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Sample records for active site gorge

  1. Flexibility of active-site gorge aromatic residues and non-gorge aromatic residues in acetylcholinesterase

    SciTech Connect

    Ghattyvenkatakrishna, Pavan K; Uberbacher, Edward C

    2013-01-01

    The presence of an unusually large number of aromatic residues in the active site gorge of acetylcholinesterase has been a topic of great interest. Flexibility of these residues has been suspected to be a key player in controlling ligand traversal in the gorge. This raises the question of whether the over representation of aromatic residues in the gorge implies higher than normal flexibility of those residues. The current study suggests that it does not. Large changes in the hydrophobic cross sectional area due to dihedral oscillations are probably the reason behind their presence in the gorge.

  2. Rapid binding of a cationic active site inhibitor to wild type and mutant mouse acetylcholinesterase: Brownian dynamics simulation including diffusion in the active site gorge.

    PubMed

    Tara, S; Elcock, A H; Kirchhoff, P D; Briggs, J M; Radic, Z; Taylor, P; McCammon, J A

    1998-12-01

    It is known that anionic surface residues play a role in the long-range electrostatic attraction between acetylcholinesterase and cationic ligands. In our current investigation, we show that anionic residues also play an important role in the behavior of the ligand within the active site gorge of acetylcholinesterase. Negatively charged residues near the gorge opening not only attract positively charged ligands from solution to the enzyme, but can also restrict the motion of the ligand once it is inside of the gorge. We use Brownian dynamics techniques to calculate the rate constant kon, for wild type and mutant acetylcholinesterase with a positively charged ligand. These calculations are performed by allowing the ligand to diffuse within the active site gorge. This is an extension of previously reported work in which a ligand was allowed to diffuse only to the enzyme surface. By setting the reaction criteria for the ligand closer to the active site, better agreement with experimental data is obtained. Although a number of residues influence the movement of the ligand within the gorge, Asp74 is shown to play a particularly important role in this function. Asp74 traps the ligand within the gorge, and in this way helps to ensure a reaction.

  3. Energetics of Ortho-7 (Oxime Drug) Translocation through the Active-Site Gorge of Tabun Conjugated Acetylcholinesterase

    PubMed Central

    Sinha, Vivek; Ganguly, Bishwajit; Bandyopadhyay, Tusar

    2012-01-01

    Oxime drugs translocate through the 20 Å active-site gorge of acetylcholinesterase in order to liberate the enzyme from organophosphorus compounds’ (such as tabun) conjugation. Here we report bidirectional steered molecular dynamics simulations of oxime drug (Ortho-7) translocation through the gorge of tabun intoxicated enzyme, in which time dependent external forces accelerate the translocation event. The simulations reveal the participation of drug-enzyme hydrogen bonding, hydrophobic interactions and water bridges between them. Employing nonequilibrium theorems that recovers the free energy from irreversible work done, we reconstruct potential of mean force along the translocation pathway such that the desired quantity represents an unperturbed system. The potential locates the binding sites and barriers for the drug to translocate inside the gorge. Configurational entropic contribution of the protein-drug binding entity and the role of solvent translational mobility in the binding energetics is further assessed. PMID:22808117

  4. Ortho-7 bound to the active-site gorge of free and OP-conjugated acetylcholinesterase: cation-π interactions.

    PubMed

    Pathak, Arup Kumar; Bandyopadhyay, Tusar

    2016-01-01

    Despite the immense importance of cation-π interactions prevailing in bispyridinium drug acetylcholinesterase (AChE) complexes, a precise description of cation-π interactions at molecular level has remained elusive. Here, we consider a bispyridinium drug, namely, ortho-7 in three different structures of AChE, with and without complexation with organophosphorus (OP) compounds for detailed investigation using all atom molecular dynamics simulation. By quantum mechanical calculations, Y72, W86, Y124, W286, Y337, and Y341 aromatic residues of the enzyme are investigated for possible cation-π interactions with ortho-7. The cation-π interactions in each of the protein-drug complexes are studied using distance, angle, a suitable functional form of them, and electrostatic criteria. The variation of cation-π functional is remarkably consistent with that of the Columbic variation. It is clearly observed that cation-π interactions for some of the residues in the catalytic active site (CAS) and peripheral anionic site (PAS) of the enzyme are either enhanced or reduced based on the nature of OP conjugation (i.e., nerve gas, tabun or pesticide, fenamiphos) when compared with the OP-free enzyme. The strength of cation-π interaction is strongly dependent on the type OP conjugation. The effect of conjugation at CAS is also seen to influence the cation-π interaction at the PAS region. The variation of cation-π interactions on the type of conjugating OP compounds might be suggestive of a reason as to why wide spectrum drug against any OP poisoning is yet to arrive in the market.

  5. A New Horned Crocodile from the Plio-Pleistocene Hominid Sites at Olduvai Gorge, Tanzania

    PubMed Central

    Brochu, Christopher A.; Njau, Jackson; Blumenschine, Robert J.; Densmore, Llewellyn D.

    2010-01-01

    Background The fossil record reveals surprising crocodile diversity in the Neogene of Africa, but relationships with their living relatives and the biogeographic origins of the modern African crocodylian fauna are poorly understood. A Plio-Pleistocene crocodile from Olduvai Gorge, Tanzania, represents a new extinct species and shows that high crocodylian diversity in Africa persisted after the Miocene. It had prominent triangular “horns” over the ears and a relatively deep snout, these resemble those of the recently extinct Malagasy crocodile Voay robustus, but the new species lacks features found among osteolaemines and shares derived similarities with living species of Crocodylus. Methodology/Principal Findings The holotype consists of a partial skull and skeleton and was collected on the surface between two tuffs dated to approximately 1.84 million years (Ma), in the same interval near the type localities for the hominids Homo habilis and Australopithecus boisei. It was compared with previously-collected material from Olduvai Gorge referable to the same species. Phylogenetic analysis places the new form within or adjacent to crown Crocodylus. Conclusions/Significance The new crocodile species was the largest predator encountered by our ancestors at Olduvai Gorge, as indicated by hominid specimens preserving crocodile bite marks from these sites. The new species also reinforces the emerging view of high crocodylian diversity throughout the Neogene, and it represents one of the few extinct species referable to crown genus Crocodylus. PMID:20195356

  6. Geomorphic impacts of active tectonics on a river course, the case of Klissoura gorge, central Greece.

    NASA Astrophysics Data System (ADS)

    Tsanakas, Konstantinos; Fubelli, Giandomenico; Karymbalis, Efthimios

    2014-05-01

    The delicate balance of the natural processes within the river systems can be easily tipped making them very sensitive to changes occurring on the earth surface. Fluvial systems are therefore profoundly influenced by endogenic processes such as active tectonics as well as global sea level fluctuations following the climatic variations during the Quaternary. This study deals with the geomorphological evolution of the broader area of the abandoned gorge of Klissoura which is located in central Greece. This 130 m deep and roughly 3 km long gorge is a characteristic example of an old drainage course preserved on the footwall blocks of two normal faults which confine both outlets of the deeply incised valley. The gorge has formed by a river that once had a N-S flow direction discharging into the Gulf of Patras. Acheloos River and the much smaller Ermitza Remma Stream are the two recent primary watercourses which drain the area close to the abandoned gorge. Both the dimensions and morphological characteristics of the abandoned deep valley indicate that the gorge has formed by a large river with high discharge in order to incise into the limestone bedrock. In order to investigate the tectonic constrains and determine the geomorphic and climatic processes that compelled the lower reaches of Acheloos River to abandon the gorge and find an outlet following its present course a GIS based analysis at a scale of 1:50.000 was applied in the drainage basin of Acheloos River. Additionally, to reconstruct the palaeolandscape and the earth surface processes, a detailed morphometric and geomorphic analysis of the abandoned gorge was also performed at a scale of 1:5.000 coupled with field observations and stratigraphic analysis of the deposits outcropping on the valley sides within the gorge as well as on both outlets. The geomorphic analysis led to the conclusion that the primary course of the gorge abandonment and diversion and reverse of the drainage is the uplift of the footwall

  7. Wind Field Predictions for the Columbia Gorge and the Goodnoe Hills Wind Turbine Site.

    SciTech Connect

    Veenhuizen, Scott D.; Lin, Jung-Tai.

    1980-08-01

    Numerical estimates of the long term seasonal mean wind speeds, wind directions, and available wind power density were conducted for comparison with the results of field wind measurements obtained by the Bonneville Power Administration for the Columbia Gorge region along the Oregon-Washngton border. The authors had previously used the numerical method of estimating wind flows in complex terrain to identify high wind energy areas within the Olympic Peninsula and Northern Cascade regions of the State of Washington. The numerical technique was used as a generalized wind prospecting tool to provide the link between regional assessments and on-site biological or geomorphological indicators of mean wind speeds and available wind energy. The wind flow model used is a two dimensional model based upon simplified hydrodynamical equations describing the fluid and thermodynamic motion of the atmosphere.

  8. Disentangling hominin and carnivore activities near a spring at FLK North (Olduvai Gorge, Tanzania)

    NASA Astrophysics Data System (ADS)

    Domínguez-Rodrigo, M.; Mabulla, A. Z. P.; Bunn, H. T.; Diez-Martin, F.; Baquedano, E.; Barboni, D.; Barba, R.; Domínguez-Solera, S.; Sánchez, P.; Ashley, G. M.; Yravedra, J.

    2010-11-01

    FLK North is one of the densest concentrations of fossils found in Olduvai Gorge. A recent taphonomic re-evaluation of the collection excavated by Leakey at the site suggests that it was a palimpsest in which most of the animals were accumulated and modified by carnivores. The lithic tools therefore seem to have an independent depositional history from most of the fauna. The present study, based on new excavations, expands the evidence supporting this interpretation and demonstrates a thicker deposit than was reported by Leakey, including new archaeological levels. It also shows that in the few instances where hominins butchered carcasses, meat, not marrow, was their main target. This argues against passive scavenging hypotheses, which emphasize the dietary role of marrow, and instead underscores the importance of meat in the diet of early Pleistocene hominins.

  9. Diel and seasonal variation of methane and carbon dioxide fluxes at site Guojiaba, the Three Gorges Reservoir.

    PubMed

    Xiao, Shangbin; Wang, Yuchun; Liu, Defu; Yang, Zhengjian; Lei, Dan; Zhang, Cheng

    2013-10-01

    In order to investigate the CH4 and CO2 fluxes across the water-gas interface and identify their controlling factors, four diel field campaigns and one monthly sampling campaign during June 2010-May 2011 were carried out at a site near the Three Gorges Dam, China. The averaged CH4 and CO2 fluxes across the air-water interface from the site were much less than those reported from reservoirs in tropic and temperate regions, and from the natural river channels of the Yangtze River. CH4 Fluxes at the site were very low compared to most other reservoirs or natural lakes. One of the most important reasons may be due to the oxidation of CH4 in the water column owing to the great water depth and high DO in water in the Three Gorges Reservoir. The averaged monthly CH4 and CO2 fluxes at the site during the observation year were 0.05 mg/(m2 x hr) and 104.43 mg/(m2 x hr) respectively with the maximum occurred in July 2010. The monthly CO2 fluxes during the observation year were positively correlated to the surface water temperature, and negatively correlated to the air pressure and the surface water pH. The CO2 flux showed a positive correlation with DOC to some extent, although not significantly, which indicated that allochthonous organic C was a major source of CO2 and biogeochemical processes in this reservoir were C-limited. The significantly positive correlation between the reservoir outflow and the seasonal gas flux indicate the disturbance condition of the water body dominated the seasonal gas emission.

  10. Diel and seasonal variation of methane and carbon dioxide fluxes at site Guojiaba, the Three Gorges Reservoir.

    PubMed

    Xiao, Shangbin; Wang, Yuchun; Liu, Defu; Yang, Zhengjian; Lei, Dan; Zhang, Cheng

    2013-10-01

    In order to investigate the CH4 and CO2 fluxes across the water-gas interface and identify their controlling factors, four diel field campaigns and one monthly sampling campaign during June 2010-May 2011 were carried out at a site near the Three Gorges Dam, China. The averaged CH4 and CO2 fluxes across the air-water interface from the site were much less than those reported from reservoirs in tropic and temperate regions, and from the natural river channels of the Yangtze River. CH4 Fluxes at the site were very low compared to most other reservoirs or natural lakes. One of the most important reasons may be due to the oxidation of CH4 in the water column owing to the great water depth and high DO in water in the Three Gorges Reservoir. The averaged monthly CH4 and CO2 fluxes at the site during the observation year were 0.05 mg/(m2 x hr) and 104.43 mg/(m2 x hr) respectively with the maximum occurred in July 2010. The monthly CO2 fluxes during the observation year were positively correlated to the surface water temperature, and negatively correlated to the air pressure and the surface water pH. The CO2 flux showed a positive correlation with DOC to some extent, although not significantly, which indicated that allochthonous organic C was a major source of CO2 and biogeochemical processes in this reservoir were C-limited. The significantly positive correlation between the reservoir outflow and the seasonal gas flux indicate the disturbance condition of the water body dominated the seasonal gas emission. PMID:24494493

  11. A Survey of Landslide Activity in the Columbia River Gorge from InSAR

    NASA Astrophysics Data System (ADS)

    Tong, X.; Schmidt, D. A.

    2015-12-01

    The Columbia River Gorge contains several large landslide complexes that have exhibited historical movement, both catastrophic and slow moving. Monitoring the kinematics of active movement helps to characterize the ongoing natural hazard. In this study, we document the status of several large landslide complexes along the Columbia River Gorge. We use synthetic aperture radar (SAR) data from multiple satellites (ERS, ENVISAT and ALOS) to reveal the spatial-temporal movement of slow-moving landslides over two decades, 1992-2011. To increase the spatial extent of the signal we developed a new InSAR time-series method based on pixel coherence and derived the time series of the landslides. We also investigate the ability of Persistent Scatterer InSAR to better illuminate active movement. While many historical landslide complexes show minimal or non-existent movement, we measure significant creep on the Redbluff landslide, which is part of the Cascade Landslide Complex near the Bonneville Dam. The InSAR time-series data reveal approximately 25 cm of line-of-sight movement from 5 years of ALOS observations, which translates into greater than 60 cm of downslope movement. The Redbluff landslide is seasonally activated, with accelerated movement observed during the early winter of each year. However, the amplitude of the seasonal signal is variable from year-to-year. To assess the triggering mechanisms, we compared the deformation time series data with local precipitation data. The deformation correlates well with precipitation, implying the slow movement is controlled by rainfall that infiltrates to the base of the slide. A preliminary comparison with the bare earth 2m-resolution digital elevation model from LiDAR reveals that the overall deformation pattern and the active perimeter is highly correlated with the morphology of the landslide.

  12. Study of Active Faults in the Three Gorges Dam region by Detecting and Relocating Aftershocks

    NASA Astrophysics Data System (ADS)

    Huang, R.; Zhu, L.; Xu, Y.

    2014-12-01

    Seismicity in the Three Gorges Dam (TGD) region and its adjacent areas increased dramatically as the water- level of the TGD reservoir rises since its completion in 2003. Accordingly, many efforts have been put forward to quantify the seismicity and geological hazards in the region. However, the precise detective of earthquakes, especially for the minor ones, remains difficulty because of sparse distribution of permanent seismic stations. From December 2013 to June 2014, we deployed 30 three-component broadband seismic stations in the TGD region. During the deployment, we recorded two earthquakes of magnitudes lager than 5.0, one occurred on December 16th 2013 in Badong and another on March 30th 2014 in Zigui. We firstly used a sliding-window cross-correlation (SCC) detection technique to supplement the events catalog from the China Earthquake Networks Center. Over 500 new events with ML lager than 0.5 were detected. We then relocated 502 events out of the total 987 events using the double-difference (DD) relocation algorithm. We also determined moment tensors of some large earthquakes using gCAP. The results clearly show two active faults along Yangtze River with dips of 50 degrees and 90 degrees to a maximum depth of 10 km, respectively. And they also reveal that water might have permeated to a depth of 6 km corresponds to the interface of sediments and metamorphic basement beneath Zigui Basin. We thus preliminarily judge that the quakes are triggered by local stress adjustment resulting of fluctuation of Three Gorges reservoir's loading.

  13. The Origin of The Acheulean: The 1.7 Million-Year-Old Site of FLK West, Olduvai Gorge (Tanzania).

    PubMed

    Diez-Martín, F; Sánchez Yustos, P; Uribelarrea, D; Baquedano, E; Mark, D F; Mabulla, A; Fraile, C; Duque, J; Díaz, I; Pérez-González, A; Yravedra, J; Egeland, C P; Organista, E; Domínguez-Rodrigo, M

    2015-01-01

    The appearance of the Acheulean is one of the hallmarks of human evolution. It represents the emergence of a complex behavior, expressed in the recurrent manufacture of large-sized tools, with standardized forms, implying more advance forethought and planning by hominins than those required by the precedent Oldowan technology. The earliest known evidence of this technology dates back to c. 1.7 Ma. and is limited to two sites (Kokiselei [Kenya] and Konso [Ethiopia]), both of which lack functionally-associated fauna. The functionality of these earliest Acheulean assemblages remains unknown. Here we present the discovery of another early Acheulean site also dating to c. 1.7 Ma from Olduvai Gorge. This site provides evidence of the earliest steps in developing the Acheulean technology and is the oldest Acheulean site in which stone tools occur spatially and functionally associated with the exploitation of fauna. Simple and elaborate large-cutting tools (LCT) and bifacial handaxes co-exist at FLK West, showing that complex cognition was present from the earliest stages of the Acheulean. Here we provide a detailed technological study and evidence of the use of these tools on the butchery and consumption of fauna, probably by early Homo erectus sensu lato. PMID:26639785

  14. The Origin of The Acheulean: The 1.7 Million-Year-Old Site of FLK West, Olduvai Gorge (Tanzania).

    PubMed

    Diez-Martín, F; Sánchez Yustos, P; Uribelarrea, D; Baquedano, E; Mark, D F; Mabulla, A; Fraile, C; Duque, J; Díaz, I; Pérez-González, A; Yravedra, J; Egeland, C P; Organista, E; Domínguez-Rodrigo, M

    2015-12-07

    The appearance of the Acheulean is one of the hallmarks of human evolution. It represents the emergence of a complex behavior, expressed in the recurrent manufacture of large-sized tools, with standardized forms, implying more advance forethought and planning by hominins than those required by the precedent Oldowan technology. The earliest known evidence of this technology dates back to c. 1.7 Ma. and is limited to two sites (Kokiselei [Kenya] and Konso [Ethiopia]), both of which lack functionally-associated fauna. The functionality of these earliest Acheulean assemblages remains unknown. Here we present the discovery of another early Acheulean site also dating to c. 1.7 Ma from Olduvai Gorge. This site provides evidence of the earliest steps in developing the Acheulean technology and is the oldest Acheulean site in which stone tools occur spatially and functionally associated with the exploitation of fauna. Simple and elaborate large-cutting tools (LCT) and bifacial handaxes co-exist at FLK West, showing that complex cognition was present from the earliest stages of the Acheulean. Here we provide a detailed technological study and evidence of the use of these tools on the butchery and consumption of fauna, probably by early Homo erectus sensu lato.

  15. The Origin of The Acheulean: The 1.7 Million-Year-Old Site of FLK West, Olduvai Gorge (Tanzania)

    PubMed Central

    Diez-Martín, F.; Sánchez Yustos, P.; Uribelarrea, D.; Baquedano, E.; Mark, D. F.; Mabulla, A.; Fraile, C.; Duque, J.; Díaz, I.; Pérez-González, A.; Yravedra, J.; Egeland, C. P.; Organista, E.; Domínguez-Rodrigo, M.

    2015-01-01

    The appearance of the Acheulean is one of the hallmarks of human evolution. It represents the emergence of a complex behavior, expressed in the recurrent manufacture of large-sized tools, with standardized forms, implying more advance forethought and planning by hominins than those required by the precedent Oldowan technology. The earliest known evidence of this technology dates back to c. 1.7 Ma. and is limited to two sites (Kokiselei [Kenya] and Konso [Ethiopia]), both of which lack functionally-associated fauna. The functionality of these earliest Acheulean assemblages remains unknown. Here we present the discovery of another early Acheulean site also dating to c. 1.7 Ma from Olduvai Gorge. This site provides evidence of the earliest steps in developing the Acheulean technology and is the oldest Acheulean site in which stone tools occur spatially and functionally associated with the exploitation of fauna. Simple and elaborate large-cutting tools (LCT) and bifacial handaxes co-exist at FLK West, showing that complex cognition was present from the earliest stages of the Acheulean. Here we provide a detailed technological study and evidence of the use of these tools on the butchery and consumption of fauna, probably by early Homo erectus sensu lato. PMID:26639785

  16. The Dynamics of Ligand Barrier Crossing Inside the Acetylcholinesterase Gorge

    SciTech Connect

    Bui, Jennifer M.; Henchman, Richard H.; Mccammon, Andy

    2003-10-01

    The dynamics of ligand movement through the constricted region of the acetylcholinesterase gorge is important in understanding how the ligand gains access to and is released from the active site of the enzyme. Molecular dynamics simulations of the simple ligand, tetramethylammonium, crossing this bottleneck region are conducted using umbrella potential sampling and activated .ux techniques. The low potential of mean force obtained is consistent with the fast reaction rate of acetylcholinesterase observed experimentally. From the results of the activated dynamics simulations, local conformational .uctuations of the gorge residues and larger scale collective motions of the protein are found to correlate highly with the ligand crossing.

  17. Three Gorges Dam, China

    NASA Technical Reports Server (NTRS)

    2002-01-01

    This ASTER image shows a 60 km stretch of the Yangtze River in China, including the Xiling Gorge, the eastern of the three gorges. In the left part of the image is the construction site of the Three Gorges Dam, the world's largest.

    This image was acquired on July 20, 2000 by the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) on NASA's Terra satellite. With its 14 spectral bands from the visible to the thermal infrared wavelength region, and its high spatial resolution of 15 to 90 meters (about 50 to 300 feet), ASTER will image Earth for the next 6 years to map and monitor the changing surface of our planet.

    ASTER is one of five Earth-observing instruments launched December 18, 1999, on NASA's Terra satellite. The instrument was built by Japan's Ministry of Economy, Trade and Industry. A joint U.S./Japan science team is responsible for validation and calibration of the instrument and the data products. Dr. Anne Kahle at NASA's Jet Propulsion Laboratory, Pasadena, California, is the U.S. Science team leader; Bjorn Eng of JPL is the project manager. The Terra mission is part of NASA's Earth Science Enterprise, a long-term research and technology program designed to examine Earth's land, oceans, atmosphere, ice and life as a total integrated system.

    The broad spectral coverage and high spectral resolution of ASTER will provide scientists in numerous disciplines with critical information for surface mapping, and monitoring dynamic conditions and temporal change. Example applications are: monitoring glacial advances and retreats; monitoring potentially active volcanoes; identifying crop stress; determining cloud morphology and physical properties; wetlands evaluation; thermal pollution monitoring; coral reef degradation; surface temperature mapping of soils and geology; and measuring surface heat balance.

    Size: 60 x 24 km (36 x 15 miles) Location: 30.6 deg. North lat., 111.2 deg. East long. Orientation: North at top Image Data: ASTER

  18. The Effect on the Flow Conditions of Chinese Sturgeons’ Spawning Sites in the Process of Peak Regulation between the Three Gorges Dam and Gezhou Dam

    NASA Astrophysics Data System (ADS)

    Hui, Guo; Minghai, Huang; Feng, Jin

    Chinese sturgeon (Acipenser sinensis Gray) is a kind of key protected fish in ChangJiang river. Recently the Three Gorges dam has run, the peak regulation process between the two dams has serious effect on the formed spawning sites. Based on the previous research results of suitable flow conditions about the spawning sites, this article builds a 2-D shallow water numerical model, calculates the flow conditions of the spawning sites in the process of peak regulation. The results show that the water depth and velocity are various and affect the spawning sites in one 24-hours process of peak regulation, as a whole, when the discharge is below 9000 m3/s and 7500 m3/s respectively, the two spawning sites will be affected seriously.

  19. Causes of haze in the Columbia River Gorge

    SciTech Connect

    Mark Green; Jin Xu

    2007-08-15

    Visibility impairment in the Columbia River Gorge National Scenic Area is an area of concern. A field study conducted from July 2003 to February 2005 was followed by data analysis and receptor modeling to better understand the temporal and spatial patterns of haze and the sources contributing to the haze in the Columbia River Gorge in the states of Washington and Oregon. The nephelometer light scattering and surface meteorological data at eight sites along the gorge showed five distinct wind patterns, each with its characteristic diurnal and spatial patterns in light scattering by particles (b{sub sp}). In summer, winds were nearly always from west to east (upgorge) and showed decreasing b{sub sp} with distance into the gorge and a pronounced effect of the Portland, OR, metropolitan area on haze, especially in the western portions of the gorge. Winter often had winds from the east with very high levels of b{sub sp}, especially at the eastern gorge sites, with sources east of the gorge responsible for much of the haze. The major chemical components responsible for haze were organic carbon, sulfate, and nitrate. Positive matrix factorization (PMF) using chemically speciated Interagency Monitoring of Protected Visual Environments data indicated seven source factors in the western gorge and five factors in the eastern gorge. Organic mass is a large contributor to haze in the gorge in all seasons, with a peak in fall. Approximately half of the organic mass is biomass smoke, with mobile sources as the second largest contributor. PMF analysis showed nitrates mainly attributed to a generic secondary nitrate factor. Sulfate is a significant contributor in all seasons, with peak sulfate concentrations in summer. Sources east of the gorge, likely a coal-fired power plant, nearby dairy farm, and upriver cities, appear to be major contributors to wintertime haze in the gorge. 22 refs., 11 figs., 6 tabs.

  20. When felids and hominins ruled at Olduvai Gorge: A machine learning analysis of the skeletal profiles of the non-anthropogenic Bed I sites

    NASA Astrophysics Data System (ADS)

    Arriaza, Mari Carmen; Domínguez-Rodrigo, Manuel

    2016-05-01

    In the past twenty years, skeletal part profiles, which are prone to equifinality, have not occupied a prominent role in the interpretation of early Pleistocene sites on Africa. Alternatively, taphonomic studies on bone surface modifications and bone breakage patterns, have provided heuristic interpretations of some of the best preserved archaeological record of this period; namely, the Olduvai Bed I sites. The most recent and comprehensive taphonomic study of these sites (Domínguez-Rodrigo et al., 2007a) showed that FLK Zinj was an anthropogenic assemblage in which hominins acquired carcasses via primary access. That study also showed that the other sites were palimpsests with minimal or no intervention by hominins. The FLK N, FLK NN and DK sequence seemed to be dominated by single-agent (mostly, felid) or multiple-agent (mostly, felid-hyenid) processes. The present study re-analyzes the Bed I sites focusing on skeletal part profiles. Machine learning methods, which incorporate complex algorithms, are powerful predictive and classification methods and have the potential to better extract information from skeletal part representation than past approaches. Here, multiple algorithms (via decision trees, neural networks, random forests and support vector machines) are combined to produce a solid interpretation of bone accumulation agency at the Olduvai Bed I sites. This new approach virtually coincides with previous taphonomic interpretations on a site by site basis and shows that felids were dominant accumulating agents over hyenas during Bed I times. The recent discovery of possibly a modern lion-accumulated assemblage at Olduvai Gorge (Arriaza et al., submitted) provides a very timely analog for this interpretation.

  1. [Effects of biological regulated measures on active organic carbon and erosion-resistance in the Three Gorges Reservoir region soil].

    PubMed

    Huang, Ru; Huang, Lin; He, Bing-Hui; Zhou, Li-Jiang; Yu, Chuan; Wang, Feng

    2013-07-01

    To gain a better knowledge of characteristics of soils and provide a scientific basis for soil erosion control in the Three Gorges Reservoir Area, contents of aggregates and total soil organic carbon (SOC), as well as soil active organic carbon fractions including particulate organic carbon (POC), readily oxidized organic carbon (ROC), dissolved organic carbon (DOC), microbial biomass carbon (MBC) in the 0-30 cm soil layer under seven different biological regulated measures were studied by the field investigation combined with the laboratory analysis. Results showed that the content of the SOC and active organic carbon fractions decreased with the increasing soil depth; the content of the SOC and active organic carbon fractions in 0-10 cm was significantly higher than that in 20-30 cm. The stability of soil aggregates were also significantly influenced by biological regulated measures, the content of > 0.25 mm water-stable aggregates in seven types of biological regulated measures was in the order of Koelreuteria bipinnata + Cassia suffruticasa > hedgerows > closed forest > natural restoration > economic forest > traditional planting > control plot, moreover, the content of 0.25 mm water-stable aggregates correlated positively with the content of SOC. Soils under different biological regulated measures all demonstrated fractal features, and soil under the measure of Koelreuteria bipinnata + Cassia suffruticasa was found to have the lowest value of fractal dimension and soil erodiable K, indicating a relatively strong structure stability and erosion-resistant capacity. Negative correlation was observed when compared the content of active organic carbon fractions with the soil erodiable K. It can be concluded that properties of soil can be managed through biological regulated measures; thence had an influence on the soil erosion-resistant capacity. PMID:24028016

  2. [Effects of biological regulated measures on active organic carbon and erosion-resistance in the Three Gorges Reservoir region soil].

    PubMed

    Huang, Ru; Huang, Lin; He, Bing-Hui; Zhou, Li-Jiang; Yu, Chuan; Wang, Feng

    2013-07-01

    To gain a better knowledge of characteristics of soils and provide a scientific basis for soil erosion control in the Three Gorges Reservoir Area, contents of aggregates and total soil organic carbon (SOC), as well as soil active organic carbon fractions including particulate organic carbon (POC), readily oxidized organic carbon (ROC), dissolved organic carbon (DOC), microbial biomass carbon (MBC) in the 0-30 cm soil layer under seven different biological regulated measures were studied by the field investigation combined with the laboratory analysis. Results showed that the content of the SOC and active organic carbon fractions decreased with the increasing soil depth; the content of the SOC and active organic carbon fractions in 0-10 cm was significantly higher than that in 20-30 cm. The stability of soil aggregates were also significantly influenced by biological regulated measures, the content of > 0.25 mm water-stable aggregates in seven types of biological regulated measures was in the order of Koelreuteria bipinnata + Cassia suffruticasa > hedgerows > closed forest > natural restoration > economic forest > traditional planting > control plot, moreover, the content of 0.25 mm water-stable aggregates correlated positively with the content of SOC. Soils under different biological regulated measures all demonstrated fractal features, and soil under the measure of Koelreuteria bipinnata + Cassia suffruticasa was found to have the lowest value of fractal dimension and soil erodiable K, indicating a relatively strong structure stability and erosion-resistant capacity. Negative correlation was observed when compared the content of active organic carbon fractions with the soil erodiable K. It can be concluded that properties of soil can be managed through biological regulated measures; thence had an influence on the soil erosion-resistant capacity.

  3. A modular treatment of molecular traffic through the active site of cholinesterase

    PubMed Central

    Botti, SA; Felder, CE; Lifson, S; Sussman, JL; Silman, I

    1999-01-01

    We present a model for the molecular traffic of ligands, substrates, and products through the active site of cholinesterases (ChEs). First, we describe a common treatment of the diffusion to a buried active site of cationic and neutral species. We then explain the specificity of ChEs for cationic ligands and substrates by introducing two additional components to this common treatment. The first module is a surface trap for cationic species at the entrance to the active-site gorge that operates through local, short-range electrostatic interactions and is independent of ionic strength. The second module is an ionic-strength-dependent steering mechanism generated by long-range electrostatic interactions arising from the overall distribution of charges in ChEs. Our calculations show that diffusion of charged ligands relative to neutral isosteric analogs is enhanced approximately 10-fold by the surface trap, while electrostatic steering contributes only a 1.5- to 2-fold rate enhancement at physiological salt concentration. We model clearance of cationic products from the active-site gorge as analogous to the escape of a particle from a one-dimensional well in the presence of a linear electrostatic potential. We evaluate the potential inside the gorge and provide evidence that while contributing to the steering of cationic species toward the active site, it does not appreciably retard their clearance. This optimal fine-tuning of global and local electrostatic interactions endows ChEs with maximum catalytic efficiency and specificity for a positively charged substrate, while at the same time not hindering clearance of the positively charged products. PMID:10545346

  4. 2. GORGE HIGH DAM. UNUSUALLY HIGH WATER IN GORGE LAKE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. GORGE HIGH DAM. UNUSUALLY HIGH WATER IN GORGE LAKE DUE TO THE COMBINATION OF UNIT 24 BEING DOWN FOR REWINDING AND TWO UNITS COMING ON LINE UNEXPECTEDLY AT ROSS POWERHOUSE LED TO WATER FLOWING OVER THE SPILLGATES. EACH GATE IF 47 FEET WIDE AND 50 FEET HIGH, 1989. - Skagit Power Development, Gorge High Dam, On Skagit River, 2.9 miles upstream from Newhalem, Newhalem, Whatcom County, WA

  5. Probing Gorge Dimensions of Cholinesterases by Freeze-Frame Click Chemistry

    PubMed Central

    Radić, Zoran; Manetsch, Roman; Fournier, Didier; Sharpless, K. Barry; Taylor, Palmer

    2008-01-01

    Freeze-frame click chemistry is a proven approach for design in situ of high affinity ligands from bioorthogonal, reactive building blocks and macromolecular template targets. We recently described in situ design of femtomolar reversible inhibitors of fish and mammalian acetylcholinesterases (EC 3.1.1.7; AChEs) using several different libraries of acetylene and azide building blocks. Active center gorge geometries of those AChEs are rather similar and identical triazole inhibitors were detected in situ when incubating the same building block libraries in different AChEs. Drosophila melanogaster AChE crystal structure and other insect AChE homology models differ more in their overall 3D structure than other members of the cholinesterase family. The portion of the gorge proximal to the catalytic triad and choline binding site has a ~50% reduction in volume, and the gorge entrance at the peripheral anionic site (PAS) is more constricted than in the fish and mammalian AChE’s. In this communication we describe rationale for using purified recombinant Drosophila AChE as a template for in situ reaction of tacrine and propidium based libraries of acetylene and azide building blocks. The structures of resulting triazole inhibitors synthesized in situ are expected to differ appreciably from the fish and mammalian AChEs. While the latter AChEs exclusively promote synthesis of syn-substituted triazoles, the best Drosophila AChE triazole inhibitors were always anti-substituted. The anti- regioisomer triazoles were by about one order of magnitude better inhibitors of Drosophila than mammalian and fish AChEs. Moreover, the preferred site of acetylene + azide reaction in insect AChE and the resulting triazole ring formation shifts from near the base of the gorge to closer to its rim due to substantial differences of the gorge geometry in Drosophila AChE. Thus, in addition to synthesizing high affinity, lead inhibitors in situ, freeze-frame, click chemistry has capacity to

  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. [Effects of Citric Acid on Activation and Methylation of Mercury in the Soils of Water-Level-Fluctuating Zone of the Three Gorges.Reservoir].

    PubMed

    Qin, Cai-qing; Liang, Li; You, Rui; Deng, Han; Wang, Ding-yong

    2015-12-01

    To investigate effects of the main component of vegetation root exudates-citric acid on activation and methylation of mercury in the soil of water-level-fluctuating zone (WLFZ) of the Three Gorges Reservoir area, simulation experiments were conducted by extracting and cultivating soil with different concentrations of citric acid. The results showed that after adding citric acid, the total mercury content in leaching solution before reaching peak were higher than that of the control, and increased with the increase of citric acid concentrations. The maximum amount of mercury complexes increased initially and then reached plateaus with the percentage against the total mercury in soil of 1.03%, 1.67%, 1.99%, 2.47%, 2.68%, 2.73% and 2.73% for different citric acid concentrations (0, 1, 2, 4, 5, 6 and 8 mmol · L⁻¹). In addition, concentrations of methylmercury ( MeHg) in soil remained stable in the first 3 hours, and then increased accompanying with the increasing rate rising with the concentration of citric acid ( besides the control group) . This result indicated that citric acid probably could promote the transformation process from inorganic mercury to MeHg in soil. which increased with the concentration of citric acid.

