landfill revealed slightly elevated concentrations of {sup 238}U and {sup 226}Ra suggestive of residuals from former Linde Plant operations. Therefore, it is recommended that additional surveying of the landfill property and of Sheridan Creek from south of the Linde property to its confluence with the Niagara River be conducted. The survey should include the measurement of gamma radiation levels and radionuclide analysis of silt samples. 6 refs., 4 figs., 1 tab.

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

    NASA Astrophysics Data System (ADS)

    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.

    2016-08-01

    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.

  18. Dynamics of the Active Sites of Dimeric Seryl tRNA Synthetase from Methanopyrus kandleri.

    PubMed

    Dutta, Saheb; Nandi, Nilashis

    2015-08-27

    Aminoacyl tRNA synthetases (aaRSs) carry out the first step of protein biosynthesis. Several aaRSs are multimeric, and coordination between the dynamics of active sites present in each monomer is a prerequisite for the fast and accurate aminoacylation. However, important lacunae of understanding exist concerning the conformational dynamics of multimeric aaRSs. Questions remained unanswered pertaining to the dynamics of the active site. Little is known concerning the conformational dynamics of the active sites in response to the substrate binding, reorganization of the catalytic residues around reactants, time-dependent changes at the reaction center, which are essential for facilitating the nucleophilic attack, and interactions at the interface of neighboring monomers. In the present work, we carried out all-atom molecular dynamics simulation of dimeric (mk)SerRS from Methanopyrus kandleri bound with tRNA using an explicit solvent system. Two dimeric states of seryl tRNA synthetase (open, substrate bound, and adenylate bound) and two monomeric states (open and substrate bound) are simulated with bound tRNA. The aim is to understand the conformational dynamics of (mk)SerRS during its reaction cycle. While the present results provide a clear dynamical perspective of the active sites of (mk)SerRS, they corroborate with the results from the time-averaged experimental data such as crystallographic and mutation analysis of methanogenic SerRS from M. kandleri and M. barkeri. It is observed from the present simulation that the motif 2 loop gates the active site and its Glu351 and Arg360 stabilizes ATP in a bent state favorable for nucleophilic attack. The flexibility of the walls of the active site gradually reduces near reaction center, which is a more organized region compared to the lid region. The motif 2 loop anchors Ser and ATP using Arg349 in a hydrogen bonded geometry crucial for nucleophilic attack and favorably influences the electrostatic potential at the

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

    PubMed Central

    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. DOI: http://dx.doi.org/10.7554/eLife.06181.001 PMID:25902402

  20. WeBSurg: An innovative educational Web site in minimally invasive surgery--principles and results.

    PubMed

    Mutter, Didier; Vix, Michel; Dallemagne, Bernard; Perretta, Silvana; Leroy, Joël; Marescaux, Jacques

    2011-03-01

    Internet has dramatically changed clinical practice and information sharing among the surgical community and has revolutionized the access to surgical education. High-speed Internet broadcasting allows display of high-quality high-definition full-screen videos. Herein, Internet access to surgical procedures plays a major role in continuing medical education (CME). The WeBSurg Web site is a virtual surgical university dedicated to post-graduate education in minimally invasive surgery. Its results measured through its members, number of visitors coming from 213 different countries, as well as the amount of data transmitted through the provider LimeLight, confirm that WeBSurg appears as the first Web site in surgical CME. The Internet offers a tailored education for all levels of surgical expertise as well as for all types of Internet access. This represents a global multimedia solution at the cutting edge of technology and surgical evolution, which responds to the modern ethos of "always, anywhere, anytime."

  1. A split active site couples cap recognition by Dcp2 to activation

    PubMed Central

    Floor, Stephen N.; Jones, Brittnee N.; Hernandez, Gail A.; Gross, John D.

    2010-01-01

    Decapping by Dcp2 is an essential step in 5′-3′ mRNA decay. In yeast, decapping requires an open-to-closed transition in Dcp2, though the link between closure and catalysis remains elusive. Here we show using NMR that cap binds conserved residues on both the catalytic and regulatory domains of Dcp2. Lesions in the cap-binding site on the regulatory domain reduce the catalytic step two orders of magnitude and block formation of the closed state whereas Dcp1 enhances the catalytic step by a factor of ten and promotes closure. We conclude that closure occurs during the rate-limiting catalytic step of decapping, juxtaposing the cap-binding region of each domain to form a composite active site. This work suggests a model for regulation of decapping, where coactivators trigger decapping by stabilizing a labile composite active site. PMID:20711189

  2. Vertical Seafloor Geodesy at Two Mid-ocean Ridge Sites: Recent Results and Lessons Learned (Invited)

    NASA Astrophysics Data System (ADS)

    Nooner, S. L.; Chadwick, B.; Webb, S. C.

    2013-12-01

    Precise measurements of ambient seawater pressure can be used as a proxy for seafloor depth and can be used to track vertical movements of the seafloor with time. We have employed two measurement techniques simultaneously to track both episodic and long-term deformation signals at active volcanic sites on mid-ocean ridges. The first technique is through the use of Bottom Pressure Recorders (BPRs), which are instruments that sit on the seafloor recording pressure continuously for 1-3 years until they are recovered for data download and battery replacement. BPRs are essential for measuring episodic events but suffer from slow instrument drift that is indistinguishable from long-term deformation. To track the long-term deformation signals and quantify drift in the BPRs, we developed a technique using ROV deployed Mobile Pressure Recorders (MPRs). In 2000 we began making MPR measurements on top of seafloor benchmarks at Axial Seamount on the Juan de Fuca Ridge after it's 1998 eruption. The combined BPR and MPR measurements have allowed us to observe and quantify an entire eruption cycle at the intermediate spreading Axial Seamount. From 2008-2011 we established another geodetic network at the fast spreading East Pacific Rise (EPR) at the site of a 2005/2006 eruption near 9°50' N. Here we show the results to date from both Axial Seamount and the EPR, and discuss lessons learned during the last 14 years. Measurements at Axial Seamount were all made using ROVs, while measurements at the EPR were made using the manned submersible Alvin in 2008 and 2009 and the Jason ROV in 2011. Our observations at Axial Seamount have enabled us to characterize its eruption cycle into 4 distinct phases: 1.) pre-eruption short-term rapid inflation, 2.) co-eruption deflation, 3.) rapid post-eruption reinflation, and 4.) subsequent long-term steady inflation. The transition between the phases 3 and 4 was not captured after the 1998 eruption and is an important impetus for continued

  3. Active-Site Monovalent Cations Revealed in a 1.55 Å Resolution Hammerhead Ribozyme Structure

    PubMed Central

    Anderson, Michael; Schultz, Eric P.; Martick, Monika; Scott, William G.

    2013-01-01

    We have obtained a 1.55 Å crystal structure of a hammerhead ribozyme derived from Schistosoma mansoni in conditions that permit detailed observations of Na+ ion binding in the ribozyme's active site. At least two such Na+ ions are observed. The first Na+ ion binds to the N7 of G10.1 and the adjacent A9 phosphate in a manner identical to that previously observed for divalent cations. A second Na+ ion binds to the Hoogsteen face of G12, the general base in the hammerhead cleavage reaction, thereby potentially dissipating the negative charge of the catalytically active enolate form of the nucleotide base. A potential but more ambiguous third site bridges the A9 and scissile phosphates in a manner consistent with previous predictions. Hammerhead ribozymes have been observed to be active in the presence of high concentrations of monovalent cations, including Na+, but the mechanism by which monovalent cations substitute for divalent cations in hammerhead catalysis remains unclear. Our results enable us to suggest that Na+ directly and specifically substitutes for divalent cations in the hammerhead active site. The detailed geometry of the pre-catalytic active site complex is also revealed with a new level of precision, thanks to the quality of the electron density maps obtained from what is currently the highest resolution ribozyme structure in the protein data bank. PMID:23711504

  4. Result Summary for the Area 5 Radioactive Waste Management Site Performance Assessment Model Version 4.113

    SciTech Connect

    Shott, G. J.

    2012-04-15

    Preliminary results for Version 4.113 of the Nevada National Security Site Area 5 Radioactive Waste Management Site performance assessment model are summarized. Version 4.113 includes the Fiscal Year 2011 inventory estimate.

  5. Status of data, major results, and plans for geophysical activities, Yucca Mountain Project

    SciTech Connect

    Oliver, H.W.; Hardin, E.L.; Nelson, P.H.

    1990-07-01

    This report describes past and planned geophysical activities associated with the Yucca Mountain Project and is intended to serve as a starting point for integration of geophysical activities. This report relates past results to site characterization plans, as presented in the Yucca Mountain Site Characterization Plan (SCP). This report discusses seismic exploration, potential field methods, geoelectrical methods, teleseismic data collection and velocity structural modeling, and remote sensing. This report discusses surface-based, airborne, borehole, surface-to-borehole, crosshole, and Exploratory Shaft Facility-related activities. The data described in this paper, and the publications discussed, have been selected based on several considerations; location with respect to Yucca Mountain, whether the success or failure of geophysical data is important to future activities, elucidation of features of interest, and judgment as to the likelihood that the method will produce information that is important for site characterization. 65 refs., 19 figs., 12 tabs.

  6. Final Report: Results of Environmental Site Investigation at Sylvan Grove, Kansas

    SciTech Connect

    LaFreniere, Lorraine M

    2014-09-01

    Sylvan Grove is located in western Lincoln County, approximately 60 mi west of Salina, Kansas (Figure 1.1). From 1954 to 1966, the Commodity Credit Corporation (CCC), an agency of the U.S. Department of Agriculture (USDA), operated a grain storage facility at the northeastern edge of Sylvan Grove. During this time, commercial grain fumigants containing carbon tetrachloride were in common use to preserve grain in storage. In 1998, the Kansas Department of Health and Environment (KDHE) found carbon tetrachloride above the maximum contaminant level (MCL) of 5 μg/L in groundwater from one private well used for livestock and lawn and garden watering. The 1998 KDHE sampling at Sylvan Grove was conducted under the USDA private well sampling program. To determine whether the former CCC/USDA facility at Sylvan Grove is a potential contaminant source and its possible relationship to the contamination in groundwater, the CCC/USDA proposed to conduct an environmental site investigation, in accordance with the Intergovernmental Agreement between the KDHE and the Farm Service Agency (FSA) of the USDA. Argonne National Laboratory, on behalf of the CCC/USDA, developed a work plan (Argonne 2012) for the site investigation and a supplemental work plan for indoor and ambient air sampling (Appendix A). The proposed work was approved by the KDHE (2012a, 2013). The investigations were performed by the Environmental Science Division of Argonne National Laboratory, on behalf of the CCC/USDA. The main activities for the site investigation were conducted in June 2012, and indoor and ambient air sampling was performed in February 2013. This report presents the findings of the investigations at Sylvan Grove.

  7. Two interacting binding sites for quinacrine derivatives in the active site of trypanothione reductase – a template for drug design

    PubMed Central

    Saravanamuthu, Ahilan; Vickers, Tim J.; Bond, Charles S.; Peterson, Mark R.; Hunter, William N.; Fairlamb, Alan H.

    2012-01-01

    SUMMARY Trypanothione reductase is a key enzyme in the trypanothione-based redox metabolism of pathogenic trypanosomes. Since this system is absent in humans, being replaced with glutathione and glutathione reductase, it offers a target for selective inhibition. The rational design of potent inhibitors requires accurate structures of enzyme-inhibitor complexes, but this is lacking for trypanothione reductase. We therefore used quinacrine mustard, an alkylating derivative of the competitive inhibitor quinacrine, to probe the active site of this dimeric flavoprotein. Quinacrine mustard irreversibly inactivates Trypanosoma cruzi trypanothione reductase, but not human glutathione reductase, in a time-dependent manner with a stoichiometry of two inhibitors bound per monomer. The rate of inactivation is dependent upon the oxidation state of trypanothione reductase, with the NADPH-reduced form being inactivated significantly faster than the oxidised form. Inactivation is slowed by clomipramine and a melarsen oxide-trypanothione adduct (both are competitive inhibitors) but accelerated by quinacrine. The structure of the trypanothione reductase-quinacrine mustard adduct was determined to 2.7 Å, revealing two molecules of inhibitor bound in the trypanothione-binding site. The acridine moieties interact with each other through π-stacking effects, and one acridine interacts in a similar fashion with a tryptophan residue. These interactions provide a molecular explanation for the differing effects of clomipramine and quinacrine on inactivation by quinacrine mustard. Synergism with quinacrine occurs as a result of these planar acridines being able to stack together in the active site cleft, thereby gaining an increased number of binding interactions, whereas antagonism occurs with non-planar molecules, such as clomipramine, where stacking is not possible. PMID:15102853

  8. 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.

  9. 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.

  10. Controlling activation site density by low-energy far-field stimulation in cardiac tissue.

    PubMed

    Hörning, Marcel; Takagi, Seiji; Yoshikawa, Kenichi

    2012-06-01

    Tachycardia and fibrillation are potentially fatal arrhythmias associated with the formation of rotating spiral waves in the heart. Presently, the termination of these types of arrhythmia is achieved by use of antitachycardia pacing or cardioversion. However, these techniques have serious drawbacks, in that they either have limited application or produce undesirable side effects. Low-energy far-field stimulation has recently been proposed as a superior therapy. This proposed therapeutic method would exploit the phenomenon in which the application of low-energy far-field shocks induces a large number of activation sites ("virtual electrodes") in tissue. It has been found that the formation of such sites can lead to the termination of undesired states in the heart and the restoration of normal beating. In this study we investigate a particular aspect of this method. Here we seek to determine how the activation site density depends on the applied electric field through in vitro experiments carried out on neonatal rat cardiac tissue cultures. The results indicate that the activation site density increases exponentially as a function of the intracellular conductivity and the level of cell isotropy. Additionally, we report numerical results obtained from bidomain simulations of the Beeler-Reuter model that are quantitatively consistent with our experimental results. Also, we derive an intuitive analytical framework that describes the activation site density and provides useful information for determining the ratio of longitudinal to transverse conductivity in a cardiac tissue culture. The results obtained here should be useful in the development of an actual therapeutic method based on low-energy far-field pacing. In addition, they provide a deeper understanding of the intrinsic properties of cardiac cells.

  11. Controlling activation site density by low-energy far-field stimulation in cardiac tissue

    NASA Astrophysics Data System (ADS)

    Hörning, Marcel; Takagi, Seiji; Yoshikawa, Kenichi

    2012-06-01

    Tachycardia and fibrillation are potentially fatal arrhythmias associated with the formation of rotating spiral waves in the heart. Presently, the termination of these types of arrhythmia is achieved by use of antitachycardia pacing or cardioversion. However, these techniques have serious drawbacks, in that they either have limited application or produce undesirable side effects. Low-energy far-field stimulation has recently been proposed as a superior therapy. This proposed therapeutic method would exploit the phenomenon in which the application of low-energy far-field shocks induces a large number of activation sites (“virtual electrodes”) in tissue. It has been found that the formation of such sites can lead to the termination of undesired states in the heart and the restoration of normal beating. In this study we investigate a particular aspect of this method. Here we seek to determine how the activation site density depends on the applied electric field through in vitro experiments carried out on neonatal rat cardiac tissue cultures. The results indicate that the activation site density increases exponentially as a function of the intracellular conductivity and the level of cell isotropy. Additionally, we report numerical results obtained from bidomain simulations of the Beeler-Reuter model that are quantitatively consistent with our experimental results. Also, we derive an intuitive analytical framework that describes the activation site density and provides useful information for determining the ratio of longitudinal to transverse conductivity in a cardiac tissue culture. The results obtained here should be useful in the development of an actual therapeutic method based on low-energy far-field pacing. In addition, they provide a deeper understanding of the intrinsic properties of cardiac cells.

  12. Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model

    PubMed Central

    Huang, Xiaoqiang; Xue, Jing; Lin, Min; Zhu, Yushan

    2016-01-01

    Active site preorganization helps native enzymes electrostatically stabilize the transition state better than the ground state for their primary substrates and achieve significant rate enhancement. In this report, we hypothesize that a complex active site model for active site preorganization modeling should help to create preorganized active site design and afford higher starting activities towards target reactions. Our matching algorithm ProdaMatch was improved by invoking effective pruning strategies and the native active sites for ten scaffolds in a benchmark test set were reproduced. The root-mean squared deviations between the matched transition states and those in the crystal structures were < 1.0 Å for the ten scaffolds, and the repacking calculation results showed that 91% of the hydrogen bonds within the active sites are recovered, indicating that the active sites can be preorganized based on the predicted positions of transition states. The application of the complex active site model for de novo enzyme design was evaluated by scaffold selection using a classic catalytic triad motif for the hydrolysis of p-nitrophenyl acetate. Eighty scaffolds were identified from a scaffold library with 1,491 proteins and four scaffolds were native esterase. Furthermore, enzyme design for complicated substrates was investigated for the hydrolysis of cephalexin using scaffold selection based on two different catalytic motifs. Only three scaffolds were identified from the scaffold library by virtue of the classic catalytic triad-based motif. In contrast, 40 scaffolds were identified using a more flexible, but still preorganized catalytic motif, where one scaffold corresponded to the α-amino acid ester hydrolase that catalyzes the hydrolysis and synthesis of cephalexin. Thus, the complex active site modeling approach for de novo enzyme design with the aid of the improved ProdaMatch program is a promising approach for the creation of active sites with high catalytic

  13. Hydrogeology and results of injection tests at waste-injection test sites in Pinellas County, Florida

    USGS Publications Warehouse

    Hickey, John J.

    1982-01-01

    Potential benefits or hazards to freshwater resources could result from subsurface injection of treated wastewater. Recognizing this, the U.S. Geological Survey, in cooperation with Pinellas County and the city of St. Petersburg, undertook an evaluation of the hydrogeology and injection of wastewater at proposed test sites on the Pinellas peninsula. The injection sites are underlain by sedimentary rocks ranging in age from Cretaceous to Pleistocene. Lower Eocene carbonate rocks were penetrated to a maximum depth of 3,504 feet and were found to have relatively low water yields. The most permeable part of the investigated section was in rocks of middle Eocene age within the Floridan aquifer. At the injection sites, the Floridan aquifer was subdivided into four permeable zones and three semiconfining beds. The test injection zone is within the Avon Park Limestone, the most productive of the identified permeable zones, with a transmissivity of about 1,000,000 feet squared per day. Two semiconfining beds are above the injection zone in the Suwannee Limestone and Ocala Limestone and have vertical hydraulic conductivities estimated to range from about 0.1 to 1 foot per day where these beds do not contain clay. Limited fresh ground-water supplies exist in the Floridan aquifer within the Pinellas peninsula. At all test sites, chloride concentration in the injection zone ranged from 19,000 to 20,000 milligrams per liter. Injection tests ranging in duration from 3 to 91.1 days were run at three different sites. Pressure buildup occurred in permeable zones above and below the injection zone during these tests. Calculated pressure buildup in observation wells close to and at some distance from the test wells was typically less than 1 pound per square inch. Injection and formation water will probably move slowly through the semiconfining bed overlying the injection zone, and long-term injection tests will be needed to determine the effectiveness of these beds to retard flow. The

  14. Locomotor activity influences muscle architecture and bone growth but not muscle attachment site morphology

    PubMed Central

    Rabey, Karyne N.; Green, David J.; Taylor, Andrea B.; Begun, David R.; Richmond, Brian G.; McFarlin, Shannon C.

    2014-01-01

    The ability to make behavioural inferences from skeletal remains is critical to understanding the lifestyles and activities of past human populations and extinct animals. Muscle attachment site (enthesis) morphology has long been assumed to reflect muscle strength and activity during life, but little experimental evidence exists to directly link activity patterns with muscle development and the morphology of their attachments to the skeleton. We used a mouse model to experimentally test how the level and type of activity influences forelimb muscle architecture of spinodeltoideus, acromiodeltoideus, and superficial pectoralis, bone growth rate and gross morphology of their insertion sites. Over an 11-week period, we collected data on activity levels in one control group and two experimental activity groups (running, climbing) of female wild-type mice. Our results show that both activity type and level increased bone growth rates influenced muscle architecture, including differences in potential muscular excursion (fibre length) and potential force production (physiological cross-sectional area). However, despite significant influences on muscle architecture and bone development, activity had no observable effect on enthesis morphology. These results suggest that the gross morphology of entheses is less reliable than internal bone structure for making inferences about an individual’s past behaviour. PMID:25467113

  15. Locomotor activity influences muscle architecture and bone growth but not muscle attachment site morphology.

    PubMed

    Rabey, Karyne N; Green, David J; Taylor, Andrea B; Begun, David R; Richmond, Brian G; McFarlin, Shannon C

    2015-01-01

    The ability to make behavioural inferences from skeletal remains is critical to understanding the lifestyles and activities of past human populations and extinct animals. Muscle attachment site (enthesis) morphology has long been assumed to reflect muscle strength and activity during life, but little experimental evidence exists to directly link activity patterns with muscle development and the morphology of their attachments to the skeleton. We used a mouse model to experimentally test how the level and type of activity influences forelimb muscle architecture of spinodeltoideus, acromiodeltoideus, and superficial pectoralis, bone growth rate and gross morphology of their insertion sites. Over an 11-week period, we collected data on activity levels in one control group and two experimental activity groups (running, climbing) of female wild-type mice. Our results show that both activity type and level increased bone growth rates influenced muscle architecture, including differences in potential muscular excursion (fibre length) and potential force production (physiological cross-sectional area). However, despite significant influences on muscle architecture and bone development, activity had no observable effect on enthesis morphology. These results suggest that the gross morphology of entheses is less reliable than internal bone structure for making inferences about an individual's past behaviour.

  16. Preliminary results of receiver function analyses at three sites across the Bransfield Strait, Antarctica

    NASA Astrophysics Data System (ADS)

    Martínez Arévalo, C.; Mancilla, F.; Almendros, J.; Aznarte, J. L.; Alguacil, G.

    2009-04-01

    In February 2008, in the framework of the International Polar Year 2008-2009 under grant POL2006-08663 of the spanish Ministry of Education, we deployed three broadband seismometers at points forming a N-S profile across the Bransfield Strait, Antarctica, in the region between the South Shetland Islands and the Antarctic Peninsula. This region is very interesting from a tectonic point of view, due to the opening of the rift of the Bransfield and the presence of the South Shetland microplate. For logistic reasons, our instruments where located in the vicinity of the Antarctic bases Juan Carlos I (Livingston Island), Gabriel de Castilla (Deception Island), and Primavera (Antarctic Peninsula). Each seismic station consisted of a broad-band, three-component electrolitic seismometer equiped with a 24-bit data acquisition system. The energy was provided by wind generators and solar panels connected to a battery bank, a combination that has been able to provide enough power at all sites, even during the Antarctic winter. All components were designed to function under the extreme conditions of the Antarctic weather. The main objective of this experiment was to use receiver function techniques on teleseism data to investigate the structure of the crust under the sites, in order to compare with other studies and shed light on the structure and tectonics of the region. During this past year, we have recorded several tens of teleseisms at distances appropriate for receiver function analyses. Preliminary results will add information on critical issues regarding the structure of the Bransfield Strait region. Although the Earth models obtained will contain extra information, we are specially interested in the determination of the depth of the Moho at each site, a controversial point in this area. These results will be compared with estimates obtained by different techniques. We are also interested in the determination of the vertical extent of the magma chamber recently imaged by

  17. Communication: Active space decomposition with multiple sites: Density matrix renormalization group algorithm

    SciTech Connect

    Parker, Shane M.; Shiozaki, Toru

    2014-12-07

    We extend the active space decomposition method, recently developed by us, to more than two active sites using the density matrix renormalization group algorithm. The fragment wave functions are described by complete or restricted active-space wave functions. Numerical results are shown on a benzene pentamer and a perylene diimide trimer. It is found that the truncation errors in our method decrease almost exponentially with respect to the number of renormalization states M, allowing for numerically exact calculations (to a few μE{sub h} or less) with M = 128 in both cases. This rapid convergence is because the renormalization steps are used only for the interfragment electron correlation.

  18. Altered binding of thioflavin t to the peripheral anionic site of acetylcholinesterase after phosphorylation of the active site by chlorpyrifos oxon or dichlorvos

    SciTech Connect

    Sultatos, L.G. Kaushik, R.

    2008-08-01

    The peripheral anionic site of acetylcholinesterase, when occupied by a ligand, is known to modulate reaction rates at the active site of this important enzyme. The current report utilized the peripheral anionic site specific fluorogenic probe thioflavin t to determine if the organophosphates chlorpyrifos oxon and dichlorvos bind to the peripheral anionic site of human recombinant acetylcholinesterase, since certain organophosphates display concentration-dependent kinetics when inhibiting this enzyme. Incubation of 3 nM acetylcholinesterase active sites with 50 nM or 2000 nM inhibitor altered both the B{sub max} and K{sub d} for thioflavin t binding to the peripheral anionic site. However, these changes resulted from phosphorylation of Ser203 since increasing either inhibitor from 50 nM to 2000 nM did not alter further thioflavin t binding kinetics. Moreover, the organophosphate-induced decrease in B{sub max} did not represent an actual reduction in binding sites, but instead likely resulted from conformational interactions between the acylation and peripheral anionic sites that led to a decrease in the rigidity of bound thioflavin t. A drop in fluorescence quantum yield, leading to an apparent decrease in B{sub max}, would accompany the decreased rigidity of bound thioflavin t molecules. The organophosphate-induced alterations in K{sub d} represented changes in binding affinity of thioflavin t, with diethylphosphorylation of Ser203 increasing K{sub d}, and dimethylphosphorylation of Ser203 decreasing K{sub d}. These results indicate that chlorpyrifos oxon and dichlorvos do not bind directly to the peripheral anionic site of acetylcholinesterase, but can affect binding to that site through phosphorylation of Ser203.

  19. Active layer dynamics in three sites with contrasted topography in the Byers Peninsula (Livingston Island, Antarctica)

    NASA Astrophysics Data System (ADS)

    Oliva, Marc; Ruiz-Fernández, Jesús; Vieira, Gonçalo

    2015-04-01

    Topography exerts a key role on permafrost distribution in areas where mean annual temperatures are slightly negative. This is the case of low-altitude environments in Maritime Antarctica, namely in the South Shetland Islands, where permafrost is marginal to discontinuous until elevations of 20-40 m asl turning to continuous at higher areas. Consequently, the active layer dynamics is also strongly conditioned by the geomorphological setting. In January 2014 we installed three sites for monitoring the active layer dynamics across the Byers Peninsula (Livingston Island, South Shetland Islands) in different geomorphological environments at elevations between 60 and 100 m. The purpose was to examine the role of the topography and microclimatic conditions on the active layer dynamics. At each site a set of loggers was set up to monitor: air temperatures, snow thickness, ground temperatures until 80 cm together with the coupling atmosphere-ground temperatures. During the first year of monitoring the mean annual air temperatures show similar values in the three sites, in all cases slightly below freezing. The snowy conditions during this year in this archipelago have resulted in a late melting of snow, which has also conditioned the duration of frozen conditions in the uppermost soil layers. Topography has a strong influence on snow cover duration, which in turn affects frozen ground conditions. The Domo site is located in a higher position with respect to the central plateau of Byers; here, the wind is stronger and snow cover thinner, which has conditioned a longer thawing season than in the other two sites (Cerro Negro, Escondido). These two sites are located in topographically protected areas favouring snow accumulation. The longer persistence of snow conditions a longer duration of negative temperatures in the active layer of the permafrost. This research was financially supported by the HOLOANTAR project (Portuguese Science Foundation) and the AXA Research Fund.

  20. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 9 2012-07-01 2012-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing...

  1. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 9 2014-07-01 2014-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing...

  2. Overview of the Manitou Experimental Forest Observatory: site description and selected science results from 2008 to 2013

    SciTech Connect

    Ortega, John; Turnipseed, A.; Guenther, Alex B.; Karl, Thomas G.; Day, D. A.; Gochis, David; Huffman, J. A.; Prenni, Anthony J.; Levin, E. J.; Kreidenweis, Sonia M.; DeMott, Paul J.; Tobo, Y.; Patton, E. G.; Hodzic, Alma; Cui, Y. Y.; Harley, P.; Hornbrook, R. S.; Apel, E. C.; Monson, Russell K.; Eller, A. S.; Greenberg, J. P.; Barth, Mary; Campuzano-Jost, Pedro; Palm, B. B.; Jiminez, J. L.; Aiken, A. C.; Dubey, Manvendra K.; Geron, Chris; Offenberg, J.; Ryan, M. G.; Fornwalt, Paula J.; Pryor, S. C.; Keutsch, Frank N.; DiGangi, J. P.; Chan, A. W.; Goldstein, Allen H.; Wolfe, G. M.; Kim, S.; Kaser, L.; Schnitzhofer, R.; Hansel, A.; Cantrell, Chris; Mauldin, R. L.; Smith, James N.

    2014-01-01

    The Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics & Nitrogen (BEACHON) project seeks to understand the feedbacks and interrelationships between hydrology, biogenic emissions, carbon assimilation, aerosol properties, clouds and associated feedbacks within water-limited ecosystems. The Manitou Experimental Forest Observatory (MEFO) was established in 2008 by the National Center for Atmospheric Research to address many of the BEACHON research objectives, and it now provides a fixed field site with significant infrastructure. MEFO is a mountainous, semi-arid ponderosa pine-dominated forest site that is normally dominated by clean continental air but is periodically influenced by anthropogenic sources from Colorado Front Range cities. This article summarizes the past and ongoing research activities at the site, and highlights some of the significant findings that have resulted from these measurements. These activities include – soil property measurements; – hydrological studies; – measurements of high-frequency turbulence parameters; – eddy covariance flux measurements of water, energy, aerosols and carbon dioxide through the canopy; – determination of biogenic and anthropogenic volatile organic compound emissions and their influence on regional atmospheric chemistry; – aerosol number and mass distributions; – chemical speciation of aerosol particles; – characterization of ice and cloud condensation nuclei; – trace gas measurements; and – model simulations using coupled chemistry and meteorology. In addition to various long-term continuous measurements, three focused measurement campaigns with state-of-the-art instrumentation have taken place since the site was established, and two of these studies are the subjects of this special issue: BEACHON-ROCS (Rocky Mountain Organic Carbon Study, 2010) and BEACHON-RoMBAS (Rocky Mountain Biogenic Aerosol Study, 2011).

  3. Overview of the Manitou Experimental Forest Observatory: site description and selected science results from 2008-2013

    NASA Astrophysics Data System (ADS)

    Ortega, J.; Turnipseed, A.; Guenther, A. B.; Karl, T. G.; Day, D. A.; Gochis, D.; Huffman, J. A.; Prenni, A. J.; Levin, E. J. T.; Kreidenweis, S. M.; DeMott, P. J.; Tobo, Y.; Patton, E. G.; Hodzic, A.; Cui, Y.; Harley, P. C.; Hornbrook, R. H.; Apel, E. C.; Monson, R. K.; Eller, A. S. D.; Greenberg, J. P.; Barth, M.; Campuzano-Jost, P.; Palm, B. B.; Jimenez, J. L.; Aiken, A. C.; Dubey, M. K.; Geron, C.; Offenberg, J.; Ryan, M. G.; Fornwalt, P. J.; Pryor, S. C.; Keutsch, F. N.; DiGangi, J. P.; Chan, A. W. H.; Goldstein, A. H.; Wolfe, G. M.; Kim, S.; Kaser, L.; Schnitzhofer, R.; Hansel, A.; Cantrell, C. A.; Mauldin, R. L., III; Smith, J. N.

    2014-01-01

    The Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics & Nitrogen (BEACHON) project seeks to understand the feedbacks and inter-relationships between hydrology, biogenic emissions, carbon assimilation, aerosol properties, clouds and associated feedbacks within water-limited ecosystems. The Manitou Experimental Forest Observatory (MEFO) was established in 2008 by the National Center for Atmospheric Research to address many of the BEACHON research objectives, and it now provides a fixed field site with significant infrastructure. MEFO is a mountainous, semi-arid ponderosa pine-dominated forest site that is normally dominated by clean continental air, but is periodically influenced by anthropogenic sources from Colorado Front Range cities. This article summarizes the past and ongoing research activities at the site, and highlights some of the significant findings that have resulted from these measurements. These activities include: - soil property measurements, - hydrological studies, - measurements of high-frequency turbulence parameters, - eddy covariance flux measurements of water, energy, aerosols and carbon dioxide through the canopy, - biogenic and anthropogenic volatile organic compound emissions and their influence on regional atmospheric chemistry, - aerosol number and mass distributions, - chemical speciation of aerosol particles, - characterization of ice and cloud condensation nuclei, - trace gas measurements, and - model simulations using coupled chemistry and meteorology. In addition to various long-term continuous measurement, three focused measurement campaigns with state-of-the-art instrumentation have taken place since the site was established, and two of these are the subjects of this special issue: BEACHON-ROCS (Rocky Mountain Organic Carbon Study, 2010) and BEACHON-RoMBAS (Rocky Mountain Biogenic Aerosol Study, 2011).

  4. Overview of the Manitou Experimental Forest Observatory: site description and selected science results from 2008 to 2013

    NASA Astrophysics Data System (ADS)

    Ortega, J.; Turnipseed, A.; Guenther, A. B.; Karl, T. G.; Day, D. A.; Gochis, D.; Huffman, J. A.; Prenni, A. J.; Levin, E. J. T.; Kreidenweis, S. M.; DeMott, P. J.; Tobo, Y.; Patton, E. G.; Hodzic, A.; Cui, Y. Y.; Harley, P. C.; Hornbrook, R. S.; Apel, E. C.; Monson, R. K.; Eller, A. S. D.; Greenberg, J. P.; Barth, M. C.; Campuzano-Jost, P.; Palm, B. B.; Jimenez, J. L.; Aiken, A. C.; Dubey, M. K.; Geron, C.; Offenberg, J.; Ryan, M. G.; Fornwalt, P. J.; Pryor, S. C.; Keutsch, F. N.; DiGangi, J. P.; Chan, A. W. H.; Goldstein, A. H.; Wolfe, G. M.; Kim, S.; Kaser, L.; Schnitzhofer, R.; Hansel, A.; Cantrell, C. A.; Mauldin, R. L.; Smith, J. N.

    2014-06-01

    The Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics & Nitrogen (BEACHON) project seeks to understand the feedbacks and inter-relationships between hydrology, biogenic emissions, carbon assimilation, aerosol properties, clouds and associated feedbacks within water-limited ecosystems. The Manitou Experimental Forest Observatory (MEFO) was established in 2008 by the National Center for Atmospheric Research to address many of the BEACHON research objectives, and it now provides a fixed field site with significant infrastructure. MEFO is a mountainous, semi-arid ponderosa pine-dominated forest site that is normally dominated by clean continental air but is periodically influenced by anthropogenic sources from Colorado Front Range cities. This article summarizes the past and ongoing research activities at the site, and highlights some of the significant findings that have resulted from these measurements. These activities include - soil property measurements; - hydrological studies; - measurements of high-frequency turbulence parameters; - eddy covariance flux measurements of water, energy, aerosols and carbon dioxide through the canopy; - determination of biogenic and anthropogenic volatile organic compound emissions and their influence on regional atmospheric chemistry; - aerosol number and mass distributions; - chemical speciation of aerosol particles; - characterization of ice and cloud condensation nuclei; - trace gas measurements; and - model simulations using coupled chemistry and meteorology. In addition to various long-term continuous measurements, three focused measurement campaigns with state-of-the-art instrumentation have taken place since the site was established, and two of these studies are the subjects of this special issue: BEACHON-ROCS (Rocky Mountain Organic Carbon Study, 2010) and BEACHON-RoMBAS (Rocky Mountain Biogenic Aerosol Study, 2011).

  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, 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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.

  11. 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.

  12. Low Noise Results From IMS Site Surveys: A Preliminary New High-Frequency Low Noise Model

    NASA Astrophysics Data System (ADS)

    Ebeling, C.; Astiz, L.; Starovoit, Y.; Tavener, N.; Perez, G.; Given, H. K.; Barrientos, S.; Yamamoto, M.; Hfaiedh, M.; Stewart, R.; Estabrook, C.

    2002-12-01

    Since the establishment of the Provisional Technical Secretariat (PTS) of the Comprehensive Nuclear-Test-Ban Treaty (CTBT) Organization, a vigorous seismic site survey program has been carried out to identify locations as necessary for International Monitoring System (IMS) primary and auxiliary seismic stations listed in Annex 1 to the Protocol to the CTBT. The IMS Seismic Section maintains for this purpose a small pool of seismic equipment comprised of Guralp CMG-3T and CMG-3ESP and Streckeisen STS-2 broadband seismometers, and Reftek and Guralp acquisition systems. Seismic site surveys are carried out by conducting continuous measurements of ground motion at temporary installations for approximately five to seven days. Seismometer installation methods, which depend on instrument type and on local conditions, range from placement within small cement-floored subsurface vaults to near-surface burial. Data are sampled at 40 Hz. Seismic noise levels are evaluated through the analysis of power spectral density distributions. Eleven 10.5-minute-long representative de-trended and mean-removed segments each of daytime and night-time data are chosen randomly, but reviewed to avoid event contamination. Fast Fourier Transforms are calculated for the five windows in each of these segments generated using a 50% overlap for Hanning-tapered sections ~200 s long. Instrument responses are removed. To date, 20 site surveys for primary and auxiliary stations have been carried out by the IMS. The sites surveyed represent a variety of physical and geological environments on most continents. The lowest high frequency (>1.4 Hz) noise levels at five sites with igneous or metamorphic geologies were as much as 6 dB below the USGS New Low Noise Model (NLNM) developed by Peterson (1993). These sites were in Oman (local geology consisting of Ordovician metasediments), Egypt (Precambrian granite), Niger (early Proterozoic tonalite and granodiorite), Saudi Arabia (Precambian metasediments), and

  13. Plutonium recycle test reactor characterization activities and results

    SciTech Connect

    Cornwell, B.C.

    1997-05-01

    Report contains results of PRTR core and associated structures characterization performed in January and February of 1997. Radiation survey data are presented, along with recommendations for stabilization activities before transitioning to a decontamination and decommissioning function. Recommendations are also made about handling the waste generated by the stabilization activities, and actions suggested by the Decontamination and Decommissioning organization.

  14. Impulse propagation over a complex site: a comparison of experimental results and numerical predictions.

    PubMed

    Dragna, Didier; Blanc-Benon, Philippe; Poisson, Franck

    2014-03-01

    Results from outdoor acoustic measurements performed in a railway site near Reims in France in May 2010 are compared to those obtained from a finite-difference time-domain solver of the linearized Euler equations. During the experiments, the ground profile and the different ground surface impedances were determined. Meteorological measurements were also performed to deduce mean vertical profiles of wind and temperature. An alarm pistol was used as a source of impulse signals and three microphones were located along a propagation path. The various measured parameters are introduced as input data into the numerical solver. In the frequency domain, the numerical results are in good accordance with the measurements up to a frequency of 2 kHz. In the time domain, except a time shift, the predicted waveforms match the measured waveforms with a close agreement.

  15. Lidar research activities and observations at NARL site, Gadanki, India

    NASA Astrophysics Data System (ADS)

    Yellapragada, Bhavani Kumar

    2016-05-01

    The National Atmospheric Research Laboratory (NARL), a unit of Department of Space (DOS), located at Gadanki village (13.5°N, 79.2°E, 370 m AMSL) in India, is involved in the development of lidar remote sensing technologies for atmospheric research. Several advanced lidar technologies employing micropulse, polarization, Raman and scanning have been developed at this site and demonstrated for atmospheric studies during the period between 2008 and 2015. The technology of micropulse lidar, operates at 532 nm wavelength, was successfully transferred to an industry and the commercial version has been identified for Indian Lidar network (I-LINK) programme. Under this lidar network activity, several lidar units were installed at different locations in India to study tropospheric aerosols and clouds. The polarization sensitive lidar technology was realized using a set of mini photomultiplier tube (PMT) units and has the capability to operate during day and night without a pause. The lidar technology uses a compact flashlamp pumped Qswitched laser and employs biaxial configuration between the transmitter and receiver units. The lidar technology has been utilized for understanding the polarization characteristics of boundary layer aerosols during the mixed layer development. The demonstrated Raman lidar technology, uses the third harmonic wavelength of Nd:YAG laser, provides the altitude profiles of aerosol backscattering, extinction and water vapor covering the boundary layer range and allows operation during nocturnal periods. The Raman lidar derived height profiles of aerosol backscattering and extinction coefficient, lidar ratio, and watervapor mixing ratio inform the tropical boundary layer aerosol characteristics. The scanning lidar technology uses a near infrared laser wavelength for probing the lower atmosphere and has been utilized for high resolution cloud profiling during convective periods. The lidar technology is also used for rain rate measurement during

  16. Dynamically achieved active site precision in enzyme catalysis.

    PubMed

    Klinman, Judith P

    2015-02-17

    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.

  17. Research plan and preliminary results - A field research site for emerging contaminants in Iowa

    USGS Publications Warehouse

    Schnoebelen, Douglas J.; Kolpin, Dana W.; Barber, Larry B.; Furlong, Edward T.; Meyer, Michael; Skopec, M.

    2006-01-01

    Research has recently documented the prevalence of a wide variety of pharmaceuticals and other emerging contaminants (ECs) in streams across the United States. Wastewater treatment plants (WWTPs) have been found to be an important source and collection point of ECs to streams as many ECs are incompletely removed during treatment. To investigate the complex in-stream processes (e.g., dilution, sorption, degradation, dispersion, etc.) that can affect ECs following their input from a WWTP and determining if such input is having an effect on the aquatic ecosystem requires the integration of multi-disciplinary efforts at a carefully selected field site. Preliminary work has identified an 8-km reach of Fourmile Creek in central Iowa as an ideal research site to investigate such important research questions pertaining to ECs. Unique aspects of Fourmile Creek included: (1) it single source effluent-dominated stream, (2) background data document the input of a wide variety of ECs from WWTP discharge, (3) small basin size, (4) relatively simple flow system, (5) background data suggest that undefined processes are taking place decreasing the level of select ECs during stream transport, (6) the WWTP uses a treatment technology (activated sludge) typical of many towns in Iowa and the United States (7) a hydrogeologic setting of a low-gradient, small stream (average discharge less than 1.41 m³/s) in glacial drift is typical of many areas in Iowa and across the Midwest, and (8) the existence of a low-head clam approximately 2 km upstream of the WWTP outfall allowing more accurate "above WWTP" and "below WWTP" comparisons in aquatic ecosystems. Furthermore, the WWTP is scheduled to close by 2011 providing a unique opportunity to determine how stream hydrology, water chemistry and aquatic biota react to the removal of the primary source of flow and ECs in this system. This will allow a novel "before" and "after" assessment not previously available in EC research. Research to date

  18. Roles of s3 site residues of nattokinase on its activity and substrate specificity.

    PubMed

    Wu, Shuming; Feng, Chi; Zhong, Jin; Huan, Liandong

    2007-09-01

    Nattokinase (Subtilisin NAT, NK) is a bacterial serine protease with high fibrinolytic activity. To probe their roles on protease activity and substrate specificity, three residues of S3 site (Gly(100), Ser(101) and Leu(126)) were mutated by site-directed mutagenesis. Kinetics parameters of 20 mutants were measured using tetrapeptides as substrates, and their fibrinolytic activities were determined by fibrin plate method. Results of mutation analysis showed that Gly(100) and Ser(101) had reverse steric and electrostatic effects. Residues with bulky or positively charged side chains at position 100 decreased the substrate binding and catalytic activity drastically, while residues with the same characters at position 101 could obviously enhance protease and fibrinolytic activity of NK. Mutation of Leu(126) might impair the structure of the active cleft and drastically decreased the activity of NK. Kinetics studies of the mutants showed that S3 residues were crucial to keep protease activity while they moderately affected substrate specificity of NK. The present study provided some original insight into the P3-S3 interaction in NK and other subtilisins, as well as showed successful protein engineering cases to improve NK as a potential therapeutic agent.