  8. [Effects of Citric Acid on Activation and Methylation of Mercury in the Soils of Water-Level-Fluctuating Zone of the Three Gorges.Reservoir].

    PubMed

    Qin, Cai-qing; Liang, Li; You, Rui; Deng, Han; Wang, Ding-yong

    2015-12-01

    To investigate effects of the main component of vegetation root exudates-citric acid on activation and methylation of mercury in the soil of water-level-fluctuating zone (WLFZ) of the Three Gorges Reservoir area, simulation experiments were conducted by extracting and cultivating soil with different concentrations of citric acid. The results showed that after adding citric acid, the total mercury content in leaching solution before reaching peak were higher than that of the control, and increased with the increase of citric acid concentrations. The maximum amount of mercury complexes increased initially and then reached plateaus with the percentage against the total mercury in soil of 1.03%, 1.67%, 1.99%, 2.47%, 2.68%, 2.73% and 2.73% for different citric acid concentrations (0, 1, 2, 4, 5, 6 and 8 mmol · L⁻¹). In addition, concentrations of methylmercury ( MeHg) in soil remained stable in the first 3 hours, and then increased accompanying with the increasing rate rising with the concentration of citric acid ( besides the control group) . This result indicated that citric acid probably could promote the transformation process from inorganic mercury to MeHg in soil. which increased with the concentration of citric acid. PMID:27011985

  9. Aryl hydrocarbon receptor (AhR) inducers and estrogen receptor (ER) activities in surface sediments of Three Gorges Reservoir, China evaluated with in vitro cell bioassays.

    PubMed

    Wang, Jingxian; Bovee, Toine F H; Bi, Yonghong; Bernhöft, Silke; Schramm, Karl-Werner

    2014-02-01

    Two types of biological tests were employed for monitoring the toxicological profile of sediment cores in the Three Gorges Reservoir (TGR), China. In the present study, sediments collected in June 2010 from TGR were analyzed for estrogen receptor (ER)- and aryl hydrocarbon receptor (AhR)-mediated activities. The estrogenic activity was assessed using a rapid yeast estrogen bioassay, based on the expression of a green fluorescent reporter protein. Weak anti-estrogenic activity was detected in sediments from an area close to the dam of the reservoir, and weak estrogenic activities ranging from 0.3 to 1 ng 17β-estradiol (E2) equivalents (EQ) g(-1) dry weight sediment (dw) were detected in sediments from the Wanzhou to Guojiaba areas. In the upstream areas Wanzhou and Wushan, sediments demonstrated additive effects in co-administration of 1 nM E2 in the yeast test system, while sediments from the downstream Badong and Guojiaba areas showed estrogenic activities which seemed to be more than additive (synergistic activity). There was an increasing tendency in estrogenic activity from upstream of TGR to downstream, while this tendency terminated and converted into anti-estrogenic activity in the area close to the dam. The AhR activity was detected employing rat hepatoma cell line (H4IIE). EROD activities were found homogenously distributed in sediments in TGR ranging from 200 to 311 pg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) EQ g(-1) dw for total AhR agonists and from 45 to 76 pg TCDD EQ g(-1) dw for more persistent AhR agonists. The known AhR agonists polycyclic aromatic hydrocarbon, polychlorinated biphenyl, and PCDD/F only explained up to 8 % of the more persistent AhR agonist activity in the samples, which suggests that unidentified AhR-active compounds represented a great proportion of the TCDD EQ in sediments from TGR. These findings of estrogenic potential and dioxin-like activity in TGR sediments provide possible weight-of-evidence of potential

  10. Aryl hydrocarbon receptor (AhR) inducers and estrogen receptor (ER) activities in surface sediments of Three Gorges Reservoir, China evaluated with in vitro cell bioassays.

    PubMed

    Wang, Jingxian; Bovee, Toine F H; Bi, Yonghong; Bernhöft, Silke; Schramm, Karl-Werner

    2014-02-01

    Two types of biological tests were employed for monitoring the toxicological profile of sediment cores in the Three Gorges Reservoir (TGR), China. In the present study, sediments collected in June 2010 from TGR were analyzed for estrogen receptor (ER)- and aryl hydrocarbon receptor (AhR)-mediated activities. The estrogenic activity was assessed using a rapid yeast estrogen bioassay, based on the expression of a green fluorescent reporter protein. Weak anti-estrogenic activity was detected in sediments from an area close to the dam of the reservoir, and weak estrogenic activities ranging from 0.3 to 1 ng 17β-estradiol (E2) equivalents (EQ) g(-1) dry weight sediment (dw) were detected in sediments from the Wanzhou to Guojiaba areas. In the upstream areas Wanzhou and Wushan, sediments demonstrated additive effects in co-administration of 1 nM E2 in the yeast test system, while sediments from the downstream Badong and Guojiaba areas showed estrogenic activities which seemed to be more than additive (synergistic activity). There was an increasing tendency in estrogenic activity from upstream of TGR to downstream, while this tendency terminated and converted into anti-estrogenic activity in the area close to the dam. The AhR activity was detected employing rat hepatoma cell line (H4IIE). EROD activities were found homogenously distributed in sediments in TGR ranging from 200 to 311 pg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) EQ g(-1) dw for total AhR agonists and from 45 to 76 pg TCDD EQ g(-1) dw for more persistent AhR agonists. The known AhR agonists polycyclic aromatic hydrocarbon, polychlorinated biphenyl, and PCDD/F only explained up to 8 % of the more persistent AhR agonist activity in the samples, which suggests that unidentified AhR-active compounds represented a great proportion of the TCDD EQ in sediments from TGR. These findings of estrogenic potential and dioxin-like activity in TGR sediments provide possible weight-of-evidence of potential

  11. Maximum safe slope angles for proposed shiplocks of the Three Gorges dam site based on kinematic analyses performed on major discontinuities

    SciTech Connect

    Um, Jeong-gi; Kulatilake, P.H.S.W.; Jianping Chen; Jianren Teng

    1996-12-31

    The Three Gorges Project has been proposed to harness the great hydrologic power potential of the Yangtze River, which is the largest river in China. The depth of rock excavation needed to construct the permanent navigation structures (shiplocks) is high, with a maximum of 170m in some locations. The granitic rock mass which exists in the shiplock region contains a number of major discontinuities and about four sets of minor discontinuities. One hundred and thirty three major discontinuities have been mapped around the shiplock covering an area of 1740x600m. Kinematic analyses were conducted using the major discontinuities to estimate maximum safe cut slope angles with respect to plane sliding, wedge sliding and toppling failure. Kinematic analysis for plane sliding has resulted in maximum safe cut slope angles greater than 65{degrees} for most of the discontinuities. For most of the wedges, maximum safe cut slope angles greater than 45{degrees} were obtained. Maximum safe slope angles greater than 85{degrees} were obtained for most of the discontinuities in the toppling case. It seems that the shiplock faces in the proposed permanent shiplock region in fresh rock are stable up to a cut slope of about 45{degrees}. However, it is important to keep in mind that this conclusion is based on the kinematic analyses performed using only the major discontinuities. Further kinematic as well as kinetic analyses are recommended incorporating minor discontinuities, water forces, earthquake forces, etc., before making the final conclusions about maximum safe cut slope angles for the shiplock region.

  12. Spatial and temporal patterns of greenhouse gas emissions from Three Gorges Reservoir of China

    NASA Astrophysics Data System (ADS)

    Zhao, Y.; Wu, B. F.; Zeng, Y.

    2013-02-01

    Anthropogenic activity has led to significant emissions of greenhouse gas (GHG), which is thought to play important roles in global climate changes. It remains unclear about the kinetics of GHG emissions, including carbon dioxide (CO2), methane (CH4) and nitrous Oxide (N2O) from the Three Gorges Reservoir (TGR) of China, which was formed after the construction of the famous Three Gorges Dam. Here we report monthly measurements for one year of the fluxes of these gases at multiple sites within the TGR region, including three major tributaries, six mainstream sites, two downstream sites and one upstream site. The tributary areas have lower CO2 fluxes than the main storage; CH4 fluxes in the tributaries and upper reach mainstream sites are relative higher. Overall, TGR showed significantly lower CH4 emission rates than most new reservoirs in temperate and tropical regions. We attribute this to the well-oxygenated deep water and high water velocities that may facilitate the consumption of CH4. TGR's CO2 fluxes were lower than most tropical reservoirs and higher than most temperate systems. This could be explained by the high load of labile soil carbon delivered through erosion to the Yangtze River. Compared to fossil-fuelled power plants of equivalent power output, TGR is a very small GHG emitter - annual CO2-equivalent emissions are approximately 1.7% of that of a coal-fired generating plant of comparable power output.

  13. Wetland plant waxes from Olduvai Gorge, Tanzania

    NASA Astrophysics Data System (ADS)

    Tamalavage, A.; Magill, C. R.; Barboni, D.; Ashley, G. M.; Freeman, K. H.

    2013-12-01

    Olduvai Gorge, northern Tanzania, exposes a Plio-Pleistocene sedimentary record that includes lake and lake-margin sediments and fossil remains of ancient plants and early humans. There are rich paleontological and cultural records at Olduvai Gorge that include thousands of vertebrate fossils and stone tools. Previous studies of plant biomarkers in lake sediments from Olduvai Gorge reveal repeated, abrupt changes in landscape dominance by woodland or grassland vegetation during the early Pleistocene, about 1.8 million years ago. However, the reconstruction of wetland vegetation in the past is limited by a dearth of published lipid signatures for modern wetland species. Here, we present lipid and isotopic data for leaf tissues from eight modern plants (i.e., sedge and Typha species) living in wetlands near Olduvai Gorge. Trends in values for molecular and leaf δ13C and average chain length (ACL) of n-alkanes in plant tissues are similar to values for underlying soils. Compound-specific δ13C values for n-alkanes C25 to C33 range between -36.4 to -23.1‰ for C3 plants and -22.3 to -19.5‰ for C4 plants. Fractionation factors between leaf and lipids, ɛ29 and ɛ33, fall within the range reported in the literature, but they differ more widely within a single plant. For C3 plants, the average difference between ɛ29 and ɛ33 is 6.5 ‰, and the difference between ɛ29 and ɛ33 for C4 plants is less than 2‰. Both plant types show a parabolic relationship between chain length and δ13C values, in which C29 typically has the most depleted value, and typically shift by 3-5‰ between alkane homologs. This pattern has not been previously reported, and could be unique for sedge lipids. If so, these data help constrain the application of plant wax biomarkers from sedges for paleo-vegetation reconstruction in paleoclimate studies and at archaeological sites.

  14. Soil properties and enzyme activities as affected by biogas slurry irrigation in the Three Gorges Reservoir areas of China.

    PubMed

    Chen, Shiling; Yu, Weiwei; Zhang, Zhi; Luo, Surong

    2015-03-01

    Biogas slurry, as a quality organic fertilizer, is widely used on large scale livestock farmland in Southwest China. In the present study, slurry collected from anaerobic tank of dairy farm was used to irrigate farmland having typical purple soil in Chongquing, China. The study revealed that irrigation with biogasslurry increased soil ammonium nitrogen and soil nitrate by 47.8 and 19% respectively as compared to control check. The average soil available phosphorus and soil phosphorus absorption co-efficient changed slightly. Relative enzyme activities of N and P transformation were indicated by catalase, urease, invertase and phosphatase activity. Irrigation period and irrigation quantity were selected as variable factor Catalase, invertase and urease activity was highest when irrigation period and irrigation quantitiy was 4 days and 500 ml; whereas highest phosphatase activity increased significantly in purple irrigated by biogas slurry. The result of the present study is helpful in finding optimum irrigation conditions required for enzyme activity within defined range. It further reveals that biogas slurry enriches soil with various nutrients by enhancing N, P content and enzyme activities as well as it also deals with large number of biogas slurry for protecting the environment.

  15. Soil properties and enzyme activities as affected by biogas slurry irrigation in the Three Gorges Reservoir areas of China.

    PubMed

    Chen, Shiling; Yu, Weiwei; Zhang, Zhi; Luo, Surong

    2015-03-01

    Biogas slurry, as a quality organic fertilizer, is widely used on large scale livestock farmland in Southwest China. In the present study, slurry collected from anaerobic tank of dairy farm was used to irrigate farmland having typical purple soil in Chongquing, China. The study revealed that irrigation with biogasslurry increased soil ammonium nitrogen and soil nitrate by 47.8 and 19% respectively as compared to control check. The average soil available phosphorus and soil phosphorus absorption co-efficient changed slightly. Relative enzyme activities of N and P transformation were indicated by catalase, urease, invertase and phosphatase activity. Irrigation period and irrigation quantity were selected as variable factor Catalase, invertase and urease activity was highest when irrigation period and irrigation quantitiy was 4 days and 500 ml; whereas highest phosphatase activity increased significantly in purple irrigated by biogas slurry. The result of the present study is helpful in finding optimum irrigation conditions required for enzyme activity within defined range. It further reveals that biogas slurry enriches soil with various nutrients by enhancing N, P content and enzyme activities as well as it also deals with large number of biogas slurry for protecting the environment. PMID:25895278

  16. Do we need big flood to cut spectacular river gorges?

    NASA Astrophysics Data System (ADS)

    Antón, Loreto; Muñoz-Martín, Alfonso; Mather, Anne; Stokes, Martin

    2016-04-01

    The study of a historical erosional process occurred in a dam spillway in NW Spain evidences extremely rapid gorge formation in granite. Historic documents, photographs and surveys preserved at the Historical Archives allowed the reconstruction of the whole erosion process. A ~270 m long, ~100 m deep and ~100 to 160 m wide amphitheater headed canyon was carved over 6 years. The study approaches the reconstruction of the scour site topography prior to the gorge formation and during the erosion events, and analyses the erosion mechanisms involved in the canyon cutting. Data reveal extremely high (>100 m/year) erosion rates, the highest reported so far on earth, associated to small-moderate floods (~100-1500m3/s). Results come to nuance the established models of erosion and gorge formation which are used to analyze the landscape evolution. The example demonstrates that moderate water discharges are capable of radical erosion suggesting that adjustments to changes such as drainage diversion and capture, or glacier outburst, may be initially much more rapid than has hereto been assumed. Structural preconditioning of the bedrock through jointing and faulting was the primary control on landscape change, conditioning gorge morphology and the rate at which erosion progress.

  17. Landslide Monitoring in Three Gorges Area Using Multi-Frequency Insar Techniques

    NASA Astrophysics Data System (ADS)

    Liao, M.; Balz, T.; Tantianuparp, P.; Shi, X.; Zhang, L.; Wang, T.

    2012-12-01

    Landslide is a term describing the downslope movement of soil, rock, and organic materials under the effects of gravity. Landslides are very destructive forces. In order to decrease landslide occurrences and its impacts, landslide monitoring is applied to analyze, forecast, and control landslides. The Three Gorges Project, the largest hydroelectric project of the world, began to function in 2003. The dam site is situated at Sandouping in China's Hubei Province. The reservoir has a length of approximately 600 km along the Yangtze River. In 2001, in a statistical survey, carried out by the Ministry of Land and Resources of China, landslides were observed in all counties surrounding the Three Gorges reservoir and nearly 2500 landslide bodies were observed. There are many landslide triggering factors in this area, for example the dam was built on a geologically unstable zone, the large surface-water level change, the construction of new buildings and roads, deforestation, etc. The potential landslide hazards are threatening the lives of millions of residents in the area. The Three Gorges area has a rough topography and is heavily vegetated. In an effort to reduce the landslide risks, advanced monitoring techniques and methods, such as a GPS network and other terrestrial surveillance technologies, are used in the area. Although these techniques can acquire highly accurate results, their results are only available over sparse measurement points and it they requires high costs for manpower and rather high costs for the instrument manipulation. Synthetic Aperture Radar (SAR), an active microwave imaging system, suffers from temporal decorrelation when monitoring heavily vegetated area as the Three Gorges. In order to analysis long-term and continuous displacement trend in this area, Differential Interferometric SAR (D-InSAR) and Persistent Scatterer Interferometry (PSI) are applied. Both techniques are able to detect surface motions. We use high resolution TerraSAR-X X

  18. Impacts of the Three Gorges Dam on microbial structure and potential function.

    PubMed

    Yan, Qingyun; Bi, Yonghong; Deng, Ye; He, Zhili; Wu, Liyou; Van Nostrand, Joy D; Shi, Zhou; Li, Jinjin; Wang, Xi; Hu, Zhengyu; Yu, Yuhe; Zhou, Jizhong

    2015-02-27

    The Three Gorges Dam has significantly altered ecological and environmental conditions within the reservoir region, but how these changes affect bacterioplankton structure and function is unknown. Here, three widely accepted metagenomic tools were employed to study the impact of damming on the bacterioplankton community in the Xiangxi River. Our results indicated that bacterioplankton communities were both taxonomically and functionally different between backwater and riverine sites, which represent communities with and without direct dam effects, respectively. There were many more nitrogen cycling Betaproteobacteria (e.g., Limnohabitans), and a higher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in the riverine sites, suggesting a higher level of bacterial activity involved in generating more nitrogenous nutrients for the growth of phytoplankton. Additionally, the KO categories involved in carbon and sulfur metabolism, as well as most of the detected functional genes also showed clear backwater and riverine patterns. As expected, these diversity patterns all significantly correlated with environmental characteristics, confirming that the bacterioplankton communities in the Xiangxi River were really affected by environmental changes from the Three Gorges Dam. This study provides a first comparative metagenomic insight for evaluating the impacts of the large dam on microbial function.

  19. Impacts of the Three Gorges Dam on microbial structure and potential function

    PubMed Central

    Yan, Qingyun; Bi, Yonghong; Deng, Ye; He, Zhili; Wu, Liyou; Van Nostrand, Joy D.; Shi, Zhou; Li, Jinjin; Wang, Xi; Hu, Zhengyu; Yu, Yuhe; Zhou, Jizhong

    2015-01-01

    The Three Gorges Dam has significantly altered ecological and environmental conditions within the reservoir region, but how these changes affect bacterioplankton structure and function is unknown. Here, three widely accepted metagenomic tools were employed to study the impact of damming on the bacterioplankton community in the Xiangxi River. Our results indicated that bacterioplankton communities were both taxonomically and functionally different between backwater and riverine sites, which represent communities with and without direct dam effects, respectively. There were many more nitrogen cycling Betaproteobacteria (e.g., Limnohabitans), and a higher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in the riverine sites, suggesting a higher level of bacterial activity involved in generating more nitrogenous nutrients for the growth of phytoplankton. Additionally, the KO categories involved in carbon and sulfur metabolism, as well as most of the detected functional genes also showed clear backwater and riverine patterns. As expected, these diversity patterns all significantly correlated with environmental characteristics, confirming that the bacterioplankton communities in the Xiangxi River were really affected by environmental changes from the Three Gorges Dam. This study provides a first comparative metagenomic insight for evaluating the impacts of the large dam on microbial function. PMID:25721383

  20. Impacts of the Three Gorges Dam on microbial structure and potential function.

    PubMed

    Yan, Qingyun; Bi, Yonghong; Deng, Ye; He, Zhili; Wu, Liyou; Van Nostrand, Joy D; Shi, Zhou; Li, Jinjin; Wang, Xi; Hu, Zhengyu; Yu, Yuhe; Zhou, Jizhong

    2015-01-01

    The Three Gorges Dam has significantly altered ecological and environmental conditions within the reservoir region, but how these changes affect bacterioplankton structure and function is unknown. Here, three widely accepted metagenomic tools were employed to study the impact of damming on the bacterioplankton community in the Xiangxi River. Our results indicated that bacterioplankton communities were both taxonomically and functionally different between backwater and riverine sites, which represent communities with and without direct dam effects, respectively. There were many more nitrogen cycling Betaproteobacteria (e.g., Limnohabitans), and a higher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in the riverine sites, suggesting a higher level of bacterial activity involved in generating more nitrogenous nutrients for the growth of phytoplankton. Additionally, the KO categories involved in carbon and sulfur metabolism, as well as most of the detected functional genes also showed clear backwater and riverine patterns. As expected, these diversity patterns all significantly correlated with environmental characteristics, confirming that the bacterioplankton communities in the Xiangxi River were really affected by environmental changes from the Three Gorges Dam. This study provides a first comparative metagenomic insight for evaluating the impacts of the large dam on microbial function. PMID:25721383

  1. Patterns in atmospheric circulation affect emission sources contributing to nitrogen deposition in the Columbia River Gorge, Pacific Northwest USA

    NASA Astrophysics Data System (ADS)

    Anderson, S. M.; Chung, S. H.; Welker, J. M.; Harlow, B.; Evans, R. D.

    2014-12-01

    The Columbia River Gorge separating Oregon and Washington provides an ideal setting to investigate how atmospheric circulation patterns determine types of emission sources contributing to atmospheric deposition. Up-gorge and down-gorge atmospheric circulation patterns each provide a different suite of emission sources. Up-gorge airflow originates in the Portland-Vancouver metro area dominated by urban and industrial sources. Down-gorge patterns originate in the Columbia River basin, which is dominated by agricultural production. We tested the dependence of emission sources contributing to atmospheric deposition on circulation patterns by measuring the isotopic composition of nitrate (NO3-) in 2003-2004 precipitation samples from the WA98-Columbia River Gorge NADP & USNIP site. Circulation patterns were determined using back-trajectory analysis with the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model using the archived EDAS meteorological dataset. We observed a significant difference (P=0.01) between up-gorge and down-gorge patterns with mean δ15N-NO3- of +1.8 and -2.1‰ for up- and down-gorge, respectively. The differences observed between these two patterns is likely tied to the different emission sources of N found in these different geographic areas. The lower δ15N of down-gorge sources is due to the large amount of agricultural production in the Columbia River basin. Observed values for the up-gorge patterns likely result from industrial and fossil fuel emissions of NOx, the precursor of deposited NO3-, in the Portland-Vancouver area. The significantly greater amount of NO3- in precipitation from up-gorge patterns (0.72 mg/L) compared to down-gorge patterns (0.36 mg/L, P=0.01) supports the influence of urban sources rather than relatively clean marine air which characteristically has low amounts of NO3-. No significant differences are found in δ18Onitrate or Δ17Onitrate between the two patterns, suggesting that atmospheric chemistry

  2. Catalysis: Elusive active site in focus

    NASA Astrophysics Data System (ADS)

    Labinger, Jay A.

    2016-08-01

    The identification of the active site of an iron-containing catalyst raises hopes of designing practically useful catalysts for the room-temperature conversion of methane to methanol, a potential fuel for vehicles. See Letter p.317

  3. Meat-eating by early hominids at the FLK 22 Zinjanthropus site, Olduvai Gorge (Tanzania): an experimental approach using cut-mark data.

    PubMed

    Domínguez-Rodrigo, M

    1997-12-01

    The meat-eating behavior of Plio-Pleistocene hominids, responsible for the bone accumulations at the earliest archaeological sites, is still a hotly-debated issue in paleoanthropology. In particular, meat-eating and bone marrow consumption are often presented as either complementary or opposing strategies of carcass exploitation. The presence of cut marks on fossil archeofauna is a potential source of information that has not been consistently used as evidence of carcass consumption by hominids. Some authors interpret cut marks as the result of hominids manipulating meat-bearing bones, while others argue that they can also be the result of hominids extracting marginal scraps of carcass flesh that have survived carnivores' initial consumption. In this study, a referential framework concerning the interpretation of cut marks is presented, based on a set of experiments conducted by the author. It is suggested, according to these experiments and data drawn from the FLK "Zinj" site, that hominids processed meat-bearing bones (on which flesh was abundant) rather than defleshed carcasses from felid kills.

  4. Low dielectric response in enzyme active site

    PubMed Central

    Mertz, Edward L.; Krishtalik, Lev I.

    2000-01-01

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

  5. Recreation planning for Tallulah Gorge

    SciTech Connect

    Gardner, J.; Vogler, E.; Merklein, G.

    1995-12-31

    Georgia Power Company`s North Georgia Project, a member of the Class of `93, offers an example of successful recreation planning and conflict resolution. Following filing of the relicense application in 1991, the American Whitewater Affiliation (AWA) filed a motion to intervene, requesting a study of the feasibility of whitewater boating in Tallulah Gorge, located within the project. Following extensive consultation Georgia Power conducted the test in May 1993. The test garnered a great deal of publicity in Atlanta and North Georgia. At about this time, public support for aesthetics flows arose, and Georgia Power eventually tested several flows to compare aesthetics benefits. Georgia Power negotiated at length with agencies and interest groups to arrive at a proposal for whitewater, aesthetic and fishery enhancement flows and in December 1993, GPC made a proposal to FERC for flows in Tallulah Gorge. During this same time period, Georgia Power and the State of Georgia entered into a partnership agreement to develop a new state park encompassing lands within the North Georgia Project.

  6. Post-glacial rock avalanche causing epigenetic gorge incision (Strassberg gorge, Eastern Alps).

    NASA Astrophysics Data System (ADS)

    Sanders, Diethard

    2015-04-01

    fractured clasts up to boulder size. Comparison with areas with intense neotectonism (e. g., Central Apennines) suggests that fracturation may have been caused by seismicity. For the area, historical earthquakes with Me 3-3.9 imply the incidence of stronger quakes on longer timescales. The considered rock avalanche thus perhaps was triggered by a seismic event. The investigated RAD is the hitherto unappreciated, easternmost outlier of a cluster of rock avalanches in the area; these rock avalanches are grouped within a seismically active belt of strike-slip faults related to the Neogene to recent deformation of the Eastern Alps. This study links structural deformation with catastrophic mass-wasting which, in turn, caused incision of an epigenetic bedrock gorge. Surface exposure dating of boulders is intended to constrain the age of rock avalanching.

  7. [Effect of Low Molecular Weight Organic Acids on the Chemical Speciation and Activity of Mercury in the Soils of the Water-Level-Fluctuating Zone of the Three Gorges Reservoir].

    PubMed

    You, Rui; Liang, Li; Qin, Cai-qing; Deng, Han; Wang, Ding-yong

    2016-01-15

    To investigate the effect of low molecular weight organic acids ( LMWOA) on the ability of migration and the species of mercury in the soil of the Water-Level-Fluctuating Zone of the Three Gorges Reservoir, citric acid, tartaric acid and oxalic acid were dded into the soil to conduct simulation experiments. The results showed that the percentage of exchangeable mercury increased with the increase of the concentration of citric acid, but the value declined slightly as the concentration of tartaric acid and oxalic acid increased. While all three acids elevated the bioavailability of mercury, which increased with the increase of the concentration of acids. Vhen the concentration of citric acid reached 15 mmol x L(-1), the activation effect was the best. But for oxalic acid and citric acid, 10 mmol x L(-1) was the optimal concentration. In general, the effect of three organic acids on the activation of mercury in the soil followed the trend of citric acid > tartaric acid > oxalic acid. In the soil supplemented with 15 mmol x L(-1) citric acid, the change of mercury pecies was more and more striking with the prolonged incubation, and the conversion did not stop until 14 d, at that time the stomach cid dissolved mercury increased obviously, which was mainly converted from elemental mercury.

  8. [Effect of Low Molecular Weight Organic Acids on the Chemical Speciation and Activity of Mercury in the Soils of the Water-Level-Fluctuating Zone of the Three Gorges Reservoir].

    PubMed

    You, Rui; Liang, Li; Qin, Cai-qing; Deng, Han; Wang, Ding-yong

    2016-01-15

    To investigate the effect of low molecular weight organic acids ( LMWOA) on the ability of migration and the species of mercury in the soil of the Water-Level-Fluctuating Zone of the Three Gorges Reservoir, citric acid, tartaric acid and oxalic acid were dded into the soil to conduct simulation experiments. The results showed that the percentage of exchangeable mercury increased with the increase of the concentration of citric acid, but the value declined slightly as the concentration of tartaric acid and oxalic acid increased. While all three acids elevated the bioavailability of mercury, which increased with the increase of the concentration of acids. Vhen the concentration of citric acid reached 15 mmol x L(-1), the activation effect was the best. But for oxalic acid and citric acid, 10 mmol x L(-1) was the optimal concentration. In general, the effect of three organic acids on the activation of mercury in the soil followed the trend of citric acid > tartaric acid > oxalic acid. In the soil supplemented with 15 mmol x L(-1) citric acid, the change of mercury pecies was more and more striking with the prolonged incubation, and the conversion did not stop until 14 d, at that time the stomach cid dissolved mercury increased obviously, which was mainly converted from elemental mercury. PMID:27078955

  9. GEOMORPHOLOGY. Comment on "Tectonic control of Yarlung Tsangpo Gorge revealed by a buried canyon in Southern Tibet".

    PubMed

    Zeitler, Peter K; Koons, Peter O; Hallet, Bernard; Meltzer, Anne S

    2015-08-21

    Wang et al. (Reports, 21 November, 2014, p. 978) describe a buried canyon upstream of the Yarlung Tsangpo Gorge and argue that rapid erosion of the gorge was merely a passive response to rapid uplift at ~2.5 million years ago (Ma). We view these data as an expected consequence emerging from feedbacks between erosion and crustal rheology active well before 2.5 Ma.

  10. GEOMORPHOLOGY. Comment on "Tectonic control of Yarlung Tsangpo Gorge revealed by a buried canyon in Southern Tibet".

    PubMed

    Zeitler, Peter K; Koons, Peter O; Hallet, Bernard; Meltzer, Anne S

    2015-08-21

    Wang et al. (Reports, 21 November, 2014, p. 978) describe a buried canyon upstream of the Yarlung Tsangpo Gorge and argue that rapid erosion of the gorge was merely a passive response to rapid uplift at ~2.5 million years ago (Ma). We view these data as an expected consequence emerging from feedbacks between erosion and crustal rheology active well before 2.5 Ma. PMID:26293946

  11. Active Sites Environmental Monitoring Program: Action levels

    SciTech Connect

    Ashwood, J.S.; Ashwood, T.L.

    1991-10-01

    The Active Sites Environmental Monitoring Program (ASEMP) was established at Oak Ridge National Laboratory to provide for early leak detection and to monitor performance of the active low-level waste disposal facilities in Solid Waste Storage Area (SWSA) 6 and the transuranic waste storage areas in SWSA 5 North. Early leak detection is accomplished by sampling runoff, groundwater, and perched water in burial trenches. Sample results are compared to action levels that represent background contamination by naturally occurring and fallout-derived radionuclides. 15 refs., 3 figs., 12 tabs.

  12. Nutritional and behavioral effects of gorge and fast feeding in captive lions.

    PubMed

    Altman, Joanne D; Gross, Kathy L; Lowry, Stephen R

    2005-01-01

    Nonhuman animals in captivity manifest behaviors and physiological conditions that are not common in the wild. Lions in captivity face problems of obesity, inactivity, and stereotypy. To mediate common problems of captive lions, this study implemented a gorge and fast feeding schedule that better models naturalistic patterns: African lions (Panthera leo) gradually adapted from a conventional feeding program to a random gorge and fast feeding schedule. Digestibility increased significantly and food intake and metabolizable energy intake correspondingly decreased. Lions also showed an increase in appetitive active behaviors, no increase in agonistic behavior, and paced half as frequently on fast days as on feeding days. Thus, switching captive lions to a gorge and fast feeding schedule resulted in improved nutritional status and increased activity.

  13. Monitoring the Dynamic of a Fluvial Channel after Lahar Disturbance: Huiloac Gorge (Popocatepetl Volcano, Mexico)

    NASA Astrophysics Data System (ADS)

    Andres, N.; Palacios, D.; Zamorano, J. J.; Tanarro, L. M.; Renschler, C.; Sanjosé, J. J.; Atkinson, A.

    2009-04-01

    Volcanic eruptions generate disturbances that affect hydrological systems (Major, 2003) by depositing large volumes of sediments in watersheds that exceed amounts common to non-volcanic river systems (Montgomery, 2005). If the eruption releases abundant melt water, the river system may respond immediately by forming hazardous flows called lahars. River system recovery following eruptive and laharic impact is an important process, but it has received little attention (Gran and Montgomery, 2005) despite the fact that Major et al. (2000) and Hayes et al. (2002) have shown that these disruptions cause long term instability and their effects persist for decades. Lahar deposits resulting from interaction between volcanic activity and the glacier located above the Huiloac Gorge on the northern slope of Popocatepetl volcano (19°02´ N, 98°62´ W, 5,424 m), have infilled the gorge (Palacios, 1995; Palacios et al., 1998 and 2001; Capra et al., 2004; Muñoz, 2007). All of the major lahars that occurred on the volcano in 1995 (4 km), 1997 (21 km), and 2001 (14 km) have channelled through Huiloac Gorge, and have dramatically altered its morphology and dynamics through erosion and deposition. The present study traces these changes in the aftermath of the laharic events that occurred from 1997-2001. A sector of the channel, located at 3200m-3240m altitude, of 500 m long and 15 to 20 m wide, in the mid-section of the gorge, was chosen as the control site. Precipitation is heaviest there and is most apt to trigger secondary post-eruptive lahars. ArcGis software was used to draw 6 geomorphic maps of the site showing spatial variations in the landforms for the period February 2002 - February 2008. In addition, 29 cross-profiles were made of the gorge for the same time interval, excluding February 2004. The volume of sediment eroded and deposited was calculated for each date by comparing variations in the height of the floor and banks of the gorge depicted in the cross-profile, and

  14. Characterization of active sites in zeolite catalysts

    SciTech Connect

    Eckert, J.; Bug, A.; Nicol, J.M.

    1997-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Atomic-level details of the interaction of adsorbed molecules with active sites in catalysts are urgently needed to facilitate development of more effective and/or environmentally benign catalysts. To this end the authors have carried out neutron scattering studies combined with theoretical calculations of the dynamics of small molecules inside the cavities of zeolite catalysts. The authors have developed the use of H{sub 2} as a probe of adsorption sites by observing the hindered rotations of the adsorbed H{sub 2} molecule, and they were able to show that an area near the four-rings is the most likely adsorption site for H{sub 2} in zeolite A while adsorption of H{sub 2} near cations located on six-ring sites decreases in strength as Ni {approximately} Co > Ca > Zn {approximately} Na. Vibrational and rotational motions of ethylene and cyclopropane adsorption complexes were used as a measure for zeolite-adsorbate interactions. Preliminary studies of the binding of water, ammonia, and methylamines were carried out in a number of related guest-host materials.

  15. 6. VIEW FROM THE ROOF OF GORGE POWERHOUSE LOOKING EAST ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. VIEW FROM THE ROOF OF GORGE POWERHOUSE LOOKING EAST TO THE FORMER GRAVITY OIL STORAGE BUILDING, 1989. - Skagit Power Development, Gorge Powerhouse, On Skagit River, 0.4 mile upstream from Newhalem, Newhalem, Whatcom County, WA

  16. 5. GORGE HIGH DAM; LOOKING TOWARD INTAKE WITH WATER FLOWING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. GORGE HIGH DAM; LOOKING TOWARD INTAKE WITH WATER FLOWING OVER THE TOP OF THE SPILLGATE, 1989. - Skagit Power Development, Gorge High Dam, On Skagit River, 2.9 miles upstream from Newhalem, Newhalem, Whatcom County, WA

  17. 10. TRANSMISSION LINES BETWEEN DIABLO AND GORGE; CONSTRUCTION DETAIL OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    10. TRANSMISSION LINES BETWEEN DIABLO AND GORGE; CONSTRUCTION DETAIL OF TOWER STRUCTURE, 1989. - Skagit Power Development, Gorge High Dam, On Skagit River, 2.9 miles upstream from Newhalem, Newhalem, Whatcom County, WA

  18. Initiation age and incision rates of inner gorges: Do they record multiple glacial-interglacial cycles?

    NASA Astrophysics Data System (ADS)

    Delunel, Romain; Casagrande, Jan; Schlunegger, Fritz; Akçar, Naki; Kubik, Peter W.

    2015-04-01

    Inner gorges represent some of the most conspicuous landforms in the European Alps. They form narrow and deep active-channel incisions that link hanging tributaries with trunk valleys in glacially-conditioned environments. Despite abundant research carried out on these objects, both their origin and evolution have remained unclear. In particular, the age of initiation, the rate of incision, and the respective contribution of fluvial and subglacial processes in the evolution of inner gorges have still been a matter of scientific debate. Indeed, answering these questions has been complicated by the lack of appropriate quantitative methods and/or suitable sampling strategies for studying inner gorges. Here, we report 10Be concentrations measured in alluvial sediments that have been collected along the main stream of a ~20-km2-catchment in the Swiss foreland (Central European Alps). This catchment hosts a ca. 100-m-deep and 2-km-long inner gorge that has been cut mainly in glacial till. Catchment wide denudation rates inferred from 10Be analyses (n = 15) vary from ~120 to 650 mm/ka and show a general downstream increasing trend. Additional field observations and GIS analyses reveal that the denudation rates within the catchment increase from the headwaters, characterized by relict glacial/periglacial landscapes, to the downstream end of the basin where the inner gorge has been formed. Using a 10Be-based sediment budget approach and the delineation of topographic domains from a 2-m-resolution LIDAR, we provide an estimate of erosion rates within the gorge that are higher than 2.5 m/ka and can reach up to ~ 7 m/ka. Combining these estimated erosion rates with the reconstruction of eroded volumes within the gorge, we obtain a rough initiation age in the early Holocene, in general agreement with previous studies reporting a postglacial origin for the inner gorges. Our results therefore appear contradictory with recent findings arguing for a gradual formation of inner

  19. Monitoring the Dynamic of a Fluvial Channel after Lahar Disturbance: Huiloac Gorge (Popocatepetl Volcano, Mexico)

    NASA Astrophysics Data System (ADS)

    Andres, N.; Palacios, D.; Zamorano, J. J.; Tanarro, L. M.; Renschler, C.; Sanjosé, J. J.; Atkinson, A.

    2009-04-01

    Volcanic eruptions generate disturbances that affect hydrological systems (Major, 2003) by depositing large volumes of sediments in watersheds that exceed amounts common to non-volcanic river systems (Montgomery, 2005). If the eruption releases abundant melt water, the river system may respond immediately by forming hazardous flows called lahars. River system recovery following eruptive and laharic impact is an important process, but it has received little attention (Gran and Montgomery, 2005) despite the fact that Major et al. (2000) and Hayes et al. (2002) have shown that these disruptions cause long term instability and their effects persist for decades. Lahar deposits resulting from interaction between volcanic activity and the glacier located above the Huiloac Gorge on the northern slope of Popocatepetl volcano (19°02´ N, 98°62´ W, 5,424 m), have infilled the gorge (Palacios, 1995; Palacios et al., 1998 and 2001; Capra et al., 2004; Muñoz, 2007). All of the major lahars that occurred on the volcano in 1995 (4 km), 1997 (21 km), and 2001 (14 km) have channelled through Huiloac Gorge, and have dramatically altered its morphology and dynamics through erosion and deposition. The present study traces these changes in the aftermath of the laharic events that occurred from 1997-2001. A sector of the channel, located at 3200m-3240m altitude, of 500 m long and 15 to 20 m wide, in the mid-section of the gorge, was chosen as the control site. Precipitation is heaviest there and is most apt to trigger secondary post-eruptive lahars. ArcGis software was used to draw 6 geomorphic maps of the site showing spatial variations in the landforms for the period February 2002 - February 2008. In addition, 29 cross-profiles were made of the gorge for the same time interval, excluding February 2004. The volume of sediment eroded and deposited was calculated for each date by comparing variations in the height of the floor and banks of the gorge depicted in the cross-profile, and

  20. 1. GORGE HIGH DAM. THIS THIN ARCH DAM WITH A ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. GORGE HIGH DAM. THIS THIN ARCH DAM WITH A GRAVITY SECTION IS THE THIRD DAM BUILT BY SEATTLE CITY LIGHT TO PROVIDE WATER FOR GORGE POWERHOUSE AND WAS COMPLETED IN 1961, 1989. - Skagit Power Development, Gorge High Dam, On Skagit River, 2.9 miles upstream from Newhalem, Newhalem, Whatcom County, WA

  1. MIDDLE GORGE POWER PLANT, OWENS RIVER STREAM FLOWING OVER TAIL ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    MIDDLE GORGE POWER PLANT, OWENS RIVER STREAM FLOWING OVER TAIL RACE OF POWER PLANT AND PENSTOCK HEADGATE TO LOWER GORGE CONTROL PLANT. A MINIMAL FLOW OF RIVER WATER IS REQUIRED TO MAINTAIN FISH LIFE - Los Angeles Aqueduct, Middle Gorge Power Plant, Los Angeles, Los Angeles County, CA

  2. Effects of hydropower operations on recreational use and nonuse values at Glen Canyon and Flaming Gorge Dams

    SciTech Connect

    Carlson, J.L.

    1995-03-01

    Increases in streamflows are generally positively related to the use values of angling and white-water boating, and constant flows tend to increase the use values more than fluctuating flows. In most instances, however, increases in streamflows beyond some threshold level cause the use values to decrease. Expenditures related to angling and white-water boating account for about $24 million of activity in the local economy around Glen Canyon Dam and $24.8 million in the local economy around flaming Gorge Dam. The range of operational scenarios being considered in the Western Area Power Administration`s Electric Power Marketing Environmental Impact Statement, when use rates are held constant, could change the combined use value of angling and white-water boating below Glen Canyon Dam, increasing it by as much as 50%, depending on prevailing hydrological conditions. Changes in the combined use value below Flaming Gorge Dam could range from a decrease of 9% to an increase of 26%. Nonuse values, such as existence and bequest values, could also make a significant contribution to the total value of each site included in this study; however, methodological and data limitations prevented estimating how each operational scenario could change nonuse values.

  3. Active site of ribulosebisphosphate carboxylase/oxygenase

    SciTech Connect

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

    1985-01-01

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

  4. 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.

  5. Ancient landslide-dam events in the Jishi Gorge, upper Yellow River valley, China

    NASA Astrophysics Data System (ADS)

    Dong, Guanghui; Zhang, Fanyu; Ma, Minmin; Fan, Yuxin; Zhang, Jiawu; Wang, Zongli; Chen, Fahu

    2014-05-01

    Some scholars have argued that the formation and outburst of an ancient dammed lake in the Jishi Gorge at ca. 3700 cal yr BP resulted in the destruction of Lajia, the site of a famous prehistoric disaster in the Guanting Basin, upper Yellow River valley, China. However, the cause of the dammed lake and the exact age of the dam breaching are still debated. We investigated ancient landslides and evidence for the dammed lake in the Jishi Gorge, including dating of soil from the shear zone of an ancient landslide, sediments of the ancient dammed lake, and loess above lacustrine sediments using radiocarbon and optically stimulated luminescence (OSL) dating methods. Six radiocarbon dates and two OSL dates suggested that the ancient landslides and dammed lake events in the Jishi Gorge probably occurred around 8100 cal yr BP, and the ancient dammed lake was breached between 6780 cal yr BP and 5750 cal yr BP. Hence, the outburst of the ancient dammed lake in the Jishi Gorge was unrelated to the ruin of the Lajia site, but likely resulted in flood disasters in the Guanting Basin around 6500 cal yr BP.

  6. Sediment delivery to the Three Gorges. 2: Local response

    NASA Astrophysics Data System (ADS)

    Lu, X. X.; Higgitt, D. L.

    2001-11-01

    Information on soil erosion and sediment yields is very limited in the immediate vicinity of the Three Gorges Project (TGP), although the inceptisols developed on Triassic shales and sandstones in this area are known to be highly susceptible to erosion. Estimated sediment yields for a small reservoir catchment (Yiwanshui) in Changshou County, downstream of Chongqing, are high (around 3500 t km -2 a -1) and similar to the data from 38 reservoir investigations in Sichuan basin, but exceeding the yields estimated in the feasibility studies for the TGP. The high sediment yield reflects severe soil erosion due to cultivation aligned with slope on steep slopes, which is very common throughout Sichuan Basin and particularly in the TGP area. The total sediment delivered to the Yangtze from the TGP area has been estimated, using small reservoir data and sediment load measured at hydrological stations. These are comparable with previous estimates but there is much temporal variability in sediment supply from different parts of the Three Gorges region, suggesting the importance of local impact on sediment flux. Resettlement of agricultural activity around the Three Gorges Reservoir is likely to further enhance soil erosion. Temporal changes in sediment yields are reconstructed by using caesium-137 ( 137Cs) dating techniques. They indicate significant changes resulting from human activity and rainfall variability during the past four decades. Comparing reservoir sedimentation against erosion estimates on catchment soils, derived from measurements, indicates that 84% of eroded soil is delivered to the reservoir and the remainder is deposited in valley floor paddy fields. It is estimated that over 60% of sediment is contributed from arable land. The trap efficiency of small catchment reservoirs, such as Yiwanshui, may be an important control on sediment delivery to the main channel of the Upper Yangtze.

  7. Altered streamflow and sediment entrainment in the Gunnison Gorge

    USGS Publications Warehouse

    Elliott, J.G.; Parker, R.S.

    1997-01-01

    The Gunnison River in the Gunnison Gorge is a canyon river where upstream dams regulate mainstem discharge but do not affect debris-flow sediment supply from tributaries entering below the reservoirs. Regulation since 1966 has altered flood frequency, streambed mobility, and fluvial geomorphology creating potential resource-management issues. The duration of moderate streamflows between 32.3 and 85.0 m3/s has increased threefold since 1966. This, along with flood-peak attenuation, has facilitated fine-sediment deposition and vegetation encroachment on stream banks. The Shields equation and on-site channel geometry and bed-material measurements were used to assess changes in sediment entrainment in four alluvial reaches. Sand and fine gravel are transported through riffle/pool reaches at most discharges, but the cobbles and boulders composing the streambed in many reaches now are infrequently entrained. Periodic debris flows add coarse sediment to rapids and can increase pool elevation and the streambed area affected by backwater and fine-sediment accumulation. Debris-flow supplied boulders accumulate on fans and in rapids and constrict the channel until reworked by larger floods. The response to streamflow-regime changes in the Gunnison Gorge could serve as an analog for alluvial reaches in other regulated canyon rivers.

  8. Raptor Use of the Rio Grande Gorge

    SciTech Connect

    Ponton, David A.

    2015-03-20

    The Rio Grande Gorge is a 115 km long river canyon located in Southern Colorado (15 km) and Northern New Mexico (100 km). The majority of the canyon is under the administration of the Bureau of Land Management {BLM), and 77 km of the canyon south of the Colorado/New Mexico border are designated Wild River under the National Wild and Scenic Rivers Act of 1968. Visits I have made to the Rio Grande Gorge over the past 15 .years disclosed some raptor utilization. As the Snake River Birds of Prey Natural Area gained publicity, its similarity to the Rio Grande Gorge became obvious, and I was intrigued by the possibility of a high raptor nesting density in the Gorge. A survey in 1979 of 20 km of the northern end of the canyon revealed a moderately high density of red-tailed hawks and prairie falcons. With the encouragement of that partial survey, and a need to assess the impact of river-running on nesting birds of prey, I made a more comprehensive survey in 1980. The results of my surveys, along with those of a 1978 helicopter survey by the BLM, are presented in this report, as well as general characterization of the area, winter use by raptors, and an assessment of factors influencing the raptor population.

  9. PAH distribution and mass fluxes in the Three Gorges Reservoir after impoundment of the Three Gorges Dam.

    PubMed

    Deyerling, Dominik; Wang, Jingxian; Hu, Wei; Westrich, Bernhard; Peng, Chengrong; Bi, Yonghong; Henkelmann, Bernhard; Schramm, Karl-Werner

    2014-09-01

    Mass fluxes of polycyclic aromatic hydrocarbons (PAHs) were calculated for the Three Gorges Reservoir (TGR) in China, based on concentration and discharge data from the Yangtze River. Virtual Organisms (VOs) have been applied during four campaigns in 2008, 2009 (twice) and 2011 at sampling sites distributed from Chongqing to Maoping. The total PAH mass fluxes ranged from 110 to 2,160 mg s(-1). Highest loads were determined at Chongqing with a decreasing trend towards Maoping in all four sampling campaigns. PAH remediation capacity of the TGR was found to be high as the mass flux reduced by more than half from upstream to downstream. Responsible processes are thought to be adsorption of PAH to suspended particles, dilution and degradation. Furthermore, the dependence of PAH concentration upon water depth was investigated at Maoping in front of the Three Gorges Dam. Although considerable differences could be revealed, there was no trend observable. Sampling of water with self-packed filter cartridges confirmed more homogenous PAH depth distribution. Moreover, PAH content of suspended particles was estimated from water concentrations gathered by VOs based on a water-particle separation model and subsequently compared to PAH concentration measured in water and in filter cartridges. It could be shown that the modeled data predicts the concentration caused by particle-bound PAHs to be about 6 times lower than PAHs dissolved in water. Besides, the model estimates the proportions of 5- and 6-ring PAHs being higher than in water phase.

  10. PAH distribution and mass fluxes in the Three Gorges Reservoir after impoundment of the Three Gorges Dam.

    PubMed

    Deyerling, Dominik; Wang, Jingxian; Hu, Wei; Westrich, Bernhard; Peng, Chengrong; Bi, Yonghong; Henkelmann, Bernhard; Schramm, Karl-Werner

    2014-09-01

    Mass fluxes of polycyclic aromatic hydrocarbons (PAHs) were calculated for the Three Gorges Reservoir (TGR) in China, based on concentration and discharge data from the Yangtze River. Virtual Organisms (VOs) have been applied during four campaigns in 2008, 2009 (twice) and 2011 at sampling sites distributed from Chongqing to Maoping. The total PAH mass fluxes ranged from 110 to 2,160 mg s(-1). Highest loads were determined at Chongqing with a decreasing trend towards Maoping in all four sampling campaigns. PAH remediation capacity of the TGR was found to be high as the mass flux reduced by more than half from upstream to downstream. Responsible processes are thought to be adsorption of PAH to suspended particles, dilution and degradation. Furthermore, the dependence of PAH concentration upon water depth was investigated at Maoping in front of the Three Gorges Dam. Although considerable differences could be revealed, there was no trend observable. Sampling of water with self-packed filter cartridges confirmed more homogenous PAH depth distribution. Moreover, PAH content of suspended particles was estimated from water concentrations gathered by VOs based on a water-particle separation model and subsequently compared to PAH concentration measured in water and in filter cartridges. It could be shown that the modeled data predicts the concentration caused by particle-bound PAHs to be about 6 times lower than PAHs dissolved in water. Besides, the model estimates the proportions of 5- and 6-ring PAHs being higher than in water phase. PMID:24726518

  11. Control of active sites in flocculation: Concept of equivalent active sites''

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Flocculation and dispersion of solids are strong functions of the amount and conformation of the adsorbed polymer. Regions of dispersion and flocculation of solids with particular polymer molecules may be deduced from saturation adsorption data. The concept of equivalent active sites'' is proposed to explain flocculation and dispersion behavior irrespective of the amount or conformation of the adsorbed polymer. The concept has been further extended to study the selective flocculation process.

  12. Assessing internal biophysical vulnerability to landslide hazards - a nested catchment approach: Xiangxi Watershed / Three Gorges Reservoir

    NASA Astrophysics Data System (ADS)

    Wiegand, Matthias; Seeber, Christoph; Hartmann, Heike; Xiang, Wei; King, Lorenz

    2010-05-01

    The Three Gorges dam construction was completed in 2006. Besides the international media, also the responsible authorities and various scholarly communities pay close attention to potential and actual environmental impacts related to the impoundment and development activities. The geo-environment within the Three Gorges region is highly conducive to landslides. Consequently, a scientific monitoring and risk mitigation system was established and is still under development. Risk analysis with regard to gravity driven mass movements is highly complex and strongly site specific - several aspects hamper a universal methodology applicable for landslide risk and site assessment. The interdisciplinary Sino-German Yangtze-Project Research co-operation aims, among others, to support the sustainable cultivation of the newly developed ecosystems within the Yangtze catchments. Land use change and increasing population growth are causing severe pressure on the scarce land resources. Landslides are acknowledged as important threat, hence vulnerability of certain landscape components have to be identified, quantified and monitored. A nested quantitative approach for vulnerability analysis is developed. The applied risk and vulnerability model understands risk as the product of hazard and vulnerability. Whereas vulnerability is characterized by: mass movement intensity and susceptibility of the respective element at risk. The watershed of Xiangxi river serves as study area. In general, catchment approaches intent and proved to be a functional geographical unit for successful integrated resources management. Several limitations with regard to data accessibility, availability and accuracy have to be considered due to restrictions of feasible scales. Comprehensive large-scale site investigations are confined to training areas for model calibration and validation. Remote sensing potentials are utilised for land use/ land cover change analysis and localization of selected elements

  13. Dissecting the active site of a photoreceptor protein

    NASA Astrophysics Data System (ADS)

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

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

  14. The Three Gorges Project: How sustainable?

    NASA Astrophysics Data System (ADS)

    Kepa Brian Morgan, Te Kipa; Sardelic, Daniel N.; Waretini, Amaria F.

    2012-08-01

    SummaryIn 1984 the Government of China approved the decision to construct the Three Gorges Dam Project, the largest project since the Great Wall. The project had many barriers to overcome, and the decision was made at a time when sustainability was a relatively unknown concept. The decision to construct the Three Gorges Project remains contentious today, especially since Deputy Director of the Three Gorges Project Construction Committee, Wang Xiaofeng, stated that "We absolutely cannot relax our guard against ecological and environmental security problems sparked by the Three Gorges Project" (Bristow, 2007; McCabe, 2007). The question therefore was posed: how sustainable is the Three Gorges Project? Conventional approaches to sustainability assessment tend to use monetary based assessment aligned to triple bottom line thinking. That is, projects are evaluated as trade-offs between economic, environmental and social costs and benefits. The question of sustainability is considered using such a traditional Cost-Benefit Analysis approach, as undertaken in 1988 by a CIPM-Yangtze Joint Venture, and the Mauri Model Decision Making Framework (MMDMF). The Mauri Model differs from other approaches in that sustainability performance indicators are considered independently from any particular stakeholder bias. Bias is then introduced subsequently as a sensitivity analysis on the raw results obtained. The MMDMF is unique in that it is based on the Māori concept of Mauri, the binding force between the physical and the spiritual attributes of something, or the capacity to support life in the air, soil, and water. This concept of Mauri is analogous to the Chinese concept of Qi, and there are many analogous concepts in other cultures. It is the universal relevance of Mauri that allows its use to assess sustainability. This research identified that the MMDMF was a strong complement to Cost-Benefit Analysis, which is not designed as a sustainability assessment tool in itself. The

  15. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

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

    1999-01-01

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

  16. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

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

    1999-01-01

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

  17. Activation of Inhibitors by Sortase Triggers Irreversible Modification of the Active Site*S

    PubMed Central

    Maresso, Anthony W.; Wu, Ruiying; Kern, Justin W.; Zhang, Rongguang; Janik, Dorota; Missiakas, Dominique M.; Duban, Mark-Eugene; Joachimiak, Andrzej; Schneewind, Olaf

    2011-01-01

    Sortases anchor surface proteins to the cell wall of Gram-positive pathogens through recognition of specific motif sequences. Loss of sortase leads to large reductions in virulence, which identifies sortase as a target for the development of antibacterials. By screening 135,625 small molecules for inhibition, we report here that aryl (β-amino)ethyl ketones inhibit sortase enzymes from staphylococci and bacilli. Inhibition of sortases occurs through an irreversible, covalent modification of their active site cysteine. Sortases specifically activate this class of molecules via β-elimination, generating a reactive olefin intermediate that covalently modifies the cysteine thiol. Analysis of the three-dimensional structure of Bacillus anthracis sortase B with and without inhibitor provides insights into the mechanism of inhibition and reveals binding pockets that can be exploited for drug discovery. PMID:17545669

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

    PubMed

    Taylor, J C; Markham, G D

    1999-11-12

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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site.

    PubMed Central

    Weaver, T.; Lees, M.; Banaszak, L.

    1997-01-01

    Two mutant forms of fumarase C from E. coli have been made using PCR and recombinant DNA. The recombinant form of the protein included a histidine arm on the C-terminal facilitating purification. Based on earlier studies, two different carboxylic acid binding sites, labeled A- and B-, were observed in crystal structures of the wild type and inhibited forms of the enzyme. A histidine at each of the sites was mutated to an asparagine. H188N at the A-site resulted in a large decrease in specific activity, while the H129N mutation at the B-site had essentially no effect. From the results, we conclude that the A-site is indeed the active site, and a dual role for H188 as a potential catalytic base is proposed. Crystal structures of the two mutant proteins produced some unexpected results. Both mutations reduced the affinity for the carboxylic acids at their respective sites. The H129N mutant should be particularly useful in future kinetic studies because it sterically blocks the B-site with the carboxyamide of asparagine assuming the position of the ligand's carboxylate. In the H188N mutation at the active site, the new asparagine side chain still interacts with an active site water that appears to have moved slightly as a result of the mutation. PMID:9098893

  4. Linking Ah receptor mediated effects of sediments and impacts on fish to key pollutants in the Yangtze Three Gorges Reservoir, China - A comprehensive perspective.

    PubMed

    Floehr, Tilman; Scholz-Starke, Björn; Xiao, Hongxia; Hercht, Hendrik; Wu, Lingling; Hou, Junli; Schmidt-Posthaus, Heike; Segner, Helmut; Kammann, Ulrike; Yuan, Xingzhong; Roß-Nickoll, Martina; Schäffer, Andreas; Hollert, Henner

    2015-12-15

    The Three Gorges Reservoir (TGR), created in consequence of the Yangtze River's impoundment by the Three Gorges Dam, faces numerous anthropogenic impacts that challenge its unique ecosystem. Organic pollutants, particularly aryl hydrocarbon receptor (AhR) agonists, have been widely detected in the Yangtze River, but only little research was yet done on AhR-mediated activities. Hence, in order to assess effects of organic pollution, with particular focus on AhR-mediated activities, several sites in the TGR area were examined applying the "triad approach". It combines chemical analysis, in vitro, in vivo and in situ investigations to a holistic assessment. Sediments and the benthic fish species Pelteobagrus vachellii were sampled in 2011/2012, respectively, to identify relevant endpoints. Sediment was tested in vitro with the ethoxyresorufin-O-deethylase (EROD) induction assay, and in vivo with the Fish Embryo Toxicity Test and Sediment Contact Assay with Danio rerio. Activities of phase I (EROD) and phase II (glutathione-S-transferase) biotransformation enzymes, pollutant metabolites and histopathological alterations were studied in situ in P. vachellii. EROD induction was tested in vitro and in situ to evaluate possible relationships. Two sites, near Chongqing and Kaixian city, were identified as regional hot-spots and further investigated in 2013. The sediments induced in the in vitro/in vivo bioassays AhR-mediated activities and embryotoxic/teratogenic effects - particularly on the cardiovascular system. These endpoints could be significantly correlated to each other and respective chemical data. However, particle-bound pollutants showed only low bioavailability. The in situ investigations suggested a rather poor condition of P. vachellii, with histopathological alterations in liver and excretory kidney. Fish from Chongqing city exhibited significant hepatic EROD induction and obvious parasitic infestations. The polycyclic aromatic hydrocarbon (PAH) metabolite 1

  5. Linking Ah receptor mediated effects of sediments and impacts on fish to key pollutants in the Yangtze Three Gorges Reservoir, China - A comprehensive perspective.

    PubMed

    Floehr, Tilman; Scholz-Starke, Björn; Xiao, Hongxia; Hercht, Hendrik; Wu, Lingling; Hou, Junli; Schmidt-Posthaus, Heike; Segner, Helmut; Kammann, Ulrike; Yuan, Xingzhong; Roß-Nickoll, Martina; Schäffer, Andreas; Hollert, Henner

    2015-12-15

    The Three Gorges Reservoir (TGR), created in consequence of the Yangtze River's impoundment by the Three Gorges Dam, faces numerous anthropogenic impacts that challenge its unique ecosystem. Organic pollutants, particularly aryl hydrocarbon receptor (AhR) agonists, have been widely detected in the Yangtze River, but only little research was yet done on AhR-mediated activities. Hence, in order to assess effects of organic pollution, with particular focus on AhR-mediated activities, several sites in the TGR area were examined applying the "triad approach". It combines chemical analysis, in vitro, in vivo and in situ investigations to a holistic assessment. Sediments and the benthic fish species Pelteobagrus vachellii were sampled in 2011/2012, respectively, to identify relevant endpoints. Sediment was tested in vitro with the ethoxyresorufin-O-deethylase (EROD) induction assay, and in vivo with the Fish Embryo Toxicity Test and Sediment Contact Assay with Danio rerio. Activities of phase I (EROD) and phase II (glutathione-S-transferase) biotransformation enzymes, pollutant metabolites and histopathological alterations were studied in situ in P. vachellii. EROD induction was tested in vitro and in situ to evaluate possible relationships. Two sites, near Chongqing and Kaixian city, were identified as regional hot-spots and further investigated in 2013. The sediments induced in the in vitro/in vivo bioassays AhR-mediated activities and embryotoxic/teratogenic effects - particularly on the cardiovascular system. These endpoints could be significantly correlated to each other and respective chemical data. However, particle-bound pollutants showed only low bioavailability. The in situ investigations suggested a rather poor condition of P. vachellii, with histopathological alterations in liver and excretory kidney. Fish from Chongqing city exhibited significant hepatic EROD induction and obvious parasitic infestations. The polycyclic aromatic hydrocarbon (PAH) metabolite 1

  6. Ionizable Side Chains at Catalytic Active Sites of Enzymes

    PubMed Central

    Jimenez-Morales, David; Liang, Jie

    2012-01-01

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

  7. 18. SHEAR PIN, UNIT 24 GORGE POWERHOUSE. THE WICKET GATES ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    18. SHEAR PIN, UNIT 24 GORGE POWERHOUSE. THE WICKET GATES ON THE TURBINE ARE EACH EQUIPPED WITH A SHEAR PIN AND OIL PRESSURE GAUGE. IF A GATE JAMS, THE PIN SMEARS AND THE CHANGE IN OIL PRESSURE TRIGGERS AN ALARM, 1989. - Skagit Power Development, Gorge Powerhouse, On Skagit River, 0.4 mile upstream from Newhalem, Newhalem, Whatcom County, WA

  8. 36 CFR 7.89 - New River Gorge National River.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 1 2011-07-01 2011-07-01 false New River Gorge National River. 7.89 Section 7.89 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR SPECIAL REGULATIONS, AREAS OF THE NATIONAL PARK SYSTEM § 7.89 New River Gorge National River....

  9. Historic interior view of gorge wall, taken shortly after battle, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Historic interior view of gorge wall, taken shortly after battle, looking northwest at the entrance and northwest shoeing damage to gorge wall as well as timber and earth blindage (see also HABS No. GA-2158-39). - Fort Pulaski, Cockspur Island, Savannah, Chatham County, GA

  10. 24. MITSUBISHI BIPLANE VALVE GORGE POWERHOUSE SEEN FROM THE SOUTH. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    24. MITSUBISHI BIPLANE VALVE GORGE POWERHOUSE SEEN FROM THE SOUTH. THE MITSUBISHI BIPLANE VALVES WERE INSTALLED IN 1980 AND REPLACED LARNER-JOHNSON NEEDLE VALVES ON UNITS 21, 22, AND 23, 1989. - Skagit Power Development, Gorge Powerhouse, On Skagit River, 0.4 mile upstream from Newhalem, Newhalem, Whatcom County, WA

  11. Rapid Gorge Formation in an Artificially Created Waterfall

    NASA Astrophysics Data System (ADS)

    Anton, L.; Mather, A. E.; Stokes, M.; Munoz Martin, A.

    2014-12-01

    A number of studies have examined rates of gorge formation, nick point retreat, and the controls on those rates via bedrock erodibility, the effectiveness of bedrock erosion mechanisms and the role of hillslope processes. Most findings are based on conceptual / empirical models or long term landscape analysis; but studies of recent quantifiable events are scarce yet highly valuable. Here we present expert eye witness account and quantitative survey of large and rapid fluvial erosion events that occurred over an artificially created waterfall at a spillway mouth. In 6 years a ~270 m long, ~100 m deep and ~100 to 160 m wide canyon was carved, and ~1.58 x106 m3 of granite bedrock was removed from the spillway site. Available flow data indicates that the erosion took place under unremarkable flood discharge conditions. The analysis of historic topographic maps enables the reconstruction of the former topography and successive erosion events, enabling the quantification of bedrock erosion amounts, and rates. Analysis of bedrock erodibility and discontinuity patterns demonstrates that the bedrock is mechanically strong, and that similar rock strength and fracture patterns are found throughout the region. It is apparent that structural pre-conditioning through fracture density and orientation in relation to flow and slope direction is of paramount importance in the gorge development. The presented example provides an exceptional opportunity for studying the evolution process of a bedrock canyon and to precisely measure the rate of bedrock channel erosion over a six year period. Results illustrate the highly episodic nature of the erosion and highlight several key observations for the adjustability of bedrock rivers. The observations have implications for the efficiency of bedrock erosion and raise important questions about incision rates, driving mechanisms and timescale assumptions' in models of landscape change.

  12. Determination of polybrominated diphenyl ethers in soils and sediment of Hanfeng Lake, Three Gorges.

    PubMed

    Zhang, Wenrui; Lu, Yingzhuan; Gao, Shutao; Jia, Xuwei; Yu, Zhiqiang; Zeng, Xiangying; Sheng, Guoying; Fu, Jiamo

    2015-01-01

    As ubiquitous organic contaminants, polybrominated diphenyl ethers (PBDEs) were evaluated to explore the impacts of the water level fluctuating zone (WLFZ) on organic pollutant behavior and the retention mechanism of organic pollutants in the bank-WLFZ-water system of Hanfeng Lake in the Three Gorges region of China. The mean concentrations of total PBDEs were 103, 75.2, and 568 ng g(-1) dry wt for bank soils, WLFZ soils, and sediment samples, respectively. Except for sampling sites S1 and S2, the levels of PBDEs decreased in the order of sediment>WLFZ soil > bank soil, suggesting that PBDEs were transferred from bank soil to WLFZ soil and finally deposited in the sediment. Decabromodiphenyl ethers (deca-BDEs) were the predominant congener in the study area, comprising 93.8% to 98.3% of the total PBDEs. Greater photolytic degradation of deca-BDEs was suggested in bank soils based on a higher relative abundance of octa- and nona-BDEs than in WLFZ soils and sediment. This may have occurred because deca-BDEs in bank soils have relatively longer sunlight exposure than in WLFZ soils and sediment due to the annual alternation of water storage and drainage in the catchments of the Three Gorges Reservoir. More in-depth investigations of contaminants in bank-WLFZ-water systems are needed due to the large areas of WLFZ created by the construction of the Three Gorges Dam and their importance to the balance of aquatic ecosystems. PMID:26181085

  13. Determination of polybrominated diphenyl ethers in soils and sediment of Hanfeng Lake, Three Gorges.

    PubMed

    Zhang, Wenrui; Lu, Yingzhuan; Gao, Shutao; Jia, Xuwei; Yu, Zhiqiang; Zeng, Xiangying; Sheng, Guoying; Fu, Jiamo

    2015-01-01

    As ubiquitous organic contaminants, polybrominated diphenyl ethers (PBDEs) were evaluated to explore the impacts of the water level fluctuating zone (WLFZ) on organic pollutant behavior and the retention mechanism of organic pollutants in the bank-WLFZ-water system of Hanfeng Lake in the Three Gorges region of China. The mean concentrations of total PBDEs were 103, 75.2, and 568 ng g(-1) dry wt for bank soils, WLFZ soils, and sediment samples, respectively. Except for sampling sites S1 and S2, the levels of PBDEs decreased in the order of sediment>WLFZ soil > bank soil, suggesting that PBDEs were transferred from bank soil to WLFZ soil and finally deposited in the sediment. Decabromodiphenyl ethers (deca-BDEs) were the predominant congener in the study area, comprising 93.8% to 98.3% of the total PBDEs. Greater photolytic degradation of deca-BDEs was suggested in bank soils based on a higher relative abundance of octa- and nona-BDEs than in WLFZ soils and sediment. This may have occurred because deca-BDEs in bank soils have relatively longer sunlight exposure than in WLFZ soils and sediment due to the annual alternation of water storage and drainage in the catchments of the Three Gorges Reservoir. More in-depth investigations of contaminants in bank-WLFZ-water systems are needed due to the large areas of WLFZ created by the construction of the Three Gorges Dam and their importance to the balance of aquatic ecosystems.

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

    SciTech Connect

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

    1986-03-20

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

  15. A novel approach to predict active sites of enzyme molecules.

    PubMed

    Chou, Kuo-Chen; Cai, Yu-dong

    2004-04-01

    Enzymes are critical in many cellular signaling cascades. With many enzyme structures being solved, there is an increasing need to develop an automated method for identifying their active sites. However, given the atomic coordinates of an enzyme molecule, how can we predict its active site? This is a vitally important problem because the core of an enzyme molecule is its active site from the viewpoints of both pure scientific research and industrial application. In this article, a topological entity was introduced to characterize the enzymatic active site. Based on such a concept, the covariant discriminant algorithm was formulated for identifying the active site. As a paradigm, the serine hydrolase family was demonstrated. The overall success rate by jackknife test for a data set of 88 enzyme molecules was 99.92%, and that for a data set of 50 independent enzyme molecules was 99.91%. Meanwhile, it was shown through an example that the prediction algorithm can also be used to find any typographic error of a PDB file in annotating the constituent amino acids of catalytic triad and to suggest a possible correction. The very high success rates are due to the introduction of a covariance matrix in the prediction algorithm that makes allowance for taking into account the coupling effects among the key constituent atoms of active site. It is anticipated that the novel approach is quite promising and may become a useful high throughput tool in enzymology, proteomics, and structural bioinformatics. PMID:14997541

  16. Growth exponents in surface models with non-active sites

    NASA Astrophysics Data System (ADS)

    Santos, M.; Figueiredo, W.; Aarão Reis, F. D. A.

    2006-11-01

    In this work, we studied the role played by the inactive sites present on the substrate of a growing surface. In our model, one particle sticks at the surface if the site where it falls is an active site. However, we allow the deposited particle to diffuse along the surface in accordance with some mechanism previously defined. Using Monte Carlo simulations, and some analytical results, we have investigated the model in (1+1) and (2+1) dimensions considering different relaxation mechanisms. We show that the consideration of non-active sites is a crucial point in the model. In fact, we have seen that the saturation regime is not observed for any value of the density of inactive sites. Besides, the growth exponent β turns to be one, at long times, whatever the mechanism of diffusion we consider in one and two dimensions.