  19. Active-site zinc ligands and activated H2O of zinc enzymes.

    PubMed Central

    Vallee, B L; Auld, D S

    1990-01-01

    The x-ray crystallographic structures of 12 zinc enzymes have been chosen as standards of reference to identify the ligands to the catalytic and structural zinc atoms of other members of their respective enzyme families. Universally, H2O is a ligand and critical component of the catalytically active zinc sites. In addition, three protein side chains bind to the catalytic zinc atom, whereas four protein ligands bind to the structural zinc atom. The geometry and coordination number of zinc can vary greatly to accommodate particular ligands. Zinc forms complexes with nitrogen and oxygen just as readily as with sulfur, and this is reflected in catalytic zinc sites having a binding frequency of His much greater than Glu greater than Asp = Cys, three of which bind to the metal atom. The systematic spacing between the ligands is striking. For all catalytic zinc sites except the coenzyme-dependent alcohol dehydrogenase, the first two ligands are separated by a "short-spacer" consisting of 1 to 3 amino acids. These ligands are separated from the third ligand by a "long spacer" of approximately 20 to approximately 120 amino acids. The spacer enables formation of a primary bidentate zinc complex, whereas the long spacer contributes flexibility to the coordination sphere, which can poise the zinc for catalysis as well as bring other catalytic and substrate binding groups into apposition with the active site. The H2O is activated by ionization, polarization, or poised for displacement. Collectively, the data imply that the preferred mechanistic pathway for activating the water--e.g., zinc hydroxide or Lewis acid catalysis--will be determined by the identity of the other three ligands and their spacing. Images PMID:2104979

  20. Results of thermal desorption treatability studies on soils from wood treatment sites

    SciTech Connect

    Shealy, S.E.; Lin, W.C.; Richards, M.K.; Culp, J.

    1997-12-31

    Thermal desorption is one of the most effective technologies for treatment of soils or wastes containing organic contaminants. This includes the polycyclic aromatic hydrocarbons, pentachlorophenol and dioxins/furans that are the typical contaminants of concern at wood treatment sites. This paper summarizes the results of bench-scale thermal desorption treatability studies on soils from two wood treatment sites. The testing identified the time-temperature combination needed for contaminant removal and provided data on the composition of the treatment residuals from the thermal treatment process. This study included testing in static trays and in a small bench-scale rotary kiln. The static tray tests are a bench-scale method of readily evaluating the effect of various target temperatures and residence times on contaminant removal. These tests use 40--50 grams, of soil, which is aliquoted into a tray and placed into a muffle furnace at a pre-determined time and temperature. These tests are used to identify effective treatment conditions. The Rotary Thermal Apparatus (RTA) is also a bench-scale device that is used to treat 1 to 1.5 kilograms of soil in an indirectly heated rotary tube. This device simulates the heat and mass transfer in rotary kiln. The RTA is a batch device and can be purged with nitrogen, oxygen or other gases to simulate the atmosphere of various thermal treatment processes.

  1. Structural role of the active-site metal in the conformation of Trypanosoma brucei phosphoglycerate mutase.

    PubMed

    Mercaldi, Gustavo F; Pereira, Humberto M; Cordeiro, Artur T; Michels, Paul A M; Thiemann, Otavio H

    2012-06-01

    Phosphoglycerate mutases (PGAMs) participate in both the glycolytic and the gluconeogenic pathways in reversible isomerization of 3-phosphoglycerate and 2-phosphoglycerate. PGAMs are members of two distinct protein families: enzymes that are dependent on or independent of the 2,3-bisphosphoglycerate cofactor. We determined the X-ray structure of the monomeric Trypanosoma brucei independent PGAM (TbiPGAM) in its apoenzyme form, and confirmed this observation by small angle X-ray scattering data. Comparing the TbiPGAM structure with the Leishmania mexicana independent PGAM structure, previously reported with a phosphoglycerate molecule bound to the active site, revealed the domain movement resulting from active site occupation. The structure reported here shows the interaction between Asp319 and the metal bound to the active site, and its contribution to the domain movement. Substitution of the metal-binding residue Asp319 by Ala resulted in complete loss of independent PGAM activity, and showed for the first time its involvement in the enzyme's function. As TbiPGAM is an attractive molecular target for drug development, the apoenzyme conformation described here provides opportunities for its use in structure-based drug design approaches. Database Structural data for the Trypanosoma brucei 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGAM) has been deposited with the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank under code 3NVL.

  2. Substrate conformational transitions in the active site of chorismate mutase: their role in the catalytic mechanism.

    PubMed

    Guo, H; Cui, Q; Lipscomb, W N; Karplus, M

    2001-07-31

    Chorismate mutase acts at the first branch-point of aromatic amino acid biosynthesis and catalyzes the conversion of chorismate to prephenate. The results of molecular dynamics simulations of the substrate in solution and in the active site of chorismate mutase are reported. Two nonreactive conformers of chorismate are found to be more stable than the reactive pseudodiaxial chair conformer in solution. It is shown by QM/MM molecular dynamics simulations, which take into account the motions of the enzyme, that when these inactive conformers are bound to the active site, they are rapidly converted to the reactive chair conformer. This result suggests that one contribution of the enzyme is to bind the more prevalent nonreactive conformers and transform them into the active form in a step before the chemical reaction. The motion of the reactive chair conformer in the active site calculated by using the QM/MM potential generates transient structures that are closer to the transition state than is the stable CHAIR conformer.

  3. The Ribotoxin Restrictocin Recognizes Its RNA Substrate by Selective Engagement of Active Site Residues

    PubMed Central

    2011-01-01

    Restrictocin and related fungal endoribonucleases from the α-sarcin family site-specifically cleave the sarcin/ricin loop (SRL) on the ribosome to inhibit translation and ultimately trigger cell death. Previous studies showed that the SRL folds into a bulged-G motif and tetraloop, with restrictocin achieving a specificity of ∼1000-fold by recognizing both motifs only after the initial binding step. Here, we identify contacts within the protein−RNA interface and determine the extent to which each one contributes to enzyme specificity by examining the effect of protein mutations on the cleavage of the SRL substrate compared to a variety of other RNA substrates. As with other biomolecular interfaces, only a subset of contacts contributes to specificity. One contact of this subset is critical, with the H49A mutation resulting in quantitative loss of specificity. Maximum catalytic activity occurs when both motifs of the SRL are present, with the major contribution involving the bulged-G motif recognized by three lysine residues located adjacent to the active site: K110, K111, and K113. Our findings support a kinetic proofreading mechanism in which the active site residues H49 and, to a lesser extent, Y47 make greater catalytic contributions to SRL cleavage than to suboptimal substrates. This systematic and quantitative analysis begins to elucidate the principles governing RNA recognition by a site-specific endonuclease and may thus serve as a mechanistic model for investigating other RNA modifying enzymes. PMID:21417210

  4. Computational approaches to find the active binding sites of biological targets against busulfan.

    PubMed

    Karthick, T; Tandon, Poonam

    2016-06-01

    Determination of electrophilic and nucleophilic sites of a molecule is the primary task to find the active sites of the lead molecule. In the present study, the active sites of busulfan have been predicted by molecular electrostatic potential surface and Fukui function analysis with the help of dispersion corrected density functional theory. Similarly, the identification of active binding sites of the proteins against lead compound plays a vital role in the field of drug discovery. Rigid and flexible molecular docking approaches are used for this purpose. For rigid docking, Hex 8.0.0 software employing fast Fourier transform (FFT) algorithm has been used. The partial flexible blind docking simulations have been performed with AutoDock 4.2 software; where a Lamarckian genetic algorithm is employed. The results showed that the most electrophilic atoms of busulfan bind with the targets. It is clear from the docking studies that busulfan has inhibition capability toward the targets 12CA and 1BZM. Graphical Abstract Docking of ligand and protein.

  5. Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation

    PubMed Central

    Lee, Tai-Sung; Giambaşu, George M.; Sosa, Carlos P.; Martick, Monika; Scott, William G.; York, Darrin M.

    2009-01-01

    The relationship between formation of active in-line attack conformations and monovalent (Na+) and divalent (Mg2+) metal ion binding in the hammerhead ribozyme has been explored with molecular dynamics simulations. To stabilize repulsions between negatively charged groups, different requirements of threshold occupancy of metal ions were observed in the reactant and activated precursor states both in the presence or absence of a Mg2+ in the active site. Specific bridging coordination patterns of the ions are correlated with the formation of active in-line attack conformations and can be accommodated in both cases. Furthermore, simulation results suggest that the hammerhead ribozyme folds to form an electronegative recruiting pocket that attracts high local concentrations of positive charge. The present simulations help to reconcile experiments that probe the metal ion sensitivity of hammerhead ribozyme catalysis and support the supposition that Mg2+, in addition to stabilizing active conformations, plays a specific chemical role in catalysis. PMID:19265710

  6. Public participation in energy facility siting. Part 1; Case study results

    SciTech Connect

    Whitlatch, E.E. . Dept. of Civil Engineering); Aldrich, J.A. ); Cristo, M. )

    1990-08-01

    The objective of this paper is to determine to what extent public participation has been effective in influencing recent energy-facility siting (EFS) decisions for nuclear and coal-fired power plants in the Ohio River Basin. Licensing requirements, review procedures, and criteria were studied for six basin states, along with utility-siting criteria and siting methodologies. Six case study power plants (four coal-fired and two nuclear) were investigated in detail. It is concluded that the current regulatory/adjudicatory EFS process is not conducive to meaningful public participation for a wide range of reasons, which include: lack of public involvement during the crucial early site screening stage; lack of public information during the long draft environmental impact statement (DEIS) stage; the negative effect on public trust caused by site purchase and limited site work before issuance of the DEIS; and siting methodologies that heavily emphasize technological criteria.

  7. Lethal Factor Active-Site Mutations Affect Catalytic Activity In Vitro

    PubMed Central

    Hammond, S. E.; Hanna, P. C.

    1998-01-01

    The lethal factor (LF) protein of Bacillus anthracis lethal toxin contains the thermolysin-like active-site and zinc-binding consensus motif HEXXH (K. R. Klimpel, N. Arora, and S. H. Leppla, Mol. Microbiol. 13:1093–1100, 1994). LF is hypothesized to act as a Zn2+ metalloprotease in the cytoplasm of macrophages, but no proteolytic activities have been previously shown on any target substrate. Here, synthetic peptides are hydrolyzed by LF in vitro. Mass spectroscopy and peptide sequencing of isolated cleavage products separated by reverse-phase high-pressure liquid chromatography indicate that LF seems to prefer proline-containing substrates. Substitution mutations within the consensus active-site residues completely abolish all in vitro catalytic functions, as does addition of 1,10-phenanthroline, EDTA, and certain amino acid hydroxamates, including the novel zinc metalloprotease inhibitor ZINCOV. In contrast, the protease inhibitors bestatin and lysine CMK, previously shown to block LF activity on macrophages, did not block LF activity in vitro. These data provide the first direct evidence that LF may act as an endopeptidase. PMID:9573135

  8. Interaction of aspartic acid-104 and proline-287 with the active site of m-calpain.

    PubMed Central

    Arthur, J S; Elce, J S

    1996-01-01

    In an ongoing study of the mechanisms of calpain catalysis and Ca(2+)-induced activation, the effects of Asp-104-->Ser and Pro-287-->Ser large subunit mutations on m-calpain activity, the pH-activity profile, Ca(2+)-sensitivity, and autolysis were measured. The importance of these positions was suggested by sequence comparisons between the calpain and papain families of cysteine proteinases. Asp-104 is adjacent to the active-site Cys-105, and Pro-287 is adjacent to the active-site Asn-286 and probably to the active-site His-262; both Asp-104 and Pro-287 are absolutely conserved in the known calpains, but are replaced by highly conserved serine residues in the papains. The single mutants had approx. 10-15% of wild-type activity, due mainly to a decrease in kcat, since Km was only slightly increased. The Pro-287-->Ser mutation appeared to cause a local perturbation of the catalytic Cys-105/His-262 catalytic ion pair, reducing its efficiency without major effect on the conformation and stability of the enzyme. The Asp-104-->Ser mutation caused a marked narrowing of the pH-activity curve, a 9-fold increase in Ca2+ requirement, and an acceleration of autolysis, when compared with the wild-type enzyme. The results indicated that Asp-104 alters the nature of its interaction with the catalytic ion pair during Ca(2+)-induced conformational change in calpain. This interaction may be direct or indirect, but is important in activation of the enzyme. PMID:8912692

  9. The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity.

    PubMed

    Xiang, Kehui; Manley, James L; Tong, Liang

    2012-07-10

    The activity of RNA polymerase II (Pol II) is controlled in part by the phosphorylation state of the C-terminal domain (CTD) of its largest subunit. Recent reports have suggested that yeast regulator of transcription protein, Rtr1, and its human homologue RPAP2, possess Pol II CTD Ser5 phosphatase activity. Here we report the crystal structure of Kluyveromyces lactis Rtr1, which reveals a new type of zinc finger protein and does not have any close structural homologues. Importantly, the structure does not show evidence of an active site, and extensive experiments to demonstrate its CTD phosphatase activity have been unsuccessful, suggesting that Rtr1 has a non-catalytic role in CTD dephosphorylation.

  10. Site-directed mutagenesis of an alkaline phytase: influencing specificity, activity and stability in acidic milieu.

    PubMed

    Tran, Thuy T; Mamo, Gashaw; Búxo, Laura; Le, Nhi N; Gaber, Yasser; Mattiasson, Bo; Hatti-Kaul, Rajni

    2011-07-10

    Site-directed mutagenesis of a thermostable alkaline phytase from Bacillus sp. MD2 was performed with an aim to increase its specific activity and activity and stability in an acidic environment. The mutation sites are distributed on the catalytic surface of the enzyme (P257R, E180N, E229V and S283R) and in the active site (K77R, K179R and E227S). Selection of the residues was based on the idea that acid active phytases are more positively charged around their catalytic surfaces. Thus, a decrease in the content of negatively charged residues or an increase in the positive charges in the catalytic region of an alkaline phytase was assumed to influence the enzyme activity and stability at low pH. Moreover, widening of the substrate-binding pocket is expected to improve the hydrolysis of substrates that are not efficiently hydrolysed by wild type alkaline phytase. Analysis of the phytase variants revealed that E229V and S283R mutants increased the specific activity by about 19% and 13%, respectively. Mutation of the active site residues K77R and K179R led to severe reduction in the specific activity of the enzyme. Analysis of the phytase mutant-phytate complexes revealed increase in hydrogen bonding between the enzyme and the substrate, which might retard the release of the product, resulting in decreased activity. On the other hand, the double mutant (K77R-K179R) phytase showed higher stability at low pH (pH 2.6-3.0). The E227S variant was optimally active at pH 5.5 (in contrast to the wild type enzyme that had an optimum pH of 6) and it exhibited higher stability in acidic condition. This mutant phytase, displayed over 80% of its initial activity after 3h incubation at pH 2.6 while the wild type phytase retained only about 40% of its original activity. Moreover, the relative activity of this mutant phytase on calcium phytate, sodium pyrophosphate and p-nitro phenyl phosphate was higher than that of the wild type phytase.

  11. Preliminary results of a seismic borehole test using downhole shaped charges at the DOE Hanford Site

    SciTech Connect

    Narbutovskih, S.M.; Michelsen, F.

    1994-02-01

    Geophysical site characterization studies can be important steps in the process of designing and monitoring remediation at hazardous waste storage facilities. Use of seismic techniques for subsurface characterization at the DOE Hanford Site has been limited. One reason is the lack of borehole velocity control, and low-velocity sediments are highly attenuative. Consequently, standard techniques to provide velocity control are not adequate. Both Vertical Seismic Profiling and reversed VSP surveys are currently being investigated to provide velocity control and for subsurface imaging capabilities. Recently a jet perforating gun was used to perforate a doubled-cased borehole in the 200 West Area. Acoustic emissions were recorded from numerous depths to obtain velocity control for a previous surface survey conducted in the same area. Both P- and S-wave data were recorded simultaneously from multiple horizons using the DAS-1 seismograph and 3-component geophones. The data were analyzed for a variety of uses besides velocity control. Signal attenuation was studied as a function of source depth and offset distance to evaluate formation absorption while vertical resolution was determined from the frequency spectrum. Preliminary results indicate that adequate P-wave velocity control can be obtained even though the near-surface sediments are very attenuative. However, we conclude that the perforating gun produces little SH energy. Preliminary velocities indicate that reflection coefficients should be great enough to use surface techniques. Results from the frequency study suggest that a swept source for both surface and borehole surveys may be necessary to obtain required resolutions. Finally, signal attenuation as a function of formation facies suggest that seismic techniques may be useful in mapping perched water zones and for long term vadose zone monitoring.

  12. Identification of active site residues of Fenugreek β-amylase: chemical modification and in silico approach.

    PubMed

    Srivastava, Garima; Singh, Vinay K; Kayastha, Arvind M

    2014-10-01

    The amino acid sequence of Fenugreek β-amylase is not available in protein data bank. Therefore, an attempt has been made to identify the catalytic amino acid residues of enzyme by employing studies of pH dependence of enzyme catalysis, chemical modification and bioinformatics. Treatment of purified Fenugreek β-amylase with EDAC in presence of glycine methyl ester and sulfhydryl group specific reagents (IAA, NEM and p-CMB), followed a pseudo first-order kinetics and resulted in effective inactivation of enzyme. The reaction with EDAC in presence of NTEE (3-nitro-l-tyrosine ethylester) resulted into modification of two carboxyl groups per molecule of enzyme and presence of one accessible sulfhydryl group at the active site, per molecule of enzyme was ascertained by titration with DTNB. The above results were supported by the prevention of inactivation of enzyme in presence of substrate. Based on MALDI-TOF analysis of purified Fenugreek β-amylase and MASCOT search, β-amylase of Medicago sativa was found to be the best match. To further confirm the amino acid involved in catalysis, homology modelling of β-amylase of M. sativa was performed. The sequence alignment, superimposition of template and target models, along with study of interactions involved in docking of sucrose and maltose at the active site, led to identification of Glu187, Glu381 and Cys344 as active site residues.

  13. Probing Oxygen Activation Sites in Two Flavoprotein Oxidases Using Chloride as an Oxygen Surrogate

    SciTech Connect

    Kommoju, Phaneeswara-Rao; Chen, Zhi-wei; Bruckner, Robert C.; Mathews, F. Scott; Jorns, Marilyn Schuman

    2011-08-16

    A single basic residue above the si-face of the flavin ring is the site of oxygen activation in glucose oxidase (GOX) (His516) and monomeric sarcosine oxidase (MSOX) (Lys265). Crystal structures of both flavoenzymes exhibit a small pocket at the oxygen activation site that might provide a preorganized binding site for superoxide anion, an obligatory intermediate in the two-electron reduction of oxygen. Chloride binds at these polar oxygen activation sites, as judged by solution and structural studies. First, chloride forms spectrally detectable complexes with GOX and MSOX. The protonated form of His516 is required for tight binding of chloride to oxidized GOX and for rapid reaction of reduced GOX with oxygen. Formation of a binary MSOX-chloride complex requires Lys265 and is not observed with Lys265Met. Binding of chloride to MSOX does not affect the binding of a sarcosine analogue (MTA, methylthioactetate) above the re-face of the flavin ring. Definitive evidence is provided by crystal structures determined for a binary MSOX-chloride complex and a ternary MSOX-chloride-MTA complex. Chloride binds in the small pocket at a position otherwise occupied by a water molecule and forms hydrogen bonds to four ligands that are arranged in approximate tetrahedral geometry: Lys265:NZ, Arg49:NH1, and two water molecules, one of which is hydrogen bonded to FAD:N5. The results show that chloride (i) acts as an oxygen surrogate, (ii) is an effective probe of polar oxygen activation sites, and (iii) provides a valuable complementary tool to the xenon gas method that is used to map nonpolar oxygen-binding cavities.

  14. Different cleavage sites are aligned differently in the active site of M1 RNA, the catalytic subunit of Escherichia coli RNase P.

    PubMed Central

    Kufel, J; Kirsebom, L A

    1996-01-01

    We have studied RNase P RNA (M1 RNA) cleavage of model tRNA precursors that are cleaved at two independent positions. Here we present data demonstrating that cleavage at both sites depends on the 2'-OH immediately 5' of the respective cleavage site. However, we show that the 2-amino group of a guanosine at the cleavage site plays a significant role in cleavage at one of these sites but not at the other. These data suggest that these two cleavage sites are handled differently by the ribozyme. This theory is supported by our finding that the cross-linking pattern between Ml RNA and tRNA precursors carrying 4-thioU showed distinct differences, depending on the location of the 4-thioU relative to the respective cleavage site. These findings lead us to suggest that different cleavage sites are aligned differently in the active site, possibly as a result of different binding modes of a substrate to M1 RNA. We discuss a model in which the interaction between the 3'-terminal "RCCA" motif (first three residues interact) of a tRNA precursor and M1 RNA plays a significant role in this process. Images Fig. 2 Fig. 3 Fig. 4 PMID:8650223

  15. Non-specific binding sites help to explain mixed inhibition in mushroom tyrosinase activities.

    PubMed

    Hassani, Sorour; Haghbeen, Kamahldin; Fazli, Mostafa

    2016-10-21

    Inhibition and activation studies of tyrosinase could prove beneficial to agricultural, food, cosmetic, and pharmaceutical industries. Although non-competitive and mixed-inhibition are frequent modes observed in kinetics studies on mushroom tyrosinase (MT) activities, the phenomena are left unexplained. In this study, dual effects of phthalic acid (PA) and cinnamic acid (CA) on MT during mono-phenolase activity were demonstrated. PA activated and inhibited MT at concentrations lower and higher than 150 μM, respectively. In contrast, CA inhibited and activated MT at concentrations lower and higher than 5 μM. The mode of inhibition for both effectors was mixed-type. Complex kinetics of MT in the presence of a modulator could partly be ascribed to its mixed-cooperativity. However, to explain mixed-inhibition mode, it is necessary to demonstrate how the ternary complex of substrate/enzyme/effector is formed. Therefore, we looked for possible non-specific binding sites using MT tropolone-bound PDB (2Y9X) in the computational studies. When tropolone was in MTPa (active site), PA and CA occupied different pockets (named MTPb and MTPc, respectively). The close Moldock scores of PA binding posed in MTPb and MTPa suggested that MTPb could be a secondary binding site for PA. Similar results were obtained for CA. Ensuing results from 10 ns molecular dynamics simulations for 2Y9X-effector complexes indicated that the structures were gradually stabilized during simulation. Tunnel analysis by using CAVER Analyst and CHEXVIS resulted in identifying two distinct channels that assumingly participate in exchanging the effectors when the direct channel to MTPa is not accessible.

  16. Results of geothermal gradient core hole TCB-1, Tecuamburro volcano geothermal site, Guatemala, Central America

    SciTech Connect

    Adams, A.I.; Chipera, S.; Counce, D.; Gardner, J.; Goff, S.; Goff, F.; Heiken, G.; Laughlin, A.W.; Musgrave, J.; Trujillo, P.E. Jr. ); Aycinena, S.; Martinelli, L. ); Castaneda, O.; Revolorio, M.; Roldan, A. . Inst. Nacional de Electrificacion); D

    1992-02-01

    Results of geological, volcanological, hydrogeochemical, and geophysical field studies conducted in 1988 and 1989 at the Tecuamburro volcano geothermal site in Guatemala indicated that there is a substantial shallow heat source beneath the area of youngest volcanism. To obtain information on subsurface temperatures and temperature gradients, stratigraphy, hydrothermal alteration, fracturing, and possible inflows of hydrothermal fluids, a geothermal gradient core hole (TCB-1) was drilled to 808 m low on the northern flank of the Tecuamburro volcano Complex, 300 km south of a 300-m-diameter phreatic crater, Laguna Ixpaco, dated at 2,910 years. Gases from acid-sulfate springs near Laguna Ixpaco consistently yield maximum estimated subsurface temperatures of 250--300{degrees}C. The temperature versus depth curve from TCB-1 does not show isothermal conditions and the calculated thermal gradients from 500--800 m is 230{degrees}C/km. Bottom hole temperature is 238{degrees}C. Calculated heat flow values are nearly 9 heat flow units (HFU). The integration of results from the TCB-1 gradient core hole with results from field studies provides strong evidence that the Tecuamburro area holds great promise for containing a commercial geothermal resource.

  17. Evaluating the results of a site-specific PSHA from the perspective of a risk analyst

    NASA Astrophysics Data System (ADS)

    Klügel, Jens-Uwe

    2016-04-01

    From 1998 till 2015 Swiss Nuclear Power Plants sponsored a set of comprehensive site-specific PSHA-studies (PEGASOS, PEGASOS Refinement Project) to obtain the requested input for their plant specific probabilistic risk assessments following the US SSHAC procedures at their most elaborated level 4. The studies were performed by well-known earth scientists working completely independent from sponsors under participatory review of the Swiss Nuclear Safety Inspectorate. Risk analysts of Swiss Nuclear Power Plants recently have been mandated to implement the final results of the studies in their risk assessment studies. This triggered an in depth assessment of the results focussed on their practical applicability for risk studies. This assessment resulted in some important insights that are of interest for future PSHA studies performed for new nuclear power plants. The assessment included a review of the completeness of results with respect to risk applications as well as plausibility checks of hazard results based on Black Swan Theory and known historical events. The key lessons and recommendations for more detailed project output specifications for future projects are presented in the paper. It was established that future PSHA projects shall provide the joint probability distribution of ground motion hazard and the associated strong motion duration as the output to allow for a technically meaningful risk assessment. The recommendation of WENRA (West European Nuclear Regulators) published in their reference levels to perform natural hazard assessment preferably based on physical grounds (deterministic method) is also rationalized by recommending an holistic approach to hazard analysis comparing PSHA insights with the results of modelling deterministic Seismic Hazard Analysis.

  18. Structural evolution of luciferase activity in Zophobas mealworm AMP/CoA-ligase (protoluciferase) through site-directed mutagenesis of the luciferin binding site.

    PubMed

    Prado, R A; Barbosa, J A; Ohmiya, Y; Viviani, V R

    2011-07-01

    The structural origin and evolution of bioluminescent activity of beetle luciferases from AMP/CoA ligases remains a mystery. Previously we cloned the luciferase-like enzyme from Zophobas morio mealworm, a reasonable protoluciferase model that could shine light on this mystery. Kinetic characterization and studies with D- and L-luciferin and their adenylates showed that stereoselectivity constitutes a critical feature for the origin of luciferase activity in AMP/CoA ligases. Comparison of the primary structures and modeling studies of this protoluciferase and the three main families of beetle luciferases showed that the carboxylic acid substrate binding site of this enzyme is smaller and more hydrophobic than the luciferin binding site of beetle luciferases, showing several substitutions of otherwise conserved residues. Thus, here we performed a site-directed mutagenesis survey of the carboxylic binding site motifs of the protoluciferase by replacing their residues by the respective conserved ones found in beetle luciferases in order to identify the structural determinants of luciferase/oxygenase activity. Although most of the substitutions had negative impact on the luminescence activity of the protoluciferase, only the substitution I327T improved the luminescence activity, resulting in a broad and 15 nm blue-shifted luminescence spectrum. Such substitution indicates the importance of the loop motif 322YGMSEI327 (341YGLTETT347 in Photinus pyralis luciferase) for luciferase activity, and indicates a possible route for the evolution of bioluminescence function of beetle luciferases.

  19. Synthesis of supported bimetallic nanoparticles with controlled size and composition distributions for active site elucidation

    SciTech Connect

    Hakim, Sikander H.; Sener, Canan; Alba Rubio, Ana C.; Gostanian, Thomas M.; O'neill, Brandon J; Ribeiro, Fabio H.; Miller, Jeffrey T.; Dumesic, James A

    2015-08-01

    Elucidation of active sites in supported bimetallic catalysts is complicated by the high level of dispersity in the nanoparticle size and composition that is inherent in conventional methods of catalyst preparation. We present a synthesis strategy that leads to highly dispersed, bimetallic nanoparticles with uniform particle size and composition by means of controlled surface reactions. We demonstrate the synthesis of three systems, RhMo, PtMo, and RhRe, consisting of a highly reducible metal with an oxophilic promoter. These catalysts are characterized by FTIR, CO chemisorption, STEM/EDS, TPR, and XAS analysis. The catalytic properties of these bimetallic nanoparticles were probed for the selective CO hydrogenolysis of (hydroxymethyl)tetrahydropyran to produce 1,6 hexanediol. Based on the characterization results and reactivity trends, the active sites in the hydrogenolysis reaction are identified to be small ensembles of the more noble metal (Rh, Pt) adjacent to highly reduced moieties of the more oxophilic metal (Mo, Re).

  20. Dynamics and Mechanism of Efficient DNA Repair Reviewed by Active-Site Mutants

    NASA Astrophysics Data System (ADS)

    Tan, Chuang; Liu, Zheyun; Li, Jiang; Guo, Xunmin; Wang, Lijuan; Zhong, Dongping

    2010-06-01

    Photolyases repair the UV-induced pyrimidine dimers in damage DNA via a photoreaction which includes a series of light-driven electron transfers between the two-electron-reduced flavin cofactor FADH^- and the dimer. We report here our systematic studies of the repair dynamics in E. coli photolyase with mutation of several active-site residues. With femtosecond resolution, we observed the significant change in the forward electron transfer from the excited FADH^- to the dimer and the back electron transfer from the repaired thymines by mutation of E274A, R226A, R342A, N378S and N378C. We also found that the mutation of E274A accelerates the bond-breaking of the thymine dimer. The dynamics changes are consistent with the quantum yield study of these mutants. These results suggest that the active-site residues play a significant role, structurally and chemically, in the DNA repair photocycle.

  1. Hazard Ranking System evaluation of CERCLA (Comprehensive Environmental Response, Compensation, and Liability Act) inactive waste sites at Hanford: Volume 1, Evaluation methods and results

    SciTech Connect

    Stenner, R.D.; Cramer, K.H.; Higley, K.A.; Jette, S.J.; Lamar, D.A.; McLaughlin, T.J.; Sherwood, D.R.; Van Houten, N.C.

    1988-10-01

    The purpose of this report is to formally document the individual site Hazard Ranking System (HRS) evaluations conducted as part of the preliminary assessment/site inspection (PA/SI) activities at the US Department of Energy (DOE) Hanford Site. These activities were carried out pursuant to the DOE orders that describe the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) Program addressing the cleanup of inactive waste sites. These orders incorporate the US Environmental Protection Agency methodology, which is based on the Superfund Amendments and Reauthorization Act of 1986 (SARA). The methodology includes six parts: PA/SI, remedial investigation/feasibility study, record of decision, design and implementation of remedial action, operation and monitoring, and verification monitoring. Volume 1 of this report discusses the CERCLA inactive waste-site evaluation process, assumptions, and results of the HRS methodology employed. Volume 2 presents the data on the individual CERCLA engineered-facility sites at Hanford, as contained in the Hanford Inactive Site Surveillance (HISS) Data Base. Volume 3 presents the data on the individual CERCLA unplanned-release sites at Hanford, as contained in the HISS Data Base. 34 refs., 43 figs., 47 tabs.

  2. TOSPAC calculations in support of the COVE 2A benchmarking activity; Yucca Mountain Site Characterization Project

    SciTech Connect

    Gauthier, J.H.; Zieman, N.B.; Miller, W.B.

    1991-10-01

    The purpose of the the Code Verification (COVE) 2A benchmarking activity is to assess the numerical accuracy of several computer programs for the Yucca Mountain Site Characterization Project of the Department of Energy. This paper presents a brief description of the computer program TOSPAC and a discussion of the calculational effort and results generated by TOSPAC for the COVE 2A problem set. The calculations were performed twice. The initial calculations provided preliminary results for comparison with the results from other COVE 2A participants. TOSPAC was modified in response to the comparison and the final calculations included a correction and several enhancements to improve efficiency. 8 refs.

  3. The New Bedford Harbor Superfund Site Long Term Monitoring Program: Results from 1993 to 2014

    EPA Science Inventory

    Background. New Bedford Harbor (NBH), located in southeastern Massachusetts, was designated as a marine Superfund site in 1983 due to sediment contamination by polychlorinated biphenyls (PCBs). Based on risks to human health and the environment, the first two phases of the site ...

  4. The Costs of Pursuing Accreditation for Methadone Treatment Sites: Results from a National Study

    ERIC Educational Resources Information Center

    Zarkin, Gary A.; Dunlap, Laura J.; Homsi, Ghada

    2006-01-01

    The use of accreditation has been widespread among medical care providers, but accreditation is relatively new to the drug abuse treatment field. This study presents estimates of the costs of pursuing accreditation for methadone treatment sites. Data are from 102 methadone treatment sites that underwent accreditation as part of the Center for…

  5. Interaction of mining activities and aquatic environment: A review from Greek mine sites.

    NASA Astrophysics Data System (ADS)

    Vasileiou, Eleni; Kallioras, Andreas

    2016-04-01

    In Greece a significant amount of mineral and ore deposits have been recorded accompanied by large industrial interest and a long mining history. Today many active and/or abandoned mine sites are scattered within the country; while mining activities take place in different sites for exploiting various deposits (clay, limestone, slate, gypsum, kaolin, mixed sulphide ores (lead, zinc, olivine, pozzolan, quartz lignite, nickel, magnesite, aluminum, bauxite, gold, marbles etc). The most prominent recent ones are: (i) the lignite exploitation that is extended in the area of Ptolemais (Western Macedonia) and Megalopolis (Central Peloponnese); and (ii) the major bauxite deposits located in central Greece within the Parnassos-Ghiona geotectonic zone and on Euboea Island. In the latter area, significant ores of magnesite were exploited and mixed sulphide ores. Centuries of intensive mining exploitation and metallurgical treatment of lead-silver deposits in Greece, have also resulted in significant abandoned sites, such as the one in Lavrion. Mining activities in Lavrio, were initiated in ancient times and continued until the 1980s, resulting in the production of significant waste stockpiles deposited in the area, crucial for the local water resources. Ιn many mining sites, environmental pressures are also recorded after the mine closure to the aquatic environment, as the surface waters flow through waste dump areas and contaminated soils. This paper aims to the geospatial visualization of the mining activities in Greece, in connection to their negative (surface- and/or ground-water pollution; overpumping due to extensive dewatering practices) or positive (enhanced groundwater recharge; pit lakes, improvement of water budget in the catchment scale) impacts on local water resources.

  6. Incomplete suppression of distractor-related activity in the frontal eye field results in curved saccades.

    PubMed

    McPeek, Robert M

    2006-11-01

    Saccades in the presence of distractors show significant trajectory curvature. Based on previous work in the superior colliculus (SC), we speculated that curvature arises when a movement is initiated before competition between the target and distractor goals has been fully resolved. To test this hypothesis, we recorded frontal eye field (FEF) activity for curved and straight saccades in search. In contrast to the SC, activity in FEF is normally poorly correlated with saccade dynamics. However, the FEF, like the SC, is involved in target selection. Thus if curvature is caused by incomplete target selection, we expect to see its neural correlates in the FEF. We found that saccades that curve toward a distractor are accompanied by an increase in perisaccadic activity of FEF neurons coding the distractor location, and saccades that curve away are accompanied by a decrease in activity. In contrast, for FEF neurons coding the target location, there is no significant difference in activity between curved and straight saccades. To establish that the distractor-related activity is causally related to saccade curvature, we applied microstimulation to sites in the FEF before saccades to targets presented without distractors. The stimulation was subthreshold for evoking saccades and the temporal structure of the stimulation train resembled the activity recorded for curved saccades. The resulting movements curved toward the location coded by the stimulation site. These results support the idea that saccade curvature results from incomplete suppression of distractor-related activity during target selection.

  7. Effect of prolonged exposure to organic solvents on the active site environment of subtilisin Carlsberg.

    PubMed

    Bansal, Vibha; Delgado, Yamixa; Fasoli, Ezio; Ferrer, Amaris; Griebenow, Kai; Secundo, Francesco; Barletta, Gabriel L

    2010-06-01

    The potential of enzyme catalysis as a tool for organic synthesis is nowadays indisputable, as is the fact that organic solvents affect an enzyme's activity, selectivity and stability. Moreover, it was recently realized that an enzyme's initial activity is substantially decreased after prolonged exposure to organic media, an effect that further hampers their potential as catalysts for organic synthesis. Regrettably, the mechanistic reasons for these effects are still debatable. In the present study we have made an attempt to explain the reasons behind the partial loss of enzyme activity on prolonged exposure to organic solvents. Fluorescence spectroscopic studies of the serine protease subtilisin Carlsberg chemically modified with polyethylene glycol (PEG-SC) and inhibited with a Dancyl fluorophore, and dissolved in two organic solvents (acetonitrile and 1,4-dioxane) indicate that when the enzyme is initially introduced into these solvents, the active site environment is similar to that in water; however prolonged exposure to the organic medium causes this environment to resemble that of the solvent in which the enzyme is dissolved. Furthermore, kinetic studies show a reduction on both V(max) and K(M) as a result of prolonged exposure to the solvents. One interpretation of these results is that during this prolonged exposure to organic solvents the active-site fluorescent label inhibitor adopts a different binding conformation. Extrapolating this to an enzymatic reaction we argue that substrates bind in a less catalytically favorable conformation after the enzyme has been exposed to organic media for several hours.

  8. The pepsin residue glycine-76 contributes to active-site loop flexibility and participates in catalysis.

    PubMed Central

    Okoniewska, M; Tanaka, T; Yada, R Y

    2000-01-01

    Glycine residues are known to contribute to conformational flexibility of polypeptide chains, and have been found to contribute to flexibility of some loops associated with enzymic catalysis. A comparison of porcine pepsin in zymogen, mature and inhibited forms revealed that a loop (a flap), consisting of residues 71--80, located near the active site changed its position upon substrate binding. The loop residue, glycine-76, has been implicated in the catalytic process and thought to participate in a hydrogen-bond network aligning the substrate. This study investigated the role of glycine-76 using site-directed mutagenesis. Three mutants, G76A, G76V and G76S, were constructed to increase conformational restriction of a polypeptide chain. In addition, the serine mutant introduced a hydrogen-bonding potential at position 76 similar to that observed in human renin. All the mutants, regardless of amino acid size and polarity, had lower catalytic efficiency and activated more slowly than the wild-type enzyme. The slower activation process was associated directly with altered proteolytic activity. Consequently, it was proposed that a proteolytic cleavage represents a limiting step of the activation process. Lower catalytic efficiency of the mutants was explained as a decrease in the flap flexibility and, therefore, a different pattern of hydrogen bonds responsible for substrate alignment and flap conformation. The results demonstrated that flap flexibility is essential for efficient catalytic and activation processes. PMID:10861225

  9. Improving the activity of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation.

    PubMed

    Weng, Meizhi; Deng, Xiongwei; Bao, Wei; Zhu, Li; Wu, Jieyuan; Cai, Yongjun; Jia, Yan; Zheng, Zhongliang; Zou, Guolin

    2015-09-25

    Nattokinase (NK), a bacterial serine protease from Bacillus subtilis var. natto, is a potential cardiovascular drug exhibiting strong fibrinolytic activity. To broaden its commercial and medical applications, we constructed a single-mutant (I31L) and two double-mutants (M222A/I31L and T220S/I31L) by site-directed mutagenesis. Active enzymes were expressed in Escherichia coli with periplasmic secretion and were purified to homogeneity. The kinetic parameters of enzymes were examined by spectroscopy assay and isothermal titration calorimetry (ITC), and their fibrinolytic activities were determined by fibrin plate method. The substitution of Leu(31) for Ile(31) resulted in about 2-fold enhancement of catalytic efficiency (Kcat/KM) compared with wild-type NK. The specific activities of both double-mutants (M222A/I31L and T220S/I31L) were significantly increased when compared with the single-mutants (M222A and T220S) and the oxidative stability of M222A/I31L mutant was enhanced with respect to wild-type NK. This study demonstrates the feasibility of improving activity of NK by site-directed mutagenesis and shows successful protein engineering cases to improve the activity of NK as a potent therapeutic agent.

  10. Discovery of Active Hydrothermal Sites Along the Mariana Volcanic Arc, Western Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Baker, E. T.; Embley, R. W.; Resing, J. A.; Lupton, J. E.; Massoth, G. J.; de Ronde, C. E.; Nakamura, K.; Walker, S. L.

    2003-12-01

    Some 20,000 km of volcanic arcs, roughly one-third the total length of the global midocean ridge (MOR) system, rim the western Pacific Ocean. But compared to 25 years of hydrothermal investigations along MORs, exploration of similar activity on the estimated 600 submarine arc volcanoes is only beginning. In February 2003, as part of the Submarine Ring of Fire project funded by NOAA's Ocean Exploration Program, we made the first systematic survey of hydrothermal activity along the 1270-km-long Mariana intraoceanic volcanic arc, which lies almost entirely within the US EEZ. Prior fieldwork had documented active (but low-temperature) hydrothermal discharge on only three volcanoes: Kasuga 2, Kasuga 3, and Esmeralda Bank. During the cruise, we conducted 70 CTD operations over more than 50 individual volcanoes from 13° N to 23° N, plus a continuous CTD survey along 75 km of the back-arc spreading center (13° 15'N to 13° 41'N) adjacent to the southern end of the arc. We found evidence for active hydrothermal venting at 11 submarine volcanoes with summit (or caldera floor) depths ranging from 50 to 1550 m. Two additional sites were identified on the back-arc spreading center. Ongoing analyses of collected water samples could increase these totals. Our results confirmed continuing hydrothermal activity at Kasuga 2 (but not Kasuga 3) and Esmeralda Bank, in addition to newly discovered sites on nine other volcanoes. Many of these sites produce intense and widely dispersed plumes indicative of vigorous, high-temperature discharge. The volcanoes with active hydrothermal systems are about equally divided between those with and without summit calderas. The addition of the Marianas data greatly improves our view of hydrothermal sources along arcs. The 20,000 km of Pacific arcs can be divided between 6380 km of intraoceanic (i.e., mostly submarine) arcs and 13,880 km of island (i.e., mostly subaerial) arcs. At present, ˜15% of the total length of Pacific arcs has been surveyed

  11. PARP promoter-mediated activation of a VSG expression site promoter in insect form Trypanosoma brucei.

    PubMed

    Urményi, T P; Van der Ploeg, L H

    1995-03-25

    In trypanosomes the rRNA, PARP and VSG gene promoters mediate alpha-amanitin-resistant transcription of protein coding genes, presumably by RNA polymerase (pol) I. We compared the activity of PARP and VSG promoters integrated at one of the alleles of the largest subunit of pol II genes in insect form trypanosomes. Even though both promoters are roughly equally active in transient transformation assays in insect form trypanosomes, only the PARP promoter functioned effectively when integrated at the pol II largest subunit or other loci. Promoter activity in transient transformation assays is therefore not necessarily predictive of transcriptional activity once integrated into the trypanosome genome. The integrated fully active PARP promoter could upregulate in cis an otherwise poorly active integrated VSG promoter. The PARP promoter nucleotide sequence elements responsible for VSG promoter activation coincided with most of the important PARP promoter elements mapped previously by linker scanning mutagenesis, indicating that it is not a single unique promoter element that was responsible for VSG promoter activation. The data suggest that PARP promoter-mediated activation of the VSG promoter does not result from complementation of the VSG promoter with a single insect form-specific transcription factor whose binding site is missing from the VSG promoter and present in the PARP promoter. We favor a model in which chromatin structure at the locus is altered by the PARP promoter, allowing VSG promoter activation in insect form trypanosomes. We discuss the significance of these observations for the control of VSG promoters in insect form trypanosomes.