  17. A small ribozyme with dual-site kinase activity

    PubMed Central

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

    2012-01-01

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

  18. Spatiotemporal characteristics of the Huangtupo landslide in the Three Gorges region (China) constrained by radar interferometry

    NASA Astrophysics Data System (ADS)

    Tomás, R.; Li, Z.; Liu, P.; Singleton, A.; Hoey, T.; Cheng, X.

    2014-04-01

    The Huangtupo landslide is one of the largest in the Three Gorges region, China. The county-seat town of Badong, located on the south shore between the Xiling and Wu gorges of the Yangtze River, was moved to this unstable slope prior to the construction of the Three Gorges Project, since the new Three Gorges reservoir completely submerged the location of the old city. The instability of the slope is affecting the new town by causing residential safety problems. The Huangtupo landslide provides scientists an opportunity to understand landslide response to fluctuating river water level and heavy rainfall episodes, which is essential to decide upon appropriate remediation measures. Interferometric Synthetic Aperture Radar (InSAR) techniques provide a very useful tool for the study of superficial and spatially variable displacement phenomena. In this paper, three sets of radar data have been processed to investigate the Huangtupo landslide. Results show that maximum displacements are affecting the northwest zone of the slope corresponding to Riverside slumping mass I#. The other main landslide bodies (i.e. Riverside slumping mass II#, Substation landslide and Garden Spot landslide) exhibit a stable behaviour in agreement with in situ data, although some active areas have been recognized in the foot of the Substation landslide and Garden Spot landslide. InSAR has allowed us to study the kinematic behaviour of the landslide and to identify its active boundaries. Furthermore, the analysis of the InSAR displacement time-series has helped recognize the different displacement patterns on the slope and their relationships with various triggering factors. For those persistent scatterers, which exhibit long-term displacements, they can be decomposed into a creep model (controlled by geological conditions) and a superimposed recoverable term (dependent on external factors), which appears closely correlated with reservoir water level changes close to the river's edge. These

  19. Exceptional river gorge formation from unexceptional floods.

    PubMed

    Anton, L; Mather, A E; Stokes, M; Muñoz-Martin, A; De Vicente, G

    2015-01-01

    An understanding of rates and mechanisms of incision and knickpoint retreat in bedrock rivers is fundamental to perceptions of landscape response to external drivers, yet only sparse field data are available. Here we present eye witness accounts and quantitative surveys of rapid, amphitheatre-headed gorge formation in unweathered granite from the overtopping of a rock-cut dam spillway by small-moderate floods (∼100-1,500 m(3) s(-1)). The amount of erosion demonstrates no relationship with flood magnitude or bedload availability. Instead, structural pattern of the bedrock through faults and joints appears to be the primary control on landscape change. These discontinuities facilitate rapid erosion (>270 m headward retreat; ∼100 m incision; and ∼160 m widening over 6 years) principally through fluvial plucking and block topple. The example demonstrates the potential for extremely rapid transient bedrock erosion even when rocks are mechanically strong and flood discharges are moderate. These observations are relevant to perceived models of gorge formation and knickpoint retreat. PMID:26242429

  20. Exceptional river gorge formation from unexceptional floods.

    PubMed

    Anton, L; Mather, A E; Stokes, M; Muñoz-Martin, A; De Vicente, G

    2015-08-05

    An understanding of rates and mechanisms of incision and knickpoint retreat in bedrock rivers is fundamental to perceptions of landscape response to external drivers, yet only sparse field data are available. Here we present eye witness accounts and quantitative surveys of rapid, amphitheatre-headed gorge formation in unweathered granite from the overtopping of a rock-cut dam spillway by small-moderate floods (∼100-1,500 m(3) s(-1)). The amount of erosion demonstrates no relationship with flood magnitude or bedload availability. Instead, structural pattern of the bedrock through faults and joints appears to be the primary control on landscape change. These discontinuities facilitate rapid erosion (>270 m headward retreat; ∼100 m incision; and ∼160 m widening over 6 years) principally through fluvial plucking and block topple. The example demonstrates the potential for extremely rapid transient bedrock erosion even when rocks are mechanically strong and flood discharges are moderate. These observations are relevant to perceived models of gorge formation and knickpoint retreat.

  1. Architecture and active site of particulate methane monooxygenase

    PubMed Central

    Culpepper, Megen A.; Rosenzweig, Amy C.

    2012-01-01

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

  2. 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. PMID:26908655

  3. 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

  4. The Volcanic Story of the Columbia River Gorge.

    ERIC Educational Resources Information Center

    Allen, John Eliot

    1982-01-01

    Uses maps, diagrams, and geological accounts to describe the Columbia River Gorge which separates Oregon from Washington and exposes an unexcelled record of Cenozoic volcanic stratigraphy, sedimentation, flooding, and landsliding for the visiting tourists, geologists, or students. (Author/DC)

  5. 36 CFR 7.89 - New River Gorge National River.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... River Gorge National River? (i) In addition to the applicable provisions in 36 CFR part 4, all... Bicycle Use—North to South Hawks Nest Connector Trail Fayetteville Trail Park Loop Trail Timber...

  6. 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.

  7. 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.

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

    PubMed

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

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

  9. Studies on the active site of pig plasma amine oxidase.

    PubMed Central

    Collison, D; Knowles, P F; Mabbs, F E; Rius, F X; Singh, I; Dooley, D M; Cote, C E; McGuirl, M

    1989-01-01

    Amine oxidase from pig plasma (PPAO) has two bound Cu2+ ions and at least one pyrroloquinoline quinone (PQQ) moiety as cofactors. It is shown that recovery of activity by copper-depleted PPAO is linear with respect to added Cu2+ ions. Recovery of e.s.r. and optical spectral characteristics of active-site copper parallel the recovery of catalytic activity. These results are consistent with both Cu2+ ions contributing to catalysis. Further e.s.r. studies indicate that the two copper sites in PPAO, unlike those in amine oxidases from other sources, are chemically distinct. These comparative studies establish that non-identity of the Cu2+ ions in PPAO is not a requirement for amine oxidase activity. It is shown through the use of a new assay procedure that there are two molecules of PQQ bound per molecule of protein in PPAO; only the more reactive of these PQQ moieties is required for activity. PMID:2559715

  10. Computer simulation of the active site of human serum cholinesterase

    SciTech Connect

    Kefang Jiao; Song Li; Zhengzheng Lu

    1996-12-31

    The first 3D-structure of acetylchelinesterase from Torpedo California electric organ (T.AChE) was published by JL. Sussman in 1991. We have simulated 3D-structure of human serum cholinesterase (H.BuChE) and the active site of H.BuChE. It is discovered by experiment that the residue of H.BuChE is still active site after a part of H.BuChE is cut. For example, the part of 21KD + 20KD is active site of H.BuChE. The 20KD as it is. Studies on these peptides by Hemelogy indicate that two active peptides have same negative electrostatic potential maps diagram. These negative electrostatic areas attached by acetyl choline with positive electrostatic potency. We predict that 147...236 peptide of AChE could be active site because it was as 20KD as with negative electrostatic potential maps. We look forward to proving from other ones.

  11. 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.

  12. Multi-site Phosphorylation Regulates Bim Stability and Apoptotic Activity

    PubMed Central

    Hübner, Anette; Barrett, Tamera; Flavell, Richard A.; Davis, Roger J.

    2008-01-01

    The pro-apoptotic BH3-only protein Bim is established to be an important mediator of signaling pathways that induce cell death. Multi-site phosphorylation of Bim by several members of the MAP kinase group is implicated as a regulatory mechanism that controls the apoptotic activity of Bim. To test the role of Bim phosphorylation in vivo, we constructed mice with a series of mutant alleles that express phosphorylation-defective Bim proteins. We show that mutation of the phosphorylation site Thr-112 causes decreased binding of Bim to the anti-apoptotic protein Bcl2 and can increase cell survival. In contrast, mutation of the phosphorylation sites Ser-55, Ser-65, and Ser-73 can cause increased apoptosis because of reduced proteasomal degradation of Bim. Together, these data indicate that phosphorylation can regulate Bim by multiple mechanisms and that the phosphorylation of Bim on different sites can contribute to the sensitivity of cellular apoptotic responses. PMID:18498746

  13. Analysis and assessment of the nutrients, biochemical indexes and heavy metals in the Three Gorges Reservoir, China, from 2008 to 2013.

    PubMed

    Gao, Qiang; Li, Yi; Cheng, Qingyuan; Yu, Mingxia; Hu, Bo; Wang, Zhigang; Yu, Zhiqiang

    2016-04-01

    The Three Gorges Reservoir, the world's largest hydropower project, has operated stably for more than five years. To understand its water quality status, the nutrient and biochemical indexes, the total nitrogen (TN), the total phosphorus (TP), the potassium permanganate index (CODMn), the five-day biochemical oxygen demand (BOD5) and fecal coliform (F. coli), as well as the heavy metals (Cu, Hg, As, Cd, Zn and Pb) of samples collected from 10 sites during the time period of 2008-2013 were studied via using multiple analysis approaches. For each parameter, pictures of the spatial and temporal distributions were presented, and the reasons behind their variation trends were elaborated. Principal component analysis (PCA) was applied to identify the types of pollution. The Canadian Council of Ministers of the Environment Water Quality Index (CCME-WQI) was calculated to concisely mark the water quality. In addition, a human health risk assessment of the heavy metals in a representative site was conducted. The results showed that the water quality state in the Three Gorges Reservoir was intricate but stable and acceptable from 2008 to 2013. The TN, TP and Pb were considered to be the key pollution indexes. Enforcements to alleviate industrial and urban pollution, along with ship management, have worked. The decrease in heavy metal concentrations from upstream to downstream was associated with the self-purification of the reservoir. However, rural pollution became worse in those years. Improper agricultural activity was an important reason for this trend. For local residents, drinking water was generally safe, but cancer caused by As and Pb is a potential issue.

  14. Analysis and assessment of the nutrients, biochemical indexes and heavy metals in the Three Gorges Reservoir, China, from 2008 to 2013.

    PubMed

    Gao, Qiang; Li, Yi; Cheng, Qingyuan; Yu, Mingxia; Hu, Bo; Wang, Zhigang; Yu, Zhiqiang

    2016-04-01

    The Three Gorges Reservoir, the world's largest hydropower project, has operated stably for more than five years. To understand its water quality status, the nutrient and biochemical indexes, the total nitrogen (TN), the total phosphorus (TP), the potassium permanganate index (CODMn), the five-day biochemical oxygen demand (BOD5) and fecal coliform (F. coli), as well as the heavy metals (Cu, Hg, As, Cd, Zn and Pb) of samples collected from 10 sites during the time period of 2008-2013 were studied via using multiple analysis approaches. For each parameter, pictures of the spatial and temporal distributions were presented, and the reasons behind their variation trends were elaborated. Principal component analysis (PCA) was applied to identify the types of pollution. The Canadian Council of Ministers of the Environment Water Quality Index (CCME-WQI) was calculated to concisely mark the water quality. In addition, a human health risk assessment of the heavy metals in a representative site was conducted. The results showed that the water quality state in the Three Gorges Reservoir was intricate but stable and acceptable from 2008 to 2013. The TN, TP and Pb were considered to be the key pollution indexes. Enforcements to alleviate industrial and urban pollution, along with ship management, have worked. The decrease in heavy metal concentrations from upstream to downstream was associated with the self-purification of the reservoir. However, rural pollution became worse in those years. Improper agricultural activity was an important reason for this trend. For local residents, drinking water was generally safe, but cancer caused by As and Pb is a potential issue. PMID:26874779

  15. Water in the Active Site of Ketosteroid Isomerase

    PubMed Central

    Hanoian, Philip; Hammes-Schiffer, Sharon

    2011-01-01

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

  16. 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.

  17. 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…

  18. 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.

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

    PubMed

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

    2016-09-01

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

  20. Conformational Transitions in Human AP Endonuclease 1 and Its Active Site Mutant during Abasic Site Repair†

    PubMed Central

    Kanazhevskaya, Lyubov Yu.; Koval, Vladimir V.; Zharkov, Dmitry O.; Strauss, Phyllis R.; Fedorova, Olga S.

    2010-01-01

    AP endonuclease 1 (APE 1) is a crucial enzyme of the base excision repair pathway (BER) in human cells. APE1 recognizes apurinic/apyrimidinic (AP) sites and makes a nick in the phosphodiester backbone 5′ to them. The conformational dynamics and presteady-state kinetics of wild-type APE1 and its active site mutant, Y171F-P173L-N174K, have been studied. To observe conformational transitions occurring in the APE1 molecule during the catalytic cycle, we detected intrinsic tryptophan fluorescence of the enzyme under single turnover conditions. DNA duplexes containing a natural AP site, its tetrahydrofuran analogue, or a 2′-deoxyguanosine residue in the same position were used as specific substrates or ligands. The stopped-flow experiments have revealed high flexibility of the APE1 molecule and the complexity of the catalytic process. The fluorescent traces indicate that wild-type APE1 undergoes at least four conformational transitions during the processing of abasic sites in DNA. In contrast, nonspecific interactions of APE1 with undamaged DNA can be described by a two-step kinetic scheme. Rate and equilibrium constants were extracted from the stopped-flow and fluorescence titration data for all substrates, ligands, and products. A replacement of three residues at the enzymatic active site including the replacement of tyrosine 171 with phenylalanine in the enzyme active site resulted in a 2 × 104-fold decrease in the reaction rate and reduced binding affinity. Our data indicate the important role of conformational changes in APE1 for substrate recognition and catalysis. PMID:20575528

  1. N-methyl-D-aspartate recognition site ligands modulate activity at the coupled glycine recognition site.

    PubMed

    Hood, W F; Compton, R P; Monahan, J B

    1990-03-01

    In synaptic plasma membranes from rat forebrain, the potencies of glycine recognition site agonists and antagonists for modulating [3H]1-[1-(2-thienyl)cyclohexyl]piperidine ([3H]TCP) binding and for displacing strychnine-insensitive [3H]glycine binding are altered in the presence of N-methyl-D-aspartate (NMDA) recognition site ligands. The NMDA competitive antagonist, cis-4-phosphonomethyl-2-piperidine carboxylate (CGS 19755), reduces [3H]glycine binding, and the reduction can be fully reversed by the NMDA recognition site agonist, L-glutamate. Scatchard analysis of [3H]glycine binding shows that in the presence of CGS 19755 there is no change in Bmax (8.81 vs. 8.79 pmol/mg of protein), but rather a decrease in the affinity of glycine (KD of 0.202 microM vs. 0.129 microM). Similar decreases in affinity are observed for the glycine site agonists, D-serine and 1-aminocyclopropane-1-carboxylate, in the presence of CGS 19755. In contrast, the affinity of glycine antagonists, 1-hydroxy-3-amino-2-pyrrolidone and 1-aminocyclobutane-1-carboxylate, at this [3H]glycine recognition site increases in the presence of CGS 19755. The functional consequence of this change in affinity was addressed using the modulation of [3H]TCP binding. In the presence of L-glutamate, the potency of glycine agonists for the stimulation of [3H]TCP binding increases, whereas the potency of glycine antagonists decreases. These data are consistent with NMDA recognition site ligands, through their interactions at the NMDA recognition site, modulating activity at the associated glycine recognition site.

  2. Geochemical "fingerprints" for Olduvai Gorge Bed II tuffs and implications for the Oldowan-Acheulean transition

    NASA Astrophysics Data System (ADS)

    McHenry, Lindsay J.; Njau, Jackson K.; de la Torre, Ignacio; Pante, Michael C.

    2016-01-01

    Bed II is a critical part of early Pleistocene Olduvai Gorge, Tanzania. Its deposits include transitions from humid to more arid conditions (with associated faunal changes), from Homo habilis to erectus, and from Oldowan to Acheulean technology. Bed II (~ 1.8-1.2 Ma) is stratigraphically and environmentally complex, with facies changes, faulting, and unconformities, making site-to-site correlation over the ~ 20 km of exposure difficult. Bed II tuffs are thinner, less evenly preserved, and more reworked than those of Bed I. Five marker tuffs (Tuffs IIA-IID, Bird Print Tuff (BPT)), plus local tephra, were collected from multiple sites and characterized using stratigraphic position, mineral assemblage, and electron probe microanalysis of phenocryst (feldspar, hornblende, augite, titanomagnetite) and glass (where available) composition. Lowermost Bed II tuffs are dominantly nephelinitic, Middle Bed II tuffs (BPT, Tuff IIC) have basaltic components, and upper Bed II Tuff IID is trachytic. The BPT and Tuff IID are identified widely using phenocryst compositions (high-Ca plagioclase and high-Ti hornblende, respectively), though IID was originally (Hay, 1976) misidentified as Tuff IIC at Loc 91 (SHK Annexe) in the Side Gorge. This work helps establish a high-resolution basin-wide paleolandscape context for the Oldowan-Acheulean transition and helps link hominin, faunal and archaeological records.

  3. Control of active sites in selective flocculation: I -- Mathematical model

    SciTech Connect

    Behl, S.; Moudgil, B.M.; Prakash, T.S. . Dept. of Materials Science and Engineering)

    1993-12-01

    Heteroflocculation has been determined to be another major reason for loss in selectivity for flocculation process. In a mathematical model developed earlier, conditions for controlling heteroflocculation were discussed. Blocking active sites to control selective adsorption of a flocculant oil a desirable solid surface is discussed. It has been demonstrated that the lower molecular weight fraction of a flocculant which is incapable of flocculating the particles is an efficient site blocking agent. The major application of selective flocculation has been in mineral processing but many potential uses exist in biological and other colloidal systems. These include purification of ceramic powders, separating hazardous solids from chemical waste, and removal of deleterious components from paper pulp.

  4. The site of activation of factor X by cancer procoagulant.

    PubMed

    Gordon, S G; Mourad, A M

    1991-12-01

    Cancer procoagulant (CP) is a cysteine proteinase found in a variety of malignant cells and tissues and in human amnion-chorion tissue. It initiates coagulation by activating factor X. However, the amino acid sequence of the substrate protein that determines the cleavage site of cysteine proteinases is different from that of the serine proteinases that normally activate factor X, such as factor IXa, VIIa and Russell's Viper Venom (RVV). Therefore, it was of interest to determine the site of cleavage of human factor X by CP. Purified CP was incubated with purified factor X and the reaction mixture was electrophoresed on a 10% Tris-tricine SDS-PAGE gel. The proteins were electroeluted on to a polyvinylidene difluoride (PVDF) membrane, and stained with Coomassie blue. The heavy chain of activated factor X was cut out of the PVDF membrane and sequenced with an Applied Biosystems 477A with on-line HPLC. The primary cleavage sequence was Asp-Ala-Ala-Asp-Leu-Asp-Pro-; two other secondary sequences Ser-Ile-Thr-Trp-Lys-Pro- and Glu-Asn-Pro-Phe-Asp-Leu were found. The penultimate amino acid on the carbonyl side of the hydrolysed amide bond plays a critical role for the recognition of the cleavage site of cysteine proteinases. These data indicate that the penultimate amino acid for the primary cleavage site of factor X by CP is proline-20 and for the secondary sites, proline-13 and proline-28. This is in contrast to arginine-52 that determines the specificity of the cleavage by normal serine proteinase activation.(ABSTRACT TRUNCATED AT 250 WORDS)

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

    SciTech Connect

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

    2012-02-06

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

  6. Functional constituents of the active site of human neutrophil collagenase.

    PubMed

    Mookhtiar, K A; Wang, F; Van Wart, H E

    1986-05-01

    A series of chemical modification reactions has been carried out to identify functional constituents of the active site of human neutrophil collagenase. The enzyme is reversibly inhibited by the transition metal chelating agent 1,10-phenanthroline, and inhibition is fully reversed by zinc. Removal of weakly bound metal ions by gel filtration inactivates collagenase, and activity is fully restored on immediate readdition of calcium. The enzyme is unaffected by reagents that modify serine, cysteine, and arginine residues. However, reaction with the carboxyl reagents cyclohexylmorpholinocarbodiimide and Woodward's Reagent K lowers the activity of the enzyme substantially. Acetylimidazole inactivates the enzyme, but activity is completely restored on addition of hydroxylamine. The enzyme is also inactivated by tetranitromethane, indicating that it contains an essential tyrosine residue. Acylation of collagenase with diethyl pyrocarbonate, diketene, acetic anhydride, or trinitrobenzenesulfonate inactivates the enzyme, and activity is not restored on addition of hydroxylamine, indicating the presence of an essential lysine residue.

  7. 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.

  8. Management of municipal solid waste in the Three Gorges region

    SciTech Connect

    Wang Liao Pei Tingquan Huang Chuan; Yuan Hui

    2009-07-15

    As the fourth phase of the Three Gorges reservoir project commenced in 2008, the rate of water flow in the Yangtze River has obviously decelerated further downstream and water clarity within the storage facility has decreased. Meanwhile, the rate of urbanization in the region is adding to the amount of municipal solid waste (MSW) being generated by every day life. The composition of the waste is becoming more diversified and complicated, thereby presenting an increasing threat to the ecological environment and water resources of the Three Gorges region. This paper is a probe into MSW in terms of its characteristics as well as methods of storage, collection, transportation, recycling, treatment and disposal, the protection of environmental ecosystems. Municipal solid waste management (MSWM) is one of the major environmental problems in the Three Gorges region, and indeed the whole of China. Based on the analysis of the present situation of MSWM and its treatment/disposal, some methods of sorting, recycling, decomposing, incineration and reuse are described, sanitary landfill as the main disposal method in Chongqing city, incineration being the second. Sanitary landfill or dump was also used for MSW treatment in the Three Gorges region, and this paper also provides some suggestions for improving MSWM in the Three Gorges region.

  9. 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.

  10. 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.

  11. Active Sites Environmental Monitoring Program: FY 1991 report

    SciTech Connect

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

    1992-11-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from April 1991 through September 1991. The ASEMP was established in 1989 by Solid Waste Operations (SWO) and the Environmental Sciences Division, both of Oak Ridge National Laboratory, 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. A new set of action levels was developed on the basis of a statistical analysis of background contamination. These new action levels have been used to evaluate results in this report. Results of ASEMP monitoring continue to demonstrate that no LLW (except [sup 3]H) is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II, which began in early FY 1991, was >90% complete at the end of September 1991. Results of sampling of groundwater and surface waters is presented.

  12. Inhibition and active-site modelling of prolidase.

    PubMed

    King, G F; Crossley, M J; Kuchel, P W

    1989-03-15

    Consideration of the active-site model of prolidase led us to examine azetidine, pyrrolidine and piperidine substrate analogs as potential in vivo inhibitors of the enzyme. One of these, N-benzyloxycarbonyl-L-proline, was shown to be a potent competitive inhibitor of porcine kidney prolidase (Ki = 90 microM); its rapid protein-mediated permeation of human and sheep erythrocytes suggests that it may be effective in vivo. The higher homolog, N-benzyloxycarbonyl-L-pipecolic acid, was also a potent inhibitor of the enzyme while the antihypertensive drugs, captopril and enalaprilat, were shown to have mild and no inhibitory effects, respectively. Analysis of inhibitor action and consideration of X-ray crystallographic data of relevant Mn2+ complexes allowed the active-site model of prolidase to be further refined; a new model is presented in which the substrate acts as a bidentate ligand towards the active-site manganous ion. Various aspects of the new model help to explain why Mn2+ has been 'chosen' by the enzyme in preference to other biologically available metal ions. PMID:2924773

  13. The Three Gorges Dam Affects Regional Precipitation

    NASA Technical Reports Server (NTRS)

    Wu, Liguang; Zhang, Qiang; Jiang, Zhihong

    2006-01-01

    Issues regarding building large-scale dams as a solution to power generation and flood control problems have been widely discussed by both natural and social scientists from various disciplines, as well as the policy-makers and public. Since the Chinese government officially approved the Three Gorges Dam (TGD) projects, this largest hydroelectric project in the world has drawn a lot of debates ranging from its social and economic to climatic impacts. The TGD has been partially in use since June 2003. The impact of the TGD is examined through analysis of the National Aeronautics and Space Administration (NASA) Tropical Rainfall Measuring Mission (TRMM) rainfall rate and Moderate Resolution Imaging Spectroradiometer (MODIS) land surface temperature and high-resolution simulation using the Pennsylvania State University-National Center for Atmospheric Research (PSU-NCAR) fifth-generation Mesoscale Model (MM5). The independent satellite data sets and numerical simulation clearly indicate that the land use change associated with the TGD construction has increased the precipitation in the region between Daba and Qinling mountains and reduced the precipitation in the vicinity of the TGD after the TGD water level abruptly rose from 66 to 135 m in June 2003. This study suggests that the climatic effect of the TGD is on the regional scale (approx.100 km) rather than on the local scale (approx.10 km) as projected in previous studies.

  14. Druggability analysis and classification of protein tyrosine phosphatase active sites

    PubMed Central

    Ghattas, Mohammad A; Raslan, Noor; Sadeq, Asil; Al Sorkhy, Mohammad; Atatreh, Noor

    2016-01-01

    Protein tyrosine phosphatases (PTP) play important roles in the pathogenesis of many diseases. The fact that no PTP inhibitors have reached the market so far has raised many questions about their druggability. In this study, the active sites of 17 PTPs were characterized and assessed for its ability to bind drug-like molecules. Consequently, PTPs were classified according to their druggability scores into four main categories. Only four members showed intermediate to very druggable pocket; interestingly, the rest of them exhibited poor druggability. Particularly focusing on PTP1B, we also demonstrated the influence of several factors on the druggability of PTP active site. For instance, the open conformation showed better druggability than the closed conformation, while the tight-bound water molecules appeared to have minimal effect on the PTP1B druggability. Finally, the allosteric site of PTP1B was found to exhibit superior druggability compared to the catalytic pocket. This analysis can prove useful in the discovery of new PTP inhibitors by assisting researchers in predicting hit rates from high throughput or virtual screening and saving unnecessary cost, time, and efforts via prioritizing PTP targets according to their predicted druggability. PMID:27757011

  15. 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.

  16. Canyons and gorges as potential geotourism destinations in Serbia: comparative analysis from two perspectives - general geotourists' and pure geotourists'

    NASA Astrophysics Data System (ADS)

    Božić, Sanja; Tomić, Nemanja

    2015-10-01

    Serbia represents one of those countries which have not yet differentiated themselves on the world tourism map. However, it has an immense but still unrevealed potential for geotourism development. In this paper we analyzed several remarkable canyons and gorges of great scientific importance and geotourism potential. These sites include the Djerdap Gorge and Lazar River Canyon, located in Eastern Serbia and the Ovcar-Kablar Gorge and Uvac Canyon located in Western Serbia. One of the main goals of this paper was to analyze and compare the current state and tourism potential of these geosites by using the M-GAM model for geosite assessment. However, the principal aim of the paper is to analyze how important is each subindicator in the assessment process for different market segments. In this paper, we also analyzed how giving different importance to subindicators can influence the position of the geosites in the matrix indicating different assessment done by two chosen market segments. The research showed that general geotourists appreciate considerably different values when assessing a geosite in comparison to pure geotourists. The paper can be used as framework for developing the tourism management strategy of geosites taking into consideration the needs and preferences of the target market segments.

  17. Electrostatic fields in the active sites of lysozymes.

    PubMed

    Sun, D P; Liao, D I; Remington, S J

    1989-07-01

    Considerable experimental evidence is in support of several aspects of the mechanism that has been proposed for the catalytic activity of lysozyme. However, the enzymatically catalyzed hydrolysis of polysaccharides proceeds over 5 orders of magnitude faster than that of model compounds that mimic the configuration of the substrate in the active site of the enzyme. Although several possible explanations for this rate enhancement have been discussed elsewhere, a definitive mechanism has not emerged. Here we report striking results obtained by classical electrodynamics, which suggest that bond breakage and the consequent separation of charge in lysozyme is promoted by a large electrostatic field across the active site cleft, produced in part by a very asymmetric distribution of charged residues on the enzyme surface. Lysozymes unrelated in amino acid sequence have similar distributions of charged residues and electric fields. The results reported here suggest that the electrostatic component of the rate enhancement is greater than 9 kcal.mol-1. Thus, electrostatic interactions may play a more important role in the enzymatic mechanism than has generally been appreciated.

  18. Histidine at the active site of Neurospora tyrosinase.

    PubMed

    Pfiffner, E; Lerch, K

    1981-10-13

    The involvement of histidyl residues as potential ligands to the binuclear active-site copper of Neurospora tyrosinase was explored by dye-sensitized photooxidation. The enzymatic activity of the holoenzyme was shown to be unaffected by exposure to light in the presence of methylene blue; however, irradiation of the apoenzyme under the same conditions led to a progressive loss of its ability to be reactivated with Cu2+. This photoinactivation was paralleled by a decrease in the histidine content whereas the number of histidyl residues in the holoenzyme remained constant. Copper measurements of photooxidized, reconstituted apoenzyme demonstrated the loss of binding of one copper atom per mole of enzyme as a consequence of photosensitized oxidation of three out of nine histidine residues. Their sequence positions were determined by a comparison of the relative yields of the histidine containing peptides of photooxidized holo- and apotyrosinases. The data obtained show the preferential modification of histidyl residues 188, 193, and 289 and suggest that they constitute metal ligands to one of the two active-site copper atoms. Substitution of copper by cobalt was found to afford complete protection of the histidyl residues from being modified by dye-sensitized photooxidation. PMID:6458322

  19. Quantifying Oldowan Stone Tool Production at Olduvai Gorge, Tanzania.

    PubMed

    Reti, Jay S

    2016-01-01

    Recent research suggests that variation exists among and between Oldowan stone tool assemblages. Oldowan variation might represent differential constraints on raw materials used to produce these stone implements. Alternatively, variation among Oldowan assemblages could represent different methods that Oldowan producing hominins utilized to produce these lithic implements. Identifying differential patterns of stone tool production within the Oldowan has implications for assessing how stone tool technology evolved, how traditions of lithic production might have been culturally transmitted, and for defining the timing and scope of these evolutionary events. At present there is no null model to predict what morphological variation in the Oldowan should look like. Without such a model, quantifying whether Oldowan assemblages vary due to raw material constraints or whether they vary due to differences in production technique is not possible. This research establishes a null model for Oldowan lithic artifact morphological variation. To establish these expectations this research 1) models the expected range of variation through large scale reduction experiments, 2) develops an algorithm to categorize archaeological flakes based on how they are produced, and 3) statistically assesses the methods of production behavior used by Oldowan producing hominins at the site of DK from Olduvai Gorge, Tanzania via the experimental model. Results indicate that a subset of quartzite flakes deviate from the null expectations in a manner that demonstrates efficiency in flake manufacture, while some basalt flakes deviate from null expectations in a manner that demonstrates inefficiency in flake manufacture. The simultaneous presence of efficiency in stone tool production for one raw material (quartzite) and inefficiency in stone tool production for another raw material (basalt) suggests that Oldowan producing hominins at DK were able to mediate the economic costs associated with stone tool

  20. Methane emissions from the surface of the Three Gorges Reservoir

    NASA Astrophysics Data System (ADS)

    Chen, Huai; Yuan, Xingzhong; Chen, Zhongli; Wu, Yuyuan; Liu, Xianshu; Zhu, Dan; Wu, Ning; Zhu, Qiu'an; Peng, Changhui; Li, Weizhong

    2011-11-01

    After our previous study about methane (CH4) emissions from littoral marshes of the Three Gorges Reservoir (TGR), Chinese dams have raised a world-wide concern. Through measurements from the surface of the TGR, a CH4 emission rate was recorded as 0.26 ± 0.38 mg CH4 m-2 h-1 (Mean ± SD), relatively low compared with those from other hydropower reservoirs. We also recorded CH4 emission rate from the surface of downstream water, which was also relatively low (0.24 ± 0.37 mg CH4 m-2 h-1). Such result may indicate that TGR is not a great CH4 emitter (not "CH4 menace"). One possible reason for such a low emission rate is that measures to maintain water quality and protect environment and ecosystem decrease the input of organic materials (for methanogenesis), which in turn limits the CH4 production in the sediment of the TGR. We also found that CH4 emission from the flooding drawdown area (0.29 ± 0.37 mg CH4 m-2 h-1) was higher than other permanently flooded sites (0.23 ± 0.38 mg CH4 m-2 h-1). Because of annual vegetation re-growth, the drawdown zone is the especially important carbon source for methanogenesis in flooding season. Interestingly, we also observed that mean CH4 emission was significantly higher in winter than in spring and summer. This was partly due to seasonal dynamics of hydrology. In order to estimate the net CH4 emissions caused by the reservoir and reservoir operation, the best approach would be Life Cycle Analysis.

  1. Quantifying Oldowan Stone Tool Production at Olduvai Gorge, Tanzania.

    PubMed

    Reti, Jay S

    2016-01-01

    Recent research suggests that variation exists among and between Oldowan stone tool assemblages. Oldowan variation might represent differential constraints on raw materials used to produce these stone implements. Alternatively, variation among Oldowan assemblages could represent different methods that Oldowan producing hominins utilized to produce these lithic implements. Identifying differential patterns of stone tool production within the Oldowan has implications for assessing how stone tool technology evolved, how traditions of lithic production might have been culturally transmitted, and for defining the timing and scope of these evolutionary events. At present there is no null model to predict what morphological variation in the Oldowan should look like. Without such a model, quantifying whether Oldowan assemblages vary due to raw material constraints or whether they vary due to differences in production technique is not possible. This research establishes a null model for Oldowan lithic artifact morphological variation. To establish these expectations this research 1) models the expected range of variation through large scale reduction experiments, 2) develops an algorithm to categorize archaeological flakes based on how they are produced, and 3) statistically assesses the methods of production behavior used by Oldowan producing hominins at the site of DK from Olduvai Gorge, Tanzania via the experimental model. Results indicate that a subset of quartzite flakes deviate from the null expectations in a manner that demonstrates efficiency in flake manufacture, while some basalt flakes deviate from null expectations in a manner that demonstrates inefficiency in flake manufacture. The simultaneous presence of efficiency in stone tool production for one raw material (quartzite) and inefficiency in stone tool production for another raw material (basalt) suggests that Oldowan producing hominins at DK were able to mediate the economic costs associated with stone tool

  2. Quantifying Oldowan Stone Tool Production at Olduvai Gorge, Tanzania

    PubMed Central

    Reti, Jay S.