  12. Revealing the nature of the active site on the carbon catalyst for C-H bond activation.

    PubMed

    Sun, XiaoYing; Li, Bo; Su, Dangsheng

    2014-09-28

    A reactivity descriptor for the C-H bond activation on the nanostructured carbon catalyst is proposed. Furthermore the calculations reveal that the single ketone group can be an active site in ODH reaction.

  13. Cellular Active N-Hydroxyurea FEN1 Inhibitors Block Substrate Entry to the Active Site

    PubMed Central

    Exell, Jack C.; Thompson, Mark J.; Finger, L. David; Shaw, Steven J.; Debreczeni, Judit; Ward, Thomas A.; McWhirter, Claire; Siöberg, Catrine L. B.; Martinez Molina, Daniel; Mark Abbott, W.; Jones, Clifford D.; Nissink, J. Willem M.; Durant, Stephen T.; Grasby, Jane A.

    2016-01-01

    The structure-specific nuclease human flap endonuclease-1 (hFEN1) plays a key role in DNA replication and repair and may be of interest as an oncology target. We present the first crystal structure of inhibitor-bound hFEN1 and show a cyclic N-hydroxyurea bound in the active site coordinated to two magnesium ions. Three such compounds had similar IC50 values but differed subtly in mode of action. One had comparable affinity for protein and protein–substrate complex and prevented reaction by binding to active site catalytic metal ions, blocking the unpairing of substrate DNA necessary for reaction. Other compounds were more competitive with substrate. Cellular thermal shift data showed engagement of both inhibitor types with hFEN1 in cells with activation of the DNA damage response evident upon treatment. However, cellular EC50s were significantly higher than in vitro inhibition constants and the implications of this for exploitation of hFEN1 as a drug target are discussed. PMID:27526030

  14. 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.

  15. 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

  16. Formycin triphosphate as a probe for the ATP binding site involved in the activation of guanylate cyclase.

    PubMed

    Chang, C H; Yu, Z N; Song, D L

    1992-10-01

    Formycin A triphosphate (FTP), a fluorescent analog of ATP, slightly increased basal guanylate cyclase activity, but significantly potentiated guanylate cyclase activity stimulated by atrial natriuretic factor (ANF) in rat lung membranes. FTP potentiated ANF-stimulated guanylate cyclase activity with an EC50 at about 90 microM and inhibited ATP-stimulated guanylate cyclase activity with an IC50 at about 100 microM. These results indicate that FTP binds more tightly than ATP for the same binding site. Therefore, FTP would be an excellent tool for studying the ATP binding site.

  17. 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.

  18. Molecular dynamics simulations of Zika virus NS3 helicase: Insights into RNA binding site activity.

    PubMed

    Mottin, Melina; Braga, Rodolpho C; da Silva, Roosevelt A; Silva, Joao H Martins da; Perryman, Alexander L; Ekins, Sean; Andrade, Carolina Horta

    2017-03-21

    America is still suffering with the outbreak of Zika virus (ZIKV) infection. Congenital ZIKV syndrome has already caused a public health emergency of international concern. However, there are still no vaccines to prevent or drugs to treat the infection caused by ZIKV. The ZIKV NS3 helicase (NS3h) protein is a promising target for drug discovery due to its essential role in viral genome replication. NS3h unwinds the viral RNA to enable the replication of the viral genome by the NS5 protein. NS3h contains two important binding sites: the NTPase binding site and the RNA binding site. Here, we used molecular dynamics (MD) simulations to study the molecular behavior of ZIKV NS3h in the presence and absence of ssRNA and the potential implications for NS3h activity and inhibition. Although there is conformational variability and poor electron densities of the RNA binding loop in various apo flaviviruses NS3h crystallographic structures, the MD trajectories of NS3h-ssRNA demonstrated that the RNA binding loop becomes more stable when NS3h is occupied by RNA. Our results suggest that the presence of RNA generates important interactions with the RNA binding loop, and these interactions stabilize the loop sufficiently that it remains in a closed conformation. This closed conformation likely keeps the ssRNA bound to the protein for a sufficient duration to enable the unwinding/replication activities of NS3h to occur. In addition, conformational changes of this RNA binding loop can change the nature and location of the optimal ligand binding site, according to ligand binding site prediction results. These are important findings to help guide the design and discovery of new inhibitors of NS3h as promising compounds to treat the ZIKV infection.

  19. Production and use of DDT containing antifouling paint resulted in high DDTs residue in three paint factory sites and two shipyard sites, China.

    PubMed

    Xin, Jia; Liu, Xiang; Liu, Wei; Jiang, Lu; Wang, Jihua; Niu, Jia

    2011-06-01

    This study provides the first intensive investigation of Dichlorodiphenyltrichloroethanes (DDT) distribution in typical paint factories and shipyards in China where DDT containing antifouling paint were mass produced and used respectively. DDTs were analyzed in soil, sludge and sediment samples collected from three major paint factories and two shipyards. The results showed that the total DDTs concentrations detected in paint factory and shipyard sites ranged from 0.06 to 8387.24 mg kg(-1). In comparison with paint factory sites, the shipyard sites were much more seriously contaminated. However, for both kinds of sites, the DDTs level was found to be largely affected by history and capacity of production and use of DDT containing antifouling paint. (DDE+DDD)/DDT ratios indicated that DDT containing antifouling paint could serve as important fresh input sources for DDTs. It can be seen that most samples in shipyards were in ranges where heavy contamination and potential ecological risk were identified.

  20. Active Aging Promotion: Results from the Vital Aging Program

    PubMed Central

    Caprara, Mariagiovanna; Molina, María Ángeles; Schettini, Rocío; Santacreu, Marta; Orosa, Teresa; Mendoza-Núñez, Víctor Manuel; Rojas, Macarena; Fernández-Ballesteros, Rocío

    2013-01-01

    Active aging is one of the terms in the semantic network of aging well, together with others such as successful, productive, competent aging. All allude to the new paradigm in gerontology, whereby aging is considered from a positive perspective. Most authors in the field agree active aging is a multidimensional concept, embracing health, physical and cognitive fitness, positive affect and control, social relationships and engagement. This paper describes Vital Aging, an individual active aging promotion program implemented through three modalities: Life, Multimedia, and e-Learning. The program was developed on the basis of extensive evidence about individual determinants of active aging. The different versions of Vital Aging are described, and four evaluation studies (both formative and summative) are reported. Formative evaluation reflected participants' satisfaction and expected changes; summative evaluations yielded some quite encouraging results using quasi-experimental designs: those who took part in the programs increased their physical exercise, significantly improved their diet, reported better memory, had better emotional balance, and enjoyed more cultural, intellectual, affective, and social activities than they did before the course, thus increasing their social relationships. These results are discussed in the context of the common literature within the field and, also, taking into account the limitations of the evaluations accomplished. PMID:23476644

  1. Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes

    PubMed Central

    Herschlag, Daniel

    2016-01-01

    Molecular recognition is central to biology and a critical aspect of RNA function. Yet structured RNAs typically lack the preorganization needed for strong binding and precise positioning. A striking example is the group I ribozyme from Tetrahymena, which binds its guanosine substrate (G) orders of magnitude slower than diffusion. Binding of G is also thermodynamically coupled to binding of the oligonucleotide substrate (S) and further work has shown that the transition from E•G to E•S•G accompanies a conformational change that allows G to make the active site interactions required for catalysis. The group I ribozyme from Azoarcus has a similarly slow association rate but lacks the coupled binding observed for the Tetrahymena ribozyme. Here we test, using G analogs and metal ion rescue experiments, whether this absence of coupling arises from a higher degree of preorganization within the Azoarcus active site. Our results suggest that the Azoarcus ribozyme forms cognate catalytic metal ion interactions with G in the E•G complex, interactions that are absent in the Tetrahymena E•G complex. Thus, RNAs that share highly similar active site architectures and catalyze the same reactions can differ in the assembly of transition state interactions. More generally, an ability to readily access distinct local conformational states may have facilitated the evolutionary exploration needed to attain RNA machines that carry out complex, multi-step processes. PMID:27501145

  2. Substrate-binding specificity of chitinase and chitosanase as revealed by active-site architecture analysis.

    PubMed

    Liu, Shijia; Shao, Shangjin; Li, Linlin; Cheng, Zhi; Tian, Li; Gao, Peiji; Wang, Lushan

    2015-12-11

    Chitinases and chitosanases, referred to as chitinolytic enzymes, are two important categories of glycoside hydrolases (GH) that play a key role in degrading chitin and chitosan, two naturally abundant polysaccharides. Here, we investigate the active site architecture of the major chitosanase (GH8, GH46) and chitinase families (GH18, GH19). Both charged (Glu, His, Arg, Asp) and aromatic amino acids (Tyr, Trp, Phe) are observed with higher frequency within chitinolytic active sites as compared to elsewhere in the enzyme structure, indicating significant roles related to enzyme function. Hydrogen bonds between chitinolytic enzymes and the substrate C2 functional groups, i.e. amino groups and N-acetyl groups, drive substrate recognition, while non-specific CH-π interactions between aromatic residues and substrate mainly contribute to tighter binding and enhanced processivity evident in GH8 and GH18 enzymes. For different families of chitinolytic enzymes, the number, type, and position of substrate atoms bound in the active site vary, resulting in different substrate-binding specificities. The data presented here explain the synergistic action of multiple enzyme families at a molecular level and provide a more reasonable method for functional annotation, which can be further applied toward the practical engineering of chitinases and chitosanases.

  3. A Relaxed Active Site After Exon Ligation by the Group I Intron

    SciTech Connect

    Lipchock,S.; Strobel, S.

    2008-01-01

    During RNA maturation, the group I intron promotes two sequential phosphorotransfer reactions resulting in exon ligation and intron release. Here, we report the crystal structure of the intron in complex with spliced exons and two additional structures that examine the role of active-site metal ions during the second step of RNA splicing. These structures reveal a relaxed active site, in which direct metal coordination by the exons is lost after ligation, while other tertiary interactions are retained between the exon and the intron. Consistent with these structural observations, kinetic and thermodynamic measurements show that the scissile phosphate makes direct contact with metals in the ground state before exon ligation and in the transition state, but not after exon ligation. Despite no direct exonic interactions and even in the absence of the scissile phosphate, two metal ions remain bound within the active site. Together, these data suggest that release of the ligated exons from the intron is preceded by a change in substrate-metal coordination before tertiary hydrogen bonding contacts to the exons are broken.

  4. Active site structure and catalytic mechanism of phosphodiesterase for degradation of intracellular second messengers

    NASA Astrophysics Data System (ADS)

    Zhan, Chang-Guo

    2002-03-01

    Phosphodiesterases are clinical targets for a variety of biological disorders, because this superfamily of enzymes regulate intracellular concentration of cyclic nucleotides that serve as the second messengers playing a critical role in a variety of physiological processes. Understanding structure and mechanism of a phosphodiesterase will provide a solid basis for rational design of the more efficient therapeutics. Although a three-dimensional X-ray crystal structure of the catalytic domain of human phosphodiesterase 4B2B was recently reported, it was uncertain whether a critical bridging ligand in the active site is a water molecule or a hydroxide ion. The identity of this bridging ligand has been determined by performing first-principles quantum chemical calculations on models of the active site. All the results obtained indicate that this critical bridging ligand in the active site of the reported X-ray crystal structure is a hydroxide ion, rather than a water molecule, expected to serve as the nucleophile to initialize the catalytic degradation of the intracellular second messengers.

  5. Aerosol measurements at a high-elevation site: composition, size, and cloud condensation nuclei activity

    SciTech Connect

    Friedman, Beth; Zelenyuk, Alla; Beranek, Josef; Kulkarni, Gourihar R.; Pekour, Mikhail S.; Hallar, Anna G.; McCubbin, Ian; Thornton, Joel A.; Cziczo, D. J.

    2013-12-09

    We present measurements of CCN concentrations and associated aerosol composition and size properties at a high-elevation research site in March 2011. CCN closure and aerosol hygroscopicity were assessed using simplified assumptions of bulk aerosol properties as well as a new method utilizing single particle composition and size to assess the importance of particle mixing state in CCN activation. Free troposphere analysis found no significant difference between the CCN activity of free tropospheric aerosol and boundary layer aerosol at this location. Closure results indicate that using only size and number information leads to adequate prediction, in the majority of cases within 50%, of CCN concentrations, while incorporating the hygroscopicity parameters of the individual aerosol components measured by single particle mass spectrometry adds to the agreement, in most cases within 20%, between predicted and measured CCN concentrations. For high-elevation continental sites, with largely aged aerosol and low amounts of local area emissions, a lack of chemical knowledge and hygroscopicity may not hinder models in predicting CCN concentrations. At sites influenced by fresh emissions or more heterogeneous particle types, single particle composition information may be more useful in predicting CCN concentrations and understanding the importance of particle mixing state on CCN activation.

  6. Extracellular matrix-specific focal adhesions in vascular smooth muscle produce mechanically active adhesion sites

    PubMed Central

    Sun, Zhe; Martinez-Lemus, Luis A.; Hill, Michael A.; Meininger, Gerald A.

    2008-01-01

    Integrin-mediated mechanotransduction in vascular smooth muscle cells (VSMCs) plays an important role in the physiological control of tissue blood flow and vascular resistance. To test whether force applied to specific extracellular matrix (ECM)-integrin interactions could induce myogenic-like mechanical activity at focal adhesion sites, we used atomic force microscopy (AFM) to apply controlled forces to specific ECM adhesion sites on arteriolar VSMCs. The tip of AFM probes were fused with a borosilicate bead (2∼5 μm) coated with fibronectin (FN), collagen type I (CNI), laminin (LN), or vitronectin (VN). ECM-coated beads induced clustering of α5- and β3-integrins and actin filaments at sites of bead-cell contact indicative of focal adhesion formation. Step increases of an upward (z-axis) pulling force (800∼1,600 pN) applied to the bead-cell contact site for FN-specific focal adhesions induced a myogenic-like, force-generating response from the VSMC, resulting in a counteracting downward pull by the cell. This micromechanical event was blocked by cytochalasin D but was enhanced by jasplakinolide. Function-blocking antibodies to α5β1- and αvβ3-integrins also blocked the micromechanical cell event in a concentration-dependent manner. Similar pulling experiments with CNI, VN, or LN failed to induce myogenic-like micromechanical events. Collectively, these results demonstrate that mechanical force applied to integrin-FN adhesion sites induces an actin-dependent, myogenic-like, micromechanical event. Focal adhesions formed by different ECM proteins exhibit different mechanical characteristics, and FN appears of particular relevance in its ability to strongly attach to VSMCs and to induce myogenic-like, force-generating reactions from sites of focal adhesion in response to externally applied forces. PMID:18495809

  7. 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.

  8. Analysis of Hydrogen Tunneling in an Enzyme Active Site using von Neumann Measurements

    PubMed Central

    Sumner, Isaiah; Iyengar, Srinivasan S.

    2010-01-01

    We build on our earlier quantum wavepacket study of hydrogen transfer in the biological enzyme, soybean lipoxygenase-1, by using von Neumann quantum measurement theory to gain qualitative insights into the transfer event. We treat the enzyme active site as a measurement device which acts on the tunneling hydrogen nucleus via the potential it exerts at each configuration. A series of changing active site geometries during the tunneling process effects a sequential projection of the initial, reactant state onto the final, product state. We study this process using several different kinds of von Neumann measurements and show how a discrete sequence of such measurements not only progressively increases the projection of the hydrogen nuclear wavepacket onto the product side but also favors proton over deuteron transfer. Several qualitative features of the hydrogen tunneling problem found in wavepacket dynamics studies are also recovered here. These include the shift in the “transition state” towards the reactant as a result of nuclear quantization, greater participation of excited states in the case of deuterium, and presence of critical points along the reaction coordinate that facilitate hydrogen and deuterium transfer and coincide with surface crossings. To further “tailor” the dynamics, we construct a perturbation to the sequence of measurements, that is a perturbation to the dynamical sequence of active site geometry evolution, which leads us to insight on the existence of sensitive regions of the reaction profile where subtle changes to the dynamics of the active site can have an effect on the hydrogen and deuterium transfer process. PMID:22933858

  9. 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.

  10. SITE PROGRAM EVALUATION OF THE SONOTECH PULSE COMBUSTION BURNER TECHNOLOGY - TECHNICAL RESULTS

    EPA Science Inventory

    A series of demonstration tests was performed at the Environmental Protection Agency's (EPA's) Incineration Research Facility (IRF) under the Superfund Innovative Technology Evaluation (SITE) program. These tests, twelve in all, evaluated a pulse combustion burner technology dev...

  11. Preliminary results of the search for possible Martian landing sites to be considered for future European exploration missions

    NASA Astrophysics Data System (ADS)

    Martin, P.

    2007-08-01

    The recently adopted European Space Policy aims at expanding and coordinating the role and activities of Europe's space actors with the purpose of increasing both scientific knowledge in selected space domains and the European presence in the Solar System, as well as optimising the relevant societal benefits. With our Moon and in particular Mars as primary targets of exploration goals for the Solar System, and following a number of very successful orbital missions performing detailed remote sensing and mapping of these planetary bodies, probe landings on the surface of the Moon and Mars represent the next stepping stone of the exploration of our close planetary environment. Along with developing the hardware capabilities required for Europe to reach such ambitious goals, it therefore becomes increasingly important to pinpoint with precision a number of landing sites well suited for the safety and scientific success of future robotic missions. Focusing on Mars, and although a number of candidate landing sites and associated catalogs with available scientific justification already exist, the results being obtained by orbiters such as Mars Express and Mars Reconnaissance Orbiter are fundamentally transforming our knowledge of the planet's surface, which in turns highlights the need to review, update and revise the candidate sites for future landing missions on Mars. Detailed investigations of possible future Martian landing sites for European missions are ongoing, based on the wealth of scientific data and high-resolution mapping products available. In order to support the identification of suitable sites, various mapping products (geological, hyperspectral and compositional) can be consolidated, and various areas of Mars identified in the recent scientific literature as primary targets for landing can be taken into account for further, refined assessment of their suitability for landing. Seasonal and climatic effects potentially influencing landing shall also be

  12. Health-Related Messages about Physical Activity Promotion: An Analysis of Photographs on Social Networking Sites of Universities

    ERIC Educational Resources Information Center

    Martínez-Bello, Vladimir E.; Martínez-Rojas, Ángela; Molina-García, Javier

    2017-01-01

    The main aim of this study was to examine how different physical activity domains are represented on the official social media sites of Spanish universities, through a content analysis of the photographs. Our results show that the representation of different physical activity domains is not balanced. While the analysed images do promote a message…

  13. PS2-45: Conducting Multi-site Quality Assurance on Laboratory Results Data Incorporated into the Virtual Data Warehouse

    PubMed Central

    Saylor, Gwyn; Bredfeldt, Christine; Butler, Melissa; Folck, Bruce; Hitz, Paul; Krajenta, Richard; Ogarek, Jessica; Ovans, Lucas; Pardee, Roy; Riedlinger, Karen; Schmidt, Mark; Sterrett, Andrew; Raebel, Marsha

    2012-01-01

    Background/Aims Assuring that complete and correct laboratory test results are brought into the VDW and associated with the correct Test_Type is an ongoing task. Many problems can occur. For example, a particular version of a test can incorrectly be left out when the data are extracted. Results can be duplicated, or results can be associated incorrectly with a Test_Type. Creating quality assurance checks to locate problems or validate data requires evaluating the same data record from several different angles. Methods We conducted quality assurance on numerous laboratory test results that had been incorporated into VDW format across as many as 11 HMORN sites. Quality assurance programs were written to provide counts of test results across sites and over time. These programs also detailed result values, result units, patient location, result location, and other specific metrics. Descriptive statistics and graphical displays were used to facilitate assessment of across-site data variability and identify potential data quality issues. Sites were provided their site-specific results and results for all participating sites. Results Masking site information, we will show examples of quality assurance checks and depict what type of problem each is designed to point out. Examples may include incorrectly mapped tests (e.g., “hemoglobin” test results where the result unit was in percent and was determined to actually be glycosylated hemoglobin results) and tests that require investigation by the site because the result unit is possible, but unusual (e.g., total cholesterol units of g/dl require verification of g/dl unit and conversion to mg/dl before use or verification that g/dl was entered or read incorrectly). Other examples can include the volume of test results now contained within the VDW (e.g., total cholesterol total n is over 26.6 million results). Conclusions Laboratory result quality assurance requires assessment of problems as well as verifying expectations

  14. Silver-Coated Nylon Dressing Plus Active DC Microcurrent for Healing of Autogenous Skin Donor Sites

    DTIC Science & Technology

    2013-08-01

    Silver-Coated Nylon Dressing Plus Active DC Microcurrent for Healing of Autogenous Skin Donor Sites Edward W. Malin, MD, Chaya M. Galin, BSN, RN... microcurrent in comparison to silver-coated dressing with sham microcurrent on wound-closure time for autogenous skin donor sites. Methods: Four...hundred five patients were screened for treatment of their donor sites using a silver-coated nylon dressing with either sham or active microcurrent

  15. 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

  16. 76 FR 30696 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-26

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... eligible active uranium and thorium processing site licensees for reimbursement under Title X of the Energy... requires DOE to reimburse eligible uranium and thorium licensees for certain costs of...

  17. 76 FR 24871 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-03

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... from eligible active uranium and thorium processing site licensees for reimbursement under Title X of...). Title X requires DOE to reimburse eligible uranium and thorium licensees for certain costs...

  18. Compensatory signals associated with the activation of human GC 5' splice sites.

    PubMed

    Kralovicova, Jana; Hwang, Gyulin; Asplund, A Charlotta; Churbanov, Alexander; Smith, C I Edvard; Vorechovsky, Igor

    2011-09-01

    GC 5' splice sites (5'ss) are present in ∼1% of human introns, but factors promoting their efficient selection are poorly understood. Here, we describe a case of X-linked agammaglobulinemia resulting from a GC 5'ss activated by a mutation in BTK intron 3. This GC 5'ss was intrinsically weak, yet it was selected in >90% primary transcripts in the presence of a strong and intact natural GT counterpart. We show that efficient selection of this GC 5'ss required a high density of GAA/CAA-containing splicing enhancers in the exonized segment and was promoted by SR proteins 9G8, Tra2β and SC35. The GC 5'ss was efficiently inhibited by splice-switching oligonucleotides targeting either the GC 5'ss itself or the enhancer. Comprehensive analysis of natural GC-AG introns and previously reported pathogenic GC 5'ss showed that their efficient activation was facilitated by higher densities of splicing enhancers and lower densities of silencers than their GT 5'ss equivalents. Removal of the GC-AG introns was promoted to a minor extent by the splice-site strength of adjacent exons and inhibited by flanking Alu repeats, with the first downstream Alus located on average at a longer distance from the GC 5'ss than other transposable elements. These results provide new insights into the splicing code that governs selection of noncanonical splice sites.

  19. 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

  20. SURFACE GEOPHYSICAL EXPLORATION OF B & BX & BY TANK FARMS AT THE HANFORD SITE RESULTS OF BACKGROUND CHARACTERIZATION WITH MAGNETICS AND ELECTROMAGNETICS

    SciTech Connect

    MYERS DA

    2007-09-28

    This report documents the results of preliminary surface geophysical exploration activities performed between October and December 2006 at the B, BX, and BY tank farms (B Complex). The B Complex is located in the 200 East Area of the U. S. Department of Energy's Hanford Site in Washington State. The objective of the preliminary investigation was to collect background characterization information with magnetic gradiometry and electromagnetic induction to understand the spatial distribution of metallic objects that could potentially interfere with the results from high resolution resistivity survey. Results of the background characterization show there are several areas located around the site with large metallic subsurface debris or metallic infrastructure.

  1. A model of the rabies virus glycoprotein active site.

    PubMed

    Rustici, M; Bracci, L; Lozzi, L; Neri, P; Santucci, A; Soldani, P; Spreafico, A; Niccolai, N

    1993-06-01

    The glycoprotein from the neurotropic rabies virus shows a significant homology with the alpha neurotoxin that binds to the nicotinic acetylcholine receptor. The crystal structure of the alpha neurotoxins suggests that the Arg 37 guanidinium group and the Asp 31 side-chain carboxylate of the erabutoxin have stereochemical features resembling those of acetylcholine. Conformational studies on the Asn194-Ser195-Arg196-Gly197 tetrapeptide, an essential part of the binding site of the rabies virus glycoprotein, indicate that the side chains of Asn and Arg could also mimic the acetylcholine structure. This observation is consistent with the recently proposed mechanism of the viral infection.

  2. Thermal regime of active layer at two lithologically contrasting sites on James Ross Island, Antarctic Peninsula.

    NASA Astrophysics Data System (ADS)

    Hrbáček, Filip; Nývlt, Daniel; Láska, Kamil

    2016-04-01

    Antarctic Peninsula region (AP) represents one of the most rapidly warming parts of our planet in the last 50 years. Despite increasing research activities along both western and eastern sides of AP in last decades, there is still a lot of gaps in our knowledge relating to permafrost, active layer and its thermal and physical properties. This study brings new results of active layer monitoring on James Ross Island, which is the largest island in northern AP. Its northern part, Ulu Peninsula, is the largest ice-free area (more than 200 km2) in the region. Due its large area, we focused this study on sites located in different lithologies, which would affect local thermal regime of active layer. Study site (1) at Abernethy Flats area (41 m a.s.l.) lies ~7 km from northern coast. Lithologically is formed by disintegrated Cretaceous calcareous sandstones and siltstones of the Santa Marta Formation. Study site (2) is located at the northern slopes of Berry Hill (56 m a.s.l.), about 0.4 km from northern coastline. Lithology is composed of muddy to intermediate diamictites, tuffaceous siltstones to fine grained sandstones of the Mendel Formation. Data of air temperature at 2 meters above ground and the active layer temperatures at 75 cm deep profiles were obtained from both sites in period 1 January 2012 to 31 December 2014. Small differences were found when comparing mean air temperatures and active temperatures at 5 and 75 cm depth in the period 2012-2014. While the mean air temperatures varied between -7.7 °C and -7.0 °C, the mean ground temperatures fluctuated between -6.6 °C and -6.1 °C at 5 cm and -6.9 °C and -6.0 °C at 75 cm at Abernethy Flats and Berry Hill slopes respectively. Even though ground temperature differences along the profiles weren't pronounced during thawing seasons, the maximum active layer thickness was significantly larger at Berry Hill slopes (80 to 82 cm) than at Abernethy Flats (52 to 64 cm). We assume this differences are affected by

  3. The Las Cruces Trench Site: Characterization, Experimental Results, and One-Dimensional Flow Predictions

    NASA Astrophysics Data System (ADS)

    Wierenga, P. J.; Hills, R. G.; Hudson, D. B.

    1991-10-01

    the layered soil model rather than the uniform soil model does not consistently improve the accuracy of the predictions for this particular field application. This result illustrates that increasing the spatial resolution of the deterministic characterization of the site in the vertical direction does not always improve the model predictions. Uncertainties due to horizontal spatial variability and due to other difficulties associated with experimental characterization appear to be more significant.

  4. RESULTS OF THE PERFORMANCE ASSESSMENT FOR THE CLASSIFIED TRANSURANIC WASTES DISPOSED AT THE NEVADA TEST SITE

    SciTech Connect

    J. COCHRAN; ET AL

    2001-02-01

    Most transuranic (TRU) wastes are destined for the Waste Isolation Pilot Plant (WIPP). However, the TRU wastes from the cleanup of US nuclear weapons accidents are classified for national security reasons and cannot be disposed in WIPP. The US Department of Energy (DOE) sought an alternative disposal method for these ''special case'' TRU wastes and from 1984 to 1987, four Greater Confinement Disposal (GCD) boreholes were used to place these special case TRU wastes a minimum of 21 m (70 ft) below the land surface and a minimum of 200 m (650 ft) above the water table. The GCD boreholes are located in arid alluvium at the DOE's Nevada Test Site (NTS). Because of state regulatory concerns, the GCD boreholes have not been used for waste disposal since 1989. DOE requires that TRU waste disposal facilities meet the US Environmental Protection Agency's (EPA's) requirements for disposal of TRU wastes, which are contained in 40 CFR 191. This EPA standard sets a number of requirements, including probabilistic limits on the cumulative releases of radionuclides to the accessible environment for 10,000 years. The DOE Nevada Operations Office (DOE/NV) has contracted with Sandia National Laboratories (Sandia) to conduct a performance assessment (PA) to determine if the TRU waste emplaced in the GCD boreholes complies with the EPA's requirements. Sandia has completed the PA using all available information and an iterative PA methodology. This paper overviews the PA of the TRU wastes in the GCD boreholes [1]. As such, there are few cited references in this paper and the reader is referred to [1] and [2] for references. The results of the PA are that disposal of TRU wastes in the GCD boreholes easily complies with the EPA's 40 CFR 191 safety standards for disposal of TRU wastes. The PA is undergoing a DOE Headquarters (DOE/HQ) peer review, and the final PA will be released in FY2001 or FY2002.

  5. Three-dimensional representations of salt-dome margins at four active strategic petroleum reserve sites.

    SciTech Connect

    Rautman, Christopher Arthur; Stein, Joshua S.

    2003-01-01

    Existing paper-based site characterization models of salt domes at the four active U.S. Strategic Petroleum Reserve sites have been converted to digital format and visualized using modern computer software. The four sites are the Bayou Choctaw dome in Iberville Parish, Louisiana; the Big Hill dome in Jefferson County, Texas; the Bryan Mound dome in Brazoria County, Texas; and the West Hackberry dome in Cameron Parish, Louisiana. A new modeling algorithm has been developed to overcome limitations of many standard geological modeling software packages in order to deal with structurally overhanging salt margins that are typical of many salt domes. This algorithm, and the implementing computer program, make use of the existing interpretive modeling conducted manually using professional geological judgement and presented in two dimensions in the original site characterization reports as structure contour maps on the top of salt. The algorithm makes use of concepts of finite-element meshes of general engineering usage. Although the specific implementation of the algorithm described in this report and the resulting output files are tailored to the modeling and visualization software used to construct the figures contained herein, the algorithm itself is generic and other implementations and output formats are possible. The graphical visualizations of the salt domes at the four Strategic Petroleum Reserve sites are believed to be major improvements over the previously available two-dimensional representations of the domes via conventional geologic drawings (cross sections and contour maps). Additionally, the numerical mesh files produced by this modeling activity are available for import into and display by other software routines. The mesh data are not explicitly tabulated in this report; however an electronic version in simple ASCII format is included on a PC-based compact disk.

  6. First Results of the TIGRE Chromospheric Activity Survey

    NASA Astrophysics Data System (ADS)

    Mittag, M.; Hempelmann, A.; Gonzalez-Perez, J. N.; Schmitt, J. H. M. M.

    2015-01-01

    We present the first results of the stellar activity survey with TIGRE (Telescopio Internacional de Guanajuato, Robótico-Espectroscópico). This long term program was started in August 2013 with the monitoring of a larger number of stars. We aim at measuring the short- and long-term variability of stellar activity for stars of different spectral types and luminosity classes, using indicators of different spectral lines (mainly Ca II S-Index, Ca II IR triplet, H_α and sodium D). A transformation equation of the TIGRE S-Index into the Mount Wilson S-index was derived in order to compare our results to the vast body of existing S-index measurements. Furthermore, the correlation between the S-index and the lines of the Ca II IR triplet has been studied, based on strictly simultaneous observations.

  7. Environmental Impacts of Petroleum Production: Initial Results from the Osage-Skiatook Petroleum Environmental Research Sites, Osage County, Oklahoma

    USGS Publications Warehouse

    Kharaka, Yousif K.; Otton, James K.

    2003-01-01

    releases from active and inactive pipes and tank batteries. The leases are typical of many depleted and aging petroleum fields in Osage County, which ranks among the top oil and gas producing counties in Oklahoma with about 39,000 wells. Oil and gas production has occurred in Osage county for over one hundred years, but current production is mainly from stripper wells (averaging ~2.8 bbl/d oil and >30 bbl/d brine) that are shallow, mostly 300-700 m in depth, and produce from several sandstones of Pennsylvanian age. Results to date show that the produced water source is a Na-Ca-Cl brine (~150,000 mg/L total dissolved solids), with relatively high concentrations of Mg, Sr, and NH4, but low SO4 and H2S. With the exception of Fe and Mn, the concentrations of trace metals are low. Results also show that some and, eventually, the bulk, of inorganic salts and some dissolved organic species in the released brine from both sites will reach Skiatook Lake. Results at the 'A' site show that the salts have essentially been removed from the sandy soil which formed in a surficial layer of eolian sand, but degraded and weathered oil persists on the surface of old oil and brine pits, close to sites of old tanks, on old channels that carried oil from tanks to the oil pits and other impacted areas. Results also show a plume of high salinity water (5,000-30,600 mg/L TDS) is present at intermediate depths that extend from below the old oil and brine pits to Skiatook Lake. No liquid petroleum was found in the contaminated groundwater, but soluble petroleum byproducts, including organic acid anions and other volatile organic compounds (VOCs) are present. Results to date clearly show that significant amounts of salts from produced-water releases and petroleum hydrocarbons still remain in the soils and rocks of the impacted area after more than 60 years of natural attenuation. At the 'B' site significant amounts of produced water from the two active brine pits percolate into th

  8. Structural plasmid evolution as a result of coupled recombinations at bom and cer sites.

    PubMed

    Zakharova, M V; Beletskaya, I V; Bolovin, D V; Yurkova, T V; Semenova, L M; Solonin, A S

    2003-12-01

    We have studied the recombination of plasmids bearing bom and cer sites. The bom ( basis of mobilization) site is required for conjugative transfer, while the cer ( Col E1 resolution) site is involved in the resolution of plasmid multimers, which increases plasmid stability. We constructed a pair of parent plasmids in such a way as to allow us select clones containing recombinant plasmids directly. Clone selection was based on the McrA sensitivity of recipient host DNA modified by M. Ecl18kI, which is encoded by one of the parent plasmids. The recombinant plasmid contains segments originating from both parental DNAs, which are bounded by bom and cer sites. Its structure is in accordance with our previously proposed model for recombination mediated by bom and cer sequences. The frequency of recombinant plasmid formation coincided with the frequency of recombination at the bom site. We also show that bom-mediated recombination in trans, unlike in cis, is independent of other genetic determinants on the conjugative plasmids.

  9. New results for geologic units mapping of Utah test sites using Landsat TM data

    NASA Technical Reports Server (NTRS)

    Short, N. M.; Marcell, R.

    1986-01-01

    This paper continues a study on the accuracy of geological mapping using Landsat Thematic Mapper data (Short, 1984). In June 1976, both the White Mountain alteration zone and the Waterpocket Fold sedimentary rock sites in Utah were surveyed by the Bendix 24-band scanner on a NASA NC-130B aircraft. Mid-June 1984 TM data for these two sites have been processed like the 1976 data to test the quality of simulation of TM data. Principal-components (PC) color composite images for White Mountain show close correspondence to the Bendix PC images. At this site carbonate strata are uniquely discriminated in both Bendix and TM composites that use an inverted PC 3 image. Alunite/kaolinite and hematite/limonite alteration zones developed on volcanic flows are also sharply separated, but iron oxide and silicified zones are less so. The accuracy of rock-units mapping at the Waterpocket Fold site by supervised classification of the June TM data is significantly better, reaching 70 percent in the best case, than for January 1983 data for that site.

  10. Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1

    PubMed Central

    2016-01-01

    Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller with a flexible loop (residues 70–81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1’s lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1’s lactonase activity is minimal, whereas the kcat for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1’s active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar “gating loop” or a highly buried solvent-excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates. PMID:28026940

  11. Musk Kinase Activity is Modulated By A Serine Phosphorylation Site in The Kinase Loop.

    PubMed

    Camurdanoglu, B Z; Hrovat, C; Dürnberger, G; Madalinski, M; Mechtler, K; Herbst, R

    2016-09-26

    The neuromuscular junction (NMJ) forms when a motor neuron contacts a muscle fibre. A reciprocal exchange of signals initiates a cascade of signalling events that result in pre- and postsynaptic differentiation. At the centre of these signalling events stands muscle specific kinase (MuSK). MuSK activation, kinase activity and subsequent downstream signalling are crucial for NMJ formation as well as maintenance. Therefore MuSK kinase activity is tightly regulated to ensure proper NMJ development. We have identified a novel serine phosphorylation site at position 751 in MuSK that is increasingly phosphorylated upon agrin stimulation. S751 is also phosphorylated in muscle tissue and its phosphorylation depends on MuSK kinase activity. A phosphomimetic mutant of S751 increases MuSK kinase activity in response to non-saturating agrin concentrations . In addition, basal MuSK and AChR phosphorylation as well as AChR cluster size are increased. We believe that the phosphorylation of S751 provides a novel mechanism to relief the autoinhibition of the MuSK activation loop. Such a lower autoinhibition could foster or stabilize MuSK kinase activation, especially during stages when no or low level of agrin are present. Phosphorylation of S751 might therefore represent a novel mechanism to modulate MuSK kinase activity during prepatterning or NMJ maintenance.

  12. Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins.

    PubMed

    Dingerdissen, Hayley; Motwani, Mona; Karagiannis, Konstantinos; Simonyan, Vahan; Mazumder, Raja

    2013-03-01

    An enzyme's active site is essential to normal protein activity such that any disruptions at this site may lead to dysfunction and disease. Nonsynonymous single-nucleotide variations (nsSNVs), which alter the amino acid sequence, are one type of disruption that can alter the active site. When this occurs, it is assumed that enzyme activity will vary because of the criticality of the site to normal protein function. We integrate nsSNV data and active site annotations from curated resources to identify all active-site-impacting nsSNVs in the human genome and search for all pathways observed to be associated with this data set to assess the likely consequences. We find that there are 934 unique nsSNVs that occur at the active sites of 559 proteins. Analysis of the nsSNV data shows an over-representation of arginine and an under-representation of cysteine, phenylalanine and tyrosine when comparing the list of nsSNV-impacted active site residues with the list of all possible proteomic active site residues, implying a potential bias for or against variation of these residues at the active site. Clustering analysis shows an abundance of hydrolases and transferases. Pathway and functional analysis shows several pathways over- or under-represented in the data set, with the most significantly affected pathways involved in carbohydrate metabolism. We provide a table of 32 variation-substrate/product pairs that can be used in targeted metabolomics experiments to assay the effects of specific variations. In addition, we report the significant prevalence of aspartic acid to histidine variation in eight proteins associated with nine diseases including glycogen storage diseases, lacrimo-auriculo-dento-digital syndrome, Parkinson's disease and several cancers.

  13. Human Ebola virus infection results in substantial immune activation.

    PubMed

    McElroy, Anita K; Akondy, Rama S; Davis, Carl W; Ellebedy, Ali H; Mehta, Aneesh K; Kraft, Colleen S; Lyon, G Marshall; Ribner, Bruce S; Varkey, Jay; Sidney, John; Sette, Alessandro; Campbell, Shelley; Ströher, Ute; Damon, Inger; Nichol, Stuart T; Spiropoulou, Christina F; Ahmed, Rafi

    2015-04-14

    Four Ebola patients received care at Emory University Hospital, presenting a unique opportunity to examine the cellular immune responses during acute Ebola virus infection. We found striking activation of both B and T cells in all four patients. Plasmablast frequencies were 10-50% of B cells, compared with less than 1% in healthy individuals. Many of these proliferating plasmablasts were IgG-positive, and this finding coincided with the presence of Ebola virus-specific IgG in the serum. Activated CD4 T cells ranged from 5 to 30%, compared with 1-2% in healthy controls. The most pronounced responses were seen in CD8 T cells, with over 50% of the CD8 T cells expressing markers of activation and proliferation. Taken together, these results suggest that all four patients developed robust immune responses during the acute phase of Ebola virus infection, a finding that would not have been predicted based on our current assumptions about the highly immunosuppressive nature of Ebola virus. Also, quite surprisingly, we found sustained immune activation after the virus was cleared from the plasma, observed most strikingly in the persistence of activated CD8 T cells, even 1 mo after the patients' discharge from the hospital. These results suggest continued antigen stimulation after resolution of the disease. From these convalescent time points, we identified CD4 and CD8 T-cell responses to several Ebola virus proteins, most notably the viral nucleoprotein. Knowledge of the viral proteins targeted by T cells during natural infection should be useful in designing vaccines against Ebola virus.

  14. Site-directed mutagenesis of the Anabaena sp. strain PCC 7120 nitrogenase active site to increase photobiological hydrogen production.

    PubMed

    Masukawa, Hajime; Inoue, Kazuhito; Sakurai, Hidehiro; Wolk, C Peter; Hausinger, Robert P

    2010-10-01

    Cyanobacteria use sunlight and water to produce hydrogen gas (H₂), which is potentially useful as a clean and renewable biofuel. Photobiological H₂ arises primarily as an inevitable by-product of N₂ fixation by nitrogenase, an oxygen-labile enzyme typically containing an iron-molybdenum cofactor (FeMo-co) active site. In Anabaena sp. strain 7120, the enzyme is localized to the microaerobic environment of heterocysts, a highly differentiated subset of the filamentous cells. In an effort to increase H₂ production by this strain, six nitrogenase amino acid residues predicted to reside within 5 Å of the FeMo-co were mutated in an attempt to direct electron flow selectively toward proton reduction in the presence of N₂. Most of the 49 variants examined were deficient in N₂-fixing growth and exhibited decreases in their in vivo rates of acetylene reduction. Of greater interest, several variants examined under an N₂ atmosphere significantly increased their in vivo rates of H₂ production, approximating rates equivalent to those under an Ar atmosphere, and accumulated high levels of H₂ compared to the reference strains. These results demonstrate the feasibility of engineering cyanobacterial strains for enhanced photobiological production of H₂ in an aerobic, nitrogen-containing environment.

  15. Preliminary results of systematic sampling of gas manifestations in geodynamically active areas of Greece

    NASA Astrophysics Data System (ADS)

    Daskalopoulou, Kyriaki; D'Alessandro, Walter; Calabrese, Sergio; Kyriakopoulos, Konstantinos

    2016-04-01

    Greece is located on a convergent plate boundary comprising the subduction of the African Plate beneath the Eurasian, while the Arabian plate approaches the Eurasian in a northwestward motion. It is considered to be one of the most tectonically active regions of Earth with a complex geodynamic setting, deriving from a long and complicated geological history. Due to this specific geological background, conditions for the formation of many thermal springs are favoured. In the past years, almost all the already known sites of degassing (fumaroles, soil gases, mofettes, gas bubbling in cold and thermal waters) located in the Hellenic area were sampled at least one time. Collected samples were analysed for their chemical (He, Ne, Ar, O2, N2, H2, H2S, CO, CH4 and CO2) and isotopic composition (He, C and N). Some of these sites have been selected for systematic sampling. Four of them have records longer than 10 years with tens of samplings also considering some literature data. Two of the sites are located in active volcanic areas (Santorini and Nisyros) while the other two are close to actively spreading graben structures with intense seismic activity (Gulf of Korinth and Sperchios basin). Results allowed to define long term background values and also some interesting variation related to seismic or volcanic activity.

  16. Active-site properties of Phrixotrix railroad worm green and red bioluminescence-eliciting luciferases.

    PubMed

    Viviani, V R; Arnoldi, F G C; Venkatesh, B; Neto, A J S; Ogawa, F G T; Oehlmeyer, A T L; Ohmiya, Y

    2006-10-01

    The luciferases of the railroad worm Phrixotrix (Coleoptera: Phengodidae) are the only beetle luciferases that naturally produce true red bioluminescence. Previously, we cloned the green- (PxGR) and red-emitting (PxRE) luciferases of railroad worms Phrixotrix viviani and P. hirtus[OLE1]. These luciferases were expressed and purified, and their active-site properties were determined. The red-emitting PxRE luciferase displays flash-like kinetics, whereas PxGR luciferase displays slow-type kinetics. The substrate affinities and catalytic efficiency of PxRE luciferase are also higher than those of PxGR luciferase. Fluorescence studies with 8-anilino-1-naphthalene sulfonic acid and 6-p-toluidino-2-naphthalene sulfonic acid showed that the PxRE luciferase luciferin-binding site is more polar than that of PxGR luciferase, and it is sensitive to guanidine. Mutagenesis and modelling studies suggest that several invariant residues in the putative luciferin-binding site of PxRE luciferase cannot interact with excited oxyluciferin. These results suggest that one portion of the luciferin-binding site of the red-emitting luciferase is tighter than that of PxGR luciferase, whereas the other portion could be more open and polar.

  17. Effect of particle surface area on ice active site densities retrieved from droplet freezing spectra

    NASA Astrophysics Data System (ADS)

    Beydoun, Hassan; Polen, Michael; Sullivan, Ryan C.

    2016-10-01

    Heterogeneous ice nucleation remains one of the outstanding problems in cloud physics and atmospheric science. Experimental challenges in properly simulating particle-induced freezing processes under atmospherically relevant conditions have largely contributed to the absence of a well-established parameterization of immersion freezing properties. Here, we formulate an ice active, surface-site-based stochastic model of heterogeneous freezing with the unique feature of invoking a continuum assumption on the ice nucleating activity (contact angle) of an aerosol particle's surface that requires no assumptions about the size or number of active sites. The result is a particle-specific property g that defines a distribution of local ice nucleation rates. Upon integration, this yields a full freezing probability function for an ice nucleating particle. Current cold plate droplet freezing measurements provide a valuable and inexpensive resource for studying the freezing properties of many atmospheric aerosol systems. We apply our g framework to explain the observed dependence of the freezing temperature of droplets in a cold plate on the concentration of the particle species investigated. Normalizing to the total particle mass or surface area present to derive the commonly used ice nuclei active surface (INAS) density (ns) often cannot account for the effects of particle concentration, yet concentration is typically varied to span a wider measurable freezing temperature range. A method based on determining what is denoted an ice nucleating species' specific critical surface area is presented and explains the concentration dependence as a result of increasing the variability in ice nucleating active sites between droplets. By applying this method to experimental droplet freezing data from four different systems, we demonstrate its ability to interpret immersion freezing temperature spectra of droplets containing variable particle concentrations. It is shown that general

  18. Characterization of the interactions between the active site of a protein tyrosine kinase and a divalent metal activator

    PubMed Central

    Lin, Xiaofeng; Ayrapetov, Marina K; Sun, Gongqin

    2005-01-01

    Background Protein tyrosine kinases are important enzymes for cell signalling and key targets for anticancer drug discovery. The catalytic mechanisms of protein tyrosine kinase-catalysed phosphorylation are not fully understood. Protein tyrosine kinase Csk requires two Mg2+ cations for activity: one (M1) binds to ATP, and the other (M2) acts as an essential activator. Results Experiments in this communication characterize the interaction between M2 and Csk. Csk activity is sensitive to pH in the range of 6 to 7. Kinetic characterization indicates that the sensitivity is not due to altered substrate binding, but caused by the sensitivity of M2 binding to pH. Several residues in the active site with potential of binding M2 are mutated and the effect on metal activation studied. An active mutant of Asn319 is generated, and this mutation does not alter the metal binding characteristics. Mutations of Glu236 or Asp332 abolish the kinase activity, precluding a positive or negative conclusion on their role in M2 coordination. Finally, the ability of divalent metal cations to activate Csk correlates to a combination of ionic radius and the coordination number. Conclusion These studies demonstrate that M2 binding to Csk is sensitive to pH, which is mainly responsible for Csk activity change in the acidic arm of the pH response curve. They also demonstrate critical differences in the metal activator coordination sphere in protein tyrosine kinase Csk and a protein Ser/Thr kinase, the cAMP-dependent protein kinase. They shed light on the physical interactions between a protein tyrosine kinase and a divalent metal activator. PMID:16305747

  19. Tricyclic covalent inhibitors selectively target Jak3 through an active site thiol.

    PubMed

    Goedken, Eric R; Argiriadi, Maria A; Banach, David L; Fiamengo, Bryan A; Foley, Sage E; Frank, Kristine E; George, Jonathan S; Harris, Christopher M; Hobson, Adrian D; Ihle, David C; Marcotte, Douglas; Merta, Philip J; Michalak, Mark E; Murdock, Sara E; Tomlinson, Medha J; Voss, Jeffrey W

    2015-02-20

    The action of Janus kinases (JAKs) is required for multiple cytokine signaling pathways, and as such, JAK inhibitors hold promise for treatment of autoimmune disorders, including rheumatoid arthritis, inflammatory bowel disease, and psoriasis. However, due to high similarity in the active sites of the four members (Jak1, Jak2, Jak3, and Tyk2), developing selective inhibitors within this family is challenging. We have designed and characterized substituted, tricyclic Jak3 inhibitors that selectively avoid inhibition of the other JAKs. This is accomplished through a covalent interaction between an inhibitor containing a terminal electrophile and an active site cysteine (Cys-909). We found that these ATP competitive compounds are irreversible inhibitors of Jak3 enzyme activity in vitro. They possess high selectivity against other kinases and can potently (IC50 < 100 nm) inhibit Jak3 activity in cell-based assays. These results suggest irreversible inhibitors of this class may be useful selective agents, both as tools to probe Jak3 biology and potentially as therapies for autoimmune diseases.

  20. Hydroxynonenal inactivates cathepsin B by forming Michael adducts with active site residues.

    PubMed

    Crabb, John W; O'Neil, June; Miyagi, Masaru; West, Karen; Hoff, Henry F

    2002-04-01

    Oxidation of plasma low-density lipoprotein (oxLDL) generates the lipid peroxidation product 4-hydroxy-2 nonenal (HNE) and also reduces proteolytic degradation of oxLDL and other proteins internalized by mouse peritoneal macrophages in culture. This leads to accumulation of undegraded material in lysosomes and formation of ceroid, a component of foam cells in atherosclerotic lesions. To explore the possibility that HNE contributes directly to the inactivation of proteases, structure-function studies of the lysosomal protease cathepsin B have been pursued. We found that treatment of mouse macrophages with HNE reduces degradation of internalized maleyl bovine serine albumin and cathepsin B activity. Purified bovine cathepsin B treated briefly with 15 microM HNE lost approximately 76% of its protease activity and also developed immunoreactivity with antibodies to HNE adducts in Western blot analysis. After stabilization of the potential Michael adducts by sodium borohydride reduction, modified amino acids were localized within the bovine cathepsin B protein structure by mass spectrometric analysis of tryptic peptides. Michael adducts were identified by tandem mass spectrometry at cathepsin B active site residues Cys 29 (mature A chain) and His 150 (mature B chain). Thus, covalent interaction between HNE and critical active site residues inactivates cathepsin B. These results support the hypothesis that the accumulation of undegraded macromolecules in lysosomes after oxidative damage are caused in part by direct protease inactivation by adduct formation with lipid peroxidation products such as HNE.

  1. Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.

    PubMed

    Pujadas, G; Palau, J

    2001-08-01

    Soybean beta-amylase (EC 3.2.1.2) has been crystallized both free and complexed with a variety of ligands. Four water molecules in the free-enzyme catalytic cleft form a multihydrogen-bond network with eight strategic residues involved in enzyme-ligand hydrogen bonds. We show here that the positions of these four water molecules are coincident with the positions of four potential oxygen atoms of the ligands within the complex. Some of these waters are displaced from the active site when the ligands bind to the enzyme. How many are displaced depends on the shape of the ligand. This means that when one of the four positions is not occupied by a ligand oxygen atom, the corresponding water remains. We studied the functional/structural role of these four waters and conclude that their presence means that the conformation of the eight side chains is fixed in all situations (free or complexed enzyme) and preserved from unwanted or forbidden conformational changes that could hamper the catalytic mechanism. The water structure at the active pocket of beta-amylase is therefore essential for providing the ligand recognition process with plasticity. It does not affect the protein active-site geometry and preserves the overall hydrogen-bonding network, irrespective of which ligand is bound to the enzyme. We also investigated whether other enzymes showed a similar role for water. Finally, we discuss the potential use of these results for predicting whether water molecules can mimic ligand atoms in the active center.

  2. Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol*

    PubMed Central

    Goedken, Eric R.; Argiriadi, Maria A.; Banach, David L.; Fiamengo, Bryan A.; Foley, Sage E.; Frank, Kristine E.; George, Jonathan S.; Harris, Christopher M.; Hobson, Adrian D.; Ihle, David C.; Marcotte, Douglas; Merta, Philip J.; Michalak, Mark E.; Murdock, Sara E.; Tomlinson, Medha J.; Voss, Jeffrey W.

    2015-01-01

    The action of Janus kinases (JAKs) is required for multiple cytokine signaling pathways, and as such, JAK inhibitors hold promise for treatment of autoimmune disorders, including rheumatoid arthritis, inflammatory bowel disease, and psoriasis. However, due to high similarity in the active sites of the four members (Jak1, Jak2, Jak3, and Tyk2), developing selective inhibitors within this family is challenging. We have designed and characterized substituted, tricyclic Jak3 inhibitors that selectively avoid inhibition of the other JAKs. This is accomplished through a covalent interaction between an inhibitor containing a terminal electrophile and an active site cysteine (Cys-909). We found that these ATP competitive compounds are irreversible inhibitors of Jak3 enzyme activity in vitro. They possess high selectivity against other kinases and can potently (IC50 < 100 nm) inhibit Jak3 activity in cell-based assays. These results suggest irreversible inhibitors of this class may be useful selective agents, both as tools to probe Jak3 biology and potentially as therapies for autoimmune diseases. PMID:25552479

  3. Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation

    SciTech Connect

    Boudreaux, David A.; Maiti, Tushar K.; Davies, Christopher W.; Das, Chittaranjan

    2010-07-06

    Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) is a Parkinson disease-associated, putative cysteine protease found abundantly and selectively expressed in neurons. The crystal structure of apo UCHL1 showed that the active-site residues are not aligned in a canonical form, with the nucleophilic cysteine being 7.7 {angstrom} from the general base histidine, an arrangement consistent with an inactive form of the enzyme. Here we report the crystal structures of the wild type and two Parkinson disease-associated variants of the enzyme, S18Y and I93M, bound to a ubiquitin-based suicide substrate, ubiquitin vinyl methyl ester. These structures reveal that ubiquitin vinyl methyl ester binds primarily at two sites on the enzyme, with its carboxy terminus at the active site and with its amino-terminal {beta}-hairpin at the distal site - a surface-exposed hydrophobic crevice 17 {angstrom} away from the active site. Binding at the distal site initiates a cascade of side-chain movements in the enzyme that starts at a highly conserved, surface-exposed phenylalanine and is relayed to the active site resulting in the reorientation and proximal placement of the general base within 4 {angstrom} of the catalytic cysteine, an arrangement found in productive cysteine proteases. Mutation of the distal-site, surface-exposed phenylalanine to alanine reduces ubiquitin binding and severely impairs the catalytic activity of the enzyme. These results suggest that the activity of UCHL1 may be regulated by its own substrate.

  4. All the catalytic active sites of MoS2 for hydrogen evolution

    DOE PAGES

    Li, Guoqing; Zhang, Du; Qiao, Qiao; ...

    2016-11-29

    MoS2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. Here, the intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated to be 7.5more » s–1 (65–75 mV/dec), 3.2 s–1 (65–85 mV/dec), and 0.1 s–1 (120–160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7–10%, and the number of sulfur vacancies in high crystalline quality MoS2 is higher than that in low crystalline quality MoS2, which may be related with the proximity of different local crystalline structures to the vacancies.« less

  5. Treatment of extraskeletal osteosarcoma at a previous injection site resulting in prolonged survival in 1 dog.

    PubMed

    Selmic, Laura E; Griffin, Lynn R; Rector, Megan H; Lafferty, Mary; Pool, Roy; Ehrhart, Nicole P

    2016-09-01

    A rare presentation of an extraskeletal osteosarcoma at a previous interscapular injection site in a dog is described. Treatment included surgical excision of the tumor followed by 6 rounds of intravenous carboplatin, oral toceranib, and cyclophosphamide. The dog survived for 20.5 months after diagnosis despite early development of pulmonary metastases.

  6. Treatment of extraskeletal osteosarcoma at a previous injection site resulting in prolonged survival in 1 dog

    PubMed Central

    Selmic, Laura E.; Griffin, Lynn R.; Rector, Megan H.; Lafferty, Mary; Pool, Roy; Ehrhart, Nicole P.

    2016-01-01

    A rare presentation of an extraskeletal osteosarcoma at a previous interscapular injection site in a dog is described. Treatment included surgical excision of the tumor followed by 6 rounds of intravenous carboplatin, oral toceranib, and cyclophosphamide. The dog survived for 20.5 months after diagnosis despite early development of pulmonary metastases. PMID:27587886

  7. Stress-induced enhancement of leukocyte trafficking into sites of surgery or immune activation

    NASA Astrophysics Data System (ADS)

    Viswanathan, Kavitha; Dhabhar, Firdaus S.

    2005-04-01

    Effective immunoprotection requires rapid recruitment of leukocytes into sites of surgery, wounding, infection, or vaccination. In contrast to immunosuppressive chronic stressors, short-term acute stressors have immunoenhancing effects. Here, we quantify leukocyte infiltration within a surgical sponge to elucidate the kinetics, magnitude, subpopulation, and chemoattractant specificity of an acute stress-induced increase in leukocyte trafficking to a site of immune activation. Mice acutely stressed before sponge implantation showed 200-300% higher neutrophil, macrophage, natural killer cell, and T cell infiltration than did nonstressed animals. We also quantified the effects of acute stress on lymphotactin- (LTN; a predominantly lymphocyte-specific chemokine), and TNF-- (a proinflammatory cytokine) stimulated leukocyte infiltration. An additional stress-induced increase in infiltration was observed for neutrophils, in response to TNF-, macrophages, in response to TNF- and LTN, and natural killer cells and T cells in response to LTN. These results show that acute stress initially increases trafficking of all major leukocyte subpopulations to a site of immune activation. Tissue damage-, antigen-, or pathogen-driven chemoattractants subsequently determine which subpopulations are recruited more vigorously. Such stress-induced increases in leukocyte trafficking may enhance immunoprotection during surgery, vaccination, or infection, but may also exacerbate immunopathology during inflammatory (cardiovascular disease or gingivitis) or autoimmune (psoriasis, arthritis, or multiple sclerosis) diseases. chemokine | psychophysiological stress | surgical sponge | wound healing | lymphotactin

  8. Identification of Arg-12 in the active site of Escherichia coli K1 CMP-sialic acid synthetase.

    PubMed Central

    Stoughton, D M; Zapata, G; Picone, R; Vann, W F

    1999-01-01

    Escherichia coli K1 CMP-sialic acid synthetase catalyses the synthesis of CMP-sialic acid from CTP and sialic acid. The active site of the 418 amino acid E. coli enzyme was localized to its N-terminal half. The bacterial CMP-sialic acid synthetase enzymes have a conserved motif, IAIIPARXXSKGLXXKN, at their N-termini. Several basic residues have been identified at or near the active site of the E. coli enzyme by chemical modification and site-directed mutagenesis. Only one of the lysines in the N-terminal motif, Lys-21, appears to be essential for activity. Mutation of Lys-21 in the N-terminal motif results in an inactive enzyme. Furthermore, Arg-12 of the N-terminal motif appears to be an active-site residue, based on the following evidence. Substituting Arg-12 with glycine or alanine resulted in inactive enzymes, indicating that this residue is required for enzymic activity. The Arg-12-->Lys mutant was partially active, demonstrating that a positive charge is required at this site. Steady-state kinetic analysis reveals changes in k(cat), K(m) and K(s) for CTP, which implicates Arg-12 in catalysis and substrate binding. PMID:10510306

  9. 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

  10. Web Based Autonomous Geophysical/Hydrological Monitoring of the Gilt Edge Mine Site: Implementation and Results

    NASA Astrophysics Data System (ADS)

    Versteeg, R. J.; Wangerud, K.; Mattson, E.; Ankeny, M.; Richardson, A.; Heath, G.

    2005-05-01

    The Ruby Gulch repository at the Gilt Edge Mine Superfund site is a capped waste rock repository. Early in the system design EPA and its subcontractor, Bureau of Reclamation, recognized the need for long-term monitoring system to provide information on the repository behavior with the following objectives: 1 Provide information on the integrity of the newly constructed surface cover and diversion system 2 Continually assess the waste's hydrological and geochemical behavior, such that rational decisions can be made for the operation of this cover and liner system 3 Easily access of information pertaining to the system performance to stakeholders 4 Integration of a variety of data sources to produce information which could be used to enhance future cover designs. Through discussions between EPA, the Bureau of Reclamation and Idaho National Laboratory a long-term monitoring system was designed and implemented allowing EPA to meet these objectives. This system was designed to provide a cost effective way to deal with massive amounts of data and information, subject to the following specifications: 1 Data acquisition should occur autonomously and automatically, 2 Data management, processing and presentation should be automated as much as possible, 3 Users should be able to access all data and information remotely through a web browser. The INL long-term monitoring system integrates the data from a set of 522 electrodes resistivity electrodes consisting of 462 surface electrodes and 60 borehole electrodes (in 4 wells with 15 electrodes each), an outflow meter at the toe of the repository, an autonomous, remotely accessible weather station, and four wells (average depths of 250 feet) with thermocouples, pressure transducers and sampling ports for water and air. The monitoring system has currently been in operation for over a year, and has collected data continuously over this period. Results from this system have shown both the diurnal variation in rockmass behavior

  11. 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…

  12. 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

  13. Prediction of P53 Mutants (Multiple Sites) Transcriptional Activity Based on Structural (2D&3D) Properties

    PubMed Central

    Geetha Ramani, R.; Jacob, Shomona Gracia

    2013-01-01

    Prediction of secondary site mutations that reinstate mutated p53 to normalcy has been the focus of intense research in the recent past owing to the fact that p53 mutants have been implicated in more than half of all human cancers and restoration of p53 causes tumor regression. However laboratory investigations are more often laborious and resource intensive but computational techniques could well surmount these drawbacks. In view of this, we formulated a novel approach utilizing computational techniques to predict the transcriptional activity of multiple site (one-site to five-site) p53 mutants. The optimal MCC obtained by the proposed approach on prediction of one-site, two-site, three-site, four-site and five-site mutants were 0.775,0.341,0.784,0.916 and 0.655 respectively, the highest reported thus far in literature. We have also demonstrated that 2D and 3D features generate higher prediction accuracy of p53 activity and our findings revealed the optimal results for prediction of p53 status, reported till date. We believe detection of the secondary site mutations that suppress tumor growth may facilitate better understanding of the relationship between p53 structure and function and further knowledge on the molecular mechanisms and biological activity of p53, a targeted source for cancer therapy. We expect that our prediction methods and reported results may provide useful insights on p53 functional mechanisms and generate more avenues for utilizing computational techniques in biological data analysis. PMID:23468845

  14. 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.

  15. Benzodiazepines: rat pinealocyte binding sites and augmentation of norepinephrine-stimulated N-acetyltransferase activity

    SciTech Connect

    Matthew, E.; Parfitt, A.G.; Sugden, D.; Engelhardt, D.L.; Zimmerman, E.A.; Klein, D.C.

    1984-02-01

    Studies of (/sup 3/H)diazepam binding to intact rat pineal cells were carried out in tissue culture preparations. The binding was saturable, reversible and proportional to the number of cells used. Scatchard analysis resulted in a linear plot (Kd . 23 nM, maximum binding sites (Bmax) . 1.56 pmol/mg of protein for cells in monolayer culture; Kd . 7 nM, Bmax . 1.3 pmol/mg of protein for cells in suspension culture). Inhibition constants (Ki) for clonazepam (500 nM), flunitrazepam (38 nM) and Ro-5-4864 (5 nM) indicated that the binding sites were probably of the ''peripheral'' type. In addition, the effects of diazepam on norepinephrine-stimulated N-acetyltransferase (NAT) activity were studied in organ culture and dissociated cell culture. Diazepam (10-50 microM) both prolonged and increased the magnitude of the norepinephrine-induced increase in NAT activity but did not affect the initial rate of rise of enzyme activity. The effect was dose-dependent and was also seen with clonazepam, flunitrazepam and Ro-5-4864, but not with Ro-15-1788. Diazepam, by itself, at these concentrations, had no effect on NAT, but enzyme activity was increased by higher concentrations (0.1-1 mM). Although a relationship between the (/sup 3/H)diazepam binding sites described here and the effect of benzodiazepines on NAT cannot be established from these studies, the data suggest that the benzodiazepines may alter melatonin levels through their action on NAT.

  16. 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.

  17. Structure and Reactivity of the Phosphotriesterase Active Site

    DTIC Science & Technology

    2002-01-01

    characterize different catalytic conformations for chorismate mutase . Preliminary evidence for water binding in phosphotriesterase suggests that activity in...MD/QM study of the chorismate mutase catalyzed Claisen rearrangement reaction. 2001.subm. J.Phys.Chem.B 22.Day, P.N.J., J.H.; Gordon,M.S.; Webb,S.P...Claisen rearrangement of an unusual substrate in chorismate mutase . 2001.subm. J.Phys.Chem.B 38.Stevens, W.J., Basch,H., Krauss,M., Compact effective

  18. The Hontomin CO2 geologic storage site: results from 2D seismic survey

    NASA Astrophysics Data System (ADS)

    Calahorrano, A.; Martí, D.; Alcalde, J.; Marzán, I.; Ayarza, P.; Carbonell, R.; Pérez-Estaún, A.

    2012-04-01

    The Spanish research program on Carbon dioxide Capture and Storage (CCS), leaded by the state-owned foundation CIUDEN, initiated the storage project with the creation of the first Spanish technological laboratory devoted to subsurface storage of carbon dioxide (CO2) in 2010 near the village of Hontomín (North West of Spain). This research site aims investigating the different phases involved in the CO2 injection process in underground geologic formations at real scale and monitoring its long-term behavior. The seismic baseline study consist on five innovative and non-standard seismic experiments including: 1) a 35 km2 of 3D seismic survey, 2) a 2D seismic survey, 3) a Seismovie survey, 4) a 30 passive-seismic network and 5) a Vertical Seismic Profile (VSP) survey programmed for this year. Here we focus on the 2D seismic reflection survey that was acquired with new generation 3-component receivers. A total of 408 receivers with 25 m interval were deployed along 2 orthogonal profiles, orientated ~NS-EW, centered near the injection point. The seismic source consisted on 4 15-Tn M22 vibroseis trucks with a 16-sec sweep vibrating at each 25 m distance. Data processing included static corrections, spherical divergence correction, airwave muting, predictive deconvolution, stack, time-variant band-pass filtering and time migration. First analysis of the vertical component data confirm the dome-geometry of the reservoir observed by previous studies and give details on the tectonic structure of the potential injection zone. The data also show two main seismic features corresponding to 1) a loss of the P-wave first arrival amplitudes resulting in a shadow zone at offsets of ~600-1500 m. and 2) a high-amplitude reflection at the base of the shadow zone. We related the presence of the shadow zone with a ~750 m-thick layer of low velocity or small velocity-gradient, associated to Early-Middle Cretaceous deposits that globally correspond to variable grain-size siliciclastic

  19. Natural Attenuation of Fuel Hydrocarbons Performance and Cost Results from Multiple Air Force Demonstration Sites

    DTIC Science & Technology

    1999-10-01

    of LTM plans. One site had sufficiently complex hydrogeology to warrant the construction of a three-dimensional (3-D) numerical model using MODFLOW ...ST-C 3 14 9 285 18 77.4 Eglin AFB, FL POL Facility F-C/S, C, Peat F-C/S 0 4 6 4380 263 657 Ellsworth, SD Area D G, ST-C G 7.5 24 9 146 5 76

  20. Results of the 1985 Radiological Survey at Fort Dix BOMARC Site, New Jersey

    DTIC Science & Technology

    1986-06-01

    8217fVft if neOLS&V end idenify by NIock nwtiber FIELD •-GROUP I SUB-GROUP BOHARC Radiological Survey WATCH-DOG PLUTO Ft Dix "Plutonium Environmental...12 Jun 73) under the operations plan entitled "WATCH-DOG PLUTO ". Since then, radiological site surveys have been completed in 1976, 1978. 1979, 1981...measurable pluto - nium was found. 2. Government Wells: Gross alpha and plutonium concentrations in all the government wells sampled met drinking water

  1. MX Siting Investigation. Water Resources Program. Results of Regional Carbonate Aquifer Testing, Coyote Spring Valley, Nevada.

    DTIC Science & Technology

    1981-12-18

    In the study area, these aquifer units include the Bird Springs Formation of Pennsylvannian age, the Monte Cristo Limestone of Mississipian age, and...Anchor Member of the Monte Cristo Limestone of Lower Mississippian age. The prominent Arrow Canyon Range lies to the south of the site. This range is an...of the range are of the Anchor Member of the Mississippian Monte Cristo Limestone. This formation has been included in hydrostratigraphic aquifer unit

  2. Control of Substrate Specificity by Active-Site Residues in Nitrobenzene Dioxygenase

    PubMed Central

    Ju, Kou-San; Parales, Rebecca E.

    2006-01-01

    Nitrobenzene 1,2-dioxygenase from Comamonas sp. strain JS765 catalyzes the initial reaction in nitrobenzene degradation, forming catechol and nitrite. The enzyme also oxidizes the aromatic rings of mono- and dinitrotoluenes at the nitro-substituted carbon, but the basis for this specificity is not understood. In this study, site-directed mutagenesis was used to modify the active site of nitrobenzene dioxygenase, and the contribution of specific residues in controlling substrate specificity and enzyme performance was evaluated. The activities of six mutant enzymes indicated that the residues at positions 258, 293, and 350 in the α subunit are important for determining regiospecificity with nitroarene substrates and enantiospecificity with naphthalene. The results provide an explanation for the characteristic specificity with nitroarene substrates. Based on the structure of nitrobenzene dioxygenase, substitution of valine for the asparagine at position 258 should eliminate a hydrogen bond between the substrate nitro group and the amino group of asparagine. Up to 99% of the mononitrotoluene oxidation products formed by the N258V mutant were nitrobenzyl alcohols rather than catechols, supporting the importance of this hydrogen bond in positioning substrates in the active site for ring oxidation. Similar results were obtained with an I350F mutant, where the formation of the hydrogen bond appeared to be prevented by steric interference. The specificity of enzymes with substitutions at position 293 varied depending on the residue present. Compared to the wild type, the F293Q mutant was 2.5 times faster at oxidizing 2,6-dinitrotoluene while retaining a similar Km for the substrate based on product formation rates and whole-cell kinetics. PMID:16517627

  3. Mutations in the BRCT binding site of BRCA1 result in hyper-recombination.

    PubMed

    Dever, Seth M; Golding, Sarah E; Rosenberg, Elizabeth; Adams, Bret R; Idowu, Michael O; Quillin, John M; Valerie, Nicholas; Xu, Bo; Povirk, Lawrence F; Valerie, Kristoffer

    2011-05-01

    We introduced a K1702M mutation in the BRCA1 BRCT domain known to prevent the binding of proteins harboring pS-X-X-F motifs such as Abraxas-RAP80, BRIP1, and CtIP. Surprisingly, rather than impairing homologous recombination repair (HRR), expression of K1702M resulted in hyper-recombination coinciding with an accumulation of cells in S-G2 and no effect on nonhomologous end-joining. These cells also showed increased RAD51 and RPA nuclear staining. More pronounced effects were seen with a naturally occurring BRCT mutant (M1775R) that also produced elevated levels of ssDNA, in part co-localizing with RPA, in line with excessive DNA resection. M1775R induced unusual, thread-like promyelocytic leukemia (PML) nuclear bodies and clustered RPA foci rather than the typical juxtaposed RPA-PML foci seen with wild-type BRCA1. Interestingly, K1702M hyper-recombination diminished with a second mutation in the BRCA1 RING domain (I26A) known to reduce BRCA1 ubiquitin-ligase activity. Thesein vitro findings correlated with elevated nuclear RAD51 and RPA staining of breast cancer tissue from a patient with the M1775R mutation. Altogether, the disruption of BRCA1 (BRCT)-pS-X-X-F protein binding results in ubiquitination-dependent hyper-recombination via excessive DNA resection and the appearance of atypical PML-NBs. Thus, certain BRCA1 mutations that cause hyper-recombination instead of reduced DSB repair might lead to breast cancer.

  4. 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.

  5. Pathways of H2 toward the Active Site of [NiFe]-Hydrogenase

    PubMed Central

    Teixeira, Vitor H.; Baptista, António M.; Soares, Cláudio M.

    2006-01-01

    Hydrogenases catalyze the reversible oxidation of molecular hydrogen (H2), but little is known about the diffusion of H2 toward the active site. Here we analyze pathways for H2 permeation using molecular dynamics (MD) simulations in explicit solvent. Various MD simulation replicates were done, to improve the sampling of the system states. H2 easily permeates hydrogenase in every simulation and it moves preferentially in channels. All H2 molecules that reach the active site made their approach from the side of the Ni ion. H2 is able to reach distances of <4 Å from the active site, although after 6 Å permeation is difficult. In this region we mutated Val-67 into alanine and perform new MD simulations. These simulations show an increase of H2 inside the protein and at lower distances from the active site. This valine can be a control point in the H2 access to the active center. PMID:16731562

  6. Relating subsurface temperature changes to microbial activity at a crude oil-contaminated site

    NASA Astrophysics Data System (ADS)

    Warren, Ean; Bekins, Barbara A.

    2015-11-01

    Crude oil at a spill site near Bemidji, Minnesota has been undergoing aerobic and anaerobic biodegradation for over 30 years, creating a 150-200 m plume of primary and secondary contaminants. Microbial degradation generates heat that should be measurable under the right conditions. To measure this heat, thermistors were installed in wells in the saturated zone and in water-filled monitoring tubes in the unsaturated zone. In the saturated zone, a thermal groundwater plume originates near the residual oil body with temperatures ranging from 2.9 °C above background near the oil to 1.2 °C down gradient. Temperatures in the unsaturated zone above the oil body were up to 2.7 °C more than background temperatures. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. Enthalpy calculations and observations demonstrate that the temperature increases primarily result from aerobic methane oxidation in the unsaturated zone above the oil. Methane oxidation rates at the site independently estimated from surface CO2 efflux data are comparable to rates estimated from the observed temperature increases. The results indicate that temperature may be useful as a low-cost measure of activity but care is required to account for the correct heat-generating reactions, other heat sources and the effects of focused recharge.

  7. Relating subsurface temperature changes to microbial activity at a crude oil-contaminated site.

    PubMed

    Warren, Ean; Bekins, Barbara A

    2015-11-01

    Crude oil at a spill site near Bemidji, Minnesota has been undergoing aerobic and anaerobic biodegradation for over 30 years, creating a 150-200 m plume of primary and secondary contaminants. Microbial degradation generates heat that should be measurable under the right conditions. To measure this heat, thermistors were installed in wells in the saturated zone and in water-filled monitoring tubes in the unsaturated zone. In the saturated zone, a thermal groundwater plume originates near the residual oil body with temperatures ranging from 2.9°C above background near the oil to 1.2°C down gradient. Temperatures in the unsaturated zone above the oil body were up to 2.7°C more than background temperatures. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. Enthalpy calculations and observations demonstrate that the temperature increases primarily result from aerobic methane oxidation in the unsaturated zone above the oil. Methane oxidation rates at the site independently estimated from surface CO2 efflux data are comparable to rates estimated from the observed temperature increases. The results indicate that temperature may be useful as a low-cost measure of activity but care is required to account for the correct heat-generating reactions, other heat sources and the effects of focused recharge.

  8. Relating subsurface temperature changes to microbial activity at a crude oil-contaminated site

    USGS Publications Warehouse

    Warren, Ean; Bekins, Barbara A.

    2015-01-01

    Crude oil at a spill site near Bemidji, Minnesota has been undergoing aerobic and anaerobic biodegradation for over 30 years, creating a 150–200 m plume of primary and secondary contaminants. Microbial degradation generates heat that should be measurable under the right conditions. To measure this heat, thermistors were installed in wells in the saturated zone and in water-filled monitoring tubes in the unsaturated zone. In the saturated zone, a thermal groundwater plume originates near the residual oil body with temperatures ranging from 2.9 °C above background near the oil to 1.2 °C down gradient. Temperatures in the unsaturated zone above the oil body were up to 2.7 °C more than background temperatures. Previous work at this site has shown that methane produced from biodegradation of the oil migrates upward and is oxidized in a methanotrophic zone midway between the water table and the surface. Enthalpy calculations and observations demonstrate that the temperature increases primarily result from aerobic methane oxidation in the unsaturated zone above the oil. Methane oxidation rates at the site independently estimated from surface CO2 efflux data are comparable to rates estimated from the observed temperature increases. The results indicate that temperature may be useful as a low-cost measure of activity but care is required to account for the correct heat-generating reactions, other heat sources and the effects of focused recharge.

  9. Continuum Level Results from Particle Simulations of Active Suspensions

    NASA Astrophysics Data System (ADS)

    Delmotte, Blaise; Climent, Eric; Plouraboue, Franck; Keaveny, Eric

    2014-11-01

    Accurately simulating active suspensions on the lab scale is a technical challenge. It requires considering large numbers of interacting swimmers with well described hydrodynamics in order to obtain representative and reliable statistics of suspension properties. We have developed a computationally scalable model based on an extension of the Force Coupling Method (FCM) to active particles. This tool can handle the many-body hydrodynamic interactions between O (105) swimmers while also accounting for finite-size effects, steady or time-dependent strokes, or variable swimmer aspect ratio. Results from our simulations of steady-stroke microswimmer suspensions coincide with those given by continuum models, but, in certain cases, we observe collective dynamics that these models do not predict. We provide robust statistics of resulting distributions and accurately characterize the growth rates of these instabilities. In addition, we explore the effect of the time-dependent stroke on the suspension properties, comparing with those from the steady-stroke simulations. Authors acknowledge the ANR project Motimo for funding and the Calmip computing centre for technical support.

  10. Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

    PubMed Central

    Sigala, Paul A.; Kraut, Daniel A.; Caaveiro, Jose M. M.; Pybus, Brandon; Ruben, Eliza A.; Ringe, Dagmar; Petsko, Gregory A.; Herschlag, Daniel

    2009-01-01

    Enzymes are classically proposed to accelerate reactions by binding substrates within active site environments that are structurally preorganized to optimize binding interactions with reaction transition states rather than ground states. This is a remarkably formidable task considering the limited 0.1 – 1 Å scale of most substrate rearrangements. The flexibility of active site functional groups along the coordinate of substrate rearrangement, the distance scale on which enzymes can distinguish structural rearrangement, and the energetic significance of discrimination on that scale remain open questions that are fundamental to a basic physical understanding of enzyme active sites and catalysis. We bring together high resolution X-ray crystallography, 1H and 19F NMR spectroscopy, quantum mechanical calculations, and transition state analog binding measurements to test the distance scale on which non-covalent forces can constrain side chain and ligand relaxation or translation along a specific coordinate and the energetic consequences of such geometric constraints within the active site of bacterial ketosteroid isomerase (KSI). Our results strongly suggest that packing and binding interactions within the KSI active site can constrain local side chain reorientation and prevent hydrogen bond shortening by 0.1 Å or less. Further, this constraint has substantial energetic effects on ligand binding and stabilization of negative charge within the oxyanion hole. These results provide evidence that subtle geometric effects, indistinguishable in most X-ray crystallographic structures, can have significant energetic consequences and highlight the importance of using synergistic experimental approaches to dissect enzyme function. PMID:18808119

  11. Idaho's surface-water-quality monitoring program: results from five sites sampled during water years 1990-93

    USGS Publications Warehouse

    ,

    1994-01-01

    In 1990, the U.S. Geological Survey (USGS), in cooperation with the Idaho Department of Health and Welfare, Division of Environmental Quality, implemented a statewide water-quality monitoring program in response to Idaho's antidegradation policy as required by the Clean Water Act. The program objective is to provide water-quality managers with a coordinated statewide network to detect trends in surface-water quality. The monitoring program includes the collection and analysis of samples from 56 sites on the Bear, Clearwater, Kootenai, Pend Oreille, Salmon, Snake, and Spokane Rivers and their tributaries (fig. 1). Samples are collected every year at 5 sites (annual sites) in drainage basins where long-term water-quality management is practiced, every other year at 19 sites (biennial sites) in basins where land and water uses change slowly, and every third year at 32 sites (triennial sites) where future development may affect water quality. Each year, 25 of the 56 sites are sampled. This report discusses results of sampling at five annual sites. During water years 1990-93 (October 1, 1989, through September 30, 1993), samples were collected six times per year at the five annual sites (fig. 1). Onsite analyses were made for discharge, specific conductance, pH, temperature, dissolved oxygen, bacteria (fecal coliform and fecal streptococci), and alkalinity. Laboratory analyses were made for major ions, nutrients, trace elements, and suspended sediment. Suspended sediment, nitrate, fecal coliform, trace elements, and specific conductance were used to characterize surface-water quality. Because concentrations of all trace elements except zinc were near detection limits, only zinc is discussed.

  12. Self-potential monitoring of a crude oil contaminated site (Trecate, Italy): first results of the modelling.

    NASA Astrophysics Data System (ADS)

    Giampaolo, V.; Rizzo, E.; Titov, K.; Maineult, A.; Lapenna, V.

    2012-04-01

    The contamination of soils and groundwater by hydrocarbon, due to blow out, leakage from tank or pipe and oil spill, is a heavy environmental problem because infiltrated oil can persist in the ground for a long time. The existing methods used for the remediation of these contaminated sites are invasive, time consuming and expensive. Therefore, in the last years, there was a growing interest in the use of geophysical methods for environmental monitoring (Atekwana et al., 2000; Chambers et al., 2004; Song et al., 2005; French et al., 2009). A particular attention is given to the self-potential (SP) method because SP is sensitive to the contaminant chemistry and redox processes generated by bacteria during the biodegradation (Atekwana et al., 2004; Naudet and Revil, 2005; Revil et al., 2010). Here we show the results of SP investigations carried out at Trecate site (Italy). This site was affected by a crude oil contamination from a well blowout in 1994. Four SP surveys (October 2009, March 2010, October 2010, and March 2011) were conducted at the site, both in the contaminated and uncontaminated regions. Significant changes are observed between SP data collected at different times. In particular, we found mostly negative electrical potential in October surveys and positive electrical potential in March surveys. The SP distributions can be interpreted as the superposition of many components, including a horizontal water-flow in the saturated shallow aquifer toward South-East, the infiltration movement of water in the unsaturated zone and, possibly, the oxidation-reduction phenomena due to bacterial activity. As the groundwater flow usually produces SP linear trends, the data were detrended by linear regression, taking into account the measured piezometric heads in the aquifer. The detrended SP data show that the SP distribution within the contaminated zone is generally bipolar in October: the southern part of the contaminated area is characterized by negative values

  13. The active site of oxidative phosphorylation and the origin of hyperhomocysteinemia in aging and dementia.

    PubMed

    McCully, Kilmer S

    2015-01-01

    The active site of oxidative phosphorylation and adenosine triphosphate (ATP) synthesis in mitochondria is proposed to consist of two molecules of thioretinamide bound to cobalamin, forming thioretinaco, complexed with ozone, oxygen, nicotinamide adenine dinucleotide. and inorganic phosphate, TR2CoO3O2NAD(+)H2PO4(-). Reduction of the pyridinium nitrogen of the nicotinamide group by an electron from electron transport complexes initiates polymerization of phosphate with adenosine diphosphate, yielding nicotinamide riboside and ATP bound to thioretinaco ozonide oxygen. A second electron reduces oxygen to hydroperoxyl radical, releasing ATP from the active site. A proton gradient is created within F1F0 ATPase complexes of mitochondria by reaction of protons with reduced nicotinamide riboside and with hydroperoxyl radical, yielding reduced nicotinamide riboside and hydroperoxide. The hyperhomocysteinemia of aging and dementia is attributed to decreased synthesis of adenosyl methionine by thioretinaco ozonide and ATP, causing decreased allosteric activation of cystathionine synthase and decreased allosteric inhibition of methylenetetrahydrofolate reductase and resulting in dysregulation of methionine metabolism.

  14. A phosphorylation site in the ftz homeodomain is required for activity.

    PubMed Central

    Dong, J; Hung, L H; Strome, R; Krause, H M

    1998-01-01

    The Drosophila homeodomain-containing protein Fushi tarazu (Ftz) is expressed sequentially in the embryo, first in alternate segments, then in specific neuroblasts and neurons in the central nervous system, and finally in parts of the gut. During these different developmental stages, the protein is heavily phosphorylated on different subsets of Ser and Thr residues. This stage-specific phosphorylation suggests possible roles for signal transduction pathways in directing tissue-specific Ftz activities. Here we show that one of the Ftz phosphorylation sites, T263 in the N-terminus of the Ftz homeodomain, is phosphorylated in vitro by Drosophila embryo extracts and protein kinase A. In the embryo, mutagenesis of this site to the non-phosphorylatable residue Ala resulted in loss of ftz-dependent segments. Conversely, substitution of T263 with Asp, which is also non-phosphorylatable, but which successfully mimics phosphorylated residues in a number of proteins, rescued the mutant phenotype. This suggests that T263 is in the phosphorylated state when functioning normally in vivo. We also demonstrate that the T263 substitutions of Ala and Asp do not affect Ftz DNA-binding activity in vitro, nor do they affect stability or transcriptional activity in transfected S2 cells. This suggests that T263 phosphorylation is most likely required for a homeodomain-mediated interaction with an embryonically expressed protein. PMID:9545243

  15. Structural changes in human cytomegalovirus cytoplasmic assembly sites in the absence of UL97 kinase activity

    SciTech Connect

    Azzeh, Maysa; Honigman, Alik; Taraboulos, Albert; Rouvinski, Alexander; Wolf, Dana G. . E-mail: wolfd@md.huji.ac.il

    2006-10-10

    Studies of human cytomegalovirus (HCMV) UL97 kinase deletion mutant ({delta}UL97) indicated a multi-step role for this kinase in early and late phases of the viral life cycle, namely, in DNA replication, capsid maturation and nuclear egress. Here, we addressed its possible involvement in cytoplasmic steps of HCMV assembly. Using the {delta}UL97 and the UL97 kinase inhibitor NGIC-I, we demonstrate that the absence of UL97 kinase activity results in a modified subcellular distribution of the viral structural protein assembly sites, from compact structures impacting upon the nucleus to diffuse perinuclear structures punctuated by large vacuoles. Infection by either wild type or {delta}UL97 viruses induced a profound reorganization of wheat germ agglutinin (WGA)-positive Golgi-related structures. Importantly, the viral-induced Golgi remodeling along with the reorganization of the nuclear architecture was substantially altered in the absence of UL97 kinase activity. These findings suggest that UL97 kinase activity might contribute to organization of the viral cytoplasmic assembly sites.