    2016-01-01

    Recent research suggests that variation exists among and between Oldowan stone tool assemblages. Oldowan variation might represent differential constraints on raw materials used to produce these stone implements. Alternatively, variation among Oldowan assemblages could represent different methods that Oldowan producing hominins utilized to produce these lithic implements. Identifying differential patterns of stone tool production within the Oldowan has implications for assessing how stone tool technology evolved, how traditions of lithic production might have been culturally transmitted, and for defining the timing and scope of these evolutionary events. At present there is no null model to predict what morphological variation in the Oldowan should look like. Without such a model, quantifying whether Oldowan assemblages vary due to raw material constraints or whether they vary due to differences in production technique is not possible. This research establishes a null model for Oldowan lithic artifact morphological variation. To establish these expectations this research 1) models the expected range of variation through large scale reduction experiments, 2) develops an algorithm to categorize archaeological flakes based on how they are produced, and 3) statistically assesses the methods of production behavior used by Oldowan producing hominins at the site of DK from Olduvai Gorge, Tanzania via the experimental model. Results indicate that a subset of quartzite flakes deviate from the null expectations in a manner that demonstrates efficiency in flake manufacture, while some basalt flakes deviate from null expectations in a manner that demonstrates inefficiency in flake manufacture. The simultaneous presence of efficiency in stone tool production for one raw material (quartzite) and inefficiency in stone tool production for another raw material (basalt) suggests that Oldowan producing hominins at DK were able to mediate the economic costs associated with stone tool

  3. Trichodiene synthase. Identification of active site residues by site-directed mutagenesis.

    PubMed

    Cane, D E; Shim, J H; Xue, Q; Fitzsimons, B C; Hohn, T M

    1995-02-28

    Derivatization of 5,5'-dithiobis(2-nitrobenzoic acid)-treated trichodiene synthase with [methyl-14C]methyl methanethiosulfonate and analysis of the derived tryptic peptides suggested the presence of two cysteine residues at the active site. The corresponding C146A and C190A mutants were constructed by site-directed mutagenesis. The C190A mutant displayed partial but significantly reduced activity, with a reduction in kcat/Km of 3000 compared to the wild-type trichodiene synthase, while the C146A mutant was essentially inactive. A hybrid trichodiene synthase, constructed from amino acids 1-309 of the Fusarium sporotrichioides enzyme and amino acids 310-383 of the Gibberella pulicaris cyclase, had steady state kinetic parameters nearly identical to those of the wild-type F. sporotrichioides enzyme. From this parent hybrid, a series of mutants was constructed by site-directed mutagenesis in which the amino acids in the base-rich region, 302-306 (DRRYR), were systematically modified. Three of these mutants were overexpressed and purified to homogeneity. The importance of Arg304 for catalysis was established by the observation that the R304K mutant showed a more than 25-fold increase in Km, as well as a 200-fold reduction in kcat. In addition, analysis of the incubation products of the R304K mutant by gas chromatography-mass spectrometry (GC-MS) indicated that farnesyl diphosphate was converted not only to trichodiene but to at least two additional C15H24 hydrocarbons, mle 204. Replacement of the Tyr305 residue of trichodiene synthase with Phe had little effect on kcat, while increasing the Km by a factor of ca. 7-8.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7873527

  4. Preliminary small mammal taphonomy of FLK NW level 20 (Olduvai Gorge, Tanzania)

    NASA Astrophysics Data System (ADS)

    Arcos, Saleta; Sevilla, Paloma; Fernández-Jalvo, Yolanda

    2010-11-01

    The Bed-I series of Olduvai Gorge (Tanzania) is a reference site in human evolution, having yielded the holotypes of Paranthropus boisei and Homo habilis, together with manufactured artefacts and abundant large and micro-fauna. Excavations in Olduvai Gorge have been recently resumed, with new aims and new results. This paper presents the results of the taphonomic analysis carried out on a fossil small-mammal assemblage recovered from FLK NW level 20, a layer overlying Tuff C, dated from 1.84 Ma. The analysis provides good evidence of a category 1 predator, most likely a barn owl, as the predator of the bone assemblage. Trampling and sediment compression might influence postdepositional breakage of the bones. This study is especially relevant since previous taphonomic analyses carried out at levels above and below this sample led to inconclusive results due to a low number of fossils ( Fernández-Jalvo et al., 1998). The new sample provides new information to reconstruct the paleoenvironmental context in which early hominins inhabited.

  5. Development and research on the GIS-based landslide prediction system of the Three Gorges area

    NASA Astrophysics Data System (ADS)

    Ge, Qiao; Tang, Zhongshi; Wang, Haiwei

    2008-10-01

    In this paper we discussed the development and research of the GIS-based landslide prediction system of the Three Gorges area. First of all, we systematically revisited the basic issues of the landslide prediction, including the principles of landslide prediction, the division of sliding-time and sliding-deformation stages, prediction parameters selection and monitoring sites selection. In addition to reviewing the landslide prediction models, this paper detailed discussed an improved model which makes an integration of the results of multiple prediction models. On the basis of those landslide prediction models, we developed a GIS-based landslide prediction system by using Visual C#.NET and ESRI ArcObjects components. Finally, this paper selected two typical landslide cases in the Three Gorges area: the Xintan landslide and the Lianzi Cliff dangerous rock body, and used the system to calculate and analyze. It validated the applicability and accuracy of the prediction models, made a test of the practicality of the system, and achieved good results.

  6. Status of two Coreius species in the Three Gorges Reservoir, China

    NASA Astrophysics Data System (ADS)

    Xia, Yuguo; Lloret, J.; Li, Zhongjie; Zhang, Tanglin; Ye, Shaowen; Li, Wei; Yuan, Jing; Perera, H. A. C. C.; Liu, Jiashou

    2016-01-01

    Dam construction alters natural flow regimes which, in turn, cause significant changes in fish communities during and after impoundment. The construction of the Three Gorges Reservoir, from impoundment of the Changjiang (Yangtze) River, China, may have affected native fish species. Thus, the status of two lotic freshwater fish species, Coreius heterodon and C. guichenoti, were monitored in the Three Gorges Reservoir, including fish abundance, individual composition, growth, condition, and mortality. Data on both species were gathered from upstream, midstream and downstream areas of the reservoir and, where available, from studies published before and after dam construction. Lower abundance, slower growth, a less diversified age structure, poorer fish condition (indicated by hepatosomatic index) and higher mortalities were recorded in sites nearest the dam compared with upstream areas. Furthermore, after final impoundment, individual Coreius species inhabiting the area changed, with young individuals becoming more abundant, while upstream of the reservoir the two Coreius species became smaller at a given age. The results show that the status of the two Coreius species was subject to dramatic changes after impoundment.

  7. Distribution and clinical features of Paragonimiasis skrjabini in Three Gorges Reservoir Region.

    PubMed

    Zhang, Xi-lin; Wang, Ying; Wang, Guang-xi; Chen, Wen-bi; He, Xie; Niu, Hui; Li, Zhen-lian; Chen, Lin; Wang, Li-fang

    2012-12-01

    Paragonimiasis has previously been reported in the Southwest Provinces of China, including Chongqing and Sichuan. The construction of Three Gorges Dam, which was begun in 1994, has resulted in substantial changes to the depth and the flow pattern of the Yangtze River. To investigate epidemiology of the paragonimiasis, 724 people aged 2-49 years were selected and examined for Paragonimus infection by intradermal test (IDT), and enzyme-linked immunosorbent assay (ELISA). A survey of eating habits was conducted face-to-face in 5 endemic counties. Freshwater crabs were collected from seven sites in the 5 counties to determine the rate of infection with Paragonimus metacercariae. Additionally, we analyzed 213 case reports from the region dated 2006 to 2009. According to the survey results, the prevalence of Paragonimus skrjabini infection in freshwater crab was 39.65%, and the human infection rates detected by IDT and ELISA were 14.36% (104/724) and 7.46% (54/724), respectively. These results show that the Three Gorges Reservoir is still an area of high paragonimiasis endemicity. The water level of the Yangtze River has risen to 175 m, and the area of water coverage in the region has increased to 1084 km(2). These conditions will favor the growth and expansion of the freshwater crab population.

  8. Distribution and clinical features of Paragonimiasis skrjabini in Three Gorges Reservoir Region.

    PubMed

    Zhang, Xi-lin; Wang, Ying; Wang, Guang-xi; Chen, Wen-bi; He, Xie; Niu, Hui; Li, Zhen-lian; Chen, Lin; Wang, Li-fang

    2012-12-01

    Paragonimiasis has previously been reported in the Southwest Provinces of China, including Chongqing and Sichuan. The construction of Three Gorges Dam, which was begun in 1994, has resulted in substantial changes to the depth and the flow pattern of the Yangtze River. To investigate epidemiology of the paragonimiasis, 724 people aged 2-49 years were selected and examined for Paragonimus infection by intradermal test (IDT), and enzyme-linked immunosorbent assay (ELISA). A survey of eating habits was conducted face-to-face in 5 endemic counties. Freshwater crabs were collected from seven sites in the 5 counties to determine the rate of infection with Paragonimus metacercariae. Additionally, we analyzed 213 case reports from the region dated 2006 to 2009. According to the survey results, the prevalence of Paragonimus skrjabini infection in freshwater crab was 39.65%, and the human infection rates detected by IDT and ELISA were 14.36% (104/724) and 7.46% (54/724), respectively. These results show that the Three Gorges Reservoir is still an area of high paragonimiasis endemicity. The water level of the Yangtze River has risen to 175 m, and the area of water coverage in the region has increased to 1084 km(2). These conditions will favor the growth and expansion of the freshwater crab population. PMID:22814214

  9. The copper active site of CBM33 polysaccharide oxygenases.

    PubMed

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

    2013-04-24

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

  10. Activation of muscarinic acetylcholine receptors via their allosteric binding sites.

    PubMed Central

    Jakubík, J; Bacáková, L; Lisá, V; el-Fakahany, E E; Tucek, S

    1996-01-01

    Ligands that bind to the allosteric-binding sites on muscarinic acetylcholine receptors alter the conformation of the classical-binding sites of these receptors and either diminish or increase their affinity for muscarinic agonists and classical antagonists. It is not known whether the resulting conformational change also affects the interaction between the receptors and the G proteins. We have now found that the muscarinic receptor allosteric modulators alcuronium, gallamine, and strychnine (acting in the absence of an agonist) alter the synthesis of cAMP in Chinese hamster ovary (CHO) cells expressing the M2 or the M4 subtype of muscarinic receptors in the same direction as the agonist carbachol. In addition, most of their effects on the production of inositol phosphates in CHO cells expressing the M1 or the M3 muscarinic receptor subtypes are also similar to (although much weaker than) those of carbachol. The agonist-like effects of the allosteric modulators are not observed in CHO cells that have not been transfected with the gene for any of the subtypes of muscarinic receptors. The effects of alcuronium on the formation of cAMP and inositol phosphates are not prevented by the classical muscarinic antagonist quinuclidinyl benzilate. These observations demonstrate for the first time that the G protein-mediated functional responses of muscarinic receptors can be evoked not only from their classical, but also from their allosteric, binding sites. This represents a new mechanism of receptor activation. PMID:8710935

  11. Radiation inactivation study of aminopeptidase: probing the active site

    NASA Astrophysics Data System (ADS)

    Jamadar, V. K.; Jamdar, S. N.; Mohan, Hari; Dandekar, S. P.; Harikumar, P.

    2004-04-01

    Ionizing radiation inactivated purified chicken intestinal aminopeptidase in media saturated with gases in the order N 2O>N 2>air. The D 37 values in the above conditions were 281, 210 and 198 Gy, respectively. OH radical scavengers such as t-butanol and isopropanol effectively nullified the radiation-induced damage in N 2O. The radicals (SCN) 2•-, Br 2•- and I 2•- inactivated the enzyme, pointing to the involvement of aromatic amino acids and cysteine in its catalytic activity. The enzyme exhibited fluorescence emission at 340 nm which is characteristic of tryptophan. The radiation-induced loss of activity was accompanied by a decrease in the fluorescence of the enzyme suggesting a predominant influence on tryptophan residues. The enzyme inhibition was associated with a marked increase in the Km and a decrease in the Vmax and kcat values, suggesting an irreversible alteration in the catalytic site. The above observations were confirmed by pulse radiolysis studies.

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

    PubMed

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

    2015-07-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  14. 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

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

    PubMed Central

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

    2008-01-01

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

  16. An active-site lysine in avian liver phosphoenolpyruvate carboxykinase

    SciTech Connect

    Guidinger, P.F.; Nowak, T. )

    1991-09-10

    The participation of lysine in the catalysis by avian liver phosphoenolpyruvate carboxykinase was studied by chemical modification and by a characterization of the modified enzyme. The rate of inactivation by 2,4-pentanedione is pseudo-first-order and linearly dependent on reagent concentration with a second-order rate constant of 0.36 {plus minus} 0.025 M{sup {minus}1} min{sup {minus}1}. Inactivation by pyridoxal 5{prime}-phosphate of the reversible reaction catalyzed by phosphoenolpyruvate carboxykinase follows bimolecular kinetics with a second-order rate constant of 7,700 {plus minus} 860 m{sup {minus}1} min{sup {minus}1}. Treatment of the enzyme or one lysine residue modified concomitant with 100% loss in activity. A stoichiometry of 1:1 is observed when either the reversible or the irreversible reactions catalyzed by the enzyme are monitored. A study of k{sub obs} vs pH suggests this active-site lysine has a pK{sub a} of 8.1 and a pH-independent rate constant of inactivation of 47,700 m{sup {minus}1} min{sup {minus}1}. Proton relaxation rate measurements suggest that pyridoxal 5{prime}-phosphate modification alters binding of the phosphate-containing substrates. {sup 31}P NMR relaxation rate measurements show altered binding of the substrates in the ternary enzyme {center dot}Mn{sup 2+}{center dot}substrate complex. Circular dichroism studies show little change in secondary structure of pyridoxal 5{prime}-phosphate modified phosphoenolpyruvate carboxykinase. These results indicate that avian liver phosphoenolpyruvate carboxykinase has one reactive lysine at the active site and it is involved in the binding and activation of the phosphate-containing substrates.

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

    PubMed

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

    2016-04-22

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

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

    SciTech Connect

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

    1986-03-01

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

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

    PubMed

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

    2016-04-22

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

  20. 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.

  1. 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.

  2. 3. RUSTIC BENCH AT THE LADDER CREEK GARDENS NEAR GORGE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. RUSTIC BENCH AT THE LADDER CREEK GARDENS NEAR GORGE POWERHOUSE AT NEWHALEM. J.D. ROSS HAD THE GROUNDS LANDSCAPED AND PLANTED WITH EXOTIC FLOWERS AND VEGETATION DURING THE 1930S AS AN ADDITIONAL TOURIST ATTRACTION, 1989. - Skagit Power Development, Skagit River & Newhalem Creek Hydroelectric Project, On Skagit River, Newhalem, Whatcom County, WA

  3. 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.

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

    PubMed Central

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

    2015-01-01

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

  5. Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426.

    PubMed

    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.

  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. Changes in monthly flows in the Yangtze River, China - With special reference to the Three Gorges Dam

    NASA Astrophysics Data System (ADS)

    Chen, Jing; Finlayson, Brian L.; Wei, Taoyuan; Sun, Qianli; Webber, Michael; Li, Maotian; Chen, Zhongyuan

    2016-05-01

    Much has been written on the hydrology of the Yangtze River in China, especially since the construction of the Three Gorges Dam. Given the range of views in the literature on the impacts of dams and other natural and anthropogenic activities in the catchment on monthly flows, we here set out to analyse the behavior of monthly flows over the period of record 1955-2014. In the literature, the Three Gorges dam has been singled out for particular comment, mostly adverse. In this paper we analyse trend in temperature, precipitation and discharge of the Yangtze River at the monthly time scale over a period that includes the 11 years since the Three Gorges Dam came into operation. The results show that for the upper basin, there has been a marked increase in discharge in the low flow months of January to March that began abruptly in 2003 and an abrupt decrease in flow in October at the same time. Similar changes are found for discharge from the lower basin but in that case the changes have occurred gradually over the period of record. These changes are the outcome of the operation of hydroelectric and flood control dams that have been built continuously in the lower basin since 1955 while in the upper basin the building of the Three Gorges Dam began a phase of rapid dam building not seen in the lower basin. The decreased flows in the late summer and autumn are not of sufficient magnitude to cause any problems for navigation or water supply. The enhanced flows in the winter low flow period are beneficial in that they reduce the likelihood of salt water intrusions in the estuary adversely affecting the supply of freshwater to Shanghai.

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  10. Occurrence of organotin compounds in river sediments under the dynamic water level conditions in the Three Gorges Reservoir Area, China.

    PubMed

    Gao, Jun-Min; Zhang, Ke; Chen, You-Peng; Guo, Jin-Song; Wei, Yun-Mei; Jiang, Wen-Chao; Zhou, Bin; Qiu, Hui

    2015-06-01

    The Three Gorges Project is the largest hydro project in the world, and the water level of the Three Gorges Reservoir (TGR) is dynamic and adjustable with the aim of flood control and electrical power generation. It is necessary to investigate the pollutants and their underlying contamination processes under dynamic water levels to determine their environmental behaviors in the Three Gorges Reservoir Area (TGRA). Here, we report the assessment of organotin compounds (OTs) pollution in the river sediments of the TGRA. Surface sediment samples were collected in the TGRA at low and high water levels. Tributyltin (TBT), triphenyltin (TPhT), and their degradation products in sediments were quantified by gas chromatography-mass spectrometry. Butyltins (BTs) and phenyltins (PhTs) were detected in sediments, and BTs predominated over PhTs in the whole study area under dynamic water level conditions. The concentrations of OTs in sediments varied markedly among locations, and significant concentrations were found in river areas with high levels of boat traffic and wastewater discharge. Sediments at all stations except Cuntan were lightly contaminated with TBT, and total organic carbon (TOC) was a significant factor affecting the fate of TBT in the TGRA. The butyltin and phenyltin degradation indices showed no recent inputs of TBT or TPhT into this region, with the exception of fresh TPhT input at Xiakou Town. Shipping activity, wastewater discharge, and agriculture are the most likely sources of OTs in the TGRA. PMID:25537288

  11. The Study on S-Wave Velocity Structure of Upper Crust in Three Gorges Region of Yangtze River

    NASA Astrophysics Data System (ADS)

    Li, X.; Zhu, P.; Zhou, Q.

    2014-12-01

    The profile of S-wave velocity structure along Badong-Maoping-Tumen is presented using the ambient noise data observed at 10 stations from mobile broadband seismic array which is located at Three Gorges Region. All of available vertical component time series during April and May,2011 have been cross-correlated to estimate the empirical Green functions. Group velocity dispersion curves were measured by applying multiple filtering technique. Using these dispersion curves,we obtain high resolution pure-path dispersions at 0.5-10 second periods. The S-wave velocity structure,which was reconstructed by inverting the pure-path dispersions,reveals the velocity variations of upper crust at Three Gorges Region. Main conclusions are as follows:(1)The velocity variations in the study region have a close relationship with the geological structure and the velocity profile suggests a anticline unit which core area is Huangling block;(2)The relative fast velocity variations beneath Jiuwanxi and its surrounding areas may correspond to the geological structure and earthquake activity there;(3) The high velocity of the upper crustal in Sandouping indicates that the Reservoir Dam of Three Gorges is located at a tectonic stable region.

  12. Metals in the active site of native protein phosphatase-1.

    PubMed

    Heroes, Ewald; Rip, Jens; Beullens, Monique; Van Meervelt, Luc; De Gendt, Stefan; Bollen, Mathieu

    2015-08-01

    Protein phosphatase-1 (PP1) is a major protein Ser/Thr phosphatase in eukaryotic cells. Its activity depends on two metal ions in the catalytic site, which were identified as manganese in the bacterially expressed phosphatase. However, the identity of the metal ions in native PP1 is unknown. In this study, total reflection X-ray fluorescence (TXRF) was used to detect iron and zinc in PP1 that was purified from rabbit skeletal muscle. Metal exchange experiments confirmed that the distinct substrate specificity of recombinant and native PP1 is determined by the nature of their associated metals. We also found that the iron level associated with native PP1 is decreased by incubation with inhibitor-2, consistent with a function of inhibitor-2 as a PP1 chaperone. PMID:25890482

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

    PubMed

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

    2012-09-01

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

  14. Zymogen Activation and Subcellular Activity of Subtilisin Kexin Isozyme 1/Site 1 Protease*

    PubMed Central

    da Palma, Joel Ramos; Burri, Dominique Julien; Oppliger, Joël; Salamina, Marco; Cendron, Laura; de Laureto, Patrizia Polverino; Seidah, Nabil Georges; Kunz, Stefan; Pasquato, Antonella

    2014-01-01

    The proprotein convertase subtilisin kexin isozyme 1 (SKI-1)/site 1 protease (S1P) plays crucial roles in cellular homeostatic functions and is hijacked by pathogenic viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P involves sequential autocatalytic processing of its N-terminal prodomain at sites B′/B followed by the herein newly identified C′/C sites. We found that SKI-1/S1P autoprocessing results in intermediates whose catalytic domain remains associated with prodomain fragments of different lengths. In contrast to other zymogen proprotein convertases, all incompletely matured intermediates of SKI-1/S1P showed full catalytic activity toward cellular substrates, whereas optimal cleavage of viral glycoproteins depended on B′/B processing. Incompletely matured forms of SKI-1/S1P further process cellular and viral substrates in distinct subcellular compartments. Using a cell-based sensor for SKI-1/S1P activity, we found that 9 amino acid residues at the cleavage site (P1–P8) and P1′ are necessary and sufficient to define the subcellular location of processing and to determine to what extent processing of a substrate depends on SKI-1/S1P maturation. In sum, our study reveals novel and unexpected features of SKI-1/S1P zymogen activation and subcellular specificity of activity toward cellular and pathogen-derived substrates. PMID:25378398

  15. Inner gorges cut by subglacial meltwater during Fennoscandian ice sheet decay.

    PubMed

    Jansen, J D; Codilean, A T; Stroeven, A P; Fabel, D; Hättestrand, C; Kleman, J; Harbor, J M; Heyman, J; Kubik, P W; Xu, S

    2014-05-09

    The century-long debate over the origins of inner gorges that were repeatedly covered by Quaternary glaciers hinges upon whether the gorges are fluvial forms eroded by subaerial rivers, or subglacial forms cut beneath ice. Here we apply cosmogenic nuclide exposure dating to seven inner gorges along ~500 km of the former Fennoscandian ice sheet margin in combination with a new deglaciation map. We show that the timing of exposure matches the advent of ice-free conditions, strongly suggesting that gorges were cut by channelized subglacial meltwater while simultaneously being shielded from cosmic rays by overlying ice. Given the exceptional hydraulic efficiency required for meltwater channels to erode bedrock and evacuate debris, we deduce that inner gorges are the product of ice sheets undergoing intense surface melting. The lack of postglacial river erosion in our seven gorges implicates subglacial meltwater as a key driver of valley deepening on the Baltic Shield over multiple glacial cycles.

  16. Environmental impact assessments of the Three Gorges Project in China: Issues and interventions

    NASA Astrophysics Data System (ADS)

    Xu, Xibao; Tan, Yan; Yang, Guishan

    2013-09-01

    The paper takes China's authoritative Environmental Impact Statement for the Yangzi (Yangtze) Three Gorges Project (TGP) in 1992 as a benchmark against which to evaluate emerging major environmental outcomes since the initial impoundment of the Three Gorges reservoir in 2003. The paper particularly examines five crucial environmental aspects and associated causal factors. The five domains include human resettlement and the carrying capacity of local environments (especially land), water quality, reservoir sedimentation and downstream riverbed erosion, soil erosion, and seismic activity and geological hazards. Lessons from the environmental impact assessments of the TGP are: (1) hydro project planning needs to take place at a broader scale, and a strategic environmental assessment at a broader scale is necessary in advance of individual environmental impact assessments; (2) national policy and planning adjustments need to react quickly to the impact changes of large projects; (3) long-term environmental monitoring systems and joint operations with other large projects in the upstream areas of a river basin should be established, and the cross-impacts of climate change on projects and possible impacts of projects on regional or local climate considered.

  17. Tomographic study of the velocity structure of the Three Gorges region, China

    NASA Astrophysics Data System (ADS)

    Zou, Z.; Gurrola, H.

    2013-12-01

    The Three Gorges (TG) located to the northern part of the Yangtze Craton. The crustal structure and tectonic history of TG region drew significant attention after the construction of the Three Gorges Dam. Since then many geophysical and geological surveys have been conducted in TG region to investigate the crustal structure. These surveys provided in-depth understanding of the distribution of general geologic features such as basin, faults, and crust-mantle interface. However, the detailed information, such as the depth of basins, dipping of faults, and the topography of the Moho, is still controversial. From 2008 to 2011, we deployed temporary networks in TG region each summer. A number of local and teleseismic events were recorded. Here we use the local small earthquakes to estimate the velocity structure of TGR region through multiscale tomography. The detailed basin structures and locations of faults are identified by comparing the resolved velocity model with the geologic map and the seismic reflection images. As part of this project we will be testing efficiency of different 2-D tomography methods to determine the relative effectiveness of each. One will use cells of constant velocity the other will have velocities at nodal point and assume continuously varying velocities as all positions. Continuing study based on the results of this paper may reveal more detail of the tectonic activity of TG region in geologic history.

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

    PubMed

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

    2015-05-01

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

  19. Controls of the Xiannvshan Fault on landslides and Reservoir induced earthquakes located at head area of the Three Gorges Reservoir

    NASA Astrophysics Data System (ADS)

    Shimei, Wang; Yeming, Zhang

    2015-04-01

    Landslides and reservoir induced earthquakes are two main types of geological disasters, which have serious influence on the Three Gorges Project. The Xiannvshan Fault is ten kilometers away from the Three Gorges Dam, and it has important control on landslides and earthquakes located at head area of the Three Gorges Reservoir. Data collected show that: (1) the fault stretch runs in northwest-west orientation with a total length of more than 80 kilometers, it north endpoint extends to the Yangtze River and Jiuwanxi Fault is one of its branches. The Xiannvshan Fault has a high level of activity with the average annual decline of 0.076mm in the west wall and the dextral sliding of 0.116mm. (2) Controls on landslides resulted from the Xiannvshan Fault lie in two aspects. One is a large of landslide accumulation bodies resulted from two collapse events, which are corresponded to the two intense faulting. The other is that the Xintan landslide occurred in 1982, which is resulted from the stress accumulation of the fault. (3) The Xiannvshan Fault is active. Three big earthquakes had been induced by the fault from 1959 to the time of impounding, of which one occurred at its southern endpoint, Panjiawan of Yidu, and was magnitude 5, one occurred at its northern section, Zhou Ping, and was magnitude 3.3, and another occurred at Huilongguan of Zigui with a magnitude 5.1. Earthquakes have been happening more frequently after the impoundment of the Three Gorges Reservoir or on the high water level than before. More than 40 earthquakes with magnitudes bigger than 3.3 were recorded after the impoundment, of which 4 ranged from 4.1 to 5.1 and occurred when the high water level was decreasing. Otherwise, most earthquakes centered on the northern endpoint of the fault, which indicates a characteristics of tectonic reservoir earthquake. This study, for the three gorges reservoir area landslide and seismic reservoir prediction is of great significance.

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

    PubMed

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

    2015-02-24

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

  1. Simulation of spatial and temporal distributions of non-point source pollution load in the Three Gorges Reservoir Region.

    PubMed

    Shen, Zhenyao; Qiu, Jiali; Hong, Qian; Chen, Lei

    2014-09-15

    Non-point source (NPS) pollution has become the largest threat to water quality in recent years. Major pollutants, particularly from agricultural activities, which include nitrogen, phosphorus and sediment that have been released into aquatic environments, have caused a range of problems in the Three Gorges Reservoir Region (TGRR), China. It is necessary to identify the spatial and temporal distributions of NPS pollutants and the highly polluted areas for the purpose of watershed management. In this study, the NPS pollutant load was simulated using the Soil and Water Assessment Tool (SWAT) and the small-scale watershed extended method (SWEM). The simulation results for four typical small catchments were extended to the entire watershed leading to estimates of the NPS load from 2001 to 2009. The results demonstrated that the NPS pollution load in the western area was the highest and that agricultural land was the primary pollutant source. The similar annual variation trends of runoff and sediment loads demonstrated that the sediment load was closely related to runoff. The loads of total nitrogen (TN) and total phosphorus (TP) were relatively stable from 2001 to 2007, except for high loads in 2006. The increase in pollution source strength was an important reason for the significant upward trend of TN and TP loads from 2008 to 2009. The rainfall from April to October contributed to the largest amount of runoff, sediment and nutrient loads for the year. The NPS load intensities in each sub-basin reveal large variations in the spatial distribution of different pollutants. It was shown that the temporal and spatial distributions of pollutant loads were positively correlated with the annual rainfall amounts and with human activities. Furthermore, this finding illustrates that conservation practices and nutrient management should be implemented in specific sites during special periods for the purpose of NPS pollution control in the TGRR.

  2. Water exposure assessment of aryl hydrocarbon receptor agonists in Three Gorges Reservoir, China using SPMD-based virtual organisms.

    PubMed

    Wang, Jingxian; Bernhöft, Silke; Pfister, Gerd; Schramm, Karl-Werner

    2014-10-15

    SPMD-based virtual organisms (VOs) were deployed at five to eight sites in the Three Gorges Reservoir (TGR), China for five periods in 2008, 2009 and 2011. The water exposure of aryl hydrocarbon receptor (AhR) agonists was assessed by the VOs. The chosen bioassay response for the extracts of the VOs, the induction of 7-ethoxyresorufin-O-deethylase (EROD) was assayed using a rat hepatoma cell line (H4IIE). The results show that the extracts from the VOs could induce AhR activity significantly, whereas the chemically derived 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) equivalent (TEQcal) accounted for <11% of the observed AhR responses (TEQbio). Unidentified AhR-active compounds represented a greater proportion of the TCDD equivalent in VOs from TGR. High TEQbio value in diluted extract and low TEQbio in concentrated extract of the same sample was observed suggesting potential non-additive effects in the mixture. The levels of AhR agonists in VOs from upstream TGR were in general higher than those from downstream reservoir, indicating urbanization effect on AhR agonist pollution. The temporal variation showed that levels of AhR agonists in 2009 and 2011 were higher than those in 2008, and the potential non-additive effects in the area close to the dam were also obviously higher in 2009 and 2011 than in 2008, indicating big changes in the composition of pollutants in the area after water level reached a maximum of 175 m. Although the aqueous concentration of AhR agonists of 0.8-4.8 pg TCDDL(-1) in TGR was not alarming, the tendency of accumulating high concentration of AhR agonists in VO lipid and existence of possible synergism or antagonism in the water may exhibit a potential hazard to local biota being exposed to AhR agonists.

  3. Water exposure assessment of aryl hydrocarbon receptor agonists in Three Gorges Reservoir, China using SPMD-based virtual organisms.

    PubMed

    Wang, Jingxian; Bernhöft, Silke; Pfister, Gerd; Schramm, Karl-Werner

    2014-10-15

    SPMD-based virtual organisms (VOs) were deployed at five to eight sites in the Three Gorges Reservoir (TGR), China for five periods in 2008, 2009 and 2011. The water exposure of aryl hydrocarbon receptor (AhR) agonists was assessed by the VOs. The chosen bioassay response for the extracts of the VOs, the induction of 7-ethoxyresorufin-O-deethylase (EROD) was assayed using a rat hepatoma cell line (H4IIE). The results show that the extracts from the VOs could induce AhR activity significantly, whereas the chemically derived 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) equivalent (TEQcal) accounted for <11% of the observed AhR responses (TEQbio). Unidentified AhR-active compounds represented a greater proportion of the TCDD equivalent in VOs from TGR. High TEQbio value in diluted extract and low TEQbio in concentrated extract of the same sample was observed suggesting potential non-additive effects in the mixture. The levels of AhR agonists in VOs from upstream TGR were in general higher than those from downstream reservoir, indicating urbanization effect on AhR agonist pollution. The temporal variation showed that levels of AhR agonists in 2009 and 2011 were higher than those in 2008, and the potential non-additive effects in the area close to the dam were also obviously higher in 2009 and 2011 than in 2008, indicating big changes in the composition of pollutants in the area after water level reached a maximum of 175 m. Although the aqueous concentration of AhR agonists of 0.8-4.8 pg TCDDL(-1) in TGR was not alarming, the tendency of accumulating high concentration of AhR agonists in VO lipid and existence of possible synergism or antagonism in the water may exhibit a potential hazard to local biota being exposed to AhR agonists. PMID:25058931

  4. Portland, Mount Hood, & Columbia River Gorge, Oregon, Perspective View

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Portland, the largest city in Oregon, is located on the Columbia River at the northern end of the Willamette Valley. On clear days, Mount Hood highlights the Cascade Mountains backdrop to the east. The Columbia is the largest river in the American Northwest and is navigable up to and well beyond Portland. It is also the only river to fully cross the Cascade Range, and has carved the Columbia River Gorge, which is seen in the left-central part of this view. A series of dams along the river, at topographically favorable sites, provide substantial hydroelectric power to the region.

    This perspective view was generated using topographic data from the Shuttle Radar Topography Mission (SRTM), a Landsat satellite image, and a false sky. Topographic expression is vertically exaggerated two times.

    Landsat has been providing visible and infrared views of the Earth since 1972. SRTM elevation data substantially help in analyzing Landsat images by revealing the third dimension of Earth's surface, topographic height. The Landsat archive is managed by the U.S. Geological Survey's Eros Data Center (USGS EDC).

    Elevation data used in this image were acquired by the Shuttle Radar Topography Mission (SRTM) aboard the Space Shuttle Endeavour, launched on February 11, 2000. SRTM used the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) that flew twice on the Space Shuttle Endeavour in 1994. SRTM was designed to collect three-dimensional measurements of the Earth's surface. To collect the 3-D data, engineers added a 60-meter-long (200-foot) mast, installed additional C-band and X-band antennas, and improved tracking and navigation devices. The mission is a cooperative project between the National Aeronautics and Space Administration (NASA), the National Geospatial-Intelligence Agency (NGA) of the U.S. Department of Defense (DoD), and the German and Italian space agencies. It is managed by NASA's Jet

  5. Spatial bedrock erosion distribution in a natural gorge

    NASA Astrophysics Data System (ADS)

    Beer, A. R.; Turowski, J. M.; Kirchner, J. W.

    2015-12-01

    Quantitative analysis of morphological evolution both in terrestrial and planetary landscapes is of increasing interest in the geosciences. In mountainous regions, bedrock channel formation as a consequence of the interaction of uplift and erosion processes is fundamental for the entire surface evolution. Hence, the accurate description of bedrock channel development is important for landscape modelling. To verify existing concepts developed in the lab and to analyse how in situ channel erosion rates depend on the interrelations of discharge, sediment transport and topography, there is a need of highly resolved topographic field data. We analyse bedrock erosion over two years in a bedrock gorge downstream of the Gorner glacier above the town of Zermatt, Switzerland. At the study site, the Gornera stream cuts through a roche moutonnée in serpentine rock of 25m length, 5m width and 8m depth. We surveyed bedrock erosion rates using repeat terrestrial laser scanning (TLS) with an average point spacing of 5mm. Bedrock erosion rates in direction of the individual surface normals were studied directly on the scanned point clouds applying the M3C2 algorithm (Lague et al., 2013, ISPRS). The surveyed erosion patterns were compared to a simple stream erosivity visualisation obtained from painted bedrock sections at the study location. Spatially distributed erosion rates on bedrock surfaces based on millions of scan points allow deduction of millimeter-scale mean annual values of lateral erosion, incision and downstream erosion on protruding streambed surfaces. The erosion rate on a specific surface point is shown to depend on the position of this surface point in the channel's cross section, its height above the streambed and its spatial orientation to the streamflow. Abrasion by impacting bedload was likely the spatially dominant erosion process, as confirmed by the observed patterns along the painted bedrock sections. However, a single plucking event accounted for the half

  6. Olduvai Gorge, Shaded Relief and Colored Height

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Three striking and important areas of Tanzania in eastern Africa are shown in this color-coded shaded relief image from the Shuttle Radar Topography Mission. The largest circular feature in the center right is the caldera, or central crater, of the extinct volcano Ngorongoro. It is surrounded by a number of smaller volcanoes, all associated with the Great Rift Valley, a geologic fault system that extends for about 4,830 kilometers (2,995 miles) from Syria to central Mozambique.

    Ngorongoro's caldera is 22.5 kilometers (14 miles) across at its widest point and is 610 meters (2,000 feet) deep. Its floor is very level, holding a lake fed by streams running down the caldera wall. It is part of the Ngorongoro Conservation Area and is home to over 75,000 animals. The lakes south of the crater are Lake Eyasi and Lake Manyara, also part of the conservation area.

    The relatively smooth region in the upper left of the image is the Serengeti National Park, the largest in Tanzania. The park encompasses the main part of the Serengeti ecosystem, supporting the greatest remaining concentration of plains game in Africa including more than 3,000,000 large mammals. The animals roam the park freely and in the spectacular migrations, huge herds of wild animals move to other areas of the park in search of greener grazing grounds (requiring over 4,000 tons of grass each day) and water.