  16. Site-specific phosphorylation and microtubule dynamics control Pyrin inflammasome activation

    PubMed Central

    Gao, Wenqing; Yang, Jieling; Liu, Wang; Wang, Yupeng; Shao, Feng

    2016-01-01

    Pyrin, encoded by the MEFV gene, is best known for its gain-of-function mutations causing familial Mediterranean fever (FMF), an autoinflammatory disease. Pyrin forms a caspase-1–activating inflammasome in response to inactivating modifications of Rho GTPases by various bacterial toxins or effectors. Pyrin-mediated innate immunity is unique in that it senses bacterial virulence rather than microbial molecules, but its mechanism of activation is unknown. Here we show that Pyrin was phosphorylated in bone marrow-derived macrophages and dendritic cells. We identified Ser-205 and Ser-241 in mouse Pyrin whose phosphorylation resulted in inhibitory binding by cellular 14-3-3 proteins. The two serines underwent dephosphorylation upon toxin stimulation or bacterial infection, triggering 14-3-3 dissociation, which correlated with Pyrin inflammasome activation. We developed antibodies specific for phosphorylated Ser-205 and Ser-241, which confirmed the stimuli-induced dephosphorylation of endogenous Pyrin. Mutational analyses indicated that both phosphorylation and signal-induced dephosphorylation of Ser-205/241 are important for Pyrin activation. Moreover, microtubule drugs, including colchicine, commonly used to treat FMF, effectively blocked activation of the Pyrin inflammasome. These drugs did not affect Pyrin dephosphorylation and 14-3-3 dissociation but inhibited Pyrin-mediated apoptosis-associated Speck-like protein containing CARD (ASC) aggregation. Our study reveals that site-specific (de)phosphorylation and microtubule dynamics critically control Pyrin inflammasome activation, illustrating a fine and complex mechanism in cytosolic immunity. PMID:27482109

  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. Initial results from seismic monitoring at the Aquistore CO2 storage site, Saskatchewan, Canada

    DOE PAGES

    White, D. J.; Roach, L. A.N.; Roberts, B.; ...

    2014-12-31

    The Aquistore Project, located near Estevan, Saskatchewan, is one of the first integrated commercial-scale CO2 storage projects in the world that is designed to demonstrate CO2 storage in a deep saline aquifer. Starting in 2014, CO2 captured from the nearby Boundary Dam coal-fired power plant will be transported via pipeline to the storage site and to nearby oil fields for enhanced oil recovery. At the Aquistore site, the CO2 will be injected into a brine-filled sandstone formation at ~3200 m depth using the deepest well in Saskatchewan. The suitability of the geological formations that will host the injected CO2 hasmore » been predetermined through 3D characterization using high-resolution 3D seismic images and deep well information. These data show that 1) there are no significant faults in the immediate area of the storage site, 2) the regional sealing formation is continuous in the area, and 3) the reservoir is not adversely affected by knolls on the surface of the underlying Precambrian basement. Furthermore, the Aquistore site is located within an intracratonic region characterized by extremely low levels of seismicity. This is in spite of oil-field related water injection in the nearby Weyburn-Midale field where a total of 656 million m3 of water have been injected since the 1960`s with no demonstrable related induced seismicity. A key element of the Aquistore research program is the further development of methods to monitor the security and subsurface distribution of the injected CO2. Toward this end, a permanent areal seismic monitoring array was deployed in 2012, comprising 630 vertical-component geophones installed at 20 m depth on a 2.5x2.5 km regular grid. This permanent array is designed to provide improved 3D time-lapse seismic imaging for monitoring subsurface CO2. Prior to the onset of CO2 injection, calibration 3D surveys were acquired in May and November of 2013. Comparison of the data from these surveys relative to the baseline 3D survey data

  19. Methane activation by platinum: critical role of edge and corner sites of metal nanoparticles.

    PubMed

    Viñes, Francesc; Lykhach, Yaroslava; Staudt, Thorsten; Lorenz, Michael P A; Papp, Christian; Steinrück, Hans-Peter; Libuda, Jörg; Neyman, Konstantin M; Görling, Andreas

    2010-06-11

    Complete dehydrogenation of methane is studied on model Pt catalysts by means of state-of-the-art DFT methods and by a combination of supersonic molecular beams with high-resolution photoelectron spectroscopy. The DFT results predict that intermediate species like CH(3) and CH(2) are specially stabilized at sites located at particles edges and corners by an amount of 50-80 kJ mol(-1). This stabilization is caused by an enhanced activity of low-coordinated sites accompanied by their special flexibility to accommodate adsorbates. The kinetics of the complete dehydrogenation of methane is substantially modified according to the reaction energy profiles when switching from Pt(111) extended surfaces to Pt nanoparticles. The CH(3) and CH(2) formation steps are endothermic on Pt(111) but markedly exothermic on Pt(79). An important decrease of the reaction barriers is observed in the latter case with values of approximately 60 kJ mol(-1) for first C-H bond scission and 40 kJ mol(-1) for methyl decomposition. DFT predictions are experimentally confirmed by methane decomposition on Pt nanoparticles supported on an ordered CeO(2) film on Cu(111). It is shown that CH(3) generated on the Pt nanoparticles undergoes spontaneous dehydrogenation at 100 K. This is in sharp contrast to previous results on Pt single-crystal surfaces in which CH(3) was stable up to much higher temperatures. This result underlines the critical role of particle edge sites in methane activation and dehydrogenation.

  20. Results of Bioventing System Monitoring at Eglin Main Base Old Fire Training Area (Site FT-28), Eglin Air Force Base, Florida

    DTIC Science & Technology

    2007-11-02

    This letter presents the results of the bioventing system monitoring performed by Parsons Engineering Science, Inc. (Parsons ES) during the week of 8...assess the extent of remediation completed during approximately 1 year of expanded-scale bioventing system operation. The purpose of this letter is to...summarize site and bioventing activities to date, present the results of the most recent respiration testing and soil gas sampling event, and make

  1. One-Year Testing Results Report for Full-Scale Bioventing at the POL Yard, Sites SS-06 and ST-40, Wurtsmith AFB, Michigan

    DTIC Science & Technology

    2007-11-02

    This letter report presents the results for the full-scale bioventing system testing performed by Parsons Engineering Science, Inc. (Parsons ES) at...ES from 15 to 18 September 1997 to assess the extent of remediation completed during approximately 1 year of air injection bioventing . The purpose of...this letter is to summarize site and bioventing activities to date, present the results of the most recent respiration testing and soil gas sampling

  2. H/V ratio: a tool for site effects evaluation. Results from 1-D noise simulations

    NASA Astrophysics Data System (ADS)

    Bonnefoy-Claudet, Sylvette; Cornou, Cécile; Bard, Pierre-Yves; Cotton, Fabrice; Moczo, Peter; Kristek, Jozef; Fäh, Donat

    2006-11-01

    Ambient vibration techniques such as the H/V method may have the potential to significantly contribute to site effect evaluation, particularly in urban areas. Previous studies interpret the so-called Nakamura's technique in relation to the ellipticity ratio of Rayleigh waves, which, for a high enough impedance contrast, exhibits a pronounced peak close to the fundamental S-wave resonance frequency. Within the European SESAME project (Site EffectS assessment using AMbient Excitations) this interpretation has been tested through noise numerical simulation under well-controlled conditions in terms of source type and distribution and propagation structure. We will present simulations for a simple realistic site (one sedimentary layer over bedrock) characterized by a rather high impedance contrast and low quality factor. Careful H/V and array analysis on these noise synthetics allow an in-depth investigation of the link between H/V ratio peaks and the noise wavefield composition for the soil model considered here: (1) when sources are near (4 to 50 times the layer thickness) and surficial, H/V curves exhibit one single peak, while the array analysis shows that the wavefield is dominated by Rayleigh waves; (2) when sources are distant (more than 50 times the layer thickness) and located inside the sedimentary layer, two peaks show up on the H/V curve, while the array analysis indicates both Rayleigh waves and strong S head waves; the first peak is due to both fundamental Rayleigh waves and resonance of head S waves, the second is only due to the resonance of head S waves; (3) when sources are deep (located inside the bedrock), whatever their distance, H/V ratio exhibit peaks at the fundamental and harmonic resonance frequencies, while array analyses indicate only non-dispersive body waves; the H/V is thus simply due to multiple reflections of S waves within the layer. Therefore, considering that experimental H/V ratio (i.e. derived from actual noise measured in the field

  3. 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...

  4. 75 FR 71677 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-24

    ... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department of... uranium and thorium processing site licensees for reimbursement under Title X of the Energy Policy Act of... requires DOE to reimburse eligible uranium and thorium licensees for certain costs of...

  5. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...). (e) For all asbestos-containing waste material received, the owner or operator of the active waste... 40 Protection of Environment 9 2013-07-01 2013-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an...

  6. QM/MM Analysis of Cellulase Active Sites and Actions of the Enzymes on Substrates

    SciTech Connect

    Saharay, Moumita; Guo, Hao-Bo; Smith, Jeremy C; Guo, Hong

    2010-01-01

    Biodegradation of cellulosic biomass requires the actions of three types of secreted enzymes; endoglucanase (EC 3.2.1.4), cellobiohydrolase or exoglucanase (EC 3.2.1.91), and -glucosidase (EC 4.2.1.21). These enzymes act synergistically to hydrolyse the -1,4 bonds of cellulose and converts it into simple sugar. Hydrolysis of the glycosidic bond can occur either by net retention or by inversion of anomeric configuration at the anomeric center. QM/MM simulations are useful tools to study the energetics of the reactions and analyze the active-site structures at different states of the catalysis, including the formation of unstable transition states. Here, a brief description of previous work on glycoside hydrolases is first given. The results of the QM/MM potential energy and free energy simulations corresponding to glycosylation and deglycosylation processes are then provided for two retaining endoglucanases, Cel12A and Cel5A. The active-site structural features are analyzed based on the QM/MM results. The role of different residues and hydrogen bonding interactions during the catalysis and the importance of the sugar ring distortion are discussed for these two enzymes.

  7. Selectivity of fungal sesquiterpene synthases: role of the active site's H-1 alpha loop in catalysis.

    PubMed

    López-Gallego, Fernando; Wawrzyn, Grayson T; Schmidt-Dannert, Claudia

    2010-12-01

    Sesquiterpene synthases are responsible for the cyclization of farnesyl pyrophosphate into a myriad of structurally diverse compounds with various biological activities. We examine here the role of the conserved active site H-α1 loop in catalysis in three previously characterized fungal sesquiterpene synthases. The H-α1 loops of Cop3, Cop4, and Cop6 from Coprinus cinereus were altered by site-directed mutagenesis and the resultant product profiles were analyzed by gas chromatography-mass spectrometry and compared to the wild-type enzymes. In addition, we examine the effect of swapping the H-α1 loop from the promiscuous enzyme Cop4 with the more selective Cop6 and the effect of acidic or basic conditions on loop mutations in Cop4. Directed mutations of the H-α1 loop had a marked effect on the product profile of Cop3 and Cop4, while little to no change was shown in Cop6. Swapping of the Cop4 and Cop6 loops with one another was again shown to influence the product profile of Cop4, while the product profile of Cop6 remained identical to the wild-type enzyme. The loop mutations in Cop4 also implicate specific residues responsible for the pH sensitivity of the enzyme. These results affirm the role of the H-α1 loop in catalysis and provide a potential target to increase the product diversity of terpene synthases.

  8. Unmasking tandem site interaction in human acetylcholinesterase. Substrate activation with a cationic acetanilide substrate.

    PubMed

    Johnson, Joseph L; Cusack, Bernadette; Davies, Matthew P; Fauq, Abdul; Rosenberry, Terrone L

    2003-05-13

    Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge, and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to catalytic efficiency by transiently binding substrates on their way to the acylation site, where a short-lived acyl enzyme intermediate is produced. A conformational interaction between the A- and P-sites has recently been found to modulate ligand affinities. We now demonstrate that this interaction is of functional importance by showing that the acetylation rate constant of a substrate bound to the A-site is increased by a factor a when a second molecule of substrate binds to the P-site. This demonstration became feasible through the introduction of a new acetanilide substrate analogue of acetylcholine, 3-(acetamido)-N,N,N-trimethylanilinium (ATMA), for which a = 4. This substrate has a low acetylation rate constant and equilibrates with the catalytic site, allowing a tractable algebraic solution to the rate equation for substrate hydrolysis. ATMA affinities for the A- and P-sites deduced from the kinetic analysis were confirmed by fluorescence titration with thioflavin T as a reporter ligand. Values of a >1 give rise to a hydrolysis profile called substrate activation, and the AChE site-specific mutant W86F, and to a lesser extent wild-type human AChE itself, showed substrate activation with acetylthiocholine as the substrate. Substrate activation was incorporated into a previous catalytic scheme for AChE in which a bound P-site ligand can also block product dissociation from the A-site, and two additional features of the AChE catalytic pathway were revealed. First, the ability of a bound P-site ligand to increase the substrate acetylation rate constant varied with the structure of the ligand: thioflavin T accelerated ATMA acetylation by a factor a(2) of 1.3, while propidium failed to accelerate. Second, catalytic rate

  9. Heparanase Activates Antithrombin through the Binding to Its Heparin Binding Site

    PubMed Central

    Águila, Sonia; Teruel-Montoya, Raúl; Vicente, Vicente; Corral, Javier; Martínez-Martínez, Irene

    2016-01-01

    Heparanase is an endoglycosidase that participates in morphogenesis, tissue repair, heparan sulphates turnover and immune response processes. It is over-expressed in tumor cells favoring the metastasis as it penetrates the endothelial layer that lines blood vessels and facilitates the metastasis by degradation of heparan sulphate proteoglycans of the extracellular matrix. Heparanase may also affect the hemostatic system in a non-enzymatic manner, up-regulating the expression of tissue factor, which is the initiator of blood coagulation, and dissociating tissue factor pathway inhibitor on the cell surface membrane of endothelial and tumor cells, thus resulting in a procoagulant state. Trying to check the effect of heparanase on heparin, a highly sulphated glycosaminoglycan, when it activates antithrombin, our results demonstrated that heparanase, but not proheparanase, interacted directly with antithrombin in a non-covalent manner. This interaction resulted in the activation of antithrombin, which is the most important endogenous anticoagulant. This activation mainly accelerated FXa inhibition, supporting an allosteric activation effect. Heparanase bound to the heparin binding site of antithrombin as the activation of Pro41Leu, Arg47Cys, Lys114Ala and Lys125Alaantithrombin mutants was impaired when it was compared to wild type antithrombin. Intrinsic fluorescence analysis showed that heparanase induced an activating conformational change in antithrombin similar to that induced by heparin and with a KD of 18.81 pM. In conclusion, under physiological pH and low levels of tissue factor, heparanase may exert a non-enzymatic function interacting and activating the inhibitory function of antithrombin. PMID:27322195

  10. Single-molecule catalysis mapping quantifies site-specific activity and uncovers radial activity gradient on single 2D nanocrystals.

    PubMed

    Andoy, Nesha May; Zhou, Xiaochun; Choudhary, Eric; Shen, Hao; Liu, Guokun; Chen, Peng

    2013-02-06

    Shape-controlled metal nanocrystals are a new generation of nanoscale catalysts. Depending on their shapes, these nanocrystals exhibit various surface facets, and the assignments of their surface facets have routinely been used to rationalize or predict their catalytic activity in a variety of chemical transformations. Recently we discovered that for 1-dimensional (1D) nanocrystals (Au nanorods), the catalytic activity is not constant along the same side facets of single nanorods but rather differs significantly and further shows a gradient along its length, which we attributed to an underlying gradient of surface defect density resulting from their linear decay in growth rate during synthesis (Nat. Nanotechnol.2012, 7, 237-241). Here we report that this behavior also extends to 2D nanocrystals, even for a different catalytic reaction. By using super-resolution fluorescence microscopy to map out the locations of catalytic events within individual triangular and hexagonal Au nanoplates in correlation with scanning electron microscopy, we find that the catalytic activity within the flat {111} surface facet of a Au nanoplate exhibits a 2D radial gradient from the center toward the edges. We propose that this activity gradient results from a growth-dependent surface defect distribution. We also quantify the site-specific activity at different regions within a nanoplate: The corner regions have the highest activity, followed by the edge regions and then the flat surface facets. These discoveries highlight the spatial complexity of catalytic activity at the nanoscale as well as the interplay amid nanocrystal growth, morphology, and surface defects in determining nanocatalyst properties.

  11. Site-directed mutagenesis of the toxin from the Chinese scorpion Buthus martensii Karsch (BmKAS): insight into sites related to analgesic activity.

    PubMed

    Cui, Yong; Song, Yong-Bo; Ma, Lin; Liu, Yan-Feng; Li, Guo-Dong; Wu, Chun-Fu; Zhang, Jing-Hai

    2010-10-01

    This study utilized the E. coli expression system to investigate the role of amino acid residues in toxin from the Chinese scorpion--Buthus martensii Karsch (BmKAS). To evaluate the extent to which residues of the toxin core contribute to its analgesic activity, ten mutants of BmKAS were obtained by PCR. Using site-directed mutagenesis, all of these residues were substituted with different amino acids. This study represents a thorough mapping and elucidation of the epitopes that form the molecular basis of the toxin's analgesic activity. Our results showed large mutant-dependent differences that emphasize the important roles of the studied residues.

  12. a New Site at Central Amazonia Dedicated to Long Term Cloud Properties Observations - Description, First Results and Future Perspectives.

    NASA Astrophysics Data System (ADS)

    Pauliquevis, T.; Barbosa, H. M.; Adams, D. K.; Artaxo, P.; Cirino, G. G.; Barja Gonzalez, B.; Correia, A. L.; Gomes, H. B.; Gouveia, D. A.; Padua, M. B.; Rosario, N. M. E. D.; Souza, R. A. F. D.; Nascimento dos Santos, R. M.; Sapucci, L.; Portela, B. T.

    2014-12-01

    Amazon basin during the wet season is one of the few places on Earth where "natural atmosphere", as it is expected to be in pre-industrial era, can be observed. Atmosphere in clean Amazonia can be regarded as a baseline state of tropical atmosphere. Its hydrological cycle is extreme active, as well as its convection. Several scientific questions with respect to convection remain unclear. Diurnal cycle of convection is far from adequately represented in numeric models. Precipitation typically occurs in models in the first few hours in the morning, whereas actual rain occurs mostly in the early afternoon. Convection parameterizations lack the ability to represent it adequately due to the models coarse resolution of parameterizations compared to the spatial scale of shallow convection. An adequate comprehension of shallow to deep convection transition is critical to improve convection representation in models. To reach this goal, long term measurements that could characterize clouds and convection diurnal cycle are fundamental. The implementation of ACONVEX (Atmospheric CONVection EXperiment) site, situated 50 km upwind from the megacity of Manaus ( -2.894263S°, -59.971452W) aims to fill the existent gap in long term measurements. It is designed to make measurements for more than 10 yrs, and characterize cloud properties in a climatological perspective. The site started its operation in August, 2011, initially with the Raman Lidar. Present time instrumentation set comprises: 1) UV Lidar Raman, 2) CIMEL Sunphotometer, 3) MultiFilter shadow band Radiometer (MFR), 4) GNSS/GPS Receiver, 5) Vertical Pointing Radar, 6) Disdrometer, 7) Ceilometer, 8) Met station. Two sky imagers and a microwave radiometer are about to be operated and will be able to derive 1) Cloud Cover, 2) Cloud Top and Cloud Base Heights, 3) Liquid Water Content, 4) Integrated Precipitable Water, 5) PBL Height, 6) Rain Rate (vertical profile and at surface). In this poster we discuss the site in more

  13. Active site similarity between human and Plasmodium falciparum phosphodiesterases: considerations for antimalarial drug design

    NASA Astrophysics Data System (ADS)

    Howard, Brittany L.; Thompson, Philip E.; Manallack, David T.

    2011-08-01

    The similarity between Plasmodium falciparum phosphodiesterase enzymes ( PfPDEs) and their human counterparts have been examined and human PDE9A was found to be a suitable template for the construction of homology models for each of the four PfPDE isoforms. In contrast, the architecture of the active sites of each model was most similar to human PDE1. Molecular docking was able to model cyclic guanosine monophosphate (cGMP) substrate binding in each case but a docking mode supporting cyclic adenosine monophosphate (cAMP) binding could not be found. Anticipating the potential of PfPDE inhibitors as anti-malarial drugs, a range of reported PDE inhibitors including zaprinast and sildenafil were docked into the model of PfPDEα. The results were consistent with their reported biological activities, and the potential of PDE1/9 inhibitor analogues was also supported by docking.

  14. Active Spacecraft Potential Control: Results From the Double Star Project

    NASA Astrophysics Data System (ADS)

    Torkar, K.; Fazakerley, A.; Steiger, W.

    2006-10-01

    The ion emitter instrument "active spacecraft potential control" (ASPOC) has been used successfully in several magnetospheric missions including the European Space Agency Cluster Project. An improved version has been developed for the equatorial spacecraft of the Chinese-European Double Star mission (TC-1) launched in December 2003. The modifications include a new design of the ion emitter modules. As a result, higher currents than in previous missions can be achieved. The main objective of the investigation is the reduction of positive spacecraft potential in order to minimize perturbations to the plasma measurements onboard, in particular to the plasma electron instrument PEACE. These data show an almost complete suppression of photoelectrons when ASPOC is emitting at 30- to 50-muA beam current. The angular distribution of the electrons in the presence of the ion beam is investigated in detail. The measurement of ambient electron distributions is highly improved.

  15. Cues Resulting in Desire for Sexual Activity in Women

    PubMed Central

    McCall, Katie; Meston, Cindy

    2010-01-01

    Introduction A number of questionnaires have been created to assess levels of sexual desire in women, but to our knowledge, there are currently no validated measures for assessing cues that result in sexual desire. A questionnaire of this nature could be useful for both clinicians and researchers, because it considers the contextual nature of sexual desire and it draws attention to individual differences in factors that can contribute to sexual desire. Aim The aim of the present study was to create a multidimensional assessment tool of cues for sexual desire in women that is validated in women with and without hypoactive sexual desire disorder (HSDD). Methods Factor analyses conducted on both an initial sample (N = 874) and a community sample (N = 138) resulted in the Cues for Sexual Desire Scale (CSDS) which included four factors: (i) Emotional Bonding Cues; (ii) Erotic/ Explicit Cues; (iii) Visual/Proximity Cues; and (iv) Implicit/Romantic Cues. Main Outcome Measures Scale construction of cues associated with sexual desire and differences between women with and without sexual dysfunction. Results The CSDS demonstrated good reliability and validity and was able to detect significant differences between women with and without HSDD. Results from regression analyses indicated that both marital status and level of sexual functioning predicted scores on the CSDS. The CSDS provided predictive validity for the Female Sexual Function Index desire and arousal domain scores, and increased cues were related to a higher reported frequency of sexual activity in women. Conclusions The findings from the present study provide valuable information regarding both internal and external triggers that can result in sexual desire for women. We believe that the CSDS could be beneficial in therapeutic settings to help identify cues that do and do not facilitate sexual desire in women with clinically diagnosed desire difficulties. PMID:16942529

  16. 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.

  17. Using Unnatural Amino Acids to Probe the Energetics of Oxyanion Hole Hydrogen Bonds in the Ketosteroid Isomerase Active Site

    PubMed Central

    2015-01-01

    Hydrogen bonds are ubiquitous in enzyme active sites, providing binding interactions and stabilizing charge rearrangements on substrate groups over the course of a reaction. But understanding the origin and magnitude of their catalytic contributions relative to hydrogen bonds made in aqueous solution remains difficult, in part because of complexities encountered in energetic interpretation of traditional site-directed mutagenesis experiments. It has been proposed for ketosteroid isomerase and other enzymes that active site hydrogen bonding groups provide energetic stabilization via “short, strong” or “low-barrier” hydrogen bonds that are formed due to matching of their pKa or proton affinity to that of the transition state. It has also been proposed that the ketosteroid isomerase and other enzyme active sites provide electrostatic environments that result in larger energetic responses (i.e., greater “sensitivity”) to ground-state to transition-state charge rearrangement, relative to aqueous solution, thereby providing catalysis relative to the corresponding reaction in water. To test these models, we substituted tyrosine with fluorotyrosines (F-Tyr’s) in the ketosteroid isomerase (KSI) oxyanion hole to systematically vary the proton affinity of an active site hydrogen bond donor while minimizing steric or structural effects. We found that a 40-fold increase in intrinsic F-Tyr acidity caused no significant change in activity for reactions with three different substrates. F-Tyr substitution did not change the solvent or primary kinetic isotope effect for proton abstraction, consistent with no change in mechanism arising from these substitutions. The observed shallow dependence of activity on the pKa of the substituted Tyr residues suggests that the KSI oxyanion hole does not provide catalysis by forming an energetically exceptional pKa-matched hydrogen bond. In addition, the shallow dependence provides no indication of an active site electrostatic

  18. The surface chemistry of heterogeneous catalysis: mechanisms, selectivity, and active sites.

    PubMed

    Zaera, Francisco

    2005-01-01

    The role of chemical kinetics in defining the requirements for the active sites of heterogeneous catalysts is discussed. A personal view is presented, with specific examples from our laboratory to illustrate the role of the chemical composition, structure, and electronic properties of specific surface sites in determining reaction activity and selectivity. Manipulation of catalytic behavior via the addition of chemical modifiers and by tuning of the reaction conditions is also introduced.

  19. The role of active site tyrosine 58 in Citrobacter freundii methionine γ-lyase.

    PubMed

    Anufrieva, Natalya V; Faleev, Nicolai G; Morozova, Elena A; Bazhulina, Natalia P; Revtovich, Svetlana V; Timofeev, Vladimir P; Tkachev, Yaroslav V; Nikulin, Alexei D; Demidkina, Tatyana V

    2015-09-01

    In the spatial structure of methionine γ-lyase (MGL, EC 4.4.1.11) from Citrobacter freundii, Tyr58 is located at H-bonding distance to the oxygen atom of the phosphate "handle" of pyridoxal 5'-phosphate (PLP). It was replaced for phenylalanine by site-directed mutagenesis. The X-ray structure of the mutant enzyme was determined at 1.96Å resolution. Comparison of spatial structures and absorption spectra of wild-type and mutant holoenzymes demonstrated that the replacement did not result in essential changes of the conformation of the active site Tyr58Phe MGL. The Kd value of PLP for Tyr58Phe MGL proved to be comparable to the Kd value for the wild-type enzyme. The replacement led to a decrease of catalytic efficiencies in both γ- and β-elimination reactions of about two orders of magnitude as compared to those for the wild-type enzyme. The rates of exchange of C-α- and C-β- protons of inhibitors in D2O catalyzed by the mutant form are comparable with those for the wild-type enzyme. Spectral data on the complexes of the mutant form with the substrates and inhibitors showed that the replacement led to a change of rate the limiting step of the physiological reaction. The results allowed us to conclude that Tyr58 is involved in an optimal positioning of the active site Lys210 at some stages of γ- and β-elimination reactions. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.

  20. Initial formulation results for in situ grouting of a waste trench at ORNL Site No. 6

    SciTech Connect

    Tallent, O.K.; McDaniel, E.W.; Spence, R.D.; Godsey, T.T.

    1987-01-01

    An investigation is being conducted by the Chemical Technology Division to assist the Environmental Sciences Division in developing a grout formulation for use in testing in situ grouting in a waste trench at ORNL Site 6. This final report satisfies the milestone of Subtack 12 entitled, ''Low Level Waste (LLW) Trench Grouting Assessment,'' which was initially issued as RAP-86-7, December 31, 1985. Grouts prepared from dry-solid blends containing Type I Portland cement, ASTM Class C or Class F fly ash, and bentonite, mixed water at ratios of 10 to 15 lb/gal, were evaluated. The grouts prepared with ASTM Class C fly ash exhibited significantly better properties than those prepared with ASTM Class F fly ash. The grouts containing ASTM Class C fly ash satisfy tentative performance criteria for the project. 8 refs., 7 tabs.

  1. Nuclear waste: Status of DOE`s nuclear waste site characterization activities

    SciTech Connect

    1987-12-31

    Three potential nuclear waste repository sites have been selected to carry out characterization activities-the detailed geological testing to determine the suitability of each site as a repository. The sites are Hanford in south-central Washington State, Yucca Mountain in southern Nevada, and Deaf Smith in the Texas Panhandle. Two key issues affecting the total program are the estimations of the site characterization completion data and costs and DOE`s relationship with the Nuclear Regulatory Commission which has been limited and its relations with affected states and Indian tribes which continue to be difficult.

  2. Active site mutants of human cyclophilin A separate peptidyl-prolyl isomerase activity from cyclosporin A binding and calcineurin inhibition.

    PubMed Central

    Zydowsky, L. D.; Etzkorn, F. A.; Chang, H. Y.; Ferguson, S. B.; Stolz, L. A.; Ho, S. I.; Walsh, C. T.

    1992-01-01

    Based on recent X-ray structural information, six site-directed mutants of human cyclophilin A (hCyPA) involving residues in the putative active site--H54, R55, F60, Q111, F113, and H126--have been constructed, overexpressed, and purified from Escherichia coli to homogeneity. The proteins W121A (Liu, J., Chen, C.-M., & Walsh, C.T., 1991a, Biochemistry 30, 2306-2310), H54Q, R55A, F60A, Q111A, F113A, and H126Q were assayed for cis-trans peptidyl-prolyl isomerase (PPIase) activity, their ability to bind the immunosuppressive drug cyclosporin A (CsA), and protein phosphatase 2B (calcineurin) inhibition in the presence of CsA. Results indicate that H54Q, Q111A, F113A, and W121A retain 3-15% of the catalytic efficiency (kcat/Km) of wild-type recombinant hCyPA. The remaining three mutants (R55A, F60A, and H126Q) each retain less than 1% of the wild-type catalytic efficiency, indicating participation by these residues in PPIase catalysis. Each of the mutants bound to a CsA affinity matrix. The mutants R55A, F60A, F113A, and H126Q inhibited calcineurin in the presence of CsA, whereas W121A did not. Although CsA is a competitive inhibitor of PPIase activity, it can complex with enzymatically inactive cyclophilins and inhibit the phosphatase activity of calcineurin. PMID:1338979

  3. Noncovalent intermolecular interactions between dehydroepiandrosterone and the active site of human dehydroepiandrosterone sulphotransferase: A density functional theory based treatment

    NASA Astrophysics Data System (ADS)

    Astani, Elahe; Heshmati, Emran; Chen, Chun-Jung; Hadipour, Nasser L.; Shekarsaraei, Setareh

    2016-04-01

    A theoretical study was performed to characterize noncovalent intermolecular interactions, especially hydrogen bond (HB), in the active site of enzyme human dehydroepiandrosterone sulphotransferase (SULT2A1/DHEA) using the local (M06-L) and hybrid (M06, M06-2X) meta-GGA functionals of density functional theory (DFT). Results revealed that DHEA is able to form HBs with residues His99, Tyr231, Met137 and Met16 in the active site of the SULT2A1/DHEA. It was found that DHEA interacts with the other residues through electrostatic and Van der Waals interactions.

  4. The Edison Environmental Center Permeable Pavement Site: Initial Results from a Stormwater Control Designed for Monitoring

    EPA Science Inventory

    There are few detailed studies of full-scale, replicated, actively-used permeable pavement systems. Practitioners need additional studies of permeable pavement systems in its intended application (parking lot, roadway, etc.) across a range of climatic events, daily usage conditio...

  5. Optimal active vibration absorber: Design and experimental results

    NASA Technical Reports Server (NTRS)

    Lee-Glauser, Gina; Juang, Jer-Nan; Sulla, Jeffrey L.

    1992-01-01

    An optimal active vibration absorber can provide guaranteed closed-loop stability and control for large flexible space structures with collocated sensors/actuators. The active vibration absorber is a second-order dynamic system which is designed to suppress any unwanted structural vibration. This can be designed with minimum knowledge of the controlled system. Two methods for optimizing the active vibration absorber parameters are illustrated: minimum resonant amplitude and frequency matched active controllers. The Controls-Structures Interaction Phase-1 Evolutionary Model at NASA LaRC is used to demonstrate the effectiveness of the active vibration absorber for vibration suppression. Performance is compared numerically and experimentally using acceleration feedback.

  6. Structure of the endonuclease IV homologue from Thermotoga maritima in the presence of active-site divalent metal ions

    SciTech Connect

    Tomanicek, Stephen J.; Hughes, Ronny C.; Ng, Joseph D.; Coates, Leighton

    2010-10-05

    The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5{prime}-phosphodiester bond at an AP site to generate a free 3{prime}-hydroxyl group and a 5{prime}-terminal sugar phosphate using their AP nuclease activity. Specifically, Thermotoga maritima endonuclease IV is a member of the second conserved AP endonuclease family that includes Escherichia coli endonuclease IV, which is the archetype of the AP endonuclease superfamily. In order to more fully characterize the AP endonuclease family of enzymes, two X-ray crystal structures of the T. maritima endonuclease IV homologue were determined in the presence of divalent metal ions bound in the active-site region. These structures of the T. maritima endonuclease IV homologue further revealed the use of the TIM-barrel fold and the trinuclear metal binding site as important highly conserved structural elements that are involved in DNA-binding and AP-site repair processes in the AP endonuclease superfamily.

  7. First tephrostratigraphic results of the DEEP site record from Lake Ohrid (Macedonia and Albania)

    NASA Astrophysics Data System (ADS)

    Leicher, Niklas; Zanchetta, Giovanni; Sulpizio, Roberto; Giaccio, Biagio; Wagner, Bernd; Nomade, Sebastien; Francke, Alexander; Del Carlo, Paola

    2016-04-01

    A tephrostratigraphic record covering the Marine Isotope Stages (MIS) 1-15 was established for the DEEP site record of Lake Ohrid (Macedonia and Albania). Major element analyses (energy dispersive spectroscopy (EDS) and wavelength-dispersive spectroscopy (WDS)) were carried out on juvenile fragments extracted from 12 tephra layers (OH-DP-0115 to OH-DP-2060). The geochemical analyses of the glass shards of all of these layers suggest an origin in the Italian volcanic provinces. They include the Y-3 (OH-DP-0115, 26.68-29.42 ka cal BP), the Campanian Ignimbrite-Y-5 (OH-DP-0169, 39.6 ± 0.1 ka), and the X-6 (OH-DP-0404, 109 ± 2 ka) from the Campanian volcanoes, the P-11 of Pantelleria (OH-DP-0499, 133.5 ± 2 ka), the Vico B (OH-DP-0617, 162 ± 6 ka) from the Vico volcano, the Pozzolane Rosse (OH-DP-1817, 457 ± 2 ka) and the Tufo di Bagni Albule (OH-DP-2060, 527 ± 2 ka) from the Colli Albani volcanic district, and the Fall A (OH-DP-2010, 496 ± 3 ka) from the Sabatini volcanic field. Furthermore, a comparison of the Ohrid record with tephrostratigraphic records of mid-distal archives related to the Mediterranean area allowed the recognition of the equivalents of other less known tephra layers, such as the TM24a-POP2 (OH-DP-0404, 102 ± 2 ka) recognized in the Lago Grande di Monticchio and the Sulmona Basin, the CF-V5-PRAD3225 (OH-DP-0624, ca. 163 ± 22 ka) identified in the Campo Felice Basin and the Adriatic Sea, the SC5 (OH-DP-1955, 493.1 ± 10.9 ka) recognized in the Mercure Basin, and the A11/12 (OH-DP-2017, 511 ± 6 ka) sampled at the Acerno Basin, whose specific volcanic sources are still poorly constrained. Additionally, one cryptotephra (OH-DP-0027) was identified by correlation of the potassium X-ray flourescence (XRF) intensities from the DEEP site with those from a short core of a previous study from Lake Ohrid. In these cores, a maximum in potassium is caused by glass shards, which were correlated with the Mercato tephra (8.43-8.63 ka cal BP) from Somma

  8. First tephrostratigraphic results of the DEEP site record from Lake Ohrid, Macedonia

    NASA Astrophysics Data System (ADS)

    Leicher, N.; Zanchetta, G.; Sulpizio, R.; Giaccio, B.; Wagner, B.; Nomade, S.; Francke, A.; Del Carlo, P.

    2015-09-01

    A~tephrostratigraphic record covering the Marine Isotope Stages (MIS) 1-15 was established for the DEEP site record of Lake Ohrid (Macedonia/Albania). Major element analyses (SEM-EDS/WDS) were carried out on juvenile fragments extracted from 12 tephra layers (OH-DP-0115 to OH-DP-2060). The geochemical analyses of the glass shards of all of these layers suggest an origin from the Italian Volcanic Provinces. They include: the Y-3 (OH-DP-0115, 26.68-29.42 cal ka BP), the Campanian Ignimbrite/Y-5 (OH-DP-0169, 39.6 ± 0.1 ka), and the X-6 (OH-DP-0404, 109 ± 2 ka) from the Campanian volcanoes, the P-11 of the Pantelleria Island (OH-DP-0499, 129 ± 6 ka), the Vico B (OH-DP-0617, 162 ± 6 ka) from the Vico volcano, the Pozzolane Rosse (OH-DP-1817, 457 ± 2 ka) and the Tufo di Bagni Albule (OH-DP-2060, 527 ± 2 ka) from the Colli Albani volcanic district, and the Fall A (OH-DP-2010, 496 ± 3 ka) from the Sabatini volcanic field. Furthermore, a comparison of the Ohrid record with tephrostratigraphic records of mid-distal archives related to the Mediterranean area, allowed the recognition of the equivalents of other less known tephra layers, such as the TM24-a/POP2 (OH-DP-0404, 101.8 ka) from the Lago Grande di Monticchio and the Sulmona basin, the CF-V5/PRAD3225 (OH-DP-0624, ca. 162 ka) from the Campo Felice basin/Adriatic Sea, the SC5 (OH-DP-1955, 493.1 ± 10.9 ka) from the Mercure basin, and the A11/12 (OH-DP-2017, 511 ± 6 ka) from the Acerno basin, whose specific volcanic sources are still poorly constrained. Additionally, one cryptotephra (OH-DP-0027) was identified by correlation of the potassium XRF intensities from the DEEP site with those from short cores of previous studies from Lake Ohrid. In these cores, a maximum in potassium is caused by glass shards, which were correlated with the Mercato tephra (8.43-8.63 cal ka BP) from Somma-Vesuvius. With the tephrostratigraphic work, a consistent part of the Middle Pleistocene tephrostratigraphic framework of Italian

  9. First tephrostratigraphic results of the DEEP site record of Lake Ohrid, Macedonia

    NASA Astrophysics Data System (ADS)

    Leicher, N.; Zanchetta, G.; Sulpizio, R.; Giaccio, B.; Wagner, B.; Nomade, S.; Francke, A.; del Carlo, P.

    2015-12-01

    A tephrostratigraphic record covering the Marine Isotope Stages (MIS) 1-15 was established for the DEEP site record of Lake Ohrid (Macedonia/Albania). Major element analyses (SEM-EDS/WDS) were carried out on juvenile fragments extracted from 12 tephra layers and one cryptotephra (OH-DP-0027 to OH-DP-2060). The geochemical analyses of all of these layers suggest an origin from the Italian Volcanic Provinces, including: the Mercato tephra (8.530 ± 0.1 cal a BP) of Somma-Vesuvius, the Y-3 (29.05 ± 0.37 ka cal BP), the Y-5/Campanian Ignimbrite (39.6 ± 0.1 ka), and the X-6 (109 ± 2 ka) of the Campi Flegrei, the P11 of the Pantelleria Island (129 ± 6 ka), the Vico B (162 ± 6 ka) of the Vico volcano, the Pozzolane Rosse (457 ± 2 ka) and the Tufo di Bagni Albule (527 ±2 ka) of the Colli Albani volcanic district, and the Fall A (496 ± 3 ka, here discussed) of the Sabatini volcanic field. Furthermore, a comparison of the Ohrid record with the tephrostratigraphic records of mid-distal archives allowed the recognition of the equivalents of other less known tephra, such as the TM24-a/POP2 (101.8 ka BP) from Lago Grande di Monticchio and the Sulmona basin, the CF-V5/PRAD3225 (~ 162 ka) from the Campo Felice basin and the Adriatic Sea, the SC5 (494 ± 11 ka) from the Mercure basin, and the A11/12 (511 ± 6 ka) from the Acerno basin, whose specific volcanic origins are still poorly defined. For the first time, the Middle Pleistocene tephrostratigraphic framework of Italian volcanoes could be extended beyond Italy to the Balkan Region. The establishment of the tephrostratigraphic framework for the Lake Ohrid record provides important, independent tie-points for the age-depth model of the DEEP site sequence, which is a prerequisite for paleoclimatic and -environmental reconstructions. Furthermore, this age-depth model helps to improve and re-evaluate the chronology of both unknown and dated tephra layers. Thus, the Lake Ohrid record is candidate to become the Rosetta stone

  10. First tephrostratigraphic results of the DEEP site record of Lake Ohrid, Macedonia

    NASA Astrophysics Data System (ADS)

    Leicher, Niklas; Zanchetta, Giovanni; Sulpizio, Roberto; Giaccio, Biagio; Nomade, Sebastien; Wagner, Bernd; Francke, Alexander; Del Carlo, Paola

    2016-04-01

    A tephrostratigraphic record covering the Marine Isotope Stages (MIS) 1-15 was established for the DEEP site record of Lake Ohrid (Macedonia/Albania). Major element analyses (SEM-EDS/WDS) were carried out on juvenile fragments extracted from 12 tephra layers and one cryptotephra (OH-DP-0027 to OH-DP-2060). The geochemical analyses of all of these layers suggest an origin from the Italian Volcanic Provinces, including: the Mercato tephra (8.530 ± 0.1 cal a BP) of Somma-Vesuvius, the Y-3 (29.05 ± 0.37 ka cal BP), the Y 5/Campanian Ignimbrite (39.6 ± 0.1 ka), and the X-6 (109 ± 2 ka) of the Campi Flegrei, the P11 of the Pantelleria Island (129 ± 6 ka), the Vico B (162 ± 6 ka) of the Vico volcano, the Pozzolane Rosse (457 ± 2 ka) and the Tufo di Bagni Albule (527 ±2 ka) of the Colli Albani volcanic district, and the Fall A (496 ± 3 ka, here discussed) of the Sabatini volcanic field. Furthermore, a comparison of the Ohrid record with the tephrostratigraphic records of mid-distal archives allowed the recognition of the equivalents of other less known tephra, such as the TM24-a/POP2 (101.8 ka BP) from Lago Grande di Monticchio and the Sulmona basin, the CF-V5/PRAD3225 (~ 162 ka) from the Campo Felice basin and the Adriatic Sea, the SC5 (494 ± 11 ka) from the Mercure basin, and the A11/12 (511 ± 6 ka) from the Acerno basin, whose specific volcanic origins are still poorly defined. For the first time, the Middle Pleistocene tephrostratigraphic framework of Italian volcanoes could be extended beyond Italy to the Balkan Region. The establishment of the tephrostratigraphic framework for the Lake Ohrid record provides important, independent tie-points for the age-depth model of the DEEP site sequence, which is a prerequisite for paleoclimatic and -environmental reconstructions. Furthermore, this age-depth model helps to improve and re-evaluate the chronology of both unknown and dated tephra layers. Thus, the Lake Ohrid record is candidate to become the template for

  11. Minimized natural versions of fungal ribotoxins show improved active site plasticity.

    PubMed

    Maestro-López, Moisés; Olombrada, Miriam; García-Ortega, Lucía; Serrano-González, Daniel; Lacadena, Javier; Oñaderra, Mercedes; Gavilanes, José G; Martínez-Del-Pozo, Álvaro

    2017-04-01

    Fungal ribotoxins are highly specific extracellular RNases which cleave a single phosphodiester bond at the ribosomal sarcin-ricin loop, inhibiting protein biosynthesis by interfering with elongation factors. Most ribotoxins show high degree of conservation, with similar sizes and amino acid sequence identities above 85%. Only two exceptions are known: hirsutellin A and anisoplin, produced by the entomopathogenic fungi Hirsutella thompsonii and Metarhizium anisopliae, respectively. Both proteins are similar but smaller than the other known ribotoxins (130 vs 150 amino acids), displaying only about 25% sequence identity with them. They can be considered minimized natural versions of their larger counterparts, best represented by α-sarcin. The conserved α-sarcin active site residue Tyr48 has been replaced by the geometrically equivalent Asp, present in the minimized ribotoxins, to produce and characterize the corresponding mutant. As a control, the inverse anisoplin mutant (D43Y) has been also studied. The results show how the smaller versions of ribotoxins represent an optimum compromise among conformational freedom, stability, specificity, and active-site plasticity which allow these toxic proteins to accommodate the characteristic abilities of ribotoxins into a shorter amino acid sequence and more stable structure of intermediate size between that of other nontoxic fungal RNases and previously known larger ribotoxins.

  12. Catalytic and Structural Role of a Conserved Active Site Histidine in Berberine Bridge Enzyme

    PubMed Central

    2012-01-01

    Berberine bridge enzyme (BBE) is a paradigm for the class of bicovalently flavinylated oxidases, which catalyzes the oxidative cyclization of (S)-reticuline to (S)-scoulerine. His174 was identified as an important active site residue because of its role in the stabilization of the reduced state of the flavin cofactor. It is also strictly conserved in the family of BBE-like oxidases. Here, we present a detailed biochemical and structural characterization of a His174Ala variant supporting its importance during catalysis and for the structural organization of the active site. Substantial changes in all kinetic parameters and a decrease in midpoint potential were observed for the BBE His174Ala variant protein. Moreover, the crystal structure of the BBE His174Ala variant showed significant structural rearrangements compared to wild-type enzyme. On the basis of our findings, we propose that His174 is part of a hydrogen bonding network that stabilizes the negative charge at the N1–C2=O locus via interaction with the hydroxyl group at C2′ of the ribityl side chain of the flavin cofactor. Hence, replacement of this residue with alanine reduces the stabilizing effect for the transiently formed negative charge and results in drastically decreased kinetic parameters as well as a lower midpoint redox potential. PMID:22757961

  13. Long-distance proton transfer with a break in the bacteriorhodopsin active site.

    PubMed

    Phatak, Prasad; Frähmcke, Jan S; Wanko, Marius; Hoffmann, Michael; Strodel, Paul; Smith, Jeremy C; Suhai, Sándor; Bondar, Ana-Nicoleta; Elstner, Marcus

    2009-05-27

    Bacteriorhodopsin is a proton-pumping membrane protein found in the plasma membrane of the archaeon Halobacterium salinarium. Light-induced isomerization of the retinal chromophore from all-trans to 13-cis leads to a sequence of five conformation-coupled proton transfer steps and the net transport of one proton from the cytoplasmic to the extracellular side of the membrane. The mechanism of the long-distance proton transfer from the primary acceptor Asp85 to the extracellular proton release group during the O --> bR is poorly understood. Experiments suggest that this long-distance transfer could involve a transient state [O] in which the proton resides on the intermediate carrier Asp212. To assess whether the transient protonation of Asp212 participates in the deprotonation of Asp85, we performed hybrid Quantum Mechanics/Molecular Mechanics proton transfer calculations using different protein structures and with different retinal geometries and active site water molecules. The structural models were assessed by computing UV-vis excitation energies and C=O vibrational frequencies. The results indicate that a transient [O] conformer with protonated Asp212 could indeed be sampled during the long-distance proton transfer to the proton release group. Our calculations suggest that, in the starting proton transfer state O, the retinal is strongly twisted and at least three water molecules are present in the active site.

  14. The effect of methyl-donated hydrogen bonding on active site conformations of hyaluronate lyase

    NASA Astrophysics Data System (ADS)

    Migues, Angela N.; Vergenz, Robert A.; Moore, Kevin B.

    2010-03-01

    Geometric evidence shows a val-A252 methyl-donated (MD) hydrogen bond (HB) in hyaluronate lyase (Streptococcus pneumoniae) interacts with nearby NH--O and OH--O HBs, distorting active-site helical structure. Results for model fragment A248-254 are based on experimental heavy atom positions with ab initio hydrogen atoms. The MDHB, with (H-O distance, donor-H-O angle) = (2.3å; 174^o), exhibits more favorable geometry than thr-A253 OH--O HB (1.8å; 170^o) to the same ala-249 C=O. Consequently, thr-253 N-H--O interaction is forced closer to lys-250 C=O than ala-249 C=O(2.6 versus 2.7å). A novel method has been developed to quantify the effects of atomic diplacements on motions of neighboring helices. A coordinate system was established to track the movement of specific residues and to ascertain the effect of such motions on active site conformations.

  15. Observing the formation of ice and organic crystals in active sites.

    PubMed

    Campbell, James M; Meldrum, Fiona C; Christenson, Hugo K

    2017-01-31

    Heterogeneous nucleation is vital to a wide range of areas as diverse as ice nucleation on atmospheric aerosols and the fabrication of high-performance thin films. There is excellent evidence that surface topography is a key factor in directing crystallization in real systems; however, the mechanisms by which nanoscale pits and pores promote nucleation remain unclear. Here, we use natural cleavage defects on Muscovite mica to investigate the activity of topographical features in the nucleation from vapor of ice and various organic crystals. Direct observation of crystallization within surface pockets using optical microscopy and also interferometry demonstrates that these sharply acute features provide extremely effective nucleation sites and allows us to determine the mechanism by which this occurs. A confined phase is first seen to form along the apex of the wedge and then grows out of the pocket opening to generate a bulk crystal after a threshold saturation has been achieved. Ice nucleation proceeds in a comparable manner, although our resolution is insufficient to directly observe a condensate before the growth of a bulk crystal. These results provide insight into the mechanism of crystal deposition from vapor on real surfaces, where this will ultimately enable us to use topography to control crystal deposition on surfaces. They are also particularly relevant to our understanding of processes such as cirrus cloud formation, where such topographical features are likely candidates for the "active sites" that make clay particles effective nucleants for ice in the atmosphere.

  16. Active-site-mutagenesis study of rat liver betaine-homocysteine S-methyltransferase.

    PubMed

    González, Beatriz; Campillo, Nuria; Garrido, Francisco; Gasset, María; Sanz-Aparicio, Juliana; Pajares, María A

    2003-03-15

    A site-directed-mutagenesis study of putative active-site residues in rat liver betaine-homocysteine S-methyltransferase has been carried out. Identification of these amino acids was based on data derived from a structural model of the enzyme. No alterations in the CD spectra or the gel-filtration chromatography elution pattern were observed with the mutants, thus suggesting no modification in the secondary structure content or in the association state of the proteins. All the mutants obtained showed a reduction of the enzyme activity, the most dramatic effect being that of Glu(159), followed by Tyr(77) and Asp(26). Changes in affinity for either of the substrates, homocysteine or betaine, were detected when substitutions were performed of Glu(21), Asp(26), Phe(74) and Cys(186). Interestingly, Asp(26), postulated to be involved in homocysteine binding, has a strong effect on affinity for betaine. The relevance of these results is discussed in the light of very recent structural data obtained for the human enzyme.

  17. Molecular dynamics explorations of active site structure in designed and evolved enzymes.

    PubMed

    Osuna, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L; Houk, K N

    2015-04-21

    This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explorations of the dynamical preorganization of active sites using MD, studying the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state and relates the populations of the catalytic conformational ensemble to the enzyme activity. This Account is organized around three case studies from our laboratory. We first describe the importance of dynamics in evaluating a series of computationally designed and experimentally evolved enzymes for the Kemp elimination, a popular subject in the enzyme design field. We find that the dynamics of the active site is influenced not only by the original sequence design and subsequent mutations but also by the nature of the ligand present in the active site. In the second example, we show how microsecond MD has been used to uncover the role of remote mutations in the active site dynamics and catalysis of a transesterase, LovD. This enzyme was evolved by Tang at UCLA and Codexis, Inc., and is a useful commercial catalyst for the production of the drug simvastatin. X-ray analysis of inactive and active mutants did not reveal differences in the active sites, but relatively long time scale MD in solution showed that the active site of the wild-type enzyme preorganizes only upon binding of the acyl carrier protein (ACP) that delivers the natural acyl group to the active site. In the absence of bound ACP

  18. Summary and results of the comprehensive environmental monitoring program at the INEL's Raft River geothermal site

    SciTech Connect

    Mayes, R.A.; Thurow, T.L.; Cahn, L.S.

    1982-01-01

    The Raft River Geothermal Program was designed to demonstrate that moderate temperature (approx. 150/sup 0/C) geothermal fluids could be used to generate electricity and provide an alternate energy source for direct-use applications. The environmental program was initiated soon after drilling began. The major elements of the monitoring program were continued during the construction and experimental testing of the 5-MW(e) power plant. The monitoring studies established pre-development baseline conditions of and assessed changes in the physical, biological, and human environment. The Physical Environmental Monitoring Program collected baseline data on geology, subsidence, seismicity, meteorology and air quality. The Biological Environmental Monitoring Program collected baseline data on the flora and fauna of the terrestrial ecosystem, studied raptor disturbances, and surveyed the aquatic communities of the Raft River. The Human Environmental Monitoring Program surveyed historic and archaeological sites, considered the socioeconomic environment, and documented incidences of fluorosis in the Raft River Valley. In addition to the environmental monitoring programs, research on biological direct applications using geothermal water was conducted at Raft River. Areas of research included biomass production of wetland and tree species, aquaculture, agricultural irrigation, and the use of wetlands as a treatment or pretreatment system for geothermal effluents.

  19. Summary Of Cold Crucible Vitrification Tests Results With Savannah River Site High Level Waste Surrogates

    SciTech Connect

    Stefanovsky, Sergey; Marra, James; Lebedev, Vladimir

    2014-01-13

    The cold crucible inductive melting (CCIM) technology successfully applied for vitrification of low- and intermediate-level waste (LILW) at SIA Radon, Russia, was tested to be implemented for vitrification of high-level waste (HLW) stored at Savannah River Site, USA. Mixtures of Sludge Batch 2 (SB2) and 4 (SB4) waste surrogates and borosilicate frits as slurries were vitrified in bench- (236 mm inner diameter) and full-scale (418 mm inner diameter) cold crucibles. Various process conditions were tested and major process variables were determined. Melts were poured into 10L canisters and cooled to room temperature in air or in heat-insulated boxes by a regime similar to Canister Centerline Cooling (CCC) used at DWPF. The products with waste loading from ~40 to ~65 wt.% were investigated in details. The products contained 40 to 55 wt.% waste oxides were predominantly amorphous; at higher waste loadings (WL) spinel structure phases and nepheline were present. Normalized release values for Li, B, Na, and Si determined by PCT procedure remain lower than those from EA glass at waste loadings of up to 60 wt.%.

  20. COMPARISON OF CONSEQUENCE ANALYSIS RESULTS FROM TWO METHODS OF PROCESSING SITE METEOROLOGICAL DATA

    SciTech Connect

    , D

    2007-04-25

    Consequence analysis to support documented safety analysis requires the use of one or more years of representative meteorological data for atmospheric transport and dispersion calculations. At minimum, the needed meteorological data for most atmospheric transport and dispersion models consist of hourly samples of wind speed and atmospheric stability class. Atmospheric stability is inferred from measured and/or observed meteorological data. Several methods exist to convert measured and observed meteorological data into atmospheric stability class data. In this paper, one year of meteorological data from a western Department of Energy (DOE) site is processed to determine atmospheric stability class using two methods. The method that is prescribed by the U.S. Nuclear Regulatory Commission (NRC) for supporting licensing of nuclear power plants makes use of measurements of vertical temperature difference to determine atmospheric stability. Another method that is preferred by the U.S. Environmental Protection Agency (EPA) relies upon measurements of incoming solar radiation, vertical temperature gradient, and wind speed. Consequences are calculated and compared using the two sets of processed meteorological data from these two methods as input data into the MELCOR Accident Consequence Code System 2 (MACCS2) code.

  1. Preliminary results of geothermal desalting operations at the East Mesa test site Imperial Valley, California

    NASA Technical Reports Server (NTRS)

    Suemoto, S. H.; Mathias, K. E.

    1974-01-01

    The Bureau of Reclamation has erected at its Geothermal Resource Development site two experimental test vehicles for the purpose of desalting hot fluids of geothermal origin. Both plants have as a feed source geothermal well Mesa 6-1 drilled to a total depth of 8,030 feet and having a bottom hole temperature of 400 F. Formation fluid collected at the surface contained 24,800 mg/1 total dissolved solids. The dissolved solids consist mainly of sodium chloride. A multistage distillation (3-stage) plant has been operated intermittently for one year with no operational problems. Functioning at steady-state conditions with a liquid feed rate of 70 g/m and a temperature of 221 F, the final brine blowdown temperature was 169 F. Product water was produced at a rate of about 2 g/m; average total dissolved solids content of the product was 170 mg/1. A product quality of 27.5 mg/1 at a pH of 9.5 was produced from the first stage.

  2. Evaluation of groundwater monitoring results at the Hanford Site 200 Area Treated Effluent Disposal Facility

    SciTech Connect

    Barnett, D.B.

    1998-09-01

    The Hanford Site 200 Area Treated Effluent Disposal Facility (TEDF) has operated since June 1995. Groundwater monitoring has been conducted quarterly in the three wells surrounding the facility since 1992, with contributing data from nearby B Pond System wells. Cumulative hydrologic and geochemical information from the TEDF well network and other surrounding wells indicate no discernable effects of TEDF operations on the uppermost aquifer in the vicinity of the TEDF. The lateral consistency and impermeable nature of the Ringold Formation lower mud unit, and the contrasts in hydraulic conductivity between this unit and the vadose zone sediments of the Hanford formation suggest that TEDF effluent is spreading laterally with negligible mounding or downward movement into the uppermost aquifer. Hydrographs of TEDF wells show that TEDF operations have had no detectable effects on hydraulic heads in the uppermost aquifer, but show a continuing decay of the hydraulic mound generated by past operations at the B Pond System. Comparison of groundwater geochemistry from TEDF wells and other, nearby RCRA wells suggests that groundwater beneath TEDF is unique; different from both effluent entering TEDF and groundwater in the B Pond area. Tritium concentrations, major ionic proportions, and lower-than-background concentrations of other species suggest that groundwater in the uppermost aquifer beneath the TEDF bears characteristics of water in the upper basalt confined aquifer system. This report recommends retaining the current groundwater well network at the TEDF, but with a reduction of sampling/analysis frequency and some modifications to the list of constituents sought.

  3. The three Mycobacterium tuberculosis antigen 85 isoforms have unique substrates and activities determined by non-active site regions.

    PubMed

    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

    2014-09-05

    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 Pro(216)-Phe(228) 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.

  4. In vitro methylation of nuclear respiratory factor-2 binding sites suppresses the promoter activity of the human TOMM70 gene.

    PubMed

    Blesa, José R; Hegde, Anita A; Hernández-Yago, José

    2008-12-31

    TOMM70 is a subunit of the outer mitochondrial membrane translocase that plays a major role as a receptor of hydrophobic preproteins targeted to mitochondria. We have previously reported that two binding sites for transcription factor NRF-2 in the promoter region of the human TOMM70 gene are essential in activating transcription (Blesa et al., Mitochondrion 2004; 3:251-59. Blesa et al., Biochem Cell Biol 2006; 84:813-22). This region contains thirteen CpG methylation sites, three of which occur in the sequence 5'-CCGG-3' that is specifically recognized by HpaII methylase which modifies the internal cytosine residue. Interestingly, each NRF-2 site contains one CCGG sequence, allowing specific methylation of the NRF-2 sites and, therefore, providing an ideal model to study how methylation of these sites affects promoter activity. In this paper we report that site-specific methylation of the NRF-2 binding sites in the TOMM70 promoter down-regulated expression of a luciferase reporter in HeLa S3 cells. Electrophoretic mobility shift assays confirmed abrogation of NRF-2 binding at the methylated sites. These results suggest that methylation of the TOMM70 promoter in mammalian cells may silence TOMM70 expression. However, studies of methylation degree on DNAs from different sources found no methylation in the promoter regions of TOMM70 and other TOMM/TIMM family genes. Thus, although in vitro methylation inactivates the expression of TOMM70, our results suggest that this is not the mechanism modulating its expression in vivo. Since a number of nuclear genes encoding mitochondrial translocases have NRF-2 binding sequences containing CpG methylation sites, a possible role of methylation as a regulatory mechanism of mitochondrial biogenesis can be ruled out.

  5. 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.

  6. All the catalytic active sites of MoS2 for hydrogen evolution

    SciTech Connect

    Li, Guoqing; Zhang, Du; Qiao, Qiao; Yu, Yifei; Peterson, David; Zafar, Abdullah; Kumar, Raj; Curtarolo, Stefano; Hunte, Frank; Shannon, Steve; Zhu, Yimei; Yang, Weitao; Cao, Linyou

    2016-11-29

    MoS2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. Here, the intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated to be 7.5 s–1 (65–75 mV/dec), 3.2 s–1 (65–85 mV/dec), and 0.1 s–1 (120–160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7–10%, and the number of sulfur vacancies in high crystalline quality MoS2 is higher than that in low crystalline quality MoS2, which may be related with the proximity of different local crystalline structures to the vacancies.

  7. Scientific results and lessons learned from an integrated crewed Mars exploration simulation at the Rio Tinto Mars analogue site

    NASA Astrophysics Data System (ADS)

    Orgel, Csilla; Kereszturi, Ákos; Váczi, Tamás; Groemer, Gernot; Sattler, Birgit

    2014-02-01

    Between 15 and 25 April 2011 in the framework of the PolAres programme of the Austrian Space Forum, a five-day field test of the Aouda.X spacesuit simulator was conducted at the Rio Tinto Mars-analogue site in southern Spain. The field crew was supported by a full-scale Mission Control Center (MCC) in Innsbruck, Austria. The field telemetry data were relayed to the MCC, enabling a Remote Science Support (RSS) team to study field data in near-real-time and adjust the flight planning in a flexible manner. We report on the experiences in the field of robotics, geophysics (Ground Penetrating Radar) and geology as well as life sciences in a simulated spaceflight operational environment. Extravehicular Activity (EVA) maps had been prepared using Google Earth and aerial images. The Rio Tinto mining area offers an excellent location for Mars analogue simulations. It is recognised as a terrestrial Mars analogue site because of the presence of jarosite and related sulphates, which have been identified by the NASA Mars Exploration Rover "Opportunity" in the El Capitan region of Meridiani Planum on Mars. The acidic, high ferric-sulphate content water of Rio Tinto is also considered as a possible analogue in astrobiology regarding the analysis of ferric sulphate related biochemical pathways and produced biomarkers. During our Mars simulation, 18 different types of soil and rock samples were collected by the spacesuit tester. The Raman results confirm the presence of minerals expected, such as jarosite, different Fe oxides and oxi-hydroxides, pyrite and complex Mg and Ca sulphates. Eight science experiments were conducted in the field. In this contribution first we list the important findings during the management and realisation of tests, and also a first summary of the scientific results. Based on these experiences suggestions for future analogue work are also summarised. We finish with recommendations for future field missions, including the preparation of the experiments

  8. Research in Support of Remediation Activities at the Savannah River Site

    SciTech Connect

    Seaman, J.C., B.B. Looney and M.K. Harris

    2007-01-01

    The USDOE Savannah River Site (SRS), an 803-km{sup 2} (310-mile{sup 2}) facility located south of Aiken, SC on the upper Atlantic Coastal Plain and bounded to the west by the Savannah River, was established in the 1950s for the production and refinement of nuclear materials. To fulfill this mission during the past 50 years SRS has operated five nuclear reactors, two large chemical separation areas, waste disposal facilities (landfills, waste ponds, waste tanks, and waste stabilization), and a large number of research and logistics support facilities. Contaminants of concern (COC) resulting from site operations include chlorinated solvents, radionuclides, metals, and metalloids, often found as complex mixtures that greatly complicate remediation efforts when compared with civilian industries. The objective of this article is to provide a description of the lithology and hydrostratigraphy of the SRS, as well as a brief history of site operations and research activities as a preface to the current special section of Vadose Zone Journal (VZJ) dedicated to SRS, focusing mainly on issues that are unique to the USDOE complex. Contributions to the special section reflect a diverse range of topics, from hydrologic tracer experiments conducted both within the vadose and saturated zones to studies specifically aimed at identifying geochemical processes controlling the migration and partitioning of specific contaminants (e.g., TCE, {sup 137}Cs, U, and Pu) in SRS subsurface environments. Addressing the diverse environmental challenges of the SRS provides a unique opportunity to conduct both fundamental and applied research across a range of experimental scales. Hence, the SRS has been a pioneering force in several areas of environmental research and remediation, often through active interdisciplinary collaboration with researchers from other USDOE facilities, academic and federal institutions, and commercial entities.

  9. Active Region Oscillations: Results from SOHO JOP 097

    NASA Astrophysics Data System (ADS)

    O'Shea, E.; Fleck, B.; Muglach, K.; Sütterlin, P.

    2001-05-01

    We present here an analysis of data obtained in a sunspot region, using the Coronal Diagnostic Spectrometer (CDS) on SOHO. These data were obtained in the context of the Joint Observing Program (JOP) 97 which, together with CDS, included the Michelson Doppler Imaging (MDI) instrument on SOHO, the TRACE satellite and various ground based observatories, e.g. the DOT on La Palma. Using the lines of Fe XVI 335, Mg IX 368, He I 584, O III 599, Mg X 624 and O V 624 of CDS time series data were obtained in the pore and plage regions of sunspots associated with active regions AR 9166, 9166 and 9169 between September 19-29 2000. In addition to the time series datasets we also obtained 240 arcsec x 240 arcsec raster images of the sunspot regions examined. Using different time series analysis techniques we analyse the different periods of oscillation found in time series datasets and present the results here. This research is part of the European Solar Magnetometry Network supported by the EC through the TMR programme.

  10. ICARUS T600: physics results and future activities

    NASA Astrophysics Data System (ADS)

    Zani, Andrea

    2016-11-01

    The ICARUS T600 detector has proven the effectiveness of Liquid Argon TPC technology with a successful three-year long run at the INFN Gran Sasso National Laboratories (LNGS). ICARUS T600 LNGS data strongly contributed to the global effort in searching for neutrino oscillations mediated by sterile states. A definitive clarification of the sterile neutrino puzzle will come from the new multi-station, Short Baseline Neutrino (SBN) experiment at the Booster Neutrino Beam (BNB) at Fermilab, where a refurbished T600 will act as Far Detector. Presently the T600 detector is located at CERN, undergoing a major overhauling which will allow its participation in the 5 years program of the Fermilab upcoming SBN project. Moreover, ICARUS T600 is also foreseen to collect data with the NUMI Beam to be later exploited in the wider picture of the DUNE Long-Baseline project, recently undertaken by the United States community. This contribution will report the present physics results obtained by the ICARUS Collaboration, as well as describe the overhauling activities and the physics program for the detector in its future deployment at Fermilab.

  11. Using the Novel Method of Nonthermal Plasma To Add Cl Active Sites on Activated Carbon for Removal of Mercury from Flue Gas.

    PubMed

    Zhang, Bi; Zeng, Xiaobo; Xu, Ping; Chen, Juan; Xu, Yang; Luo, Guangqian; Xu, Minghou; Yao, Hong

    2016-11-01

    A new method using nonthermal plasma to add Cl active sites on activated carbon was proposed to improve the efficiency of activated carbon (AC) for removal of mercury from flue gas. The experiments were conducted via a lab-scale dielectric barrier discharge nonthermal plasma system and a vertical adsorption reactor. The results showed that the nonthermal plasma treatment with a small amount of Cl2 successfully added Cl active sites on AC and greatly increased the mercury removal efficiency of AC by chemisorption in a very short treatment time. The increase in Cl2 concentration for AC treatment promoted the efficiency of AC. The capacity of mercury adsorption positively correlated with the content of Cl2 for AC treatment, which depends on the number of Cl active sites on activated carbon. The treated AC maintained a high mercury removal efficiency within a temperature range of 30-210 °C. SO2 and H2O in flue gas inhibited the removal of mercury by AC, while HCl had a promotional effect. Scanning electron microscopy and X-ray photoelectron spectroscopy analysis indicated the chemisorption of mercury was attributed to the C-Cl groups generated on AC surfaces during Cl2 nonthermal plasma treatment. The C-Cl groups as active sites had strong adsorption energy for mercury, which converted elemental mercury to HgCl2.

  12. DFT study of the active site of the XoxF-type natural, cerium-dependent methanol dehydrogenase enzyme.

    PubMed

    Bogart, Justin A; Lewis, Andrew J; Schelter, Eric J

    2015-01-19

    Rare-earth metal cations have recently been demonstrated to be essential co-factors for the growth of the methanotrophic bacterium Methylacidiphilum fumariolicum SolV. A crystal structure of the rare-earth-dependent methanol dehydrogenase (MDH) includes a cerium cation in the active site. Herein, the Ce-MDH active site has been analyzed through DFT calculations. The results show the stability of the Ce(III)-pyrroloquinoline quinone (PQQ) semiquinone configuration. Calculations on the active oxidized form of this complex indicate a 0.81 eV stabilization of the PQQ(0) LUMO at cerium versus calcium, supporting the observation that the cerium cation in the active site confers a competitive advantage to Methylacidiphilum fumariolicum SolV. Using reported aqueous electrochemical data, a semi-empirical correlation was established based on cerium(IV/III) redox potentials. The correlation allowed estimation of the cerium oxidation potential of +1.35 V versus saturated calomel electrode (SCE) in the active site. The results are expected to guide the design of functional model complexes and alcohol-oxidation catalysts based on lanthanide complexes of biologically relevant quinones.

  13. The roles of active site residues in the catalytic mechanism of methylaspartate ammonia-lyase.

    PubMed

    Raj, Hans; Poelarends, Gerrit J

    2013-01-01

    Methylaspartate ammonia-lyase (MAL; EC 4.3.1.2) catalyzes the reversible addition of ammonia to mesaconate to yield l-threo-(2S,3S)-3-methylaspartate and l-erythro-(2S,3R)-3-methylaspartate as products. In the proposed minimal mechanism for MAL of Clostridium tetanomorphum, Lys-331 acts as the (S)-specific base catalyst and abstracts the 3S-proton from l-threo-3-methylaspartate, resulting in an enolate anion intermediate. This enolic intermediate is stabilized by coordination to the essential active site Mg(2+) ion and hydrogen bonding to the Gln-329 residue. Collapse of this intermediate results in the release of ammonia and the formation of mesaconate. His-194 likely acts as the (R)-specific base catalyst and abstracts the 3R-proton from the l-erythro isomer of 3-methylaspartate, yielding the enolic intermediate. In the present study, we have investigated the importance of the residues Gln-73, Phe-170, Gln-172, Tyr-356, Thr-360, Cys-361 and Leu-384 for the catalytic activity of C. tetanomorphum MAL. These residues, which are part of the enzyme surface lining the substrate binding pocket, were subjected to site-directed mutagenesis and the mutant enzymes were characterized for their structural integrity, ability to catalyze the amination of mesaconate, and regio- and diastereoselectivity. Based on the observed properties of the mutant enzymes, combined with previous structural studies and protein engineering work, we propose a detailed catalytic mechanism for the MAL-catalyzed reaction, in which the side chains of Gln-73, Gln-172, Tyr-356, Thr-360, and Leu-384 provide favorable interactions with the substrate, which are important for substrate binding and activation. This detailed knowledge of the catalytic mechanism of MAL can serve as a guide for future protein engineering experiments.

  14. Functional properties and active-site topographies of factor X Gla- and prothrombin Gla-domain chimeras of activated protein C.

    PubMed

    Qureshi, Shabir H; Yang, Likui; Manithody, Chandrashekhara; Bae, Jong-Sup; Rezaie, Alireza R

    2008-09-01

    Substitution of the Gla-domain of activated protein C (APC) with the Gla-domain of prothrombin (APC-PTGla) improves the anticoagulant activity of APC independent of protein S. Previous FRET studies showed that this substitution alters the active-site topography of this mutant, rendering it identical to the active site of the APC-protein S complex. In this study, we characterized the functional properties and the active-site topography of another APC chimera containing the Gla-domain of factor X (APC-FXGla). We discovered that the anticoagulant activity of this mutant was similarly improved independent of protein S. The average distance of the closest approach (L) between the donor dye fluorescein attached to the active site of APC derivatives and the acceptor dye octadecylrhodamine incorporated into PC/PS vesicles was determined to be 99 A for APC and 84-86 A for both APC-PTGla and APC-FXGla. Protein S minimally influenced the L values of the APC chimeras, however, it lowered this value to 87 A for wild-type APC. Further studies revealed that neither chimera elicits a protective signaling response in the TNF-alpha-activated endothelial cells. These results suggest that unique structural features within the Gla-domain of APC enable the protease to interact with endothelial protein C receptor in the antiinflammatory pathway, while the same features also cause an inherently lower specific activity for APC in the anticoagulant pathway. This adaptation has made APC a cofactor-dependent protease, requiring the cofactor function of protein S for its optimal anticoagulant function, which appears to involve the alteration of the active-site topography of APC above the membrane surface.

  15. Linking Hydrologic Drivers to Arsenic Contamination in Asia, Results From a Field Site in Cambodia

    NASA Astrophysics Data System (ADS)

    Benner, S. G.; Polizzotto, M. L.; Kocar, B. D.; Sampson, M.; Fendorf, S.

    2008-12-01

    Attempts to resolve the specific release mechanisms associated with arsenic contamination on the deltas of Asia have been hampered, especially in Bangladesh, by the difficulty of linking geochemical mechanisms with hydrologic drivers. At an arsenic-contaminated (100-1200 ug/L) aquifer in Cambodia, where pumping for irrigation is limited and the hydrologic system is much less complex than in Bangladesh, we have developed a conceptual model of arsenic behavior that integrates the system hydrology and depositional history, providing strong evidence that arsenic release is sensitive to human activities. Specifically, the hydrogeologic regime is dominated by seasonally-variable head gradients between the river and adjacent wetland basins but the net annual flow is from the wetlands downwards into the aquifer (0.04-0.4 m/a) followed by discharge to the river (1-13 m/a). These flow rates produce aquifer residence times on the order of 100-1000 years. When coupled with elevated concentrations throughout the aquifer, this indicates that arsenic contamination predates recent human activities. Within this flow regime, it is possible to track spatial changes in arsenic concentrations along specific flow lines: The greatest increases in dissolved arsenic concentrations (150 ug/L/m) occur in shallow sediments along the first 2-10 m of the flow path, consistent with the depth at which reducing conditions are no longer seasonally disrupted by fluctuating water levels. Estimates of arsenic delivery to the wetlands by flood deposition (1,300,000 kg/a) are of a similar magnitude to the estimated flux, via groundwater, out of the aquifer (1,000,000 kg/a), indicating that arsenic delivery, release, and transport are in approximate steady-state. Given the dependency of arsenic release and transport on hydrologic drivers, human activities that alter the hydrology (inclusive of pumping for irrigation, soil excavation, and upstream river damming) will likely also alter arsenic behavior.

  16. Assessment Results Following Inquiry and Traditional Physics Laboratory Activities

    ERIC Educational Resources Information Center

    Bryan, Joel Arthur

    2006-01-01

    Preservice elementary teachers in a conceptual physics course were given multiple resources to use during several inquiry activities in order to investigate how materials were chosen, used, and valued. These students performed significantly better on assessment items related to the inquiry physics activities than on items related to traditional…

  17. 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

  18. Bidentate ligation of heme analogues; novel biomimetics of peroxidase active site.

    PubMed

    Ashkenasy, Gonen; Margulies, David; Felder, Clifford E; Shanzer, Abraham; Powers, Linda S

    2002-09-02

    The multifunctional nature of proteins that have iron-heme cofactors with noncovalent histidine linkage to the protein is controlled by the heme environment. Previous studies of these active-site structures show that the primary difference is the length of the iron-proximal histidine bond, which can be controlled by the degree of H-bonding to this histidine. Great efforts to mimic these functions with synthetic analogues have been made for more than two decades. The peroxidase models resulted in several catalytic systems capable of a large range of oxidative transformations. Most of these model systems modified the porphyrin ring covalently by directly binding auxiliary elements that control and facilitate reactivity; for example, electron-donating or -withdrawing substituents. A biomimetic approach to enzyme mimicking would have taken a different route, by attempting to keep the porphyrin ring system unaltered, as close as possible to its native form, and introducing all modifications at or close to the axial coordination sites. Such a model system would be less demanding synthetically, would make it easy to study the effect of a single structural modification, and might even provide a way to probe effects resulting from porphyrin exchange. We introduce here an alternative model system based on these principles. It consists of a two component system: a bis-imidazolyl ligand and an iron-porphyrin (readily substituted by a hemin). All modifications were introduced only to the ligand that engulfs the porphyrin and binds to the iron's fifth and sixth coordination sites. We describe the design, synthesis, and characterization of nine different model compounds with increased complexity. The primary tool for characterizing the environment of each complex Fe(III) center was the Extended X-ray Absorption Fine Structure (EXAFS) measurements, supported by UV/Vis, IR, and NMR spectroscopy and by molecular modeling. Introduction of asymmetry, by attaching different imidazoles

  19. MASCARA: the multi-site all-sky CAameRA: concept and first results

    NASA Astrophysics Data System (ADS)

    Lesage, A.-L.; Spronck, J. F. P.; Stuik, R.; Bettonvil, F.; Pollaco, D.; Snellen, I. A. G.

    2014-07-01

    MASCARA, the Multi-site All-Sky CAmeRA, will consist of several fully-automated stations distributed across the globe. Its goal is to find exoplanets transiting the brightest stars, in the mV = 4 to 8 magnitude range, currently probed neither by space- nor by ground-based surveys. The nearby transiting planet systems that MASCARA is expected to discover will be key targets for future detailed planet atmosphere observations. The target population for MASCARA consists mostly of hot Jupiters. The main requirement set on MASCARA to detect these planets around stars down to magnitude 8 is to reach a minimum Signal-to-Noise Ratio of 100 within one hour of observation. Each MASCARA station consists of five low-noise off-the-shelf full-frame CCD cameras, fitted with standard Canon 24 mm , f/1.4 lenses, monitoring the near-entire sky down to magnitude 8 at that location. Measurements have demonstrated that the required Signal-to-Noise Ratio of 100, can be achieved in less than thirty minutes. MASCARA aims at deploying several stations world-wide to provide a nearly continuous coverage of the dark sky, at sub-minute cadence. While at the faint end MASCARA is limited mainly by photon noise, at the bright end scintillation and red noise become the limiting factors. Instrumental noise sources are reduced by placing the cameras in a fixed orientation and in a temperature controlled environment. By defocusing and allowing stars to drift over the detector, the impact of pixel-to-pixel variations on the photometry are minimized, while taking exposures at fixed sidereal times allows accurate cross-calibration of consecutive nights. The exposure time of 6.4 seconds gives rise to a high data acquisition rate of a MASCARA station, around 500GB per night. In order to minimize data transport and data storage requirements, the raw images are reduced to produce accurate light curves in nearly real time. The first MASCARA station will be integrated on La Palma during the summer of 2014

  20. Joint NRC/EPA Sewage Sludge Radiological Survey: Survey Design & Test Site Results

    EPA Pesticide Factsheets

    This report contains the results of a radiological survey of nine publicly POTWs around the country, which was commissioned by the Sewage Sludge Subcommittee, to determine whether and to what extent radionuclides concentrate in sewage treatment wastes.

  1. Mutagenesis and crystallographic studies of the catalytic residues of the papain family protease bleomycin hydrolase: new insights into active-site structure

    PubMed Central

    O'Farrell, Paul A.; Joshua-Tor, Leemor

    2006-01-01

    Bleomycin hydrolase (BH) is a hexameric papain family cysteine protease which is involved in preparing peptides for antigen presentation and has been implicated in tumour cell resistance to bleomycin chemotherapy. Structures of active-site mutants of yeast BH yielded unexpected results. Replacement of the active-site asparagine with alanine, valine or leucine results in the destabilization of the histidine side chain, demonstrating unambiguously the role of the asparagine residue in correctly positioning the histidine for catalysis. Replacement of the histidine with alanine or leucine destabilizes the asparagine position, indicating a delicate arrangement of the active-site residues. In all of the mutants, the C-terminus of the protein, which lies in the active site, protrudes further into the active site. All mutants were compromised in their catalytic activity. The structures also revealed the importance of a tightly bound water molecule which stabilizes a loop near the active site and which is conserved throughout the papain family. It is displaced in a number of the mutants, causing destabilization of this loop and a nearby loop, resulting in a large movement of the active-site cysteine. The results imply that this water molecule plays a key structural role in this family of enzymes. PMID:17007609

  2. Exploring the role of putative active site amino acids and pro-region motif of recombinant falcipain-2: a principal hemoglobinase of Plasmodium falciparum.

    PubMed

    Kumar, Amit; Dasaradhi, P V N; Chauhan, Virander S; Malhotra, Pawan

    2004-04-23

    Falcipain-2 is one of the principal hemoglobinases of Plasmodium falciparum, a human malaria parasite. It has a typical papain family cysteine protease structural organization, a large pro-domain, a mature domain with conserved active site amino acids. Pro-domain of falcipain-2 also contains two important conserved motifs, "GNFD" and "ERFNIN." The "GNFD" motif has been shown to be responsible for correct folding and stability in case of many papain family proteases. In the present study, we carried out site-directed mutagenesis to assess the roles of active site residues and pro-domain residues for the activity of falcipain-2. Our results showed that substitutions of putative active site residues; Q36, C42, H174, and N204 resulted in complete loss of falcipain-2 activity, while W206 and D155 mutants retained partial/complete activity in comparison to the wild type falcipain-2. Homology modeling data also corroborate the results of mutagenesis; Q36, C42, H174, N204, and W206 residues form the active site loop of the enzyme and D155 lie outside the active pocket. Substitutions in the pro-region did not affect the activity of falcipain-2. This implies that falcipain-2 shares active site residues with other members of papain family, however pro-region of falcipain-2 does not play any role in the activity of enzyme.

  3. QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis.

    PubMed

    van der Kamp, Marc W; Chaudret, Robin; Mulholland, Adrian J

    2013-07-01

    Ketosteroid isomerase (Δ⁵-3-keto steroid isomerase or steroid Δ-isomerase) is a highly efficient enzyme at the centre of current debates on enzyme catalysis. We have modelled the reaction mechanism of the isomerization of 3-oxo-Δ⁵-steroids into their Δ⁴-conjugated isomers using high-level combined quantum mechanics/molecular mechanics (QM/MM) methods, and semi-empirical QM/MM molecular dynamics simulations. Energy profiles were obtained at various levels of QM theory (AM1, B3LYP and SCS-MP2). The high-level QM/MM profile is consistent with experimental data. QM/MM dynamics simulations indicate that active site closure and desolvation of the catalytic Asp38 occur before or during formation of dienolate intermediates. These changes have a significant effect on the reaction barrier. A low barrier to reaction is found only when the active site is closed, poising it for catalysis. This conformational change is thus integral to the whole process. The effects on the barrier are apparently largely due to changes in solvation. The combination of high-level QM/MM energy profiles and QM/MM dynamics simulation shows that the reaction involves active site closure, desolvation of the catalytic base, efficient isomerization and re-opening of the active site. These changes highlight the transition between the ligand binding/releasing form and the catalytic form of the enzyme. The results demonstrate that electrostatic interactions (as a consequence of pre-organization of the active site) are crucial for stabilization during the chemical reaction step, but closure of the active site is essential for efficient catalysis to occur.

  4. Evidence for the participation of Cys sub 558 and Cys sub 559 at the active site of mercuric reductase

    SciTech Connect

    Miller, S.M.; Moore, M.J.; Massey, V.; Williams, C.H. Jr.; Distefano, M.D.; Ballou, D.P.; Walsh, C.T. )

    1989-02-07

    Mercuric reductase, with FAD and a reducible disulfide at the active site, catalyzes the two-electron reduction of Hg(II) by NADPH. Addition of reducing equivalents rapidly produces a spectrally distinct EH{sub 2} form of the enzyme containing oxidized FAD and reduced active site thiols. Formation of EH{sub 2} has previously been reported to require only 2 electrons for reduction of the active site disulfide. The authors present results of anaerobic titrations of mercuric reductase with NADPH and dithionite showing that the equilibrium conversion of oxidized enzyme to EH{sub 2} actually requires 2 equiv of reducing agent or 4 electrons. Kinetic studies conducted both at 4{degree}C and at 25{degree}C indicate that reduction of the active site occurs rapidly, as previously reported; this is followed by a slower reduction of another redox group via reaction with the active site. ({sup 14}C)Iodoacetamide labeling experiments demonstrate that the C-terminal residues, Cys{sub 558} and Cys{sub 559}, are involved in this disulfide. The fluorescence, but not the absorbance, of the enzyme-bound FAD was found to be highly dependent on the redox state of the C-terminal thiols. Thus, E{sub ox} with Cys{sub 558} and Cys{sub 559} as thiols exhibits less than 50% of the fluorescence of E{sub ox} where these residues are present as a disulfide, indicating that the thiols remain intimately associated with the active site. Initial velocity measurements show that the auxiliary disulfide must be reduced before catalytic Hg(II) reduction can occur, consistent with the report of a preactivation phenomenon with NADPH or cysteine. A modified minimal catalytic mechanism is proposed as well as several chemical mechanisms for the Hg(II) reduction step.