    The faint, nearly horizontal line near the center of the image is Olduvai Gorge, made famous by the discovery of remains of the earliest humans to exist. Between 1.9 and 1.2 million years ago a salt lake occupied this area, followed by the appearance of fresh water streams and small ponds. Exposed deposits show rich fossil fauna, many hominid remains and items belonging to one of the oldest stone tool technologies, called Olduwan. The time span of the objects recovered dates from 2,100,000 to 15,000 years ago.

    Two visualization methods were combined to produce the image: shading and

  7. Characterization of the active site of chloroperoxidase using physical techniques

    SciTech Connect

    Hall, K.S.

    1986-01-01

    Chloroperoxidase (CPO) and Cytochrome P-450, two very different hemeproteins, have been shown to have similar active sites by several techniques. Recent work has demonstrated thiolate ligation from a cysteine residue to the iron in P-450. A major portion of this research has been devoted to obtaining direct evidence that CPO also has a thiolate 5th ligand from a cysteine residue. This information will provide the framework for a detailed analysis of the structure-function relationships between peroxidases, catalase and cytochrome P-450 hemeproteins. To determine whether the 5th ligand is a cysteine, methionine or a unique amino acid, specific isotope enrichment experiments were used. Preliminary /sup 1/H-NMR studies show that the carbon monoxide-CPO complex has a peak in the upfield region corresponding to alpha-protons of a thiolate amino acid. C. fumago was grown on 95% D/sub 2/O media with a small amount of /sup 1/H-cysteine added. Under these conditions C. fumago slows down the biosynthesis of cysteine by at least 50% and utilizes the exogenous cysteine in the media. GC-MS was able to show that the methylene protons next to the sulfur atom in cysteine are 80-90% protonated while these positions in methionine are approximately 73% deuterated. Comparison of the /sup 1/H-NMR spectra of CO-CPO and CO-CPO indicate the presence of a cysteine ligand in chloroperoxidase.

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

    PubMed Central

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

    2015-01-01

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

  9. 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.

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

    PubMed

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

    2016-01-01

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

  11. Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

    PubMed

    Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

    2016-09-01

    A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

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

    PubMed

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

    2014-06-01

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

  13. Ecology. Three-Gorges Dam--experiment in habitat fragmentation?

    PubMed

    Wu, Jianguo; Huang, Jianhui; Han, Xingguo; Xie, Zongqiang; Gao, Xianming

    2003-05-23

    Habitat fragmentation is the primary cause of the loss of biodiversity and ecosystem services, but its underlying processes and mechanisms remain poorly understood. Studies of islands and insular terrestrial habitats are essential for improving our understanding of habitat fragmentation. We argue that the Three-Gorges Dam, the largest that humans have ever created, presents a unique grand-scale natural experiment that allows ecologists to address a range of critical questions concerning the theory and practice of biodiversity conservation.

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. The influence of the impoundment of Three Gorges Reservoir on the M5.1 Badong earthquake

    NASA Astrophysics Data System (ADS)

    Cheng, Huihong; Zhang, Huai; Shi, Yaolin

    2014-05-01

    The Three Gorges Reservoir constructed on Yangzi River is the world's largest power station on installed capacity (39.3×109m3), it extends 660km from the western part of Hubei province and eastern part of Chongqing municipality. It is a major concern if it can trigger reservoir earthquakes. After the impoundment of the Three Gorges Reservoir since 7 June 2003, there were many micro-earthquakes in the head segment of the reservoir area including Badong area. The prior researches had suggested the micro-seismic activity will be weak as time goes on, even disappear, and the maximum magnitude of earthquake triggered by the reservoir should not be more than M5.5. However, ten year later, a moderate M5.1 earthquake happened around BaDong Country on 16 December 2013, after the annual highest water level. The epicenter was about 5.5km away from the Yangzi River and nearly 100km from the Three Gorges Reservoir dam. The focal depth of this earthquake was about 5km and the focal mechanism solutions show the NNW-striking thrust seismogenic fault (www.ceic.ac.cn). So, if this earthquake was related to the impoundment of the Three Gorges Reservoir? Would this pose an important impact on the earthquake triggered by the Three Gorges Reservoir? In order to quantitatively analyze these considerations, a three-dimensional fully coupled poroelastic finite element model is proposed in this study by taking the consideration of the realistic observation data, such as the high resolution topography, water level fluctuation, flood zone boundary and water depth variation, fault parameters and etc. The change of Coulomb Failure Stress (ΔCFS) in correspondence to elastic stress and pore pressure change induced by fluid diffusion is calculated. Meanwhile, the elastic strain energy accumulation in reservoir region due to the water-filling load is obtained. Our primary results indicate that both pore pressure and coulomb stress on the hypocenter gradually increases with the respect of time

  20. 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.

  1. Control of active sites in selective flocculation: III -- Mechanism of site blocking

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    It has been shown in Parts I and II of this paper that heteroflocculation can be controlled by poisoning the sites for flocculant adsorption using a site blocking agent (SBA). An efficient SBA was determined to be the lower molecular weight fraction of the flocculant. In this paper, the underlying mechanism of SBA action is described. Also, the mathematical model detailed in Part I is used to determine the effect of different SBAs on apatite-dolomite separation efficiency. It has been demonstrated that the depression in flocculation is directly related to the site blocking parameter ([bar [Phi

  2. Rainfall-Runoff and Erosion Data from the Mancos Shale Formation in the Gunnison Gorge National Conservation Area, Southwestern Colorado, 2003-2006

    USGS Publications Warehouse

    Elliott, John G.; Herring, James R.; Ingersoll, George P.; Kosovich, John J.; Fahy, Juli

    2008-01-01

    Data were collected and experiments were conducted from 2003 to 2006 by the U.S. Geological Survey, in cooperation with the Bureau of Land Management, to support research into understanding processes that liberate, disperse, and concentrate erosion byproducts in Mancos Shale landscapes. The study area was the Gunnison Gorge National Conservation Area near Montrose and Delta, Colorado. This report includes data collected from 24, small-plot, rainfall-runoff simulations, 6 hillslope-erosion monitoring plots, 20 hillslope-creep monitoring sites, and 3 precipitation gages. Small-plot rainfall-runoff simulations were performed on paired (undisturbed and disturbed) plots to examine the effect of off-highway vehicle use on runoff and erosion. These data were collected in conjunction with several other studies done by the U.S. Geological Survey in the Gunnison Gorge National Conservation Area. Data collected in companion studies are published in separate open-file reports.

  3. Paleoenvironmental reconstruction of a paleosol catena, the Zinj archeological level, Olduvai Gorge, Tanzania

    NASA Astrophysics Data System (ADS)

    Driese, Steven G.; Ashley, Gail M.

    2016-01-01

    Paleosols record paleoclimatic processes in the Earth's Critical Zone and are archives of ancient landscapes associated with archeological sites. Detailed field, micromorphologic, and bulk geochemical analysis of paleosols were conducted near four sites at Olduvai Gorge, Tanzania within the same stratigraphic horizon as the Zinjanthropus (Paranthropus) boisei archeological site. Paleosols are thin (< 35 cm), smectitic, and exhibit Vertisol shrink-swell features. Traced across the paleolandscape over 1 km and just beneath Tuff IC (1.845 Ma), the paleosols record a paleocatena in which soil moisture at the four sites was supplemented by seepage additions from adjacent springs, and soil development was enhanced by this additional moisture. Field evidence revealed an abrupt lateral transition in paleosol composition at the PTK site (< 1.5 m apart) in which paleosol B, formed nearest the spring system, is highly siliceous, vs. paleosol A, formed in smectitic clay. Thin-section investigations combined with mass-balance geochemistry, using Chapati Tuff as parent material and assuming immobile Ti, show moderately intense weathering. Pedotransfer functions indicate a fertile soil system, but sodicity may have limited some plant growth. Paleosol bulk geochemical proxies used to estimate paleoprecipitation (733-944 mm/yr), are higher than published estimates of 250-700 mm/yr using δD values of lipid biomarkers.

  4. 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.

  5. 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

  6. Monoclonal antibody against the active site of caeruloplasmin and the ELISA system detecting active caeruloplasmin.

    PubMed

    Hiyamuta, S; Ito, K

    1994-04-01

    Serum caeruloplasmin deficiency is a characteristic biochemical abnormality found in patients with Wilson's disease, but the mechanism of this disease is unknown. Although the phenylenediamine oxidase activity of serum caeruloplasmin is markedly low in patients with Wilson's disease, mRNA of caeruloplasmin exists to some extent. To investigate the deficiency of caeruloplasmin oxidase activity in Wilson's disease, we generated 14 monoclonal antibodies (MAbs) and selected ID1, which had the strongest reactivity, and ID2, which had neutralizing ability. We also established a system to measure active caeruloplasmin specifically using these MAbs. These MAbs and the system will be useful tools in analyzing the active site of caeruloplasmin in patients with Wilson's disease.

  7. Comparison of two methods for detection of fecal indicator bacteria used in water quality monitoring of the Three Gorges Reservoir.

    PubMed

    Wang, Zhaodan; Xiao, Guosheng; Zhou, Nong; Qi, Wenhua; Han, Lin; Ruan, Yu; Guo, Dongqin; Zhou, Hong

    2015-12-01

    Scientifically sound methods to rapidly measure fecal indicator bacteria are important to ensure safe water for drinking and recreational purposes. A total of 200 water samples obtained from the Three Gorges Reservoir during three successive one-year study periods (October 2009 to September 2012) were analyzed using multiple-tube fermentation (MTF) and most probable numbers combined with polymerase chain reaction (MPN-PCR). The MPN-PCR method was found to be significantly more sensitive than the MTF method for detecting Escherichia coli and Enterococcus spp., and of equal sensitivity for detecting total coliforms when all surface water samples were grouped together. The two analytical methods had a strong, significant relationship, but MPN-PCR took only 12-18hr, compared with the 3-8days needed using the MTF method. Bacterial concentrations varied per sampling site but were significantly lower in the mainstream of the Yangtze River than those in the backwater areas of tributaries. The water quality of 85.8% of water samples from the mainstream was suitable for use as a centralized potable water source, while the water quality of 52.5% of water samples from the backwater areas was unsuitable for recreational activities. Relationships between fecal indicator bacteria showed significant correlation (r=0.636-0.909, p<0.01, n=200), while a weak but significant correlation was found between fecal indicators and water turbidity, water temperature, daily inflow, and total dissolved solids (r=0.237-0.532, p<0.05, n=200). The study indicated that MPN-PCR is a rapid and easily performed deoxyribonucleic acid (DNA)-based method for quantitative detection of viable total coliforms, E. coli, and Enterococcus spp. in surface water.

  8. Comparison of two methods for detection of fecal indicator bacteria used in water quality monitoring of the Three Gorges Reservoir.

    PubMed

    Wang, Zhaodan; Xiao, Guosheng; Zhou, Nong; Qi, Wenhua; Han, Lin; Ruan, Yu; Guo, Dongqin; Zhou, Hong

    2015-12-01

    Scientifically sound methods to rapidly measure fecal indicator bacteria are important to ensure safe water for drinking and recreational purposes. A total of 200 water samples obtained from the Three Gorges Reservoir during three successive one-year study periods (October 2009 to September 2012) were analyzed using multiple-tube fermentation (MTF) and most probable numbers combined with polymerase chain reaction (MPN-PCR). The MPN-PCR method was found to be significantly more sensitive than the MTF method for detecting Escherichia coli and Enterococcus spp., and of equal sensitivity for detecting total coliforms when all surface water samples were grouped together. The two analytical methods had a strong, significant relationship, but MPN-PCR took only 12-18hr, compared with the 3-8days needed using the MTF method. Bacterial concentrations varied per sampling site but were significantly lower in the mainstream of the Yangtze River than those in the backwater areas of tributaries. The water quality of 85.8% of water samples from the mainstream was suitable for use as a centralized potable water source, while the water quality of 52.5% of water samples from the backwater areas was unsuitable for recreational activities. Relationships between fecal indicator bacteria showed significant correlation (r=0.636-0.909, p<0.01, n=200), while a weak but significant correlation was found between fecal indicators and water turbidity, water temperature, daily inflow, and total dissolved solids (r=0.237-0.532, p<0.05, n=200). The study indicated that MPN-PCR is a rapid and easily performed deoxyribonucleic acid (DNA)-based method for quantitative detection of viable total coliforms, E. coli, and Enterococcus spp. in surface water. PMID:26702967

  9. 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.

  10. Control of active sites in selective flocculation: II -- Role of site blocking agents

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Control of heteroflocculation using a lower molecular weight fraction of the flocculant as a site blocking agent is demonstrated in the apatite-dolomite-polyethylene oxide system. The most effective SBA (site blocking agent) was determined to be the highest molecular weight fraction of the flocculant itself which was not capable of flocculating any of the components of the mixture. In the presence of the SBA, flocculant adsorption decreased significantly on apatite particles, thereby inhibiting coflocculation.

  11. A reconnaissance of the Archean complex of the Granite Gorge, Grand Canyon, Arizona

    USGS Publications Warehouse

    Noble, L.F.; Hunter, J. Fred

    1917-01-01

    The field work upon which this article is based was done in March and April, 1914. From Garnet Canyon, near the west end of the Granite Gorge, the route followed the Tonto trail along the so-called lower plateau, or Tonto platform, to Red Canyon, at the east end of the Granite Gorge.

  12. Landslides in the western Columbia Gorge, Skamania County, Washington

    USGS Publications Warehouse

    Pierson, Thomas C.; Evarts, Russell C.; Bard, Joseph A.

    2016-11-04

    SummaryRecent light detection and ranging (lidar) imagery has allowed us to identify and map a large number of previously unrecognized landslides, or slides, in heavily forested terrain in the western Columbia Gorge, Skamania County, Washington, and it has revealed that the few previously recognized areas of instability are actually composites of multiple smaller landslides. The high resolution of the imagery further reveals that landslides in the map area have complex movement histories and span a wide range of relative ages. Movement histories are inferred from relative landslide locations and crosscutting relations of surface features. Estimated age ranges are based on (1) limited absolute dating; (2) relative fineness of landscape surface textures, calibrated by comparison with surfaces of currently active and dated landslides as interpreted from interferometric synthetic aperture radar (InSAR), global positioning system (GPS), and historical records; (3) sharpness and steepness of larger-scale surface morphologic features, calibrated by comparison with similar dated features in other regions; (4) degree of surface erosion; and (5) evidence of erosion or deposition by late Pleistocene (15–22 ka) Missoula floods at or below 200 m altitude. The relative age categories are recent (0 to ~1,000 years old), intermediate-age (~1,000 to ~15,000 years old), and old (>~15,000 years old). Within the 221.5 km2 map area, we identified 215 discrete landslides, covering 140.9 km2 (64 percent of the map area). At least 12 of the recent landslides are currently moving or have moved within the last two decades. Mapping for this study expanded the area of previously recognized unstable terrain by 56 percent. Landslide geometries suggest that more than half (62 percent) of these slope failures are translational landslides or composite landslides with translational elements, with failure occurring along gently sloping bedding planes in zones of deeply weathered, locally clay rich

  13. Statistical evaluation of the effects of fall and winter flows on the spring condition of rainbow and brown trout in the green river downstream of Flaming Gorge Dam.

    SciTech Connect

    Magnusson, A. K.; LaGory, K. E.; Hayse, J. W.; Environmental Science Division

    2009-01-09

    Flaming Gorge Dam, a hydroelectric facility operated by the Bureau of Reclamation (Reclamation), is located on the Green River in Daggett County, northeastern Utah. In recent years, single peak releases each day or steady flows have been the operational pattern during the winter period. A double-peak pattern (two flow peaks each day) was implemented during the winter of 2006-2007 by Reclamation. Because there is no recent history of double-peaking at Flaming Gorge Dam, the potential effects of double-peaking operations on the body condition of trout in the dam's tailwater are not known. A study plan was developed that identified research activities to evaluate potential effects from double-peaking operations during winter months. Along with other tasks, the study plan identified the need to conduct a statistical analysis of existing data on trout condition and macroinvertebrate abundance to evaluate potential effects of hydropower operations. This report presents the results of this analysis. We analyzed historical data to (1) describe temporal patterns and relationships among flows, benthic macroinvertebrate abundance, and condition of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) in the tailwaters of Flaming Gorge Dam and (2) to evaluate the degree to which flow characteristics (i.e., flow volumes and flow variability) and benthic macroinvertebrate abundance affect the condition of trout in this area. This information, together with further analyses of size-stratified trout data, may also serve as baseline data to which the effects of potential future double-peaking flows can be compared. The condition (length, weight and/or relative weight) of rainbow trout (Oncorhynchus mykiss) at two sites in the Green River downstream of Flaming Gorge Dam (Tailrace and Little Hole) and weight of brown trout (Salmo trutta) at the Little Hole site has been decreasing since 1990 while the abundance of brown trout has been increasing at the two sites. At the

  14. The natural product dihydrotanshinone I provides a prototype for uncharged inhibitors that bind specifically to the acetylcholinesterase peripheral site with nanomolar affinity.

    PubMed

    Beri, Veena; Wildman, Scott A; Shiomi, Kazuro; Al-Rashid, Ziyad F; Cheung, Jonah; Rosenberry, Terrone L

    2013-10-22

    Cholinergic synaptic transmission often requires extremely rapid hydrolysis of acetylcholine by acetylcholinesterase (AChE). AChE is inactivated by organophosphates (OPs) in chemical warfare nerve agents. The resulting accumulation of acetylcholine disrupts cholinergic synaptic transmission and can lead to death. A potential long-term strategy for preventing AChE inactivation by OPs is based on evidence that OPs must pass through a peripheral site or P-site near the mouth of the AChE active site gorge before reacting with a catalytic serine in an acylation site or A-site at the base of the gorge. An ultimate goal of this strategy is to design compounds that bind tightly at or near the P-site and exclude OPs from the active site while interfering minimally with the passage of acetylcholine. However, to target the AChE P-site with ligands and potential drugs that selectively restrict access, much more information must be gathered about the structure-activity relationships of ligands that bind specifically to the P-site. We apply here an inhibitor competition assay that can correctly determine whether an AChE inhibitor binds to the P-site, the A-site, or both sites. We have used this assay to examine three uncharged, natural product inhibitors of AChE, including aflatoxin B1, dihydrotanshinone I, and territrem B. The first two of these inhibitors are predicted by the competition assay to bind selectively to the P-site, while territrem B is predicted to span both the P- and A-sites. These predictions have recently been confirmed by X-ray crystallography. Dihydrotanshinone I, with an observed binding constant (KI) of 750 nM, provides a good lead compound for the development of high-affinity, uncharged inhibitors with specificity for the P-site. PMID:24040835

  15. Nutrient spatial pattern of the upstream, mainstream and tributaries of the Three Gorges Reservoir in China.

    PubMed

    Huang, YuLing; Zhang, Ping; Liu, DeFu; Yang, ZhengJian; Ji, DaoBin

    2014-10-01

    A comprehensive monitoring program was conducted to investigate the nutrient spatial pattern in the mainstream of the Yangtze River from the Baihetan Dam down to the Three Gorges Dam located at the upper region of the Yangtze River in China. Samples were taken from 33 different sites from July 30 to August 19, 2011. The nutrient patterns of the three representative tributaries of the Three Gorges Reservoir (TGR)--the Modao, the Daning, and the Xiangxi Rivers--were also investigated. The results show that the mainstream of the TGR has a higher concentration of nitrogen and a lower concentration of phosphorus than that of the upper mainstream before the TGR. Moreover, it was found that nitrate-nitrogen (NO₃-N) is the main nitrogen component, while particulate phosphorus predominates the total phosphorus (TP). It was found that the three representative tributaries of the TGR have lower total nitrogen (TN) concentrations compared to the corresponding sections of the mainstream TGR. Based on the nutrient spatial pattern, the nutrient flux was calculated. The total fluxes of TN, NO₃-N, TP, and orthophosphate (PO₄-P) from the upstream reach into the TGR are 2,155.06, 1,674.97, 212.98, and 83.42 t day(-1), respectively. The amount of nutrients imported from the TGR into its tributaries is more than the amount exported. It was determined that the Xiangxi River has the largest net rate of imported nitrogen at 7.66 t day(-1), whereas the Daning River has the largest net rate of imported phosphorus at 1.75 t day(-1). In addition, compared with the nutrients imported from the TGR into its tributaries, the nutrient flux from the upstream reach into the TGR contributes approximately less than 3 %.

  16. Nutrient spatial pattern of the upstream, mainstream and tributaries of the Three Gorges Reservoir in China.

    PubMed

    Huang, YuLing; Zhang, Ping; Liu, DeFu; Yang, ZhengJian; Ji, DaoBin

    2014-10-01

    A comprehensive monitoring program was conducted to investigate the nutrient spatial pattern in the mainstream of the Yangtze River from the Baihetan Dam down to the Three Gorges Dam located at the upper region of the Yangtze River in China. Samples were taken from 33 different sites from July 30 to August 19, 2011. The nutrient patterns of the three representative tributaries of the Three Gorges Reservoir (TGR)--the Modao, the Daning, and the Xiangxi Rivers--were also investigated. The results show that the mainstream of the TGR has a higher concentration of nitrogen and a lower concentration of phosphorus than that of the upper mainstream before the TGR. Moreover, it was found that nitrate-nitrogen (NO₃-N) is the main nitrogen component, while particulate phosphorus predominates the total phosphorus (TP). It was found that the three representative tributaries of the TGR have lower total nitrogen (TN) concentrations compared to the corresponding sections of the mainstream TGR. Based on the nutrient spatial pattern, the nutrient flux was calculated. The total fluxes of TN, NO₃-N, TP, and orthophosphate (PO₄-P) from the upstream reach into the TGR are 2,155.06, 1,674.97, 212.98, and 83.42 t day(-1), respectively. The amount of nutrients imported from the TGR into its tributaries is more than the amount exported. It was determined that the Xiangxi River has the largest net rate of imported nitrogen at 7.66 t day(-1), whereas the Daning River has the largest net rate of imported phosphorus at 1.75 t day(-1). In addition, compared with the nutrients imported from the TGR into its tributaries, the nutrient flux from the upstream reach into the TGR contributes approximately less than 3 %. PMID:24990348

  17. Use of aerial videography to evaluate the effects of Flaming Gorge Dam operations on natural resources of the Green River

    SciTech Connect

    Snider, M.A.; Hayse, J.W.; Hlohowskyj, I.; LaGory, K.E.; Greaney, M.M.; Kuiper, J.A.; Van Lonkhuyzen, R.A.

    1993-07-01

    Peaking hydropower operations can profoundly alter natural stream flow and thereby affect the natural resources dependent on these flows. In this paper, we describe how aerial videography was used to collect environmental data and evaluate impacts of hydropower operations at Flaming Gorge Dam on natural resources of the Green River. An airborne multispectral video/radiometer remote sensing system was used to collect resource data under four different flow conditions from seven sites (each about one mile in length) located downstream from the dam. Releases from Flaming Gorge Dam during data collection ranged from approximately 800 to 4,000 cubic feet/sec (cfs), spanning most of the normal operating range for this facility. For each site a series of contiguous, non-overlapping images was prepared from the videotapes and used to quantify surface water area, backwater habitats, and areas of riparian vegetation under varying flow conditions. From this information, relationships between flow and habitat parameters were developed and used in conjunction with hydrologic modeling and ecological information to evaluate impacts of various modes of operation.

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

    SciTech Connect

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

    2010-09-07

    The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site pocket must facilitate both reactions, individual active site residues may serve multiple roles. We have examined the roles of a strictly conserved active site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically (Dubois and Klinman (2006) Biochemistry 45, 3178), and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy intermediates in cofactor biogenesis but also indicates the critical control of oxidation chemistry that can be conferred by a single active site residue.

  19. Advancing analysis of spatio-temporal variations of soil nutrients in the water level fluctuation zone of China's Three Gorges Reservoir using self-organizing map.

    PubMed

    Ye, Chen; Li, Siyue; Yang, Yuyi; Shu, Xiao; Zhang, Jiaquan; Zhang, Quanfa

    2015-01-01

    The ~350 km2 water level fluctuation zone (WLFZ) in the Three Gorges Reservoir (TGR) of China, situated at the intersection of terrestrial and aquatic ecosystems, experiences a great hydrological change with prolonged winter inundation. Soil samples were collected in 12 sites pre- (September 2008) and post submergence (June 2009) in the WLFZ and analyzed for soil nutrients. Self-organizing map (SOM) and statistical analysis including multi-way ANOVA, paired-T test, and stepwise least squares multiple regression were employed to determine the spatio-temporal variations of soil nutrients in relation to submergence, and their correlations with soil physical characteristics. Results showed significant spatial variability in nutrients along ~600 km long shoreline of the TGR before and after submergence. There were higher contents of organic matter, total nitrogen (TN), and nitrate (NO3-) in the lower reach and total phosphorus (TP) in the upper reach that were primarily due to the spatial variations in soil particle size composition and anthropogenic activities. Submergence enhanced soil available potassium (K), while significantly decreased soil N, possibly due to the alterations of soil particle size composition and increase in soil pH. In addition, SOM analysis determined important roles of soil pH value, bulk density, soil particle size (i.e., silt and sand) and nutrients (TP, TK, and AK) on the spatial and temporal variations in soil quality. Our results suggest that urban sewage and agricultural runoffs are primary pollutants that affect soil nutrients in the WLFZ of TGR. PMID:25789612

  20. Advancing Analysis of Spatio-Temporal Variations of Soil Nutrients in the Water Level Fluctuation Zone of China’s Three Gorges Reservoir Using Self-Organizing Map

    PubMed Central

    Ye, Chen; Li, Siyue; Yang, Yuyi; Shu, Xiao; Zhang, Jiaquan; Zhang, Quanfa

    2015-01-01

    The ~350 km2 water level fluctuation zone (WLFZ) in the Three Gorges Reservoir (TGR) of China, situated at the intersection of terrestrial and aquatic ecosystems, experiences a great hydrological change with prolonged winter inundation. Soil samples were collected in 12 sites pre- (September 2008) and post submergence (June 2009) in the WLFZ and analyzed for soil nutrients. Self-organizing map (SOM) and statistical analysis including multi-way ANOVA, paired-T test, and stepwise least squares multiple regression were employed to determine the spatio-temporal variations of soil nutrients in relation to submergence, and their correlations with soil physical characteristics. Results showed significant spatial variability in nutrients along ~600 km long shoreline of the TGR before and after submergence. There were higher contents of organic matter, total nitrogen (TN), and nitrate (NO3-) in the lower reach and total phosphorus (TP) in the upper reach that were primarily due to the spatial variations in soil particle size composition and anthropogenic activities. Submergence enhanced soil available potassium (K), while significantly decreased soil N, possibly due to the alterations of soil particle size composition and increase in soil pH. In addition, SOM analysis determined important roles of soil pH value, bulk density, soil particle size (i.e., silt and sand) and nutrients (TP, TK, and AK) on the spatial and temporal variations in soil quality. Our results suggest that urban sewage and agricultural runoffs are primary pollutants that affect soil nutrients in the WLFZ of TGR. PMID:25789612

  1. Surface gravity and deformation effects of water storage changes in China's Three Gorges Reservoir constrained by modeled results and in situ measurements

    NASA Astrophysics Data System (ADS)

    Wang, Linsong; Chen, Chao; Zou, Rong; Du, Jinsong

    2014-09-01

    The water impoundment of China's Three Gorges Reservoir (TGR), with the largest dam in the world, makes a large mass concentrated and thus influences the surface gravity field and crustal deformation field. In the TGR area, water impoundment began in 2003, and the Earth is responding to the ongoing changes of water storage. These responses can be investigated using the gravimeter and the GPS. In this paper, using a water load model derived from Digital Elevation Model (DEM) data and elastic loading Green's function, we modeled the surface gravity and displacement changes in the front area of TGR caused by water storage variations. Predictive results are compared with the measurements derived from absolute gravity by A10, continuous gravity by gPhone and GPS time series at the sites of front area in TGR. The observations agree well with the prediction spatially and temporally. The quantitative comparison and analysis indicate that the ground gravity and the vertical displacement are more sensitive to water storage changes than the horizontal displacement. The predictions from the water load model are consistent with the in situ measurements reported in this work and therefore can be utilized for water effect corrections for exacting the further signals related to lithospheric dynamics and geological hazards, such as abnormal deformation of active faults and landslides.

  2. Advancing analysis of spatio-temporal variations of soil nutrients in the water level fluctuation zone of China's Three Gorges Reservoir using self-organizing map.

    PubMed

    Ye, Chen; Li, Siyue; Yang, Yuyi; Shu, Xiao; Zhang, Jiaquan; Zhang, Quanfa

    2015-01-01

    The ~350 km2 water level fluctuation zone (WLFZ) in the Three Gorges Reservoir (TGR) of China, situated at the intersection of terrestrial and aquatic ecosystems, experiences a great hydrological change with prolonged winter inundation. Soil samples were collected in 12 sites pre- (September 2008) and post submergence (June 2009) in the WLFZ and analyzed for soil nutrients. Self-organizing map (SOM) and statistical analysis including multi-way ANOVA, paired-T test, and stepwise least squares multiple regression were employed to determine the spatio-temporal variations of soil nutrients in relation to submergence, and their correlations with soil physical characteristics. Results showed significant spatial variability in nutrients along ~600 km long shoreline of the TGR before and after submergence. There were higher contents of organic matter, total nitrogen (TN), and nitrate (NO3-) in the lower reach and total phosphorus (TP) in the upper reach that were primarily due to the spatial variations in soil particle size composition and anthropogenic activities. Submergence enhanced soil available potassium (K), while significantly decreased soil N, possibly due to the alterations of soil particle size composition and increase in soil pH. In addition, SOM analysis determined important roles of soil pH value, bulk density, soil particle size (i.e., silt and sand) and nutrients (TP, TK, and AK) on the spatial and temporal variations in soil quality. Our results suggest that urban sewage and agricultural runoffs are primary pollutants that affect soil nutrients in the WLFZ of TGR.

  3. 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

  4. An ionizable active-site tryptophan imparts catalase activity to a peroxidase core.

    PubMed

    Loewen, Peter C; Carpena, Xavi; Vidossich, Pietro; Fita, Ignacio; Rovira, Carme

    2014-05-21

    Catalase peroxidases (KatG's) are bifunctional heme proteins that can disproportionate hydrogen peroxide (catalatic reaction) despite their structural dissimilarity with monofunctional catalases. Using X-ray crystallography and QM/MM calculations, we demonstrate that the catalatic reaction of KatG's involves deprotonation of the active-site Trp, which plays a role similar to that of the distal His in monofunctional catalases. The interaction of a nearby mobile arginine with the distal Met-Tyr-Trp essential adduct (in/out) acts as an electronic switch, triggering deprotonation of the adduct Trp.

  5. 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)

  6. 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.

  7. 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.

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

    PubMed Central

    Stec, Boguslaw

    2012-01-01

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO2. We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O2 and CO2 bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO2 defines an elusive, preactivation complex that contains a metal cation Mg2+ surrounded by three H2O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming. PMID:23112176

  9. Using catalytic atom maps to predict the catalytic functions present in enzyme active sites.

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-09-18

    Catalytic atom maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the "crowdedness" of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å rmsd of the CAM with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these CAMs were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5'-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase rmsd to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  10. Using Catalytic Atom Maps to Predict the Catalytic Functions Present in Enzyme Active Sites

    PubMed Central

    Nosrati, Geoffrey R.; Houk, K. N.

    2012-01-01

    Catalytic Atom Maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the “crowdedness” of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å RMSD of the Catalytic Atom Map with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these Catalytic Atom Maps were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5′-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase RMSD to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  11. Breeding systems, hybridization and continuing evolution in Avon Gorge Sorbus

    PubMed Central

    Ludwig, Shanna; Robertson, Ashley; Rich, Timothy C. G.; Djordjević, Milena; Cerović, Radosav; Houston, Libby; Harris, Stephen A.; Hiscock, Simon J.

    2013-01-01

    Background and Aims Interspecific hybridization and polyploidy are key processes in plant evolution and are responsible for ongoing genetic diversification in the genus Sorbus (Rosaceae). The Avon Gorge, Bristol, UK, is a world ‘hotspot’ for Sorbus diversity and home to diploid sexual species and polyploid apomictic species. This research investigated how mating system variation, hybridization and polyploidy interact to generate this biological diversity. Methods Mating systems of diploid, triploid and tetraploid Sorbus taxa were analysed using pollen tube growth and seed set assays from controlled pollinations, and parent–offspring genotyping of progeny from open and manual pollinations. Key Results Diploid Sorbus are outcrossing and self-incompatible (SI). Triploid taxa are pseudogamous apomicts and genetically invariable, but because they also display self-incompatibility, apomictic seed set requires pollen from other Sorbus taxa – a phenomenon which offers direct opportunities for hybridization. In contrast tetraploid taxa are pseudogamous but self-compatible, so do not have the same obligate requirement for intertaxon pollination. Conclusions The mating inter-relationships among Avon Gorge Sorbus taxa are complex and are the driving force for hybridization and ongoing genetic diversification. In particular, the presence of self-incompatibility in triploid pseudogamous apomicts imposes a requirement for interspecific cross-pollination, thereby facilitating continuing diversification and evolution through rare sexual hybridization events. This is the first report of naturally occurring pseudogamous apomictic SI plant populations, and we suggest that interspecific pollination, in combination with a relaxed endosperm balance requirement, is the most likely route to the persistence of these populations. We propose that Avon Gorge Sorbus represents a model system for studying the establishment and persistence of SI apomicts in natural populations. PMID

  12. Examining time trends in the Oldowan technology at Beds I and II, Olduvai Gorge.

    PubMed

    Kimura, Yuki

    2002-09-01

    The lithic analysis of the Bed I and II assemblages from Olduvai Gorge reveals both static and dynamic time trends in early hominids' technology from 1.8 to 1.2 m.y.a. The Bed I Oldowan (1.87-1.75 m.y.a.) is characterized by the least effort strategy in terms of raw material exploitation and tool production. The inclusion of new raw material, chert, for toolmaking in the following Developed Oldowan A (DOA, 1.65-1.53 m.y.a.) facilitated more distinctive and variable flaking strategies depending on the kind of raw materials. The unique characters of DOA are explainable by this raw material factor, rather than technological development of hominids. The disappearance of chert in the subsequent Developed Oldowan B and Acheulian (1.53-1.2 m.y.a.) necessitated a shift in tool production strategy more similar to that of Bed I Oldowan than DOA. However, the evidence suggests that Bed II hominids might have been more skillful toolmakers, intensive tool-users, and engaged in more active transport of stone tools than the Bed I predecessors. Koobi Fora hominids maintained a more static tool-using behavior than their Olduvai counterparts due mainly to a stable supply of raw materials. They differed from Olduvai hominids in terms of less battering of cores, consistent transport behavior, and few productions of side-struck flakes, indicating a regional variation of toolmaking and using practice. However, they shared with Olduvai hominids a temporal trend toward the production of larger flakes from larger cores after 1.6 m.y.a. Increased intake of animal resources and the expansion of ranging area of Homo ergaster would have led to the development of technological organization. Technological changes in the Oldowan industry are attested at Olduvai Gorge, Koobi Fora, and Sterkfontein, suggesting that it was a pan-African synchronous phenomenon, beginning at 1.5 m.y.a.

  13. 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.

  14. Parameterization of an Active Thermal Erosion Site, Caribou Creek, Alaska

    NASA Astrophysics Data System (ADS)

    Busey, R.; Bolton, W. R.; Cherry, J. E.; Hinzman, L. D.