  5. Fluconazole Binding and Sterol Demethylation in Three CYP51 Isoforms Indicate Differences in Active Site Topology

    SciTech Connect

    Bellamine, A.; Lepesheva, Galina I.; Waterman, Mike

    2010-11-16

    14{alpha}-Demethylase (CYP51) is a key enzyme in all sterol biosynthetic pathways (animals, fungi, plants, protists, and some bacteria), catalyzing the removal of the C-14 methyl group following cyclization of squalene. Based on mutations found in CYP51 genes from Candida albicans azole-resistant isolates obtained after fluconazole treatment of fungal infections, and using site-directed mutagenesis, we have found that fluconazole binding and substrate metabolism vary among three different CYP51 isoforms: human, fungal, and mycobacterial. In C. albicans, the Y132H mutant from isolates shows no effect on fluconazole binding, whereas the F145L mutant results in a 5-fold increase in its IC{sub 50} for fluconazole, suggesting that F145 (conserved only in fungal 14{alpha}-demethylases) interacts with this azole. In C. albicans, F145L accounts, in part, for the difference in fluconazole sensitivity reported between mammals and fungi, providing a basis for treatment of fungal infections. The C. albicans Y132H and human Y145H CYP51 mutants show essentially no effect on substrate metabolism, but the Mycobacterium tuberculosis F89H CYP51 mutant loses both its substrate binding and metabolism. Because these three residues align in the three isoforms, the results indicate that their active sites contain important structural differences, and further emphasize that fluconazole and substrate binding are uncoupled properties.

  6. Direct Visualization of Catalytically Active Sites at the FeO-Pt(111) Interface

    SciTech Connect

    Kudernatsch, Wilhelmine; Peng, Guowen; Zeuthen, Helene; Bai, Yunhai; Merte, L. R.; Lammich, Lutz; Besenbacher, Fleming; Mavrikakis, Manos; Wendt, Stefen

    2015-08-25

    Within the area of surface science, one of the “holy grails” is to directly visualize a chemical reaction at the atomic scale. Whereas this goal has been reached by high-resolution scanning tunneling microscopy (STM) in a number of cases for reactions occurring at flat surfaces, such a direct view is often inhibited for reaction occurring at steps and interfaces. Here we have studied the CO oxidation reaction at the interface between ultrathin FeO islands and a Pt(111) support by in situ STM and density functional theory (DFT) calculations. Time-lapsed STM imaging on this inverse model catalyst in O2 and CO environments revealed catalytic activity occurring at the FeO-Pt(111) interface and directly showed that the Fe-edges host the catalytically most active sites for the CO oxidation reaction. This is an important result since previous evidence for the catalytic activity of the FeO-Pt(111) interface is essentially based on averaging techniques in conjunction with DFT calculations. The presented STM results are in accord with DFTþU calculations, in which we compare possible CO oxidation pathways on oxidized Fe-edges and O-edges. We found that the CO oxidation reaction is more favorable on the oxidized Fe-edges, both thermodynamically and kinetically.

  7. Synergistic effect between defect sites and functional groups on the hydrolysis of cellulose over activated carbon.

    PubMed

    Foo, Guo Shiou; Sievers, Carsten

    2015-02-01

    The chemical oxidation of activated carbon by H2 O2 and H2 SO4 is investigated, structural and chemical modifications are characterized, and the materials are used as catalysts for the hydrolysis of cellulose. Treatment with H2 O2 enlarges the pore size and imparts functional groups such as phenols, lactones, and carboxylic acids. H2 SO4 treatment targets the edges of carbon sheets primarily, and this effect is more pronounced with a higher temperature. Adsorption isotherms demonstrate that the adsorption of oligomers on functionalized carbon is dominated by van der Waals forces. The materials treated chemically are active for the hydrolysis of cellulose despite the relative weakness of most of their acid sites. It is proposed that a synergistic effect between defect sites and functional groups enhances the activity by inducing a conformational change in the glucan chains if they are adsorbed at defect sites. This activates the glycosidic bonds for hydrolysis by in-plane functional groups.

  8. Enhancement of Polymerase Activity of the Large Fragment in DNA Polymerase I from Geobacillus stearothermophilus by Site-Directed Mutagenesis at the Active Site

    PubMed Central

    Ma, Yi; Zhang, Beilei; Wang, Meng; Ou, Yanghui

    2016-01-01

    The large fragment of DNA polymerase I from Geobacillus stearothermophilus GIM1.543 (Bst DNA polymerase) with 5′-3′ DNA polymerase activity while in absence of 5′-3′ exonuclease activity possesses high thermal stability and polymerase activity. Bst DNA polymerase was employed in isothermal multiple self-matching initiated amplification (IMSA) which amplified the interest sequence with high selectivity and was widely applied in the rapid detection of human epidemic diseases. However, the detailed information of commercial Bst DNA polymerase is unpublished and well protected by patents, which makes the high price of commercial kits. In this study, wild-type Bst DNA polymerase (WT) and substitution mutations for improving the efficiency of DNA polymerization were expressed and purified in E. coli. Site-directed substitutions of four conserved residues (Gly310, Arg412, Lys416, and Asp540) in the activity site of Bst DNA polymerase influenced efficiency of polymerizing dNTPs. The substitution of residue Gly310 by alanine or leucine and residue Asp540 by glutamic acid increased the efficiency of polymerase activity. All mutants with higher polymerizing efficiency were employed to complete the rapid detection of EV71-associated hand, foot, and mouth disease (HFMD) by IMSA approach with relatively shorter period which is suitable for the primary diagnostics setting in rural and underdeveloped areas. PMID:27981047

  9. Results of the JOSE site evaluation project for adaptive optics at the William Herschel Telescope

    NASA Astrophysics Data System (ADS)

    Wilson, R.

    1998-11-01

    Results are presented from a long-term study of the seeing properties at the William Herschel Telescope on La Palma. The measurements have been made over a two-year period using a Shack-Hartmann wavefront sensor equipped with high frame-rate CCD camera. The aim of the campaign is to characterize those aspects of the seeing relevant to the design and performance of astronomical adaptive optical systems for the WHT. Statistical results are presented for the value of Fried's parameter, power spectra of Zernike mode coefficients, isoplanatism and the outer scale of turbulence.

  10. Stellar activity and coronal heating: an overview of recent results

    PubMed Central

    Testa, Paola; Saar, Steven H.; Drake, Jeremy J.

    2015-01-01

    Observations of the coronae of the Sun and of solar-like stars provide complementary information to advance our understanding of stellar magnetic activity, and of the processes leading to the heating of their outer atmospheres. While solar observations allow us to study the corona at high spatial and temporal resolution, the study of stellar coronae allows us to probe stellar activity over a wide range of ages and stellar parameters. Stellar studies therefore provide us with additional tools for understanding coronal heating processes, as well as the long-term evolution of solar X-ray activity. We discuss how recent studies of stellar magnetic fields and coronae contribute to our understanding of the phenomenon of activity and coronal heating in late-type stars. PMID:25897087

  11. Stellar activity and coronal heating: an overview of recent results.

    PubMed

    Testa, Paola; Saar, Steven H; Drake, Jeremy J

    2015-05-28

    Observations of the coronae of the Sun and of solar-like stars provide complementary information to advance our understanding of stellar magnetic activity, and of the processes leading to the heating of their outer atmospheres. While solar observations allow us to study the corona at high spatial and temporal resolution, the study of stellar coronae allows us to probe stellar activity over a wide range of ages and stellar parameters. Stellar studies therefore provide us with additional tools for understanding coronal heating processes, as well as the long-term evolution of solar X-ray activity. We discuss how recent studies of stellar magnetic fields and coronae contribute to our understanding of the phenomenon of activity and coronal heating in late-type stars.

  12. The active site of hen egg-white lysozyme: flexibility and chemical bonding

    SciTech Connect

    Held, Jeanette Smaalen, Sander van

    2014-04-01

    Chemical bonding at the active site of lysozyme is analyzed on the basis of a multipole model employing transferable multipole parameters from a database. Large B factors at low temperatures reflect frozen-in disorder, but therefore prevent a meaningful free refinement of multipole parameters. Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader’s quantum theory of atoms in molecules [QTAIM; Bader (1994 ▶), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C

  13. Performance assessment methodology as applied to the Greater Confinement Disposal site: Preliminary results of the third performance iteration

    SciTech Connect

    Brown, T.J.; Baer, T.A.

    1994-12-31

    The US Department of Energy has contracted Sandia National Laboratories to conduct a performance assessment of the Greater Confinement Disposal facility, Nevada. The performance assessment is an iterative process in which transport models are used to prioritize site characterization data collection. Then the data are used to refine the conceptual and performance assessment models. The results of the first two performance assessment iterations indicate that the site is likely to comply with the performance standards under the existing hydrologic conditions. The third performance iteration expands the conceptual model of the existing transport system to include possible future events and incorporates these processes in the performance assessment models. The processes included in the third performance assessment are climate change, bioturbation, plant uptake, erosion, upward advection, human intrusion and subsidence. The work completed to date incorporates the effects of bioturbation, erosion and subsidence in the performance assessment model. Preliminary analyses indicate that the development of relatively deep-rooting plant species at the site, which could occur due to climate change, irrigated farming or subsidence, poses the greatest threat to the site`s performance.

  14. Charpy impact test results for low-activation ferritic alloys

    SciTech Connect

    Cannon, N.S.; Hu, W.L.; Gelles, D.S.

    1987-05-01

    The objective of this work is to evaluate the shift of the ductile to brittle transition temperature (DBTT) and the reduction of the upper shelf energy (USE) due to neutron irradiation of low activation ferritic alloys. Six low activation ferritic alloys have been tested following irradiation at 365/sup 0/C to 10 dpa and compared with control specimens in order to assess the effect of irradiation on Charpy impact properties.

  15. Chemical Analysis of the Moon at the Surveyor VI Landing Site: Preliminary Results.

    PubMed

    Turkevich, A L; Patterson, J H; Franzgrote, E J

    1968-06-07

    The alpha-scattering experiment aboard soft-landing Surveyor VI has provided a chemical analysis of the surface of the moon in Sinus Medii. The preliminary results indicate that, within experimental errors, the composition is the same as that found by Surveyor V in Mare Tranquillitatis. This finding suggests that large portions of the lunar maria resemble basalt in composition.

  16. Tc-99 Adsorption on Selected Activated Carbons - Batch Testing Results

    SciTech Connect

    Mattigod, Shas V.; Wellman, Dawn M.; Golovich, Elizabeth C.; Cordova, Elsa A.; Smith, Ronald M.

    2010-12-01

    CH2M HILL Plateau Remediation Company (CHPRC) is currently developing a 200-West Area groundwater pump-and-treat system as the remedial action selected under the Comprehensive Environmental Response, Compensation, and Liability Act Record of Decision for Operable Unit (OU) 200-ZP-1. This report documents the results of treatability tests Pacific Northwest National Laboratory researchers conducted to quantify the ability of selected activated carbon products (or carbons) to adsorb technetium-99 (Tc-99) from 200-West Area groundwater. The Tc-99 adsorption performance of seven activated carbons (J177601 Calgon Fitrasorb 400, J177606 Siemens AC1230AWC, J177609 Carbon Resources CR-1240-AW, J177611 General Carbon GC20X50, J177612 Norit GAC830, J177613 Norit GAC830, and J177617 Nucon LW1230) were evaluated using water from well 299-W19-36. Four of the best performing carbons (J177606 Siemens AC1230AWC, J177609 Carbon Resources CR-1240-AW, J177611 General Carbon GC20X50, and J177613 Norit GAC830) were selected for batch isotherm testing. The batch isotherm tests on four of the selected carbons indicated that under lower nitrate concentration conditions (382 mg/L), Kd values ranged from 6,000 to 20,000 mL/g. In comparison. Under higher nitrate (750 mg/L) conditions, there was a measureable decrease in Tc-99 adsorption with Kd values ranging from 3,000 to 7,000 mL/g. The adsorption data fit both the Langmuir and the Freundlich equations. Supplemental tests were conducted using the two carbons that demonstrated the highest adsorption capacity to resolve the issue of the best fit isotherm. These tests indicated that Langmuir isotherms provided the best fit for Tc-99 adsorption under low nitrate concentration conditions. At the design basis concentration of Tc 0.865 µg/L(14,700 pCi/L), the predicted Kd values from using Langmuir isotherm constants were 5,980 mL/g and 6,870 mL/g for for the two carbons. These Kd values did not meet the target Kd value of 9,000 mL/g. Tests

  17. The oxidation state of active site thiols determines activity of saccharopine dehydrogenase at low pH.

    PubMed

    Bobyk, Kostyantyn D; Kim, Sang Gon; Kumar, Vidya Prasanna; Kim, Sung-Kun; West, Ann H; Cook, Paul F

    2011-09-15

    Saccharopine dehydrogenase catalyzes the NAD-dependent conversion of saccharopine to generate L-lysine and α-ketoglutarate. A disulfide bond between cysteine 205 and cysteine 249, in the vicinity of the dinucleotide-binding site, is observed in structures of the apoenzyme, while a dithiol is observed in a structure with AMP bound, suggesting preferential binding of the dinucleotide to reduced enzyme. Mutation of C205 to S gave increased values of V/E(t) and V/KE(t) at pH 7 compared to wild type. Primary deuterium and solvent deuterium kinetic isotope effects suggest the catalytic pathway, which includes the hydride transfer and hydrolysis steps, contributes more to rate limitation in C205S, but the rates of the two steps relative to one another remain the same. There is a large increase in the rate constants V₁/E(t) and V₁/K(NAD)Et at pH values below 7 compared to WT. Data indicate the low pH increase in activity results from a decreased sensitivity of the C205S mutant enzyme to the protonation state of an enzyme group with a pK(a) of about 7, likely responsible for a pH-dependent conformational change. Reduction of WT and C205S mutant enzymes with TCEP gives equal activities at pH 6, consistent with the increased activity observed for the C205S mutant enzyme.

  18. Conformational Change in the Active Site of Streptococcal Unsaturated Glucuronyl Hydrolase Through Site-Directed Mutagenesis at Asp-115.

    PubMed

    Nakamichi, Yusuke; Oiki, Sayoko; Mikami, Bunzo; Murata, Kousaku; Hashimoto, Wataru

    2016-08-01

    Bacterial unsaturated glucuronyl hydrolase (UGL) degrades unsaturated disaccharides generated from mammalian extracellular matrices, glycosaminoglycans, by polysaccharide lyases. Two Asp residues, Asp-115 and Asp-175 of Streptococcus agalactiae UGL (SagUGL), are completely conserved in other bacterial UGLs, one of which (Asp-175 of SagUGL) acts as a general acid and base catalyst. The other Asp (Asp-115 of SagUGL) also affects the enzyme activity, although its role in the enzyme reaction has not been well understood. Here, we show substitution of Asp-115 in SagUGL with Asn caused a conformational change in the active site. Tertiary structures of SagUGL mutants D115N and D115N/K370S with negligible enzyme activity were determined at 2.00 and 1.79 Å resolution, respectively, by X-ray crystallography. The side chain of Asn-115 is drastically shifted in both mutants owing to the interaction with several residues, including Asp-175, by formation of hydrogen bonds. This interaction between Asn-115 and Asp-175 probably prevents the mutants from triggering the enzyme reaction using Asp-175 as an acid catalyst.

  19. Spectroscopic insights into the nature of active sites in iron–nitrogen–carbon electrocatalysts for oxygen reduction in acid

    SciTech Connect

    Jia, Qingying; Ramaswamy, Nagappan; Tylus, Urszula; Strickland, Kara; Li, Jingkun; Serov, Alexey; Artyushkova, Kateryna; Atanassov, Plamen; Anibal, Jacob; Gumeci, Cenk; Barton, Scott Calabrese; Sougrati, Moulay-Tahar; Jaouen, Frederic; Halevi, Barr; Mukerjee, Sanjeev

    2016-11-01

    of the site-blocking effect. Moreover, a highly active MOF-based catalyst without Fe–N moieties was developed, and the active sites were identified as nitrogen-doped carbon fibers with embedded iron particles that are not directly involved in the oxygen reduction pathway. The high ORR activity and durability of catalysts involving this second site, as demonstrated in fuel cell, are attributed to the high density of active sites and the elimination or reduction of Fenton-type processes. The latter are initiated by hydrogen peroxide but are known to be accelerated by iron ions exposed to the surface, resulting in the formation of damaging free-radicals.

  20. AMS 14C analysis of teeth from archaeological sites showing anomalous esr dating results

    NASA Astrophysics Data System (ADS)

    Grün, Rainer; Abeyratne, Mohan; Head, John; Tuniz, Claudio; Hedges, Robert E. M.

    We have carried out AMS radiocarbon analysis on two groups of samples: the first one gave reasonable ESR age estimates and the second one yielded serious age underestinations. All samples were supposedly older than 35 ka, the oldest being around 160 ka. Two pretreatment techniques were used for radiocarbon dating: acid evolution and thermal release. Heating to 600, 750 and 900°C combined with total de-gassing at these temperatures was chosen to obtain age estimates on the organic fraction, secondary carbonates and original carbonate present in the hydroxyapatite mineral phase, respectively. All radiocarbon results present serious age underestimations. The secondary carbonate fraction gives almost modern results indicating an extremely rapid exchange of this component. Owing to this very rapid carbonate exchange it is not likely that the ESR signals used for dating are associated with the secondary carbonates. One tooth from Tabun with independent age estimates of >150 ka was further investigated by the Oxford AMS laboratory, yielding an age estimate of 1930±100 BP on the residual collagen from dentine and 18,000±160 BP on the carbonate component of the enamel bioapatite. We did not, however, find an explanation of why some samples give serious ESR underestimatioils whilst many others provide reasonable results.

  1. 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.

  2. Transcriptional activation by LR1 at the Eµ enhancer and switch region sites

    PubMed Central

    Hanakahi, L. A.; Maizels, Nancy

    2000-01-01

    LR1 is a B cell-specific, sequence-specific duplex DNA binding activity which is induced in B cells carrying out class switch recombination. Here we identify several properties of LR1 which enable it to function in transcriptional regulation. We show that LR1 contributes to transcriptional activation by the Eµ immunoglobulin heavy chain intron enhancer by binding to a site within the enhancer core. We further show that LR1 bends DNA upon binding. In addition, we show that LR1 is itself a bona fide transcriptional activator, as multimerized LR1 sites produce an element which can enhance transcription from a minimal promoter. In order for class switch recombination to occur, an activating signal must be transmitted via the Eµ core, and both S regions targeted for recombination must be actively transcribed. The properties of LR1 that we have identified suggest distinct potential functions of LR1 duplex DNA binding activity in class switch recombination. First, LR1 may contribute to recombinational activation by the Eµ core. Second, there are multiple potential LR1 duplex binding sites in each of the G-rich switch regions, and LR1 bound at contiguous sites may enhance recombination by stimulating transcription of the S regions. PMID:10908319

  3. Benchmarking Evaluation Results for Prototype Extravehicular Activity Gloves

    NASA Technical Reports Server (NTRS)

    Aitchison, Lindsay; McFarland, Shane

    2012-01-01

    The Space Suit Assembly (SSA) Development Team at NASA Johnson Space Center has invested heavily in the advancement of rear-entry planetary exploration suit design but largely deferred development of extravehicular activity (EVA) glove designs, and accepted the risk of using the current flight gloves, Phase VI, for unique mission scenarios outside the Space Shuttle and International Space Station (ISS) Program realm of experience. However, as design reference missions mature, the risks of using heritage hardware have highlighted the need for developing robust new glove technologies. To address the technology gap, the NASA Game-Changing Technology group provided start-up funding for the High Performance EVA Glove (HPEG) Project in the spring of 2012. The overarching goal of the HPEG Project is to develop a robust glove design that increases human performance during EVA and creates pathway for future implementation of emergent technologies, with specific aims of increasing pressurized mobility to 60% of barehanded capability, increasing the durability by 100%, and decreasing the potential of gloves to cause injury during use. The HPEG Project focused initial efforts on identifying potential new technologies and benchmarking the performance of current state of the art gloves to identify trends in design and fit leading to establish standards and metrics against which emerging technologies can be assessed at both the component and assembly levels. The first of the benchmarking tests evaluated the quantitative mobility performance and subjective fit of four prototype gloves developed by Flagsuit LLC, Final Frontier Designs, LLC Dover, and David Clark Company as compared to the Phase VI. All of the companies were asked to design and fabricate gloves to the same set of NASA provided hand measurements (which corresponded to a single size of Phase Vi glove) and focus their efforts on improving mobility in the metacarpal phalangeal and carpometacarpal joints. Four test

  4. Tertiary Contacts Distant from the Active Site Prime a Ribozyme for Catalysis

    PubMed Central

    Martick, Monika; Scott, William G.

    2015-01-01

    SUMMARY Minimal hammerhead ribozymes have been characterized extensively by static and time-resolved crystallography as well as numerous biochemical analyses, leading to mutually contradictory mechanistic explanations for catalysis. We present the 2.2 Å resolution crystal structure of a full-length Schistosoma mansoni hammerhead ribozyme that permits us to explain the structural basis for its 1000-fold catalytic enhancement. The full-length hammerhead structure reveals how tertiary interactions occurring remotely from the active site prime this ribozyme for catalysis. G-12 and G-8 are positioned consistent with their previously suggested roles in acid-base catalysis, the nucleophile is aligned with a scissile phosphate positioned proximal to the A-9 phosphate, and previously unexplained roles of other conserved nucleotides become apparent within the context of a distinctly new fold that nonetheless accommodates the previous structural studies. These interactions permit us to explain the previously irreconcilable sets of experimental results in a unified, consistent, and unambiguous manner. PMID:16859740

  5. Atomistic characterization of the active-site solvation dynamics of a model photocatalyst

    NASA Astrophysics Data System (ADS)

    van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; Dohn, Asmus O.; Harlang, Tobias; Chollet, Matthieu; Christensen, Morten; Gawelda, Wojciech; Henriksen, Niels E.; Kim, Jong Goo; Haldrup, Kristoffer; Kim, Kyung Hwan; Ihee, Hyotcherl; Kim, Jeongho; Lemke, Henrik; Sun, Zheng; Sundström, Villy; Zhang, Wenkai; Zhu, Diling; Møller, Klaus B.; Nielsen, Martin M.; Gaffney, Kelly J.

    2016-11-01

    The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir2(dimen)4]2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute-solvent pair distribution function, enabling the solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis.

  6. Regulation of Dpp activity by tissue-specific cleavage of an upstream site within the prodomain

    PubMed Central

    Sopory, Shailaja; Kwon, Sunjong; Wehrli, Marcel; Christian, Jan L.

    2010-01-01

    BMP4 is synthesized as an inactive precursor that is cleaved at two sites during maturation: initially at a site (S1) adjacent to the ligand domain, and then at an upstream site (S2) within the prodomain. Cleavage at the second site regulates the stability of mature BMP4 and this in turn influences its signaling intensity and range of action. The Drosophila ortholog of BMP4, Dpp, functions as a long- or short-range signaling molecule in the wing disc or embryonic midgut, respectively but mechanisms that differentially regulate its bioactivity in these tissues have not been explored. In the current studies we demonstrate, by dpp mutant rescue, that cleavage at the S2 site of proDpp is required for development of the wing and leg imaginal discs, whereas cleavage at the S1 site is sufficient to rescue Dpp function in the midgut. Both the S1 and S2 site of proDpp are cleaved in the wing disc, and S2-cleavage is essential to generate sufficient ligand to exceed the threshold for pMAD activation at both short- and long-range in most cells. By contrast, proDpp is cleaved at the S1 site alone in the embryonic mesoderm and this generates sufficient ligand to activate physiological target genes in neighboring cells. These studies provide the first biochemical and genetic evidence that that selective cleavage of the S2 site of proDPP provides a tissue-specific mechanism for regulating Dpp activity, and that differential cleavage can contribute to, but is not an absolute determinant of signaling range. PMID:20659445

  7. 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.

  8. Elevated Ground Temperatures at Crude Oil Spill Sites due to Microbial Activity

    NASA Astrophysics Data System (ADS)

    Warren, E.; Bekins, B. A.

    2009-12-01

    Crude oil near the water table at spill sites near Bemidji and Cass Lake, Minnesota, has been undergoing aerobic and anaerobic biodegradation for decades. Because the reactions are exothermic, biodegradation of oil compounds will produce measurable temperature increases if heat is generated faster than it is transported away from the oil body. Subsurface temperatures at the two spill sites were measured with thermistors at multiple depths in groundwater monitoring wells and water-filled tubes in the vadose zone. Temperatures in selected wells were measured in the summer of 2007, 2008, and 2009. At the Bemidji site, temperatures measured in the summer ranged from a low of 6.3 oC in the background well to a high of 9.2 oC within wells in the oil-contaminated zone. From year to year, background minimum temperatures were constant within +/- 0.05 oC while maximum temperatures within the oil-contaminated zone remained within +/- 0.25 oC. Seasonal changes in temperature in the plume as measured by data loggers exceeded 4 oC, which was far greater than the year to year change in the summer measurements. Seasonal variability was greater near the water table than at depth. It is unclear whether this variability is due to subsurface hydrology or microbial activity. Temperatures in the vadose zone were warmer near and down-gradient from the oil body compared to the background indicating the heat from the oil and plume propagates up and outward into the vadose zone. At the Cass Lake site, summer temperatures in 2009 were 6.4 oC in the background and 11.5 oC in wells near the oil. Reaction rates inferred from chemical data were compared to heating required in a 3-dimension energy transport model of the subsurface. The increased temperature compared well to the expected heat production from biodegradation reactions occurring in the oil and plume. Results indicate that microbial activity in sediments contaminated with crude oil undergoing biodegradation can be detected using

  9. An Electromagnetic Interference Study of Potential Transmitter Sites for the HF Active Auroral Research Program (HAARP)

    DTIC Science & Technology

    1993-07-19

    heating . The measurements described in this report were conducted at a number of candidate HAARP transmitter sites in the vicinity of Fairbanks...employ the High Power Auroral Stimulation (HIPAS) RF heating facility [1], located in the Chena River valley area near Fairbanks. HAARP will be an...Potential Transmitter Sites for the HF Active Auroral Research Program ( HAARP ) JOSEP11 A. GOLDSTEIN EDWARD 1. KENNEDY ADRIAN S. ELEY 4 IMICHlAEL A. RuPAR C

  10. Effects of protein flexibility and active site water molecules on the prediction of sites of metabolism for cytochrome P450 2C19 substrates.

    PubMed

    Li, Junhao; Cai, Jinya; Su, Haixia; Du, Hanwen; Zhang, Juan; Ding, Shihui; Liu, Guixia; Tang, Yun; Li, Weihua

    2016-03-01

    Structure-based prediction of sites of metabolism (SOMs) mediated by cytochrome P450s (CYPs) is of great interest in drug discovery and development. However, protein flexibility and active site water molecules remain a challenge for accurate SOM prediction. CYP2C19 is one of the major drug-metabolizing enzymes and has attracted considerable attention because of its polymorphism and capability of metabolizing ∼7% clinically used drugs. In this study, we systematically evaluated the effects of protein flexibility and active site water molecules on SOM prediction for CYP2C19 substrates. Multiple conformational sampling techniques including GOLD flexible residues sampling, molecular dynamics (MD) and tCONCOORD side-chain sampling were adopted for assessing the influence of protein flexibility on SOM prediction. The prediction accuracy could be significantly improved when protein flexibility was considered using the tCONCOORD sampling method, which indicated that the side-chain conformation was important for accurate prediction. However, the inclusion of the crystallographic or MD-derived water molecule(s) does not necessarily improve the prediction accuracy. Finally, a combination of docking results with SMARTCyp was found to be able to increase the SOM prediction accuracy.

  11. Active-site concentrations of chemicals - are they a better predictor of effect than plasma/organ/tissue concentrations?

    PubMed

    Hammarlund-Udenaes, Margareta

    2010-03-01

    Active-site concentrations can be defined as the concentrations of unbound, pharmacologically active substances at the site of action. In contrast, the total concentrations of the drug in plasma/organ/tissue also include the protein- or tissue-bound molecules that are pharmacologically inactive. Plasma and whole tissue concentrations are used as predictors of effects and side effects because of their ease of sampling, while the concentrations of unbound drug in tissue are more difficult to measure. However, with the introduction of microdialysis and subsequently developed techniques, it has become possible to test the free drug hypothesis. The brain is an interesting organ in this regard because of the presence of the blood-brain barrier with its tight junctions and active efflux and influx transporters. We have proposed that research into brain drug delivery be divided into three main areas: the rate of delivery (PS, CL(in)), the extent of delivery (K(p,uu)) and the non-specific affinity of the drug to brain tissue, described by the volume of distribution of unbound drug in the brain (V(u,brain)). In this way, the concentration of unbound drug at the target site can be estimated from the total brain concentration and the plasma concentration after measuring the fraction of unbound drug. Results so far fully support the theory that active site concentrations are the best predictors when active transport is present. However, there is an urgent need to collect more relevant data for predicting active site concentrations in tissues with active transporters in their plasma membranes.

  12. Probing the catalytic mechanism of bovine CD38/NAD+ glycohydrolase by site directed mutagenesis of key active site residues.

    PubMed

    Kuhn, Isabelle; Kellenberger, Esther; Cakir-Kiefer, Céline; Muller-Steffner, Hélène; Schuber, Francis

    2014-07-01

    Bovine CD38/NAD(+) glycohydrolase catalyzes the hydrolysis of NAD(+) to nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose via a stepwise reaction mechanism. Our recent crystallographic study of its Michaelis complex and covalently-trapped intermediates provided insights into the modalities of substrate binding and the molecular mechanism of bCD38. The aim of the present work was to determine the precise role of key conserved active site residues (Trp118, Glu138, Asp147, Trp181 and Glu218) by focusing mainly on the cleavage of the nicotinamide-ribosyl bond. We analyzed the kinetic parameters of mutants of these residues which reside within the bCD38 subdomain in the vicinity of the scissile bond of bound NAD(+). To address the reaction mechanism we also performed chemical rescue experiments with neutral (methanol) and ionic (azide, formate) nucleophiles. The crucial role of Glu218, which orients the substrate for cleavage by interacting with the N-ribosyl 2'-OH group of NAD(+), was highlighted. This contribution to catalysis accounts for almost half of the reaction energy barrier. Other contributions can be ascribed notably to Glu138 and Asp147 via ground-state destabilization and desolvation in the vicinity of the scissile bond. Key interactions with Trp118 and Trp181 were also proven to stabilize the ribooxocarbenium ion-like transition state. Altogether we propose that, as an alternative to a covalent acylal reaction intermediate with Glu218, catalysis by bCD38 proceeds through the formation of a discrete and transient ribooxocarbenium intermediate which is stabilized within the active site mostly by electrostatic interactions.

  13. Characterization of the active site topography of manganese peroxidase using mechanism based inhibitors

    SciTech Connect

    Harris, R.; Wartishi, H.; Gold. M.; de Montellano, P.O. Oregon Graduate Inst. of Science and Technology, Beaverton )

    1991-03-11

    Manganese peroxidase (MnP), extracellular heme enzyme from the lignin-degrading fungus Phanerochaete chrysosporium, normally oxidizes Mn(II) to Mn(III). MnP is rapidly and completely inactivated in a H{sub 2}O{sub 2}-dependent reaction by 2 equivalents of sodium azide. The inactivation is paralleled by formation of azidyl radicals and high yield conversion of the prosthetic heme into a mexo-azido adduct. The meso-azido enzyme is oxidized by H{sub 2}O{sub 2} to a Compound II-like species. MnP is also inactivated by phenyl-, methyl- and ethylhydrazine. The phenylhydrazine reaction is too rapid for kinetic analysis, but K{sub I} = 402 mM and k{sub inact} = 0.22 min{sup {minus}1} for the inactivation by methylhydrazine. Reaction with phenylhydrazine at pH 4.5 does not yield iron-phenyl, N-phenyl, or meso-phenyl heme adducts. Ethylhydrazine inactivates the enzyme both at pH 4.5 and 7.0 but a {delta}-meso-ethylheme product is detected only at pH 7.0. Reconstitution of apo-MnP with {delta}-meso-ethylheme yields enzyme still capable of forming a Compound II-like species yet having diminished catalytic activity. Finally, Co(II) inhibits the enzyme competitively with respect to Mn(II) but does not inhibit its inactivation by azide or the alkylhydrazines. The results argue that substrates interact with the heme edge in the vicinity of the {delta}-meso carbon. They also suggest that Mn(II) and Co(II) bind to a common site close to the {delta}-meso carbon without blocking the approach of small molecules to the heme edge. An active site model is proposed that accommodates these results.

  14. Chondroitinase ABC I from Proteus vulgaris: cloning, recombinant expression and active site identification.

    PubMed

    Prabhakar, Vikas; Capila, Ishan; Bosques, Carlos J; Pojasek, Kevin; Sasisekharan, Ram

    2005-02-15

    GalAGs (galactosaminoglycans) are one subset of the GAG (glycosaminoglycan) family of chemically heterogeneous polysaccharides that are involved in a wide range of biological processes. These complex biomacromolecules are believed to be responsible for the inhibition of nerve regeneration following injury to the central nervous system. The enzymic degradation of GAG chains in damaged nervous tissue by cABC I (chondroitinase ABC I), a broad-specificity lyase that degrades GalAGs, promotes neural recovery. In the present paper, we report the subcloning of cABC I from Proteus vulgaris, and discuss a simple methodology for the recombinant expression and purification of this enzyme. The originally expressed cABC I clone resulted in an enzyme with negligible activity against a variety of GalAG substrates. Sequencing of the cABC I clone revealed four point mutations at issue with the electron-density data of the cABC I crystal structure. Site-directed mutagenesis produced a clone with restored GalAG-degrading function. We have characterized this enzyme biochemically, including an analysis of its substrate specificity. By coupling structural inspections of cABC I and an evaluation of sequence homology against other GAG-degrading lyases, a set of amino acids was chosen for further study. Mutagenesis studies of these residues resulted in the first experimental evidence of cABC I's active site. This work will facilitate the structure-function characterization of biomedically relevant GalAGs and further the development of therapeutics for nerve regeneration.

  15. Modification and activation of Ras proteins by electrophilic prostanoids with different structure are site-selective.

    PubMed

    Renedo, Marta; Gayarre, Javier; García-Domínguez, Carlota A; Pérez-Rodríguez, Andrea; Prieto, Alicia; Cañada, F Javier; Rojas, José M; Pérez-Sala, Dolores

    2007-06-05

    Cyclopentenone prostanoids (cyP) arise as important modulators of inflammation and cell proliferation. Although their physiological significance has not been fully elucidated, their potent biological effects have spurred their study as leads for the development of therapeutic agents. A key determinant of cyP action is their ability to bind to thiol groups in proteins or in glutathione through Michael addition. Even though several protein targets for cyP addition have been identified, little is known about the structural determinants from the protein or the cyP that drive this modification. The results herein presented provide the first evidence that cyP with different structures target distinct thiol sites in a protein molecule, namely, H-Ras. Whereas 15-deoxy-Delta12,14-prostaglandin J2 (15d-PGJ2) and Delta12-PGJ2 preferentially target the C-terminal region containing cysteines 181 and 184, PGA1 and 8-iso-PGA1 bind mainly to cysteine 118, located in the GTP-binding motif. The biological counterparts of this specificity are the site-selective modification and activation of H-Ras in cells and the differential interaction of cyP with H, N, and K-Ras proteins. Cysteine 184 is unique to H-Ras, whereas cysteine 118 is present in the three Ras homologues. Consistent with this, PGA1 binds to and activates H-, N-, and K-Ras, thus differing from the preferential interaction of 15d-PGJ2 with H-Ras. These results put forward the possibility of influencing the selectivity of cyP-protein addition by modifying cyP structure. Furthermore, they may open new avenues for the development of cyP-based drugs.

  16. Field and laboratory results for the evaluation of metal contaminants at a Superfund site

    SciTech Connect

    Callahan, C.A.; Svirsky, S.; Bollman, M.

    1994-12-31

    Measurements were made for seed germination plant uptake, laboratory biomass (lettuce, Lactuca saliva), mortality and bioaccumulation tests (earthworm, Eisenia fetida) in the field and laboratory, field and laboratory uptake with small mammals and laboratory uptake with Xenopus. Metals included cadmium, arsenic, chromium, copper, lead, nickel, and zinc collected in soils at five stations and a reference station, and in earthworm tissue, gut contents, in plants, small mammals and frogs exposed in the laboratory. These measurement endpoints were selected to assess the potential risks of the metal plating wastes to avian, mammalian, and wetland assessment endpoints in support of ecological risk assessment. Mortality was observed in the field earthworm test after a 7 day exposure. No inhibition of 4 day seed germination was observed at any station in field or greenhouse studies, however 28 day biomass tests for lettuce resulted in significant reductions in biomass. Cadmium measured in earthworm tissue was considerably greater for indigenous earthworms compared to laboratory exposed earthworms for 28 days, or to earthworms exposed in the field for 26 days. Differences in the results obtained from field and laboratory exposures for bioaccumulation of metals demonstrates the importance of infield exposure in studies to support ecological risk assessment.

  17. Results of Aquifer Tests Performed Near R-Area, Savannah River Site

    SciTech Connect

    Hiergesell, R.A.

    2001-01-31

    The aquifer testing described in this report was conducted in response to USEPA comments (WSRC, 1998) on the Rev. 0 R-Reactor Seepage Basins RFI/RI Report (WSRC, 1998a), Appendix G, Groundwater Contaminant Transport Modeling for the R-Reactor Seepage Basins (RRSB)/108-4R Overflow Basin Operable Unit. The R-area regional flow model described in Appendix G of the RFI/RI is based on small-scale and/or indirect measures of hydraulic conductivity, including laboratory tests, slug tests, cone penetration testing (CPT) and lithologic core descriptions. The USEPA proposed and SRS- agreed that large-scale conductivity estimates from multiple well pumping tests would be beneficial for validating the model conductivity field. Overall, the aquifer test results validate the 1998 R-area regional groundwater flow model.

  18. The influence of small-mammal burrowing activity on water storage at the Hanford Site

    SciTech Connect

    Landeen, D.S.

    1994-12-31

    This paper summarizes the activities that were conducted in support of the long-term surface barrier development program by Westinghouse Hanford Company to determine the degree that small-mammal burrow systems affect the loss or retention of water in the soils at the Hanford Site in Washington state. An animal intrusion lysimeter facility was constructed, consisting of two outer boxes buried at grade, which served as receptacles for six animal intrusion lysimeters. Small burrowing animals common the Hanford Site were introduced over a 3- to 4-month period. Supplemental precipitation was added monthly to three of the lysimeters with a rainfall simulator (rainulator). Information collected from the five tests indicated that (1) during summer months, water was lost in all the lysimeters, including the supplemental precipitation added with the rainulator; and (2) during winter months, all lysimeters gained water. The data indicate little difference in the amount of water stored between control and animal lysimeters. The overall water loss was attributed to surface evaporation, a process that occurred equally in control and treatment lysimeters. Other causes of water loss are a result of (1) constant soil turnover and subsequent drying, and (2) burrow ventilation effects. This suggests that burrow systems will not contribute to any significant water storage at depth and, in fact, may enhance the removal of water from the soil.

  19. The cytochrome P-450 active site. Regiospecificity of prosthetic heme alkylation by olefins and acetylenes.

    PubMed

    Kunze, K L; Mangold, B L; Wheeler, C; Beilan, H S; Ortiz de Montellano, P R

    1983-04-10

    Hepatic microsomal cytochrome P-450 from phenobarbital-pretreated rats is inactivated during the metabolism of linear olefins (ethylene, propene, and octene) and acetylenes (acetylene, propyne, and octyne). As expected from previous work, the inactivation is due to N-alkylation of the prosthetic heme group by the substrate. The N-alkyl group in each adduct is formally obtained by addition of a porphyrin nitrogen to the terminal carbon and of an oxygen atom (as a hydroxyl function) to the internal carbon of the pi-bond. The oxygen is shown here by 18O studies to be catalytically introduced by the enzyme. The olefins exclusively alkylate the nitrogen of pyrrole ring D, but the acetylenes alkylate that of pyrrole ring A. Acetylene is an exception in that it reacts with more than one nitrogen. Circular dichroism studies of the ethylene adduct and of the ring D regioisomer of N-ethylprotoporphyrin IX obtained by alkylation of the prosthetic heme of hemoglobin have been used to determine which face of cytochrome P-450 heme is alkylated by the unsaturated substrates. These results implicate an active site that is sterically encumbered in the region over pyrrole ring B and has a lipophilic binding site that accommodates chains of at least six carbon atoms over pyrrole ring C.

  20. Structure-guided inhibitor design for human FAAH by interspecies active site conversion.

    PubMed

    Mileni, Mauro; Johnson, Douglas S; Wang, Zhigang; Everdeen, Daniel S; Liimatta, Marya; Pabst, Brandon; Bhattacharya, Keshab; Nugent, Richard A; Kamtekar, Satwik; Cravatt, Benjamin F; Ahn, Kay; Stevens, Raymond C

    2008-09-02

    The integral membrane enzyme fatty acid amide hydrolase (FAAH) hydrolyzes the endocannabinoid anandamide and related amidated signaling lipids. Genetic or pharmacological inactivation of FAAH produces analgesic, anxiolytic, and antiinflammatory phenotypes but not the undesirable side effects of direct cannabinoid receptor agonists, indicating that FAAH may be a promising therapeutic target. Structure-based inhibitor design has, however, been hampered by difficulties in expressing the human FAAH enzyme. Here, we address this problem by interconverting the active sites of rat and human FAAH using site-directed mutagenesis. The resulting humanized rat (h/r) FAAH protein exhibits the inhibitor sensitivity profiles of human FAAH but maintains the high-expression yield of the rat enzyme. We report a 2.75-A crystal structure of h/rFAAH complexed with an inhibitor, N-phenyl-4-(quinolin-3-ylmethyl)piperidine-1-carboxamide (PF-750), that shows strong preference for human FAAH. This structure offers compelling insights to explain the species selectivity of FAAH inhibitors, which should guide future drug design programs.

  1. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    DOE PAGES

    Wang, Yanggang; Mei, Donghai; Glezakou, Vassiliki Alexandra; ...

    2015-03-04

    Ab initio Molecular Dynamics simulations and static Density Functional Theory calculations have been performed to investigate the reaction mechanism of CO oxidation on Au/CeO2 catalyst. It is found that under reaction condition CO adsorption significantly labializes the surface atoms of the Au cluster and leads to the formation of isolated Au+-CO species that resides on the support in the vicinity of the Au particle. In this context, we identified a dynamic single-atom catalytic mechanism at the interfacial area for CO oxidation on Au/CeO2 catalyst, which is a lower energy pathway than that of CO oxidation at the interface with themore » metal particle. This results from the ability of the single atom site to strongly couple with the redox properties of the support in a synergistic manner thereby lowering the barrier for redox reactions. We find that the single Au+ ion, which only exists under reaction conditions, breaks away from the Au cluster to catalyze CO oxidation and returns to the Au cluster after the catalytic cycle is completed. Generally, our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in a catalytic process.« less

  2. Dynamic formation of single-atom catalytic active sites on ceria-supported gold nanoparticles

    SciTech Connect

    Wang, Yanggang; Mei, Donghai; Glezakou, Vassiliki Alexandra; Li, Jun; Rousseau, Roger J.

    2015-03-04

    Ab initio Molecular Dynamics simulations and static Density Functional Theory calculations have been performed to investigate the reaction mechanism of CO oxidation on Au/CeO2 catalyst. It is found that under reaction condition CO adsorption significantly labializes the surface atoms of the Au cluster and leads to the formation of isolated Au+-CO species that resides on the support in the vicinity of the Au particle. In this context, we identified a dynamic single-atom catalytic mechanism at the interfacial area for CO oxidation on Au/CeO2 catalyst, which is a lower energy pathway than that of CO oxidation at the interface with the metal particle. This results from the ability of the single atom site to strongly couple with the redox properties of the support in a synergistic manner thereby lowering the barrier for redox reactions. We find that the single Au+ ion, which only exists under reaction conditions, breaks away from the Au cluster to catalyze CO oxidation and returns to the Au cluster after the catalytic cycle is completed. Generally, our study highlights the importance of the dynamic creation of active sites under reaction conditions and their essential role in a catalytic process.