    2012-12-01

    Thermokarst features are thought to be an important mechanism for landscape change in permafrost-dominated cold regions, but few such features have been incorporated into full featured landscape models. The root of this shortcoming is that historic observations are not detailed enough to parameterize a model, and the models typically do not include the relevant processes for thermal erosion. A new, dynamic thermokarst feature has been identified at the Caribou-Poker Creek Research Watershed (CPCRW) in the boreal forest of Interior Alaska. Located adjacent to a traditional use trail, this feature terminates directly in Caribou Creek. Erosion within the feature is driven predominantly by fluvial interflow. CPCRW is a Long-Term Ecological Research site underlain by varying degrees of relatively warm, discontinuous permafrost. This poster will describe the suite of measurements that have been undertaken to parameterize the ERODE model for this site, including thorough surveys, time lapse- and aerial photography, and 3-D structure from motion algorithms.

  15. Lions as Bone Accumulators? Paleontological and Ecological Implications of a Modern Bone Assemblage from Olduvai Gorge

    PubMed Central

    Arriaza, Mari Carmen; Domínguez-Rodrigo, Manuel; Yravedra, José; Baquedano, Enrique

    2016-01-01

    Analytic models have been developed to reconstruct early hominin behaviour, especially their subsistence patterns, revealed mainly through taphonomic analyses of archaeofaunal assemblages. Taphonomic research is used to discern which agents (carnivores, humans or both) generate the bone assemblages recovered at archaeological sites. Taphonomic frameworks developed during the last decades show that the only large-sized carnivores in African biomes able to create bone assemblages are leopards and hyenas. A carnivore-made bone assemblage located in the short-grassland ecological unit of the Serengeti (within Olduvai Gorge) was studied. Taphonomic analyses of this assemblage including skeletal part representation, bone density, breakage patterns and anatomical distribution of tooth marks, along with an ecological approach to the prey selection made by large carnivores of the Serengeti, were carried out. The results show that this bone assemblage may be the first lion-accumulated assemblage documented, although other carnivores (namely spotted hyenas) may have also intervened through postdepositional ravaging. This first faunal assemblage potentially created by lions constitutes a new framework for neotaphonomic studies. Since lions may accumulate carcasses under exceptional circumstances, such as those documented at the site reported here, this finding may have important consequences for interpretations of early archaeological and paleontological sites, which provide key information about human evolution. PMID:27144649

  16. Lions as Bone Accumulators? Paleontological and Ecological Implications of a Modern Bone Assemblage from Olduvai Gorge.

    PubMed

    Arriaza, Mari Carmen; Domínguez-Rodrigo, Manuel; Yravedra, José; Baquedano, Enrique

    2016-01-01

    Analytic models have been developed to reconstruct early hominin behaviour, especially their subsistence patterns, revealed mainly through taphonomic analyses of archaeofaunal assemblages. Taphonomic research is used to discern which agents (carnivores, humans or both) generate the bone assemblages recovered at archaeological sites. Taphonomic frameworks developed during the last decades show that the only large-sized carnivores in African biomes able to create bone assemblages are leopards and hyenas. A carnivore-made bone assemblage located in the short-grassland ecological unit of the Serengeti (within Olduvai Gorge) was studied. Taphonomic analyses of this assemblage including skeletal part representation, bone density, breakage patterns and anatomical distribution of tooth marks, along with an ecological approach to the prey selection made by large carnivores of the Serengeti, were carried out. The results show that this bone assemblage may be the first lion-accumulated assemblage documented, although other carnivores (namely spotted hyenas) may have also intervened through postdepositional ravaging. This first faunal assemblage potentially created by lions constitutes a new framework for neotaphonomic studies. Since lions may accumulate carcasses under exceptional circumstances, such as those documented at the site reported here, this finding may have important consequences for interpretations of early archaeological and paleontological sites, which provide key information about human evolution. PMID:27144649

  17. Geomagnetic polarity epochs: new data from Olduvai Gorge, Tanganyika

    USGS Publications Warehouse

    Gromme, C.S.; Hay, R.L.

    1967-01-01

    The lower lava flow of Bed I in Olduvai Gorge, Tanganyika, carries natural remanent magnetization (NRM) having normal polarity. Thermal demagnetization experiments demonstrate the stability of this NRM. Thus the Olduvai geomagnetic polarity event, which was originally named from the upper lava flow in Bed I, is represented in its type locality by two normally magnetized lavas. These lavas have been shown to be 1.9 m.y. old, and although they are distinct from each other in composition and surface structure, their eruptions appear to have been closely spaced in time. ?? 1967.

  18. Blogs and Social Network Sites as Activity Systems: Exploring Adult Informal Learning Process through Activity Theory Framework

    ERIC Educational Resources Information Center

    Heo, Gyeong Mi; Lee, Romee

    2013-01-01

    This paper uses an Activity Theory framework to explore adult user activities and informal learning processes as reflected in their blogs and social network sites (SNS). Using the assumption that a web-based space is an activity system in which learning occurs, typical features of the components were investigated and each activity system then…

  19. Mice that gorged during dietary restriction increased foraging related behaviors and differed in their macronutrient preference when released from restriction

    PubMed Central

    Speakman, John R.

    2015-01-01

    Caloric restriction (CR) can trigger gorging behavior. We examined macronutrient choice and behavior in mice that gorged during restriction compared to restricted non-gorgers and controls. Fifty MF1 male mice were restricted to 75% of ad-libitum food intake (FI), while ten controls were fed ad-lib. Body mass (BM) and FI were measured two and 24-h after food inclusion over 14-days. ‘Gorging’ mice were defined as those which ate over 25% of their daily FI in 2-h. The top 11 gorgers and the lowest 9 gorgers, along with 10 controls, had their behavior analysed during restriction, and were then provided with an unrestricted food choice, consisting of three diets that were high in fat, protein or carbohydrate. During restriction gorgers ate on average 51% of their daily FI in the 2-h following food introduction while the non-gorgers ate only 16%. Gorgers lost significantly more BM than non-gorgers possibly due to an increased physical activity linked to anticipation of daily food provision. Controls and non-gorgers spent most of their time sleeping. After restriction, both gorgers and non-gorgers were hyperphagic until their lost weight was regained. All 3 groups favoured high fat food. Gorgers and non-gorgers had a significantly greater high carbohydrate diet intake than controls, and gorgers also had a significantly greater high protein diet intake than non-gorgers and controls. On unrestricted food, they did not continue to gorge, although they still had a significantly greater 2-h FI than the other groups. Elevated protein intake may play an important role in the recovery of the lost lean tissue of gorgers after restriction. PMID:26157640

  20. 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.

  1. Active Site Structure and Peroxidase Activity of Oxidatively Modified Cytochrome c Species in Complexes with Cardiolipin.

    PubMed

    Capdevila, Daiana A; Oviedo Rouco, Santiago; Tomasina, Florencia; Tortora, Verónica; Demicheli, Verónica; Radi, Rafael; Murgida, Daniel H

    2015-12-29

    We report a resonance Raman and UV-vis characterization of the active site structure of oxidatively modified forms of cytochrome c (Cyt-c) free in solution and in complexes with cardiolipin (CL). The studied post-translational modifications of Cyt-c include methionine sulfoxidation and tyrosine nitration, which lead to altered heme axial ligation and increased peroxidase activity with respect to those of the wild-type protein. In spite of the structural and activity differences between the protein variants free in solution, binding to CL liposomes induces in all cases the formation of a spectroscopically identical bis-His axial coordination conformer that more efficiently promotes lipid peroxidation. The spectroscopic results indicate that the bis-His form is in equilibrium with small amounts of high-spin species, thus suggesting a labile distal His ligand as the basis for the CL-induced increase in enzymatic activity observed for all protein variants. For Cyt-c nitrated at Tyr74 and sulfoxidized at Met80, the measured apparent binding affinities for CL are ∼4 times larger than for wild-type Cyt-c. On the basis of these results, we propose that these post-translational modifications may amplify the pro-apoptotic signal of Cyt-c under oxidative stress conditions at CL concentrations lower than for the unmodified protein.

  2. Identification of ice nucleation active sites on feldspar dust particles.

    PubMed

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

    2015-03-19

    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

  3. 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

  4. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination.

    PubMed

    Rowley, Paul A; Kachroo, Aashiq H; Ma, Chien-Hui; Maciaszek, Anna D; Guga, Piotr; Jayaram, Makkuni

    2015-07-13

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions. PMID:25999343

  5. 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.

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

    PubMed

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

    2016-07-01

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

  7. Possible active site of the sweet-tasting protein thaumatin.

    PubMed

    Slootstra, J W; De Geus, P; Haas, H; Verrips, C T; Meloen, R H

    1995-10-01

    Epitopes on thaumatin and monellin were studied using the PEPSCAN-technology. The antibodies used were raised against thaumatin. Only antibodies that, in an ELISA, both recognized thaumatin and monellin were used in the PEPSCAN-analyses. On thaumatin two major overlapping epitopes were identified. On monellin no epitopes could be identified. The identified epitope region on thaumatin shares structural features with various peptide and protein sweeteners. It contains an aspartame-like site which is formed by Asp21 and Phe80, tips of the two extruding loops KGDAALDAGGR19-29 and CKRFGRPP77-84, which are spatially positioned next to each other. Furthermore, sub-sequences of the KGDAALDAGGR19-29 loop are similar to peptide-sweeteners such as L-Asp-D-Ala-L-Ala-methyl ester and L-Asp-D-Ala-Gly-methyl ester. Since the aspartame-like Asp21-Phe80 site and the peptide-sweetener-like sequences are also not present in non-sweet thaumatin-like proteins it is postulated that the KGDAALDAGGR19-29- and CKRFGRPP77-84 loop contain important sweet-taste determinants. This region has previously not been implicated as a sweet-taste determinant of thaumatin.

  8. 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.

  9. Tiny bubbles challenge giant turbines: Three Gorges puzzle.

    PubMed

    Li, Shengcai

    2015-10-01

    Since the birth of the first prototype of the modern reaction turbine, cavitation as conjectured by Euler in 1754 always presents as a challenge. Following his theory, the evolution of modern reaction (Francis and Kaplan) turbines has been completed by adding the final piece of the element 'draft-tube' that enables turbines to explore water energy at efficiencies of almost 100%. However, during the last two and a half centuries, with increasing unit capacity and specific speed, the problem of cavitation has been manifested and complicated by the draft-tube surges rather than being solved. Particularly, during the last 20 years, the fierce competition in the international market for extremely large turbines with compact design has encouraged the development of giant Francis turbines of 700-1000 MW. The first group (24 units) of such giant turbines of 700 MW each was installed in the Three Gorges project. Immediately after commission, a strange erosion phenomenon appeared on the guide vane of the machines that has puzzled professionals. From a multi-disciplinary analysis, this Three Gorges puzzle could reflect an unknown type of cavitation inception presumably triggered by turbulence production from the boundary-layer streak transitional process. It thus presents a fresh challenge not only to this old turbine industry, but also to the fundamental sciences. PMID:26442144

  10. Accumulation of floating microplastics behind the Three Gorges Dam.

    PubMed

    Zhang, Kai; Gong, Wen; Lv, Jizhong; Xiong, Xiong; Wu, Chenxi

    2015-09-01

    We investigated the occurrence and distribution of microplastics in surface water from the Three Gorges Reservoir. Nine samples were collected via trawl sampling with a 112 μmmesh net. The abundances of microplastics were from 3407.7 × 10(3) to 13,617.5 × 10(3) items per square kilometer in the main stream of the Yangtze River and from 192.5 × 10(3) to 11,889.7 × 10(3) items per square kilometer in the estuarine areas of four tributaries. The abundance of microplastics in the main stream of the Yangtze River generally increased as moving closer to the Three Gorges Dam. The microplastics are made exclusively of polyethylene (PE), polypropylene (PP), and polystyrene (PS). Together with microplastics, high abundance of coal/fly ash was also observed in the surface water samples. Comparing with previously reported data, microplastics in the TGR were approximately one to three orders of magnitudes greater, suggesting reservoirs as potential hot spot for microplastic pollution.

  11. Tiny bubbles challenge giant turbines: Three Gorges puzzle

    PubMed Central

    Li, Shengcai

    2015-01-01

    Since the birth of the first prototype of the modern reaction turbine, cavitation as conjectured by Euler in 1754 always presents as a challenge. Following his theory, the evolution of modern reaction (Francis and Kaplan) turbines has been completed by adding the final piece of the element ‘draft-tube’ that enables turbines to explore water energy at efficiencies of almost 100%. However, during the last two and a half centuries, with increasing unit capacity and specific speed, the problem of cavitation has been manifested and complicated by the draft-tube surges rather than being solved. Particularly, during the last 20 years, the fierce competition in the international market for extremely large turbines with compact design has encouraged the development of giant Francis turbines of 700–1000 MW. The first group (24 units) of such giant turbines of 700 MW each was installed in the Three Gorges project. Immediately after commission, a strange erosion phenomenon appeared on the guide vane of the machines that has puzzled professionals. From a multi-disciplinary analysis, this Three Gorges puzzle could reflect an unknown type of cavitation inception presumably triggered by turbulence production from the boundary-layer streak transitional process. It thus presents a fresh challenge not only to this old turbine industry, but also to the fundamental sciences. PMID:26442144

  12. Local Climate Sensitivity of the Three Gorges Dam

    SciTech Connect

    Miller, Norman L.; Jin, Jiming; Tsang, Chin-Fu

    2005-02-18

    Two simulations, control and land use change, were performed for an eight week period (2 April-16 May 1990) to determine the net sensitivity of the local climate around the Three Gorges Dam. The analysis indicates that the large reservoir acts as a potential evaporating surface that decreases the surface temperature, cools the lower atmosphere, decreasing upward motion, and increasing sinking air mass. Such sinking results in low level moisture divergence, decreasing cloudiness, and increasing net downward radiation, which increases the surface temperature. However, results indicate that evaporative cooling dominates radiative warming in this initial study. The strong evaporation also supplies moisture to the atmosphere, suggesting an increase in precipitation, but the sinking moist air diverges away from the TGD region with no net change in precipitation. This numerical study represents an initial methodology for quantification of the impact of the Three Gorges Dam on the local climate and a more comprehensive, fine-scale set of multi-season simulations with additional observational data is needed for a more complete analysis.

  13. Accumulation of floating microplastics behind the Three Gorges Dam.

    PubMed

    Zhang, Kai; Gong, Wen; Lv, Jizhong; Xiong, Xiong; Wu, Chenxi

    2015-09-01

    We investigated the occurrence and distribution of microplastics in surface water from the Three Gorges Reservoir. Nine samples were collected via trawl sampling with a 112 μmmesh net. The abundances of microplastics were from 3407.7 × 10(3) to 13,617.5 × 10(3) items per square kilometer in the main stream of the Yangtze River and from 192.5 × 10(3) to 11,889.7 × 10(3) items per square kilometer in the estuarine areas of four tributaries. The abundance of microplastics in the main stream of the Yangtze River generally increased as moving closer to the Three Gorges Dam. The microplastics are made exclusively of polyethylene (PE), polypropylene (PP), and polystyrene (PS). Together with microplastics, high abundance of coal/fly ash was also observed in the surface water samples. Comparing with previously reported data, microplastics in the TGR were approximately one to three orders of magnitudes greater, suggesting reservoirs as potential hot spot for microplastic pollution. PMID:25935612

  14. 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

  15. [Research progress on remote sensing of ecological and environmental changes in the Three Gorges Reservoir area, China].

    PubMed

    Teng, Ming-jun; Zeng, Li-xiong; Xiao, Wen-fa; Zhou, Zhi-xiang; Huang, Zhi-lin; Wang, Peng-cheng; Dian, Yuan-yong

    2014-12-01

    The Three Gorges Reservoir area (TGR area) , one of the most sensitive ecological zones in China, has dramatically changes in ecosystem configurations and services driven by the Three Gorges Engineering Project and its related human activities. Thus, understanding the dynamics of ecosystem configurations, ecological processes and ecosystem services is an attractive and critical issue to promote regional ecological security of the TGR area. The remote sensing of environment is a promising approach to the target and is thus increasingly applied to and ecosystem dynamics of the TGR area on mid- and macro-scales. However, current researches often showed controversial results in ecological and environmental changes in the TGR area due to the differences in remote sensing data, scale, and land-use/cover classification. Due to the complexity of ecological configurations and human activities, challenges still exist in the remote-sensing based research of ecological and environmental changes in the TGR area. The purpose of this review was to summarize the research advances in remote sensing of ecological and environmental changes in the TGR area. The status, challenges and trends of ecological and environmental remote-sensing in the TGR area were further discussed and concluded in the aspect of land-use/land-cover, vegetation dynamics, soil and water security, ecosystem services, ecosystem health and its management. The further researches on the remote sensing of ecological and environmental changes were proposed to improve the ecosystem management of the TGR area.

  16. Impact of the Three Gorges Dam on the spawning stock and natural reproduction of Chinese sturgeon in Changjiang River, China

    NASA Astrophysics Data System (ADS)

    Gao, Xin; Lin, Pengcheng; Li, Mingzheng; Duan, Zhonghua; Liu, Huanzhang

    2016-09-01

    Chinese sturgeon ( Acipenser sinensis) is the flagship species of the Changjiang River. The migration route of this species is blocked by the first dam, the Gezhou Dam, and its reproduction is affected by the Three Gorges Dam (TGD), one of the largest dams in the world. We studied the impact of the impoundment of the Three Gorges Reservoir (TGR) since 2003 on the spawning stock and the natural reproduction of the Chinese sturgeon by using our monitoring data from 1997 to 2013. Results indicate that TGR impoundment has delayed the first spawning dates of the fish from middle-late October to late November, decreased the amount of spawning activities from twice to only once each year, and significantly reduced egg production. In particular, the fish did not demonstrate any spawning activities in 2013. Therefore, TGR impoundment significantly affects the natural reproduction of the fish downstream of the TGD. The spawning stock size of the fish is also predicted to further decrease in the future, which will lead to a risk of population extinction. Ecological regulations must be imposed on decreasing the water temperature to 20°C before mid-October and increasing water discharge downstream of the TGD in October to induce spawning of the Chinese sturgeon.

  17. Characterization of an Active Thermal Erosion Site, Caribou Creek, Alaska

    NASA Astrophysics Data System (ADS)

    Busey, R.; Bolton, W. R.; Cherry, J. E.; Hinzman, L. D.

    2013-12-01

    The goal of this project is to estimate volume loss of soil over time from this site, provide parameterizations on erodibility of ice rich permafrost and serve as a baseline for future landscape evolution simulations. Located in the zone of discontinuous permafrost, the interior region of Alaska (USA) is home to a large quantity of warm, unstable permafrost that is both high in ice content and has soil temperatures near the freezing point. Much of this permafrost maintains a frozen state despite the general warming air temperature trend in the region due to the presence of a thick insulating organic mat and a dense root network in the upper sub-surface of the soil column. At a rapidly evolving thermo-erosion site, located within the Caribou-Poker Creeks Research Watershed (part of the Bonanza Creek LTER) near Chatanika, Alaska (N65.140, W147.570), the protective organic layer and associated plants were disturbed by an adjacent traditional use trail and the shifting of a groundwater spring. These triggers have led to rapid geomorphological change on the landscape as the soil thaws and sediment is transported into the creek at the valley bottom. Since 2006 (approximately the time of initiation), the thermal erosion has grown to 170 meters length, 3 meters max depth, and 15 meters maximum width. This research combines several data sets: DGPS survey, imagery from an extremely low altitude pole-based remote sensing (3 to 5 meters above ground level), and imagery from an Unmanned Aerial System (UAS) at about 60m altitude.

  18. 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.

  19. After Three Gorges Dam: What have we learned?

    NASA Astrophysics Data System (ADS)

    Natali, J.; Williams, P.; Wong, R.; Kondolf, G. M.

    2013-12-01

    China is at a critical point in its development path. By investing heavily in large-scale infrastructure, the rewards of economic growth weigh against long-term environmental and social costs. The construction of Three Gorges Dam, the world's largest hydroelectric project, began in 1994. Between 2002 and 2010, its 660 kilometer reservoir filled behind a 181 meter dam, displacing at least 1.4 million people and transforming Asia's longest river (the Yangtze) while generating nearly 100 billion kWh/yr of electricity -- 2.85% of China's current electric power usage. As the mega-project progenitor in a cascade of planned dams, the Three Gorges Dam emerges as a test case for how China will plan, execute and mitigate its development pathway and the transformation of its environment. Post-Project Assessments (PPA) provide a systematic, scientific method for improving the practice of environmental management - particularly as they apply to human intervention in river systems. In 2012, the Department of Landscape Architecture and Environmental Planning at University of California, Berkeley organized a symposium-based PPA for the Three Gorges Dam on the Yangtze River. Prior to this symposium, the twelve invited Chinese scientists, engineers and economists with recent research on Three Gorges Dam had not had the opportunity to present their evaluations together in an open, public forum. With a 50-year planning horizon, the symposium's five sessions centered on impacts on flows, geomorphology, geologic hazards, the environment and socioeconomic effects. Three Gorges' project goals focused on flood control, hydropower and improved navigation. According to expert research, major changes in sediment budget and flow regime from reservoir operation have significantly reduced sediment discharge into the downstream river and estuary, initiating a series of geomorphic changes with ecological and social impacts. While the dam reduces high flow stages from floods originating above the

  20. Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

    PubMed

    Miner, Kyle D; Kurtz, Donald M

    2016-02-16

    HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites.

  1. A rapid and direct method for the determination of active site accessibility in proteins based on ESI-MS and active site titrations.

    PubMed

    O'Farrell, Norah; Kreiner, Michaela; Moore, Barry D; Parker, Marie-Claire

    2006-11-01

    We have developed an electrospray ionisation mass spectrometry (ESI-MS) technique that can be applied to rapidly determine the number of intact active sites in proteins. The methodology relies on inhibiting the protein with an active-site irreversible inhibitor and then using ESI-MS to determine the extent of inhibition. We have applied this methodology to a test system: a serine protease, subtilisin Carlsberg, and monitored the extent of inhibition by phenylmethylsulfonyl fluoride (PMSF), an irreversible serine hydrolase inhibitor as a function of the changes in immobilisation and hydration conditions. Two types of enzyme preparation were investigated, lyophilised enzymes and protein-coated microcrystals (PCMC).

  2. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand.

    PubMed

    Parashar, Abhinav; Venkatachalam, Avanthika; Gideon, Daniel Andrew; Manoj, Kelath Murali

    2014-12-12

    The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins' active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes.

  3. 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…

  4. Endolysosomes Are the Principal Intracellular Sites of Acid Hydrolase Activity.

    PubMed

    Bright, Nicholas A; Davis, Luther J; Luzio, J Paul

    2016-09-12

    The endocytic delivery of macromolecules from the mammalian cell surface for degradation by lysosomal acid hydrolases requires traffic through early endosomes to late endosomes followed by transient (kissing) or complete fusions between late endosomes and lysosomes. Transient or complete fusion results in the formation of endolysosomes, which are hybrid organelles from which lysosomes are re-formed. We have used synthetic membrane-permeable cathepsin substrates, which liberate fluorescent reporters upon proteolytic cleavage, as well as acid phosphatase cytochemistry to identify which endocytic compartments are acid hydrolase active. We found that endolysosomes are the principal organelles in which acid hydrolase substrates are cleaved. Endolysosomes also accumulated acidotropic probes and could be distinguished from terminal storage lysosomes, which were acid hydrolase inactive and did not accumulate acidotropic probes. Using live-cell microscopy, we have demonstrated that fusion events, which form endolysosomes, precede the onset of acid hydrolase activity. By means of sucrose and invertase uptake experiments, we have also shown that acid-hydrolase-active endolysosomes and acid-hydrolase-inactive, terminal storage lysosomes exist in dynamic equilibrium. We conclude that the terminal endocytic compartment is composed of acid-hydrolase-active, acidic endolysosomes and acid hydrolase-inactive, non-acidic, terminal storage lysosomes, which are linked and function in a lysosome regeneration cycle. PMID:27498570

  5. Outside-binding site mutations modify the active site's shapes in neuraminidase from influenza A H1N1.

    PubMed

    Tolentino-Lopez, Luis; Segura-Cabrera, Aldo; Reyes-Loyola, Paola; Zimic, Mirko; Quiliano, Miguel; Briz, Veronica; Muñoz-Fernández, Angeles; Rodríguez-Pérez, Mario; Ilizaliturri-Flores, Ian; Correa-Basurto, Jose

    2013-01-01

    The recent occurrence of 2009 influenza A (H1N1) pandemic as well as others has raised concern of a far more dangerous outcome should this virus becomes resistant to current drug therapies. The number of clinical cases that are resistant to oseltamivir (Tamiflu®) is larger than the limited number of neuraminidase (NA) mutations (H275Y, N295S, and I223R) that have been identified at the active site and that are associated to oseltamivir resistance. In this study, we have performed a comparative analysis between a set of NAs that have the most representative mutations located outside the active site. The recently crystallized NA-oseltamivir complex (PDB ID: 3NSS) was used as a wild-type structure. After selecting the target NA sequences, their three-dimensional (3D) structure was built using 3NSS as a template by homology modeling. The 3D NA models were refined by molecular dynamics (MD) simulations. The refined models were used to perform a docking study, using oseltamivir as a ligand. Furthermore, the docking results were refined by free-energy analysis using the MM-PBSA method. The analysis of the MD simulation results showed that the NA models reached convergence during the first 10 ns. Visual inspection and structural measures showed that the mutated NA active sites show structural variations. The docking and MM-PBSA results from the complexes showed different binding modes and free energy values. These results suggest that distant mutations located outside the active site of NA affect its structure and could be considered to be a new source of resistance to oseltamivir, which agrees with reports in the clinical literature.

  6. 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.

  7. 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.

  8. 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

  9. Reduction of Urease Activity by Interaction with the Flap Covering the Active Site

    PubMed Central

    Macomber, Lee; Minkara, Mona S.; Hausinger, Robert P.; Merz, Kenneth M.

    2015-01-01

    With the increasing appreciation for the human microbiome coupled with the global rise of antibiotic resistant organisms, it is imperative that new methods be developed to specifically target pathogens. To that end, a novel computational approach was devised to identify compounds that reduce the activity of urease, a medically important enzyme of Helicobacter pylori, Proteus mirabilis, and many other microorganisms. Urease contains a flexible loop that covers its active site; Glide was used to identify small molecules predicted to lock this loop in an open conformation. These compounds were screened against the model urease from Klebsiella aerogenes and the natural products epigallocatechin and quercetin were shown to inhibit at low and high micromolar concentrations, respectively. These molecules exhibit a strong time-dependent inactivation of urease that was not due to their oxygen sensitivity. Rather, these compounds appear to inactivate urease by reacting with a specific Cys residue located on the flexible loop. Substitution of this cysteine by alanine in the C319A variant increased the urease resistance to both epigallocatechin and quercetin, as predicted by the computational studies. Protein dynamics are integral to the function of many enzymes; thus, identification of compounds that lock an enzyme into a single conformation presents a useful approach to define potential inhibitors. PMID:25594724

  10. Spectroscopic definition of the copper active sites in mordenite: selective methane oxidation.

    PubMed

    Vanelderen, Pieter; Snyder, Benjamin E R; Tsai, Ming-Li; Hadt, Ryan G; Vancauwenbergh, Julie; Coussens, Olivier; Schoonheydt, Robert A; Sels, Bert F; Solomon, Edward I

    2015-05-20

    Two distinct [Cu-O-Cu](2+) sites with methane monooxygenase activity are identified in the zeolite Cu-MOR, emphasizing that this Cu-O-Cu active site geometry, having a ∠Cu-O-Cu ∼140°, is particularly formed and stabilized in zeolite topologies. Whereas in ZSM-5 a similar [Cu-O-Cu](2+) active site is located in the intersection of the two 10 membered rings, Cu-MOR provides two distinct local structures, situated in the 8 membered ring windows of the side pockets. Despite their structural similarity, as ascertained by electronic absorption and resonance Raman spectroscopy, the two Cu-O-Cu active sites in Cu-MOR clearly show different kinetic behaviors in selective methane oxidation. This difference in reactivity is too large to be ascribed to subtle differences in the ground states of the Cu-O-Cu sites, indicating the zeolite lattice tunes their reactivity through second-sphere effects. The MOR lattice is therefore functionally analogous to the active site pocket of a metalloenzyme, demonstrating that both the active site and its framework environment contribute to and direct reactivity in transition metal ion-zeolites.

  11. School Pharmacist/School Environmental Hygienic Activities at School Site.

    PubMed

    Muramatsu, Akiyoshi

    2016-01-01

    The "School Health and Safety Act" was enforced in April 2009 in Japan, and "school environmental health standards" were established by the Minister of Education, Culture, Sports, Science and Technology. In Article 24 of the Enforcement Regulations, the duties of the school pharmacist have been clarified; school pharmacists have charged with promoting health activities in schools and carrying out complete and regular checks based on the "school environmental health standards" in order to protect the health of students and staff. In supported of this, the school pharmacist group of Japan Pharmaceutical Association has created and distributed digital video discs (DVDs) on "check methods of school environmental health standards" as support material. We use the DVD to ensure the basic issues that school pharmacists deal with, such as objectives, criteria, and methods for each item to be checked, advice, and post-measures. We conduct various workshops and classes, and set up Q&A committees so that inquiries from members are answered with the help of such activities. In addition, school pharmacists try to improve the knowledge of the school staff on environmental hygiene during their in-service training. They also conduct "drug abuse prevention classes" at school and seek to improve knowledge and recognition of drugs, including "dangerous drugs". PMID:27252053

  12. Excavation of Tunnel Valleys and Inner Gorges by Subglacial Meltwater Erosion

    NASA Astrophysics Data System (ADS)

    Beaud, F.; Flowers, G. E.; Venditti, J. G.; Koppes, M. N.

    2015-12-01

    Subglacial meltwater erosion (SME) is thought to contribute to the excavation of tunnel valleys and inner gorges, yet the underpinnings of the formation of these landforms remain obscure. Tunnel valleys are large channel-like features (100s of metres to few kilometres wide and up to 10s of kilometres in length) commonly found in the vicinity of former continental ice-sheet margins. The main question concerning their formation is: does SME excavate them gradually or by large subglacial floods? Inner gorges are V-shaped incisions in an otherwise glacially overprinted landscape. The initial assertion of their fluvial origin has recently been disputed, as they have been shown to persist through multiple glaciations and SME has been invoked to explain some inner gorges in Scandinavia and the Alps. The question is therefore: can SME explain the excavation of an inner gorge? In order to test these hypotheses related to the genesis of tunnel valleys and inner gorges, we use a 1-D model of subglacial hydrology to drive a model of bedrock erosion by total sediment load based on the tools and cover effect. Calculated values of subglacial transport stage in response to ordinary seasonal processes are comparable to those during large floods in rivers. Subglacial floods therefore limit bedrock erosion by transporting sediment farther from the bed, thus inhibiting impacts. Consequently, we find that gradual SME is likely to produce more incision over a glacial cycle. When we simulate the total SME that occurs through a glacial cycle under a synthetic ice-sheet margin, we are able to produce tunnel valleys or inner gorges over the timespan of a glaciation. Based on these results, we propose that (1) tunnel valleys and inner gorges can both be the result of SME, (2) tunnel valleys in bedrock can be formed through gradual processes rather than floods, and (3) SME enhances inner gorge relief.

  13. An Accessory Agonist Binding Site Promotes Activation of α4β2* Nicotinic Acetylcholine Receptors.

    PubMed

    Wang, Jingyi; Kuryatov, Alexander; Sriram, Aarati; Jin, Zhuang; Kamenecka, Theodore M; Kenny, Paul J; Lindstrom, Jon

    2015-05-29

    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.

  14. Isolated metal active site concentration and stability control catalytic CO2 reduction selectivity.

    PubMed

    Matsubu, John C; Yang, Vanessa N; Christopher, Phillip

    2015-03-01

    CO2 reduction by H2 on heterogeneous catalysts is an important class of reactions that has been studied for decades. However, atomic scale details of structure-function relationships are still poorly understood. Particularly, it has been suggested that metal particle size plays a unique role in controlling the stability of CO2 hydrogenation catalysts and the distribution of active sites, which dictates reactivity and selectivity. These studies often have not considered the possible role of isolated metal active sites in the observed dependences. Here, we utilize probe molecule diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) with known site-specific extinction coefficients to quantify the fraction of Rh sites residing as atomically dispersed isolated sites (Rhiso), as well as Rh sites on the surface of Rh nanoparticles (RhNP) for a series of TiO2 supported Rh catalysts. Strong correlations were observed between the catalytic reverse water gas shift turn over frequency (TOF) and the fraction of Rhiso sites and between catalytic methanation TOF and the fraction of RhNP sites. Furthermore, it was observed that reaction condition-induced disintegration of Rh nanoparticles, forming Rhiso active sites, controls the changing reactivity with time on stream. This work demonstrates that isolated atoms and nanoparticles of the same metal on the same support can exhibit uniquely different catalytic selectivity in competing parallel reaction pathways and that disintegration of nanoparticles under reaction conditions can play a significant role in controlling stability.

  15. Isolated metal active site concentration and stability control catalytic CO2 reduction selectivity.

    PubMed

    Matsubu, John C; Yang, Vanessa N; Christopher, Phillip

    2015-03-01

    CO2 reduction by H2 on heterogeneous catalysts is an important class of reactions that has been studied for decades. However, atomic scale details of structure-function relationships are still poorly understood. Particularly, it has been suggested that metal particle size plays a unique role in controlling the stability of CO2 hydrogenation catalysts and the distribution of active sites, which dictates reactivity and selectivity. These studies often have not considered the possible role of isolated metal active sites in the observed dependences. Here, we utilize probe molecule diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) with known site-specific extinction coefficients to quantify the fraction of Rh sites residing as atomically dispersed isolated sites (Rhiso), as well as Rh sites on the surface of Rh nanoparticles (RhNP) for a series of TiO2 supported Rh catalysts. Strong correlations were observed between the catalytic reverse water gas shift turn over frequency (TOF) and the fraction of Rhiso sites and between catalytic methanation TOF and the fraction of RhNP sites. Furthermore, it was observed that reaction condition-induced disintegration of Rh nanoparticles, forming Rhiso active sites, controls the changing reactivity with time on stream. This work demonstrates that isolated atoms and nanoparticles of the same metal on the same support can exhibit uniquely different catalytic selectivity in competing parallel reaction pathways and that disintegration of nanoparticles under reaction conditions can play a significant role in controlling stability. PMID:25671686

  16. Site specific rationale for technical impracticability of active groundwater restoration at a former manufactured gas plant site

    SciTech Connect

    Logan, C.M.; Walden, R.H.; MacFarlane, I.D.

    1995-12-31

    The National Contingency Plan (40 CFR Part 300 ) requires that remedial strategies must, at minimum, protect human health and the environment and meet applicable and relevant or appropriate requirements (ARARs). Where groundwater is impacted, maximum contaminant levels (MCLs) and maximum contaminant level goals (MCLGs) set under the Safe Drinking Water Act are often used as ARARs, whether or not the aquifer is a reasonably anticipated future source of drinking water. The US Environmental Protection Agency now recognizes the difficulty of groundwater restoration at sites where dense nonaqueous phase liquids are present, particularly in certain complex hydrogeological settings (EPA 1993). However, demonstration of impracticability generally does not occur until active remediation (e.g., pump and treat) has been shown to be ineffective. A case study of a former manufactured gas plant (MGP) is used to demonstrate how physical and chemical properties of the aquifer and coal tar, the major waste product from MGP sites, influence the feasibility of active restoration. Field characterization investigations, laboratory studies, and groundwater modeling are integrated into a demonstration following EPA guidelines. Laboratory studies included microbiological characterization and natural biodegradation and suggest that intrinsic bioremediation is occurring at this site. This work will be useful as EPA continues to develop presumptive remedies for cleanup under Superfund.