  3. Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine-200

    PubMed Central

    Kovaleva, Elena G.; Rogers, Melanie S.; Lipscomb, John D.

    2015-01-01

    Kinetic and spectroscopic studies have shown that the conserved active site residue His200 of the extradiol ring-cleaving homoprotocatechuate 2,3-dioxygenase (FeHPCD) from Brevibacterium fuscum is critical for efficient catalysis. The roles played by this residue are probed here by analysis of the steady state kinetics, pH dependence, and X-ray crystal structures of the FeHPCD position 200 variants His200Asn, His200Gln, and His200Glu alone and in complex with three catecholic substrates (homoprotocatechuate, 4-sulfonylcatechol, and 4-nitrocatechol) possessing substituents with different inductive capacity. Structures solved at 1.35 –1.75 Å resolution show that there is essentially no change in overall active site architecture or substrate binding mode for these variants when compared to the structures of the wild type enzyme and its analogous complexes. This shows that the maximal 50-fold decrease in kcat for ring cleavage, the dramatic changes in pH dependence, and the switch from ring cleavage to ring oxidation of 4-nitrocatechol by the FeHPCD variants can be attributed specifically to the properties of the altered second sphere residue and the substrate. The results suggest that proton transfer is necessary for catalysis, and that it occurs most efficiently when the substrate provides the proton and His200 serves as a catalyst. However, in the absence of an available substrate proton, a defined proton-transfer pathway in the protein can be utilized. Changes in steric bulk and charge of the residue at position 200 appear capable of altering the rate-limiting step in catalysis, and perhaps, the nature of the reactive species. PMID:26267790

  4. Microbial community changes along the active seepage site of one cold seep in the Red Sea

    PubMed Central

    Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

    2015-01-01

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep. PMID:26284035

  5. Analysis of the activity of virus internal ribosome entry site in silkworm Bombyx mori.

    PubMed

    Ye, Lupeng; Zhuang, Lanfang; Li, Jisheng; You, Zhengying; Liang, Jianshe; Wei, Hao; Lin, Jianrong; Zhong, Boxiong

    2013-07-01

    Internal ribosome entry site (IRES) has been widely used in genetic engineering; however, the application in silkworm (Bombyx mori) has hardly been reported. In this study, the biological activity of partial sequence of Encephalomyocarditis virus (EMCV) IRES, Rhopalosiphum padi virus (RhPV) IRES, and the hybrid of IRES of EMCV and RhPV were investigated in Spodoptera frugiperda (Sf9) cell line and silkworm tissues. The hybrid IRES of EMCV and RhPV showed more effective than EMCV IRES or RhPV IRES in promoting downstream gene expression in insect and silkworm. The activities of all IRESs in middle silk gland of silkworm were higher than those in the fat body and posterior silk gland. The hybrid IRES of EMCV and RhPV was integrated into silkworm genome by transgenic technology to test biological activity of IRES. Each of the positive transgenic individuals had significant expression of report gene EGFP. These results suggested that IRES has a potential to be used in the genetic engineering research of silkworm.

  6. Actinobacterial diversity in limestone deposit sites in Hundung, Manipur (India) and their antimicrobial activities.

    PubMed

    Nimaichand, Salam; Devi, Asem Mipeshwaree; Tamreihao, K; Ningthoujam, Debananda S; Li, Wen-Jun

    2015-01-01

    Studies on actinobacterial diversity in limestone habitats are scarce. This paper reports profiling of actinobacteria isolated from Hundung limestone samples in Manipur, India using ARDRA as the molecular tool for preliminary classification. A total of 137 actinobacteria were clustered into 31 phylotypic groups based on the ARDRA pattern generated and representative of each group was subjected to 16S rRNA gene sequencing. Generic diversity of the limestone isolates consisted of Streptomyces (15 phylotypic groups), Micromonospora (4), Amycolatopsis (3), Arthrobacter (3), Kitasatospora (2), Janibacter (1), Nocardia (1), Pseudonocardia (1) and Rhodococcus (1). Considering the antimicrobial potential of these actinobacteria, 19 showed antimicrobial activities against at least one of the bacterial and candidal test pathogens, while 45 exhibit biocontrol activities against at least one of the rice fungal pathogens. Out of the 137 actinobacterial isolates, 118 were found to have at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, NRPS). The results indicate that 86% of the strains isolated from Hundung limestone deposit sites possessed biosynthetic gene clusters of which 40% exhibited antimicrobial activities. It can, therefore, be concluded that limestone habitat is a promising source for search of novel secondary metabolites.

  7. In situ probing of the active site geometry of ultrathin nanowires for the oxygen reduction reaction

    SciTech Connect

    Liu, Haiqing; Wong, Stanislaus S.; An, Wei; Li, Yuanyuan; Frenkel, Anatoly I.; Sasaki, Kotaro; Koenigsmann, Christopher; Su, Dong; Anderson, Rachel M.; Crooks, Richard M.; Adzic, Radoslav R.; Liu, Ping

    2015-09-24

    To create truly effective electrocatalysts for the cathodic reaction governing proton exchange membrane fuel cells (PEMFC), namely the oxygen reduction reaction (ORR), necessitates an accurate and detailed structural understanding of these electrocatalysts, especially at the nanoscale, and to precisely correlate that structure with demonstrable performance enhancement. To address this key issue, we have combined and interwoven theoretical calculations with experimental, spectroscopic observations in order to acquire useful structural insights into the active site geometry with implications for designing optimized nanoscale electrocatalysts with rationally predicted properties. Specifically, we have probed ultrathin (~2 nm) core–shell Pt~Pd9Au nanowires, which have been previously shown to be excellent candidates for ORR in terms of both activity and long-term stability, from the complementary perspectives of both DFT calculations and X-ray absorption spectroscopy (XAS). The combination and correlation of data from both experimental and theoretical studies has revealed for the first time that the catalytically active structure of our ternary nanowires can actually be ascribed to a PtAu~Pd configuration, comprising a PtAu binary shell and a pure inner Pd core. Moreover, we have plausibly attributed the resulting structure to a specific synthesis step, namely the Cu underpotential deposition (UPD) followed by galvanic replacement with Pt. Thus, the fundamental insights gained into the performance of our ultrathin nanowires from our demonstrated approach will likely guide future directed efforts aimed at broadly improving upon the durability and stability of nanoscale electrocatalysts in general.

  8. In Situ Probing of the Active Site Geometry of Ultrathin Nanowires for the Oxygen Reduction Reaction.

    PubMed

    Liu, Haiqing; An, Wei; Li, Yuanyuan; Frenkel, Anatoly I; Sasaki, Kotaro; Koenigsmann, Christopher; Su, Dong; Anderson, Rachel M; Crooks, Richard M; Adzic, Radoslav R; Liu, Ping; Wong, Stanislaus S

    2015-10-07

    To create truly effective electrocatalysts for the cathodic reaction governing proton exchange membrane fuel cells (PEMFC), namely the oxygen reduction reaction (ORR), necessitates an accurate and detailed structural understanding of these electrocatalysts, especially at the nanoscale, and to precisely correlate that structure with demonstrable performance enhancement. To address this key issue, we have combined and interwoven theoretical calculations with experimental, spectroscopic observations in order to acquire useful structural insights into the active site geometry with implications for designing optimized nanoscale electrocatalysts with rationally predicted properties. Specifically, we have probed ultrathin (∼2 nm) core-shell Pt∼Pd9Au nanowires, which have been previously shown to be excellent candidates for ORR in terms of both activity and long-term stability, from the complementary perspectives of both DFT calculations and X-ray absorption spectroscopy (XAS). The combination and correlation of data from both experimental and theoretical studies has revealed for the first time that the catalytically active structure of our ternary nanowires can actually be ascribed to a PtAu∼Pd configuration, comprising a PtAu binary shell and a pure inner Pd core. Moreover, we have plausibly attributed the resulting structure to a specific synthesis step, namely the Cu underpotential deposition (UPD) followed by galvanic replacement with Pt. Hence, the fundamental insights gained into the performance of our ultrathin nanowires from our demonstrated approach will likely guide future directed efforts aimed at broadly improving upon the durability and stability of nanoscale electrocatalysts in general.

  9. Microbial community changes along the active seepage site of one cold seep in the Red Sea.

    PubMed

    Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

    2015-01-01

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

  10. Nanoscale electrochemical patterning reveals the active sites for catechol oxidation at graphite surfaces.

    PubMed

    Patel, Anisha N; McKelvey, Kim; Unwin, Patrick R

    2012-12-19

    Graphite-based electrodes (graphite, graphene, and nanotubes) are used widely in electrochemistry, and there is a long-standing view that graphite step edges are needed to catalyze many reactions, with the basal surface considered to be inert. In the present work, this model was tested directly for the first time using scanning electrochemical cell microscopy reactive patterning and shown to be incorrect. For the electro-oxidation of dopamine as a model process, the reaction rate was measured at high spatial resolution across a surface of highly oriented pyrolytic graphite. Oxidation products left behind in a pattern defined by the scanned electrochemical cell served as surface-site markers, allowing the electrochemical activity to be correlated directly with the graphite structure on the nanoscale. This process produced tens of thousands of electrochemical measurements at different locations across the basal surface, unambiguously revealing it to be highly electrochemically active, with step edges providing no enhanced activity. This new model of graphite electrodes has significant implications for the design of carbon-based biosensors, and the results are additionally important for understanding electrochemical processes on related sp(2)-hybridized materials such as pristine graphene and nanotubes.

  11. Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme

    SciTech Connect

    Berezniak, Tomasz; Zahran, Mai; Imhof, Petra; Jaeschke, Andres; Smith, Jeremy C

    2010-10-01

    The Diels-Alderase ribozyme, an in vitro-evolved ribonucleic acid enzyme, accelerates the formation of carbon-carbon bonds between an anthracene diene and a maleimide dienophile in a [4 + 2] cycloaddition, a reaction with broad application in organic chemistry. Here, the Diels-Alderase ribozyme is examined via molecular dynamics (MD) simulations in both crystalline and aqueous solution environments. The simulations indicate that the catalytic pocket is highly dynamic. At low Mg(2+) ion concentrations, inactive states with the catalytic pocket closed dominate. Stabilization of the enzymatically active, open state of the catalytic pocket requires a high concentration of Mg(2+) ions (e.g., 54 mM), with cations binding to specific phosphate sites on the backbone of the residues bridging the opposite strands of the pocket. The free energy profile for pocket opening at high Mg(2+) cation concentration exhibits a double minimum, with a barrier to opening of approximately 5.5 kJ/mol and the closed state approximately 3 kJ/mol lower than the open state. Selection of the open state on substrate binding leads to the catalytic activity of the ribozyme. The simulation results explain structurally the experimental observation that full catalytic activity depends on the Mg(2+) ion concentration

  12. The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine.

    PubMed

    Cottrell, Joseph W; Scott, Lincoln G; Fedor, Martha J

    2011-05-20

    Understanding how self-cleaving ribozymes mediate catalysis is crucial in light of compelling evidence that human and bacterial gene expression can be regulated through RNA self-cleavage. The hairpin ribozyme catalyzes reversible phosphodiester bond cleavage through a mechanism that does not require divalent metal cations. Previous structural and biochemical evidence implicated the amidine group of an active site adenosine, A38, in a pH-dependent step in catalysis. We developed a way to determine microscopic pK(a) values in active ribozymes based on the pH-dependent fluorescence of 8-azaadenosine (8azaA). We compared the microscopic pK(a) for ionization of 8azaA at position 38 with the apparent pK(a) for the self-cleavage reaction in a fully functional hairpin ribozyme with a unique 8azaA at position 38. Microscopic and apparent pK(a) values were virtually the same, evidence that A38 protonation accounts for the decrease in catalytic activity with decreasing pH. These results implicate the neutral unprotonated form of A38 in a transition state that involves formation of the 5'-oxygen-phosphorus bond.

  13. In situ probing of the active site geometry of ultrathin nanowires for the oxygen reduction reaction

    DOE PAGES

    Liu, Haiqing; Wong, Stanislaus S.; An, Wei; ...

    2015-09-24

    To create truly effective electrocatalysts for the cathodic reaction governing proton exchange membrane fuel cells (PEMFC), namely the oxygen reduction reaction (ORR), necessitates an accurate and detailed structural understanding of these electrocatalysts, especially at the nanoscale, and to precisely correlate that structure with demonstrable performance enhancement. To address this key issue, we have combined and interwoven theoretical calculations with experimental, spectroscopic observations in order to acquire useful structural insights into the active site geometry with implications for designing optimized nanoscale electrocatalysts with rationally predicted properties. Specifically, we have probed ultrathin (~2 nm) core–shell Pt~Pd9Au nanowires, which have been previously shownmore » to be excellent candidates for ORR in terms of both activity and long-term stability, from the complementary perspectives of both DFT calculations and X-ray absorption spectroscopy (XAS). The combination and correlation of data from both experimental and theoretical studies has revealed for the first time that the catalytically active structure of our ternary nanowires can actually be ascribed to a PtAu~Pd configuration, comprising a PtAu binary shell and a pure inner Pd core. Moreover, we have plausibly attributed the resulting structure to a specific synthesis step, namely the Cu underpotential deposition (UPD) followed by galvanic replacement with Pt. Thus, the fundamental insights gained into the performance of our ultrathin nanowires from our demonstrated approach will likely guide future directed efforts aimed at broadly improving upon the durability and stability of nanoscale electrocatalysts in general.« less

  14. A Site Characterization Protocol for Evaluating the Potential for Triggered or Induced Seismicity Resulting from Wastewater Injection and Hydraulic Fracturing

    NASA Astrophysics Data System (ADS)

    Walters, R. J.; Zoback, M. D.; Gupta, A.; Baker, J.; Beroza, G. C.

    2014-12-01

    Regulatory and governmental agencies, individual companies and industry groups and others have recently proposed, or are developing, guidelines aimed at reducing the risk associated with earthquakes triggered by waste water injection or hydraulic fracturing. While there are a number of elements common to the guidelines proposed, not surprisingly, there are also some significant differences among them and, in a number of cases, important considerations that are not addressed. The goal of this work is to develop a comprehensive protocol for site characterization based on a rigorous scientific understanding of the responsible processes. Topics addressed will include the geologic setting (emphasizing faults that might be affected), historical seismicity, hydraulic characterization of injection and adjacent intervals, geomechanical characterization to identify potentially active faults, plans for seismic monitoring and reporting, plans for monitoring and reporting injection (pressure, volumes, and rates), other factors contributing to risk (potentially affected population centers, structures, and facilities), and implementing a modified Probabilistic Seismic Hazard Analysis (PSHA). The guidelines will be risk based and adaptable, rather than prescriptive, for a proposed activity and region of interest. They will be goal oriented and will rely, to the degree possible, on established best practice procedures, referring to existing procedures and recommendations. By developing a risk-based site characterization protocol, we hope to contribute to the development of rational and effective measures for reducing the risk posed by activities that potentially trigger earthquakes.

  15. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase

    SciTech Connect

    Fenwick, Michael K.; Mehta, Angad P.; Zhang, Yang; Abdelwahed, Sameh H.; Begley, Tadhg P.; Ealick, Steven E.

    2015-03-27

    Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

  16. Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.

    PubMed

    Wang, Beibei; Sexton, Rachel E; Feig, Michael

    2017-04-01

    During transcription, RNA polymerase II elongates RNA by adding nucleotide triphosphates (NTPs) complementary to a DNA template. Structural studies have suggested that NTPs enter and exit the active site via the narrow secondary pore but details have remained unclear. A kinetic model is presented that integrates molecular dynamics simulations with experimental data. Previous simulations of trigger loop dynamics and the dynamics of matched and mismatched NTPs in and near the active site were combined with new simulations describing NTP exit from the active site via the secondary pore. Markov state analysis was applied to identify major states and estimate kinetic rates for transitions between those states. The kinetic model predicts elongation and misincorporation rates in close agreement with experiment and provides mechanistic hypotheses for how NTP entry and exit via the secondary pore is feasible and a key feature for achieving high elongation and low misincorporation rates during RNA elongation.

  17. 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

  18. 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.

  19. A mutational analysis of the active site of human type II inosine 5'-monophosphate dehydrogenase.

    PubMed

    Futer, Olga; Sintchak, Michael D; Caron, Paul R; Nimmesgern, Elmar; DeCenzo, Maureen T; Livingston, David J; Raybuck, Scott A

    2002-01-31

    The oxidation of IMP to XMP is the rate-limiting step in the de novo synthesis of guanine ribonucleotides. This NAD-dependent reaction is catalyzed by the enzyme inosine monophosphate dehydrogenase (IMPDH). Based upon the recent structural determination of IMPDH complexed to oxidized IMP (XMP*) and the potent uncompetitive inhibitor mycophenolic acid (MPA), we have selected active site residues and prepared mutants of human type II IMPDH. The catalytic parameters of these mutants were determined. Mutations G326A, D364A, and the active site nucleophile C331A all abolish enzyme activity to less than 0.1% of wild type. These residues line the IMP binding pocket and are necessary for correct positioning of the substrate, Asp364 serving to anchor the ribose ring of the nucleotide. In the MPA/NAD binding site, significant loss of activity was seen by mutation of any residue of the triad Arg322, Asn303, Asp274 which form a hydrogen bonding network lining one side of this pocket. From a model of NAD bound to the active site consistent with the mutational data, we propose that these resides are important in binding the ribose ring of the nicotinamide substrate. Additionally, mutations in the pair Thr333, Gln441, which lies close to the xanthine ring, cause a significant drop in the catalytic activity of IMPDH. It is proposed that these residues serve to deliver the catalytic water molecule required for hydrolysis of the cysteine-bound XMP* intermediate formed after oxidation by NAD.

  20. Two-Year Soil Gas Sampling and Respiration Testing Results Report for Full-Scale Bioventing at the POL Yard, Sites SS-06 and ST-40, Wurtsmith AFB, Michigan

    DTIC Science & Technology

    2007-11-02

    Parsons ES) for the full-scale bioventing system at the former Petroleum, Oils, and Lubricants, (POL) Yard, Sites SS-06 and ST-40, Wurtsmith AFB, Michigan...remediation completed during approximately 2 years of air injection bioventing . The purpose of this letter is to summarize site and bioventing activities to...testing and monitoring results. A site layout and two tables are attached. The as-built bioventing system and sampling/respiration testing locations are

  1. The Moon Zoo citizen science project: Preliminary results for the Apollo 17 landing site

    NASA Astrophysics Data System (ADS)

    Bugiolacchi, Roberto; Bamford, Steven; Tar, Paul; Thacker, Neil; Crawford, Ian A.; Joy, Katherine H.; Grindrod, Peter M.; Lintott, Chris

    2016-06-01

    Moon Zoo is a citizen science project that utilises internet crowd-sourcing techniques. Moon Zoo users are asked to review high spatial resolution images from the Lunar Reconnaissance Orbiter Camera (LROC), onboard NASA's LRO spacecraft, and perform characterisation such as measuring impact crater sizes and identify morphological 'features of interest'. The tasks are designed to address issues in lunar science and to aid future exploration of the Moon. We have tested various methodologies and parameters therein to interrogate and reduce the Moon Zoo crater location and size dataset against a validated expert survey. We chose the Apollo 17 region as a test area since it offers a broad range of cratered terrains, including secondary-rich areas, older maria, and uplands. The assessment involved parallel testing in three key areas: (1) filtering of data to remove problematic mark-ups; (2) clustering methods of multiple notations per crater; and (3) derivation of alternative crater degradation indices, based on the statistical variability of multiple notations and the smoothness of local image structures. We compared different combinations of methods and parameters and assessed correlations between resulting crater summaries and the expert census. We derived the optimal data reduction steps and settings of the existing Moon Zoo crater data to agree with the expert census. Further, the regolith depth and crater degradation states derived from the data are also found to be in broad agreement with other estimates for the Apollo 17 region. Our study supports the validity of this citizen science project but also recommends improvements in key elements of the data acquisition planning and production.

  2. Threatened and endangered wildlife species of the Hanford Site related to CERCLA characterization activities

    SciTech Connect

    Fitzner, R.E.; Weiss, S.G.; Stegen, J.A.

    1994-06-01

    The US Department of Energy`s (DOE) Hanford Site has been placed on the National Priorities List, which requires that it be remediated under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) or Superfund. Potentially contaminated areas of the Hanford Site were grouped into operable units, and detailed characterization and investigation plans were formulated. The DOE Richland Operations Office requested Westinghouse Hanford Company (WHC) to conduct a biological assessment of the potential impact of these characterization activities on the threatened, endangered, and sensitive wildlife species of the Hanford Site. Additional direction for WHC compliances with wildlife protection can be found in the Environmental Compliance Manual. This document is intended to meet these requirements, in part, for the CERCLA characterization activities, as well as for other work comparable in scope. This report documents the biological assessment and describes the pertinent components of the Hanford Site as well as the planned characterization activities. Also provided are accounts of endangered, threatened, and federal candidate wildlife species on the Hanford Site and information as to how human disturbances can affect these species. Potential effects of the characterization activities are described with recommendations for mitigation measures.

  3. Identification of a putative binding site critical for general anesthetic activation of TRPA1.

    PubMed

    Ton, Hoai T; Phan, Thieu X; Abramyan, Ara M; Shi, Lei; Ahern, Gerard P

    2017-04-04

    General anesthetics suppress CNS activity by modulating the function of membrane ion channels, in particular, by enhancing activity of GABAA receptors. In contrast, several volatile (isoflurane, desflurane) and i.v. (propofol) general anesthetics excite peripheral sensory nerves to cause pain and irritation upon administration. These noxious anesthetics activate transient receptor potential ankyrin repeat 1 (TRPA1), a major nociceptive ion channel, but the underlying mechanisms and site of action are unknown. Here we exploit the observation that pungent anesthetics activate mammalian but not Drosophila TRPA1. Analysis of chimeric Drosophila and mouse TRPA1 channels reveal a critical role for the fifth transmembrane domain (S5) in sensing anesthetics. Interestingly, we show that anesthetics share with the antagonist A-967079 a potential binding pocket lined by residues in the S5, S6, and the first pore helix; isoflurane competitively disrupts A-967079 antagonism, and introducing these mammalian TRPA1 residues into dTRPA1 recapitulates anesthetic agonism. Furthermore, molecular modeling predicts that isoflurane and propofol bind to this pocket by forming H-bond and halogen-bond interactions with Ser-876, Met-915, and Met-956. Mutagenizing Met-915 or Met-956 selectively abolishes activation by isoflurane and propofol without affecting actions of A-967079 or the agonist, menthol. Thus, our combined experimental and computational results reveal the potential binding mode of noxious general anesthetics at TRPA1. These data may provide a structural basis for designing drugs to counter the noxious and vasorelaxant properties of general anesthetics and may prove useful in understanding effects of anesthetics on related ion channels.

  4. Multiple-site mutations of phage Bp7 endolysin improves its activities against target bacteria.

    PubMed

    Zhang, Can; Wang, Yuanchao; Sun, Huzhi; Ren, Huiying

    2015-10-01

    The widespread use of antibiotics has caused serious drug resistance. Bacteria that were once easily treatable are now extremely difficult to treat. Endolysin can be used as an alternative to antibiotics for the treatment of drug-resistant bacteria. To analyze the antibacterial activity of the endolysin of phage Bp7 (Bp7e), a 489-bp DNA fragment of endolysin Bp7e was PCR-amplified from a phage Bp7 genome and cloned, and then a pET28a-Bp7e prokaryotic expression vector was constructed. Two amino acids were mutated (L99A, M102E) to construct pET28a-Bp7Δe, with pET28a-Bp7e as a template. Phylogenetic analysis suggested that BP7e belongs to a T4-like phage endolysin group. Bp7e and its mutant Bp7Δe were expressed in Escherichia coli BL21(DE3) as soluble proteins. They were purified by affinity chromatography, and then their antibacterial activities were analyzed. The results demonstrated that the recombinant proteins Bp7e and Bp7Δe showed obvious antibacterial activity against Micrococcus lysodeikticus but no activity against Staphylococcus aureus. In the presence of malic acid, Bp7e and Bp7Δe exhibited an effect on most E. coli strains which could be lysed by phage Bp7, but no effect on Salmonella paratyphi or Pseudomonas aeruginosa. Moreover, Bp7Δe with double-site mutations showed stronger antibacterial activity and a broader lysis range than Bp7e.

  5. A Variable Active Site Residue Influences the Kinetics of Response Regulator Phosphorylation and Dephosphorylation.

    PubMed

    Immormino, Robert M; Silversmith, Ruth E; Bourret, Robert B

    2016-10-04

    Two-component regulatory systems, minimally composed of a sensor kinase and a response regulator protein, are common mediators of signal transduction in microorganisms. All response regulators contain a receiver domain with conserved active site residues that catalyze the signal activating and deactivating phosphorylation and dephosphorylation reactions. We explored the impact of variable active site position T+1 (one residue C-terminal to the conserved Thr/Ser) on reaction kinetics and signaling fidelity, using wild type and mutant Escherichia coli CheY, CheB, and NarL to represent the three major sequence classes observed across response regulators: Ala/Gly, Ser/Thr, and Val/Ile/Met, respectively, at T+1. Biochemical and structural data together suggested that different amino acids at T+1 impacted reaction kinetics by altering access to the active site while not perturbing overall protein structure. A given amino acid at position T+1 had similar effects on autodephosphorylation in each protein background tested, likely by modulating access of the attacking water molecule to the active site. Similarly, rate constants for CheY autophosphorylation with three different small molecule phosphodonors were consistent with the steric constraints on access to the phosphorylation site arising from combination of specific phosphodonors with particular amino acids at T+1. Because other variable active site residues also influence response regulator phosphorylation biochemistry, we began to explore how context (here, the amino acid at T+2) affected the influence of position T+1 on CheY autocatalytic reactions. Finally, position T+1 affected the fidelity and kinetics of phosphotransfer between sensor kinases and response regulators but was not a primary determinant of their interaction.

  6. Annoyance resulting from intrusion of aircraft sounds upon various activities

    NASA Technical Reports Server (NTRS)

    Gunn, W. J.; Shepherd, W. T.; Fletcher, J. L.

    1975-01-01

    An experiment was conducted in which subjects were engaged in TV viewing, telephone listening, or reverie (no activity) for a 1/2-hour session. During the session, they were exposed to a series of recorded aircraft sounds at the rate of one flight every 2 minutes. Within each session, four levels of flyover noise, separated by dB increments, were presented several times in a Latin Square balanced sequence. The peak level of the noisiest flyover in any session was fixed at 95, 90, 85, 75, or 70 dBA. At the end of the test session, subjects recorded their responses to the aircraft sounds, using a bipolar scale which covered the range from very pleasant to extremely annoying. Responses to aircraft noises were found to be significantly affected by the particular activity in which the subjects were engaged. Not all subjects found the aircraft sounds to be annoying.

  7. Mechanical forces regulate elastase activity and binding site availability in lung elastin.

    PubMed

    Jesudason, Rajiv; Sato, Susumu; Parameswaran, Harikrishnan; Araujo, Ascanio D; Majumdar, Arnab; Allen, Philip G; Bartolák-Suki, Erzsébet; Suki, Béla

    2010-11-03

    Many fundamental cellular and extracellular processes in the body are mediated by enzymes. At the single molecule level, enzyme activity is influenced by mechanical forces. However, the effects of mechanical forces on the kinetics of enzymatic reactions in complex tissues with intact extracellular matrix (ECM) have not been identified. Here we report that physiologically relevant macroscopic mechanical forces modify enzyme activity at the molecular level in the ECM of the lung parenchyma. Porcine pancreatic elastase (PPE), which binds to and digests elastin, was fluorescently conjugated (f-PPE) and fluorescent recovery after photobleach was used to evaluate the binding kinetics of f-PPE in the alveolar walls of normal mouse lungs. Fluorescent recovery after photobleach indicated that the dissociation rate constant (k(off)) for f-PPE was significantly larger in stretched than in relaxed alveolar walls with a linear relation between k(off) and macroscopic strain. Using a network model of the parenchyma, a linear relation was also found between k(off) and microscopic strain on elastin fibers. Further, the binding pattern of f-PPE suggested that binding sites on elastin unfold with strain. The increased overall reaction rate also resulted in stronger structural breakdown at the level of alveolar walls, as well as accelerated decay of stiffness and decreased failure stress of the ECM at the macroscopic scale. These results suggest an important role for the coupling between mechanical forces and enzyme activity in ECM breakdown and remodeling in development, and during diseases such as pulmonary emphysema or vascular aneurysm. Our findings may also have broader implications because in vivo, enzyme activity in nearly all cellular and extracellular processes takes place in the presence of mechanical forces.

  8. 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.

  9. Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands

    PubMed Central

    2012-01-01

    Background Structural genomics approaches, particularly those solving the 3D structures of many proteins with unknown functions, have increased the desire for structure-based function predictions. However, prediction of enzyme function is difficult because one member of a superfamily may catalyze a different reaction than other members, whereas members of different superfamilies can catalyze the same reaction. In addition, conformational changes, mutations or the absence of a particular catalytic residue can prevent inference of the mechanism by which catalytic residues stabilize and promote the elementary reaction. A major hurdle for alignment-based methods for prediction of function is the absence (despite its importance) of a measure of similarity of the physicochemical properties of catalytic sites. To solve this problem, the physicochemical features radially distributed around catalytic sites should be considered in addition to structural and sequence similarities. Results We showed that radial distribution functions (RDFs), which are associated with the local structural and physicochemical properties of catalytic active sites, are capable of clustering oxidoreductases and transferases by function. The catalytic sites of these enzymes were also characterized using the RDFs. The RDFs provided a measure of the similarity among the catalytic sites, detecting conformational changes caused by mutation of catalytic residues. Furthermore, the RDFs reinforced the classification of enzyme functions based on conventional sequence and structural alignments. Conclusions Our results demonstrate that the application of RDFs provides advantages in the functional classification of enzymes by providing information about catalytic sites. PMID:22536854

  10. Site-specific albumination of a therapeutic protein with multi-subunit to prolong activity in vivo

    PubMed Central

    Lim, Sung In; Hahn, Young S.; Kwon, Inchan

    2015-01-01

    Albumin fusion/conjugation (albumination) has been an effective method to prolong in vivo half-life of therapeutic proteins. However, its broader application to proteins with complex folding pathway or multi-subunit is restricted by incorrect folding, poor expression, heterogeneity, and loss of native activity of the proteins linked to albumin. We hypothesized that the site-specific conjugation of albumin to a permissive site of a target protein will expand the utilities of albumin as a therapeutic activity extender to proteins with a complex structure. We show here the genetic incorporation of a non-natural amino acid (NNAA) followed by chemoselective albumin conjugation to prolong therapeutic activity in vivo. Urate oxidase (Uox), a therapeutic enzyme for treatment of hyperuricemia, is a homotetramer with multiple surface lysines, limiting conventional approaches for albumination. Incorporation of p-azido-l-phenylalanine into two predetermined positions of Uox allowed site-specific linkage of dibenzocyclooctyne-derivatized human serum albumin (HSA) through strain-promoted azide-alkyne cycloaddition (SPAAC). The bio-orthogonality of SPAAC resulted in the production of a chemically well-defined conjugate, Uox-HSA, with a retained enzymatic activity. Uox-HSA had a half-life of 8.8 h in mice, while wild-type Uox had a half-life of 1.3 h. The AUC increased 5.5-fold (1657 vs. 303 mU/mL × h). These results clearly demonstrated that site-specific albumination led to the prolonged enzymatic activity of Uox in vivo. Site-specific albumination enabled by NNAA incorporation and orthogonal chemistry demonstrates its promise for the development of long-acting protein therapeutics with high potency and safety. PMID:25862515

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

    PubMed Central

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

    2015-01-01

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

  12. Characteristics of Physical Activity Programs for Older Adults: Results of a Multisite Survey

    ERIC Educational Resources Information Center

    Hughes, Susan L.; Williams, Barbara; Molina, Lourdes C.; Bayles, Constance; Bryant, Lucinda L.; Harris, Jeffrey R.; Hunter, Rebecca; Ivey, Susan; Watkins, Ken

    2005-01-01

    Purpose: Although increased participation in physical activity by older adults is a major public health goal, little is known about the supply and use of physical activity programs in the United States. Design and Methods: Seven academic centers in diverse geographic areas surveyed physical activity programs for older adults. Five sites conducted…

  13. Functional biomimetic models for the active site in the respiratory enzyme cytochrome c oxidase.

    PubMed

    Collman, James P; Decréau, Richard A

    2008-11-07

    A functional analog of the active site in the respiratory enzyme, cytochrome c oxidase (CcO) reproduces every feature in CcO's active site: a myoglobin-like heme (heme a3), a distal tridentate imidazole copper complex (Cu(B)), a phenol (Tyr244), and a proximal imidazole. When covalently attached to a liquid-crystalline SAM film on an Au electrode, this functional model continuously catalyzes the selective four-electron reduction of dioxygen at physiological potential and pH, under rate-limiting electron flux (as occurs in CcO).

  14. Investigating the Potential Contribution of Patient Rating Sites to Hospital Supervision: Exploratory Results From an Interview Study in the Netherlands

    PubMed Central

    Zandbelt, Linda C; Borghans, Ine; de Haes, Hanneke J.C.J.M; Kool, Rudolf B

    2016-01-01

    Background Over the last decades, the patient perspective on health care quality has been unconditionally integrated into quality management. For several years now, patient rating sites have been rapidly gaining attention. These offer a new approach toward hearing the patient’s perspective on the quality of health care. Objective The aim of our study was to explore whether and how patient reviews of hospitals, as reported on rating sites, have the potential to contribute to health care inspector’s daily supervision of hospital care. Methods Given the unexplored nature of the topic, an interview study among hospital inspectors was designed in the Netherlands. We performed 2 rounds of interviews with 10 senior inspectors, addressing their use and their judgment on the relevance of review data from a rating site. Results All 10 Dutch senior hospital inspectors participated in this research. The inspectors initially showed some reluctance to use the major patient rating site in their daily supervision. This was mainly because of objections such as worries about how representative they are, subjectivity, and doubts about the relevance of patient reviews for supervision. However, confrontation with, and assessment of, negative reviews by the inspectors resulted in 23% of the reviews being deemed relevant for risk identification. Most inspectors were cautiously positive about the contribution of the reviews to their risk identification. Conclusions Patient rating sites may be of value to the risk-based supervision of hospital care carried out by the Health Care Inspectorate. Health care inspectors do have several objections against the use of patient rating sites for daily supervision. However, when they are presented with texts of negative reviews from a hospital under their supervision, it appears that most inspectors consider it as an additional source of information to detect poor quality of care. Still, it should always be accompanied and verified by other

  15. A Web Site to Improve Management of Patients with Inherited Bleeding Disorders in the Emergency Department: Results at 2 Years.

    PubMed

    Tagliaferri, Annarita; Di Perna, Caterina; Biasoli, Chiara; Rivolta, Gianna Franca; Quintavalle, Gabriele; Cervellin, Gianfranco; Barozzi, Marco; Benedettini, Laura; Pattacini, Corrado

    2016-07-01

    Treatment of patients with inherited bleeding disorders (PWIBD) in the emergency department (ED) is challenging. In 2010, a project was started involving all eight hemophilia centers (HC) and all 44 EDs of the Region of Emilia-Romagna (Italy) to improve emergency care for PWIBD. The project incorporates guidelines for emergency treatment, education for ED staff, and a dedicated Web site providing extensive information, proposing treatments, and sharing data with patients' electronic clinical records. A Web algorithm, accessible to PWIBD as well as ED and HC staff, suggests the first dose of concentrate for each type and severity of bleed or trauma. Following training courses in each ED, the network was activated. During 2012 and 2013, the site was visited 14,000 times, the EDs accessed the Web site 1,739 times, and used the algorithms 206 times. In two reference EDs, triage-assessment and triage-treatment times were reduced in 2013 and 2012 (27/20 and 110/71.5 minutes, respectively) and medical advice from the HC increased (54 vs. 24% cases). The main advantages of this system are better management of patients in ED (shorter triage-to-treatment times) and improved collaboration between HCs and EDs. The most critical point remaining is staff turnover in EDs, necessitating continual training.

  16. A Mutational Analysis of the Active Site Loop Residues in cis-3-Chloroacrylic Acid Dehalogenase

    PubMed Central

    Schroeder, Gottfried K.; Huddleston, Jamison P.; Johnson, William H.; Whitman, Christian P.

    2013-01-01

    cis -3-Chloroacrylic acid dehalogenase (cis-CaaD) from Pseudomonas pavonaceae 170 and a homologue from Corynebacterium glutamicum designated Cg10062 share 34% sequence identity (54% similarity). The former catalyzes a key step in a bacterial catabolic pathway for the nematocide 1,3-dichloropropene, whereas the latter has no known biological activity. Although Cg10062 has the six active site residues (Pro-1, His-28, Arg-70, Arg-73, Tyr-103, Glu-114) that are critical for cis-CaaD activity, it shows only a low level cis-CaaD activity and lacks the specificity of cis-CaaD: Cg10062 processes both isomers of 3-chloroacrylate with a preference for the cis-isomer. Although the basis for these differences is unknown, a comparison of the crystal structures of the enzymes covalently modified by an adduct resulting from their incubation with the same inhibitor offers a possible explanation. A 6-residue active site loop in cis-CaaD shows a strikingly different conformation from that observed in Cg10062: the loop closes down on the active site of cis-CaaD, but not on that of Cg10062. In order to examine what this loop might contribute to cis-CaaD catalysis and specificity, the residues were changed individually to those found in Cg10062. Subsequent kinetic and mechanistic analysis suggests that the T34A mutant of cis-CaaD is more Cg10062-like. The mutant enzyme shows a 4-fold increase in Km (using cis-3-bromoacrylate), but not to the degree observed for Cg10062 (687-fold). The mutation also causes a 4-fold decrease in the burst rate (compared to the wild type cis-CaaD), whereas Cg10062 shows no burst rate. More telling is the reaction of the T34A mutant of cis-CaaD with the alternate substrate, 2,3-butadienoate. In the presence of NaBH4 and the allene, cis-CaaD is completely inactivated after one turnover due to the covalent modification of Pro-1. The same experiment with Cg10062 does not result in the covalent modification of Pro-1. The different outcomes are attributed to

  17. The Role of an Active Site Mg2+ in HDV Ribozyme Self-Cleavage: Insights from QM/MM Calculations

    PubMed Central

    Mlýnský, Vojtěch; Šponer, Jiří

    2014-01-01

    The hepatitis delta virus (HDV) ribozyme is a catalytic RNA motif embedded in the human pathogenic HDV RNA. It catalyzes self-cleavage of its sugar-phosphate backbone with direct participation of the active site cytosine C75. Biochemical and structural data support a general acid role of C75. Here, we used hybrid quantum mechanical/molecular mechanical (QM/MM) calculations to probe the reaction mechanism and changes in Gibbs energy along the ribozyme's reaction pathway with an N3-protonated C75H+ in the active site, which acts as the general acid, and a partially hydrated Mg2+ ion with one deprotonated, inner-shell coordinated water molecule that acts as the general base. We followed eight reaction paths with distinct position and coordination of the catalytically important active site Mg2+ ion. For six of them, we observed feasible activation barriers ranging from 14.2 to 21.9 kcal/mol, indicating that the specific position of the Mg2+ ion in the active site is predicted to strongly affect the kinetics of self-cleavage. The deprotonation of the U-1(2′-OH) nucleophile and the nucleophilic attack of the resulting U-1(2′-O−) on the scissile phosphodiester are found to be separate steps, as deprotonation precedes the nucleophilic attack. This sequential mechanism of the HDV ribozyme differs from the concerted nucleophilic activation and attack suggested for the hairpin ribozyme. We estimated the pKa of the U-1(2′-OH) group to range from 8.8 to 11.2, suggesting that the pKa is lowered by several units from that of a free ribose, comparable to and most likely smaller than the pKa of the solvated active site Mg2+ ion. Our results thus support the notion that the structure of the HDV ribozyme, and particularly the positioning of the active site Mg2+ ion, facilitates deprotonation and activation of the 2′-OH nucleophile. PMID:25412464

  18. Phosphorylation of serine 264 impedes active site accessibility in the E1 component of the human pyruvate dehydrogenase multienzyme complex.

    PubMed

    Seifert, Franziska; Ciszak, Ewa; Korotchkina, Lioubov; Golbik, Ralph; Spinka, Michael; Dominiak, Paulina; Sidhu, Sukhdeep; Brauer, Johanna; Patel, Mulchand S; Tittmann, Kai

    2007-05-29

    At the junction of glycolysis and the Krebs cycle in cellular metabolism, the pyruvate dehydrogenase multienzyme complex (PDHc) catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA. In mammals, PDHc is tightly regulated by phosphorylation-dephosphorylation of three serine residues in the thiamin-dependent pyruvate dehydrogenase (E1) component. In vivo, inactivation of human PDHc correlates mostly with phosphorylation of serine 264, which is located at the entrance of the substrate channel leading to the active site of E1. Despite intense investigations, the molecular mechanism of this inactivation has remained enigmatic. Here, a detailed analysis of microscopic steps of catalysis in human wild-type PDHc-E1 and pseudophosphorylation variant Ser264Glu elucidates how phosphorylation of Ser264 affects catalysis. Whereas the intrinsic reactivity of the active site in catalysis of pyruvate decarboxylation remains nearly unaltered, the preceding binding of substrate to the enzyme's active site via the substrate channel and the subsequent reductive acetylation of the E2 component are severely slowed in the phosphorylation variant. The structure of pseudophosphorylation variant Ser264Glu determined by X-ray crystallography reveals no differences in the three-dimensional architecture of the phosphorylation loop or of the active site, when compared to those of the wild-type enzyme. However, the channel leading to the active site is partially obstructed by the side chain of residue 264 in the variant. By analogy, a similar obstruction of the substrate channel can be anticipated to result from a phosphorylation of Ser264. The kinetic and thermodynamic results in conjunction with the structure of Ser264Glu suggest that phosphorylation blocks access to the active site by imposing a steric and electrostatic barrier for substrate binding and active site coupling with the E2 component. As a Ser264Gln variant, which carries no charge at position 264, is also selectively

  19. Structural Characterization of Mutations at the Oxygen Activation Site in Monomeric Sarcosine Oxidase

    SciTech Connect

    Schuman Jorns, Marilyn; Chen, Zhi-wei; Mathews, F. Scott

    2010-04-30

    Oxygen reduction and sarcosine oxidation in monomeric sarcosine oxidase (MSOX) occur at separate sites above the si- and re-faces, respectively, of the flavin ring. Mutagenesis studies implicate Lys265 as the oxygen activation site. Substitution of Lys265 with a neutral (Met, Gln, or Ala) or basic (Arg) residue results in an {approx}10{sup 4}- or 250-fold decrease, respectively, in the reaction rate. The overall structure of MSOX and residue conformation in the sarcosine binding cavity are unaffected by replacement of Lys265 with Met or Arg. The side chain of Met265 exhibits the same configuration in each molecule of Lys265Met crystals and is nearly congruent with Lys265 in wild-type MSOX. The side chain of Arg265 is, however, dramatically shi