  17. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-11-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  18. The calculation of surface orbital energies for specific types of active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.; Cole, F.

    1992-01-01

    An angular overlap calculation has been used to determine the s, p, and d orbital energy levels of the different types of surface sites present on dispersed metal catalysts. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  19. 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...

  20. Activity of site-specific endonucleases on complexes of plasmid DNA with multiwalled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Egorova, V. P.; Krylova, H. V.; Lipnevich, I. V.; Veligura, A. A.; Shulitsky, B. G.; Asayonok, A. A.; Vaskovtsev, E. V.

    2016-08-01

    We have synthesized and investigated structural and functional properties of plasmid DNA complexes with multi-walled carbon nanotubes (MWCNTs) for detection of changes in structural state of the plasmid DNA at its recognition by site-specific endonuclease. It has been also established that the site-specific endonuclease is functionally active on the surface of MWCNTs.

  1. 77 FR 5560 - Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-03

    ... project proposals on those leases) in identified Wind Energy Areas (WEAs) on the OCS offshore New Jersey... Bureau of Ocean Energy Management Commercial Wind Lease Issuance and Site Assessment Activities on the... site assessment plans (SAPs) on those leases. BOEM may issue one or more commercial wind energy...

  2. The balance of flexibility and rigidity in the active site residues of hen egg white lysozyme

    NASA Astrophysics Data System (ADS)

    Qi, Jian-Xun; Jiang, Fan

    2011-05-01

    The crystallographic temperature factors (B factor) of individual atoms contain important information about the thermal motion of the atoms in a macromolecule. Previously the theory of flexibility of active site has been established based on the observation that the enzyme activity is sensitive to low concentration denaturing agents. It has been found that the loss of enzyme activity occurs well before the disruption of the three-dimensional structural scaffold of the enzyme. To test the theory of conformational flexibility of enzyme active site, crystal structures were perturbed by soaking in low concentration guanidine hydrochloride solutions. It was found that many lysozyme crystals tested could still diffract until the concentration of guanidine hydrochloride reached 3 M. It was also found that the B factors averaged over individually collected data sets were more accurate. Thus it suggested that accurate measurement of crystal temperature factors could be achieved for medium-high or even medium resolution crystals by averaging over multiple data sets. Furthermore, we found that the correctly predicted active sites included not only the more flexible residues, but also some more rigid residues. Both the flexible and the rigid residues in the active site played an important role in forming the active site residue network, covering the majority of the substrate binding residues. Therefore, this experimental prediction method may be useful for characterizing the binding site and the function of a protein, such as drug targeting.

  3. Chemical modification studies on arginine kinase: essential cysteine and arginine residues at the active site.

    PubMed

    Zhu, Wen-Jing; Li, Miao; Wang, Xiao-Yun

    2007-12-01

    Chemical modification was used to elucidate the essential amino acids in the catalytic activity of arginine kinase (AK) from Migratoria manilensis. Among six cysteine (Cys) residues only one Cys residue was determined to be essential in the active site by Tsou's method. Furthermore, the AK modified by DTNB can be fully reactivated by dithiothreitol (DTT) in a monophasic kinetic course. At the same time, this reactivation can be slowed down in the presence of ATP, suggesting that the essential Cys is located near the ATP binding site. The ionizing groups at the AK active site were studied and the standard dissociation enthalpy (DeltaH degrees ) was 12.38kcal/mol, showing that the dissociation group may be the guanidino of arginine (Arg). Using the specific chemical modifier phenylglyoxal (PG) demonstrated that only one Arg, located near the ATP binding site, is essential for the activity of AK. PMID:17765964

  4. 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.

  5. Anisotropic Covalency Contributions to Superexchange Pathways in Type One Copper Active Sites

    PubMed Central

    2015-01-01

    Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu–S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (HDA) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu–S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites. PMID:25310460

  6. Molecular Characterization of Monoclonal Antibodies that Inhibit Acetylcholinesterase by Targeting the Peripheral Site and Backdoor Region

    PubMed Central

    Essono, Sosthène; Mondielli, Grégoire; Lamourette, Patricia; Boquet, Didier; Grassi, Jacques; Marchot, Pascale

    2013-01-01

    The inhibition properties and target sites of monoclonal antibodies (mAbs) Elec403, Elec408 and Elec410, generated against Electrophorus electricus acetylcholinesterase (AChE), have been defined previously using biochemical and mutagenesis approaches. Elec403 and Elec410, which bind competitively with each other and with the peptidic toxin inhibitor fasciculin, are directed toward distinctive albeit overlapping epitopes located at the AChE peripheral anionic site, which surrounds the entrance of the active site gorge. Elec408, which is not competitive with the other two mAbs nor fasciculin, targets a second epitope located in the backdoor region, distant from the gorge entrance. To characterize the molecular determinants dictating their binding site specificity, we cloned and sequenced the mAbs; generated antigen-binding fragments (Fab) retaining the parental inhibition properties; and explored their structure-function relationships using complementary x-ray crystallography, homology modeling and flexible docking approaches. Hypermutation of one Elec403 complementarity-determining region suggests occurrence of antigen-driven selection towards recognition of the AChE peripheral site. Comparative analysis of the 1.9Å-resolution structure of Fab408 and of theoretical models of its Fab403 and Fab410 congeners evidences distinctive surface topographies and anisotropic repartitions of charges, consistent with their respective target sites and inhibition properties. Finally, a validated, data-driven docking model of the Fab403-AChE complex suggests a mode of binding at the PAS that fully correlates with the functional data. This comprehensive study documents the molecular peculiarities of Fab403 and Fab410, as the largest peptidic inhibitors directed towards the peripheral site, and those of Fab408, as the first inhibitor directed toward the backdoor region of an AChE and a unique template for the design of new, specific modulators of AChE catalysis. PMID:24146971

  7. Probing impact of active site residue mutations on stability and activity of Neisseria polysaccharea amylosucrase.

    PubMed

    Daudé, David; Topham, Christopher M; Remaud-Siméon, Magali; André, Isabelle

    2013-12-01

    The amylosucrase from Neisseria polysaccharea is a transglucosidase from the GH13 family of glycoside-hydrolases that naturally catalyzes the synthesis of α-glucans from the widely available donor sucrose. Interestingly, natural molecular evolution has modeled a dense hydrogen bond network at subsite -1 responsible for the specific recognition of sucrose and conversely, it has loosened interactions at the subsite +1 creating a highly promiscuous subsite +1. The residues forming these subsites are considered to be likely involved in the activity as well as the overall stability of the enzyme. To assess their role, a structure-based approach was followed to reshape the subsite -1. A strategy based on stability change predictions, using the FoldX algorithm, was considered to identify the best candidates for site-directed mutagenesis and guide the construction of a small targeted library. A miniaturized purification protocol was developed and both mutant stability and substrate promiscuity were explored. A range of 8 °C between extreme melting temperature values was observed and some variants were able to synthesize series of oligosaccharides with distributions differing from that of the parental enzyme. The crucial role of subsite -1 was thus highlighted and the biocatalysts generated can now be considered as starting points for further engineering purposes.

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

    PubMed

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

    2014-04-01

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

  9. Site-directed mutagenesis and high-resolution NMR spectroscopy of the active site of porphobilinogen deaminase

    SciTech Connect

    Scott, A.I.; Roessner, C.A.; Stolowich, N.J.; Karuso, P.; Williams, H.J.; Grant, S.K.; Gonzalez, M.D.; Hoshino, T. )

    1988-10-18

    The active site of porphobilinogen (PBG){sup 1} deaminase from Escherichia coli has been found to contain an unusual dipyrromethane derived from four molecules of 5-aminolevulinic acid (ALA) covalently linked to Cys-242, one of the two cysteine residues conserved in E. coli and human deaminase. By use of a hemA{sup {minus}} strain of E. coli the enzyme was enriched from (5-{sup 13}C)ALA and examined by {sup 1}H-detected multiple quantum coherence spectroscopy, which revealed all of the salient features of a dipyrromethane composed of two PBG units linked heat to tail and terminating in a CH{sub 2}-S bond to a cysteine residue. Site-specific mutagenesis of Cys-99 and Cys-242, respectively, has shown that substitution of Ser for Cys-99 does not affect the enzymatic activity, whereas substitution of Ser for Cys-242 removes essentially all of the catalytic activity as measured by the conversion of the substrate PBG to uro'gen I. The NMR spectrum of the covalent complex of deaminase with the suicide inhibitor 2-bromo-(2,11-{sup 13}C{sub 2})PBG reveals that the aminomethyl terminus of the inhibitor reacts with the enzyme's cofactor at the {alpha}-free pyrrole. NMR spectroscopy of the ES{sub 2} complex confirmed a PBG-derived head-to-tail dipyrromethane attached to the {alpha}-free pyrrole position of the enzyme. A mechanistic rationale for deaminase is presented.

  10. 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.

  11. XAFS Study of the Photo-Active Site of Mo/MCM-41

    NASA Astrophysics Data System (ADS)

    Miyamoto, Daisuke; Ichikuni, Nobuyuki; Shimazu, Shogo

    2007-02-01

    An Mo/MCM-41 catalyst was prepared and used for study of propene and 1-butene photo-metathesis reactions. XAFS analysis revealed that hydrogen reduction leads to a decreased role for the Mo=O site. The Mo-O site plays an important role for the olefin photo-metathesis reaction on the H2 reduced Mo/MCM-41. From EXAFS analysis, the active site of photo-metathesis reaction is the Mo=O part for oxidized Mo/MCM-41, whereas it is the Mo-O site for reduced Mo/MCM-41.

  12. Occurrence and potential health risk of Cryptosporidium and Giardia in the Three Gorges Reservoir, China.

    PubMed

    Xiao, Guosheng; Qiu, Zhiqun; Qi, Junsheng; Chen, Ji-an; Liu, Fengdan; Liu, Wenyi; Luo, Jiaohua; Shu, Weiqun

    2013-05-01

    The Three Gorges Reservoir (TGR) is the biggest lake in the world and a major water source in China. There is no information about occurrence and impact of Cryptosporidium and Giardia on the aquatic ecosystem. 61 surface water samples from 23 monitoring sites and 5 treated effluent samples were collected and analyzed. Cryptosporidium oocysts and Giardia cysts were found, respectively, in 86.4% and 65.2% of a total of 66 water samples, with high concentrations in treated effluent. The mean percent recovery was 29.14% for oocysts and 34.86% for cysts. A seasonal pattern was observed, with positive samples for Cryptosporidium more frequent in flood period and positive samples for Giardia more frequent in impounding period. Counts of enterococci, fecal coliforms and total coliforms, and turbidity were significantly associated with Cryptosporidium concentration in backwater (water in a main river which is backed up by the Three Gorges Dam) areas of tributaries but not Giardia. High associations were also found between oocyst and cyst in backwater areas of tributaries and cities. The risks of infection and illness due to water consumption in four different exposure routes were estimated. The results showed that swimming in the TGR has the highest infection risk with 1.39 × 10(-3) per time (95% confidence interval (CI): 0.05-600.3 × 10(-5)) for Cryptosporidium and 2.08 × 10(-4) per time (95% CI: 0.05-878.87 × 10(-6)) for Giardia, while directly drinking unboiled tap water treated with the conventional process has the highest morbidity with 524.98 per 100,000 population per year (95% CI: 10.35-2040.26) for Cryptosporidium and 5.89 per 100,000 population per year (95% CI: 0.08-22.67) for Giardia. This study provides new useful information for drinking water plants, health care workers and managers to improve the safety of tap water and deduce the risk of surface water contamination in China.

  13. Occurrence and potential health risk of Cryptosporidium and Giardia in the Three Gorges Reservoir, China.

    PubMed

    Xiao, Guosheng; Qiu, Zhiqun; Qi, Junsheng; Chen, Ji-an; Liu, Fengdan; Liu, Wenyi; Luo, Jiaohua; Shu, Weiqun

    2013-05-01

    The Three Gorges Reservoir (TGR) is the biggest lake in the world and a major water source in China. There is no information about occurrence and impact of Cryptosporidium and Giardia on the aquatic ecosystem. 61 surface water samples from 23 monitoring sites and 5 treated effluent samples were collected and analyzed. Cryptosporidium oocysts and Giardia cysts were found, respectively, in 86.4% and 65.2% of a total of 66 water samples, with high concentrations in treated effluent. The mean percent recovery was 29.14% for oocysts and 34.86% for cysts. A seasonal pattern was observed, with positive samples for Cryptosporidium more frequent in flood period and positive samples for Giardia more frequent in impounding period. Counts of enterococci, fecal coliforms and total coliforms, and turbidity were significantly associated with Cryptosporidium concentration in backwater (water in a main river which is backed up by the Three Gorges Dam) areas of tributaries but not Giardia. High associations were also found between oocyst and cyst in backwater areas of tributaries and cities. The risks of infection and illness due to water consumption in four different exposure routes were estimated. The results showed that swimming in the TGR has the highest infection risk with 1.39 × 10(-3) per time (95% confidence interval (CI): 0.05-600.3 × 10(-5)) for Cryptosporidium and 2.08 × 10(-4) per time (95% CI: 0.05-878.87 × 10(-6)) for Giardia, while directly drinking unboiled tap water treated with the conventional process has the highest morbidity with 524.98 per 100,000 population per year (95% CI: 10.35-2040.26) for Cryptosporidium and 5.89 per 100,000 population per year (95% CI: 0.08-22.67) for Giardia. This study provides new useful information for drinking water plants, health care workers and managers to improve the safety of tap water and deduce the risk of surface water contamination in China. PMID:23478072

  14. The Three Mycobacterium tuberculosis Antigen 85 Isoforms Have Unique Substrates and Activities Determined by Non-active Site Regions*

    PubMed Central

    Backus, Keriann M.; Dolan, Michael A.; Barry, Conor S.; Joe, Maju; McPhie, Peter; Boshoff, Helena I. M.; Lowary, Todd L.; Davis, Benjamin G.; Barry, Clifton E.

    2014-01-01

    The three isoforms of antigen 85 (A, B, and C) are the most abundant secreted mycobacterial proteins and catalyze transesterification reactions that synthesize mycolated arabinogalactan, trehalose monomycolate (TMM), and trehalose dimycolate (TDM), important constituents of the outermost layer of the cellular envelope of Mycobacterium tuberculosis. These three enzymes are nearly identical at the active site and have therefore been postulated to exist to evade host immunity. Distal to the active site is a second putative carbohydrate-binding site of lower homology. Mutagenesis of the three isoforms at this second site affected both substrate selectivity and overall catalytic activity in vitro. Using synthetic and natural substrates, we show that these three enzymes exhibit unique selectivity; antigen 85A more efficiently mycolates TMM to form TDM, whereas C (and to a lesser extent B) has a higher rate of activity using free trehalose to form TMM. This difference in substrate selectivity extends to the hexasaccharide fragment of cell wall arabinan. Mutation of secondary site residues from the most active isoform (C) into those present in A or B partially interconverts this substrate selectivity. These experiments in combination with molecular dynamics simulations reveal that differences in the N-terminal helix α9, the adjacent Pro216–Phe228 loop, and helix α5 are the likely cause of changes in activity and substrate selectivity. These differences explain the existence of three isoforms and will allow for future work in developing inhibitors. PMID:25028517

  15. Diel and seasonal variation of methane and carbon dioxide fluxes from the Three Gorges Reservoir

    NASA Astrophysics Data System (ADS)

    Xiao, Shangbin; Liu, Defu; Wang, Yuchun; Zhang, Cheng

    2014-05-01

    In order to investigate the CH4 and CO2 fluxes across the water-gas interface of the Three Gorges Reservoirs and identify their controlling factors, four diel field campaigns and one monthly sampling campaign during June 2010~May 2011 were carried out at two site. Site Guojiaba was located at the mainstream of the Yangtze River and near the Three Gorges Dam, and Site XX06 was located at the middle of the Xiangxi Bay, which was a tributary of the Yangtze River before impounding. Hydrodynamic situation of the two sites was completely different, and the current velocity was big at Site Guojiaba and very low at Site XX06 at all times. CH4 fluxes at the sites were much lower than those from most other reservoirs or natural lakes. One of the most important reasons may be due to the oxidation of CH4 in water column owing to the huge water depth and high DO in water in the TGR. At XX06, the diel CH4 flux varied greatly during April 27-28, 2011 and October 4-5, 2010, and changed less during August 23-24, 2010. The average CH4 flux during October 4-5, 2010 is ~0.081 mg m- h-1, which is approximate to that of August 23-24 and much less than that during April 27-28, 2011. The diel average of flux observed during April 27-28, 2011 was ~3.6 and ~3.8 times of that during August 23-24, 2010 and October 4-5, 2010 respectively. Eutrophication of the bay occurred frequently as a consequence of large influxes of nutrients in most time of the observation year. The four highest Chl-a occurred in the time of low water level and warm season. The CH4 fluxes during the observation year ranged from -0.120 to 31.008 mg m-2 h-1 with an average of 3.288 mg m-2 d-1, which was much less than that reported from reservoirs in tropic and temperate regions. The maximum flux, which occurred in June 2010, was corresponding to the lowest water level. Water temperature, sediment temperature, and TOC did not have significant correlation with the monthly CH4 fluxes. Continuously decreasing hydrostatic

  16. Impacts of the Three Gorges Project on Local Climate

    NASA Astrophysics Data System (ADS)

    Song, Z.; Liang, S.; Feng, L.

    2015-12-01

    Three Gorges Project (TGP) is the largest hydroelectric project in the world and has led to significant land cover changes in Three Gorges Reservoir Area (TGRA). Since its construction the debates on its environmental and climatic impacts have never stopped, especially after the extreme drought and flood in Yangtze River Basin these years. TGP reached its final impounding water level in 2010. However, studies on systematically monitoring the long-term variations in surface and atmospheric parameters in TGRA are still lacking. In this study, three important surface parameters - surface albedo, land surface temperature (LST) and evapotranspiration (ET) and two climatic parameters - air temperature and precipitation were investigated from 2000 to 2013 by combining multiple remote sensing data and ground measurements. Results showed that along the reservoir albedo decreased significantly as a result of water impounding. Correspondingly, in the same region daytime LST decreased in spring and summer and nighttime LST increased in autumn and winter. In the western region of TGRA, albedo increased due to resettlement and LST also changed. The average ET increased by 20% in TGR but kept stable in the whole TGRA. In contrast to LST, air temperature showed less apparent spatial and temporal variability. Only in the region near the dam air temperature experienced a decrease at daytime and an increase at nighttime. Further analysis demonstrated precipitation revealed no apparent changes in TGRA and the precipitation anomaly in northwest of TGRA may not be connected with TGP. All of the findings provide a more substantial clues of local climate change caused by TGP.

  17. Transcriptional activation through ETS domain binding sites in the cytochrome c oxidase subunit IV gene

    SciTech Connect

    Virbasius, J.V.; Scarpulla, R.C. )

    1991-11-01

    A mutational analysis of the rat cytochrome c oxidase subunit IV (RCO4) promoter region revealed the presence of a major control element consisting of a tandemly repeated pair of binding sites for a nuclear factor from HeLa cells. This factor was designated NRF-2 (nuclear respiratory factor 2) because a functional recognition site was also found in the human ATP synthase {beta}-subunit gene. Deletion or site-directed point mutations of the NRF-2 binding sites in the RCO4 promoter resulted in substantial loss of transcriptional activity, and synthetic oligomers of the NRF-2 binding sites from both genes stimulated a heterologous promoter when cloned in cis. NRF-2 binding a transcriptional activation required a purine-rich core sequence, GGAA. This motif is characteristic of the recognition site for a family of activators referred to as ETS domain proteins because of the similarity within their DNA-binding domains to the ets-1 proto-oncogene product. NRF-2 recognized an authentic Ets-1 site within the Moloney murine sarcoma virus long terminal repeat, and this site was able to compete for NRF-2 binding to the RCO4 promoter sequence. However, in contrast to Ets-1, which appears to be exclusive to lymphoid tissues, NRF-2 has the broad tissue distribution expected of a regulator of respiratory chain expression.

  18. Geomorphological evolution of volcanic fluvial channels: Eighteen years of morphological monitoring of the upper strect of the Tenenepanco Gorge, Popocatépetl volcano, Mexico

    NASA Astrophysics Data System (ADS)

    Tanarro, Luis Miguel; Juan Zamorano, Jose; Andres, Nuria; Palacios, David

    2015-04-01

    During volcanic eruptions a significant volume of material accumulates on the slopes and pre-existing gorges of the stratovolcanoes. This abundance of loose and unconsolidated material is very likely to be mobilized by rapid flows or lahars generated by sudden heavy rain or melting snow and ice. Thus, volcanic gorges are affected by complex cycles of incision, filling and widening, altering the equilibrium of river systems due to the major changes that lahars cause in channel morphology. These geomorphological dynamics characterize the gorges located on the north flank of the Popocatépetl volcano (19°02' N, 98°62' W, 5424 m). This volcano, located in the centre of the Trans-Mexican Volcanic Belt, began its most recent eruptive period in December 1994, when a glacier partially covered the northern slope. Since then, the interaction of volcanic and glacier activity triggered the formation of lahars in the gorges, causing significant morphological changes in the channel (especially in April 1995, July 1997 and January 2001). The most recent major eruption at Popocatépetl took place on 19 July 2003, and since then a series of smaller eruptions has reduced the glacier to near extinction. The aim of this study is to assess the morphological response of the Tenenepanco channel over an 18-year period, from 1995-2013, where two main scenarios can be observed: a) the period from 1995 to 2001 of volcanic activity and glacier retreat with the formation of flows and b) the period from 2002 to 2013 of relative volcanic calm, the almost complete extinction of the glacier, and the formation of secondary lahars associated with heavy rainfall. Monitoring of the gorge has consisted in the elaboration of 14 geomorphological maps during field studies (November 14, 1995, December 5, 1997, February 7, 1998, October 6, 2001, November 14, 1995, December 5, 1997, February 7, 1998, October 6, 2001, Julio 16, 2002, February 11, 2004, September 8, 2004, February 5, 2006, November 2, 2008

  19. Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.

    PubMed

    Fafarman, Aaron T; Sigala, Paul A; Schwans, Jason P; Fenn, Timothy D; Herschlag, Daniel; Boxer, Steven G

    2012-02-01

    Understanding the electrostatic forces and features within highly heterogeneous, anisotropic, and chemically complex enzyme active sites and their connection to biological catalysis remains a longstanding challenge, in part due to the paucity of incisive experimental probes of electrostatic properties within proteins. To quantitatively assess the landscape of electrostatic fields at discrete locations and orientations within an enzyme active site, we have incorporated site-specific thiocyanate vibrational probes into multiple positions within bacterial ketosteroid isomerase. A battery of X-ray crystallographic, vibrational Stark spectroscopy, and NMR studies revealed electrostatic field heterogeneity of 8 MV/cm between active site probe locations and widely differing sensitivities of discrete probes to common electrostatic perturbations from mutation, ligand binding, and pH changes. Electrostatic calculations based on active site ionization states assigned by literature precedent and computational pK(a) prediction were unable to quantitatively account for the observed vibrational band shifts. However, electrostatic models of the D40N mutant gave qualitative agreement with the observed vibrational effects when an unusual ionization of an active site tyrosine with a pK(a) near 7 was included. UV-absorbance and (13)C NMR experiments confirmed the presence of a tyrosinate in the active site, in agreement with electrostatic models. This work provides the most direct measure of the heterogeneous and anisotropic nature of the electrostatic environment within an enzyme active site, and these measurements provide incisive benchmarks for further developing accurate computational models and a foundation for future tests of electrostatics in enzymatic catalysis.

  20. Flood characteristics for the New River in the New River Gorge National River, West Virginia

    USGS Publications Warehouse

    Wiley, J.B.; Cunningham, M.K.

    1994-01-01

    The frequency and magnitude of flooding of the New River in the New River Gorge National River was studied. A steady-state, one-dimensional flow model was applied to the study reach. Rating curves, cross sections, and Manning's roughness coefficients that were used are presented in this report. Manning's roughness coefficients were evaluated by comparing computed elevations (from application of the steady-state, one-dimensional flow model) to rated elevations at U.S. Geological Survey (USGS) streamflow-gaging stations and miscellaneous-rating sites. Manning's roughness coefficients ranged from 0.030 to 0.075 and varied with hydraulic depth. The 2-, 25-, and 100-year flood discharges were esti- mated on the basis of information from flood- insurance studies of Summers County, Fayette County, and the city of Hinton, and flood-frequency analysis of discharge records for the USGS streamflow-gaging stations at Hinton and Thurmond. The 100-year discharge ranged from 107,000 cubic feet per second at Hinton to 150,000 cubic feet per second at Fayette.

  1. Spatial and temporal aspects of greenhouse gas emissions from Three Gorges Reservoir, China

    NASA Astrophysics Data System (ADS)

    Zhao, Y.; Wu, B. F.; Zeng, Y.

    2012-10-01

    Before completion of the Three Gorges Reservoir (TGR), China, there was growing apprehension that it would become a major emitter of greenhouse gases (GHG): Carbon Dioxide (CO2), Methane (CH4) and Nitrous Oxide (N2O). We report monthly measurements for one year of the fluxes of these gases at multiple sites within the TGR, Yangtze River, China, and from several major tributaries, and immediately downstream of the dam. The tributary areas have lower CO2 fluxes than the main storage; CH4 fluxes to the atmosphere after passage through the turbines are negligible. Overall, TGR showed significantly lower CH4 emission rates than most new reservoirs in temperate and tropical regions. We attribute this to the well-oxygenated deep water and high water velocities which produce oxic mainstem conditions inimical to CH4 emission. TGR's CO2 fluxes were lower than most tropical reservoirs and higher than most temperate systems. This is due to the high load of metabolizable soil carbon delivered through erosion to the Yangtze River. Compared to fossil fuelled power plants of equivalent power output TGR is a very small GHG emitter, annual CO2-equivalent emissions are approximately 1.7% of a coal-fired generating plant of comparable power output.

  2. Surface energy and radiation budgets in a steppe ecosystem in the Upper Columbia River Gorge

    SciTech Connect

    Whiteman, C.D.; Allwine, K.J.; Bian, X.

    1994-08-01

    Measurements of radiation and surface energy budget components are presented for a semiarid grassland-steppe ecosystem in the Upper Columbia River Gorge (45{degrees}45`25.6 inches N, 120{degrees}01`39.3 inches W, 190 m) for June 2-27, 1991. Over this period, the ratio of sensible to latent heat flux (the Bowen ratio) averaged 5.0, and mean daily surface energy balance totals were: net radiation, 9.23; ground heat flux, 1.25; latent heat flux, 1.32; and sensible heat flux, 6.66 MJ m{sup {minus}2} d{sup {minus}1}, where the mean daily nonradiative fluxes were directed away from the surface, and the mean daily radiative flux was directed toward the surface. On clear days, the site received from 0.71 to 0.76 of the theoretical extraterrestrial solar radiation. Albedo over the 26-d period varied from 0.17 to 0.21. Daily and daytime average values of the components are summarized, and a plot is presented of the 30-min average values of all components for the entire period.

  3. 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

  4. Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.

    PubMed

    Schöne, Stefanie; Jurk, Marcel; Helabad, Mahdi Bagherpoor; Dror, Iris; Lebars, Isabelle; Kieffer, Bruno; Imhof, Petra; Rohs, Remo; Vingron, Martin; Thomas-Chollier, Morgane; Meijsing, Sebastiaan H

    2016-09-01

    The glucocorticoid receptor (GR) binds as a homodimer to genomic response elements, which have particular sequence and shape characteristics. Here we show that the nucleotides directly flanking the core-binding site, differ depending on the strength of GR-dependent activation of nearby genes. Our study indicates that these flanking nucleotides change the three-dimensional structure of the DNA-binding site, the DNA-binding domain of GR and the quaternary structure of the dimeric complex. Functional studies in a defined genomic context show that sequence-induced changes in GR activity cannot be explained by differences in GR occupancy. Rather, mutating the dimerization interface mitigates DNA-induced changes in both activity and structure, arguing for a role of DNA-induced structural changes in modulating GR activity. Together, our study shows that DNA sequence identity of genomic binding sites modulates GR activity downstream of binding, which may play a role in achieving regulatory specificity towards individual target genes.

  5. 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.

  6. An overlapping kinase and phosphatase docking site regulates activity of the retinoblastoma protein.

    PubMed

    Hirschi, Alexander; Cecchini, Matthew; Steinhardt, Rachel C; Schamber, Michael R; Dick, Frederick A; Rubin, Seth M

    2010-09-01

    The phosphorylation state and corresponding activity of the retinoblastoma tumor suppressor protein (Rb) are modulated by a balance of kinase and phosphatase activities. Here we characterize the association of Rb with the catalytic subunit of protein phosphatase 1 (PP1c). A crystal structure identifies an enzyme docking site in the Rb C-terminal domain that is required for efficient PP1c activity toward Rb. The phosphatase docking site overlaps with the known docking site for cyclin-dependent kinase (Cdk), and PP1 competition with Cdk-cyclins for Rb binding is sufficient to retain Rb activity and block cell-cycle advancement. These results provide the first detailed molecular insights into Rb activation and establish a novel mechanism for Rb regulation in which kinase and phosphatase compete for substrate docking. PMID:20694007

  7. Formation of inner gorge and landslide occurrence by knickpoint recession in the Kii Mountains, southwest Japan

    NASA Astrophysics Data System (ADS)

    Hiraishi, Narumi; Chigira, Masahiro

    2010-05-01

    Fluvial and hillslope landforms, especially knick point, inner gorge and gravitationally deformed slope, have been investigated to reveal how landslides develop in the context of long-term slope development. We analyzed mountain topographies by using 10-m mesh DEM, topographic maps and aerial photographs in the Kii Mountains, southwest Japan. Airborne Laser Scanning has been applied for typical gravitational slope deformation area to examine the topography in detail. Field geological investigation has been conducted to reveal the effect of geology on knickpoint formation and landslide occurrence. We found widely extended relict paleosurfaces in higher elevations (900-1700 m) and inner gorges along the present rivers. The average slope angle was 27 degrees for the paleosurfaces and 37 degrees for the inner gorge slopes, respectively. The upstream end of an inner gorge coincided with a knickpoint of the river, which suggests that the inner gorges were made by the recession of knickpoint, which is the "erosion front". Field geological investigation indicated that these knickpoints and inner gorges are not due to lithological effect. The boundaries of inner gorges and paleosurfaces were convex slope breaks except for the places where gravitational slope deformation occurred. Gravitational slope deformation occurred on inner gorge slopes with outfacing structure, where convex slope breaks were not clearly observed. These facts suggest that gravitational deformation was induced by the instability caused by the undercut of outfacing slopes and that convex slope breaks were not made or erased by the gravitational slope deformation. Many recent large, catastrophic landslides occurred on these gravitationally deformed slopes, suggesting that these slopes were susceptible to landslides. In addition, the crown of rock slope failures are aligned along the convex slope breaks, which indicates that inner gorge slopes below the slope breaks are susceptible to slope failures

  8. Phytoplankton development and ecological status during a cyanobacterial bloom in a tributary bay of the Three Gorges Reservoir, China.

    PubMed

    Wang, Lan; Cai, Qinghua; Tan, Lu; Kong, Linghui

    2011-09-01

    Reservoirs can provide suitable conditions for cyanobacterial bloom development, which may impact on water quality and biological communities. Weekly surveys in a cyanobacterial bloom process were carried out in the mainstream and Xiangxi Bay of the Three Gorges Reservoir (China), from June 6 to July 18 in 2008. By application of the phytoplankton functional group approach, the spatiotemporal pattern, impact factors, and the ecological status based on Q index (assemblage index) were analyzed. The depth of euphotic layer was apparently the key factor driving the phytoplankton functional group variations. Longitudinal patterns of phytoplankton distribution were detected during this bloom: in the beginning phase, groups D (mainly Stephanodiscus hantzschii) and B (Cyclotella stelligera) dominated in the mainstream of the Three Gorges Reservoir and the mouth area of Xiangxi Bay, group Y (Cryptomonas species) dominated in the upper area, while groups J (mainly Pediastrum duplex), F (mainly Sphaerocystis schroeteri) and G (Pandorina morum and Eudorina elegans) were important in other areas; in the mid phase, group M became absolutely dominant in the whole region; and in the ending phase, besides groups M and Y, groups X2 (Chroomonas acuta, Pyramimonas nanella, etc.) and Lo (Ceratium hirundinella) became more important in the lower and upper area respectively. Generally the ecological status was bad, temporally varied with the bloom process. No spatial difference of ecological status was found in the mainstream, while longitudinal patterns in Xiangxi Bay were detected for different phases: firstly a few sites had relatively better status than the others, then nearly all the sites were in the bad condition, and at last the status in the downstream was better than that in the upstream. The longitudinal patterns of ecological status were related to phytoplankton distribution, disturbed by jacking from the downstream and flood from the upstream of Xiangxi Bay.

  9. 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.

  10. Multi-Orbit Ps-Insar for Landslide Monitoring in Three Gorges Area (Invited)

    NASA Astrophysics Data System (ADS)

    Liao, M.; Zhang, L.; Balz, T.; Shi, X.; Tantianuparp, P.

    2013-12-01

    The Three Gorges Project, the largest hydroelectric project of the world, became operational in 2003. The construction and operation of the dam significantly increased the number of active landslide bodies in the reservoir area. The reservoir area is huge, with approximately 600 km length along the Yangtze River starting from the dam at Sandouping in China's Hubei province. The dam itself was built on a rather geologically unstable zone, causing many concerns before, during, and after construction. Landslides are activated by the large surface-water level changes in each store-and-release cycle, but also by the construction of new buildings and roads and the deforestation in the area. Landslides are a huge safety concern in the area. To reduce the risks, various methods are applied in the area, such as a GPS networks and terrestrial surveillance. However, this sparse point information cannot cover the vast reservoir area. Furthermore, the area is densely vegetated and has a rough topography with steep mountainsides. Vast areas are practically inaccessible for terrestrial surveillance, due to the difficult terrain. Such a vast and inaccessible area is best to be surveyed using remote sensing techniques. Synthetic Aperture Radar (SAR) can measure long-term and continuous displacement trends using Differential Interferometric SAR (D-InSAR) and Persistent Scatterer Interferometry (PSI). However, the steep mountainside and the dense vegetation are also hindering the use of interferometric SAR techniques. The very dense vegetation causes a strong temporal decorrelation of the interferometric signal in the area. This especially affects shorter wavelength systems, like the X-band systems of TerraSAR-X and COSMO-SkyMed, but also the C-band systems. The longer wavelength L-band of ALOS PALSAR was less affected by the temporal decorrelation in the area, but unfortunately PALSAR is not operational anymore. The steep mountainsides also cause problems in the analysis of the

  11. Observation and analysis of time-variable gravity signal in China's Three Gorges Reservoir during the experimental water impoundment

    NASA Astrophysics Data System (ADS)

    Wang, L.; Chen, C.; Liang, Q.; Du, J.

    2012-12-01

    as underground water penetration and surface deformation. When the water level rose rapidly, the gravity field within 1 km of the river bank increase rapidly and the amplitude was relatively high. In the high water level stable period, gravity response was delayed in certain degree due to the huge water loads, the underground water penetration and the surface deformation. In addition, both water level and gravity curves represented the similar cycle responses of diurnal and semidiurnal features generated by local tides. During observations, the high-frequency signals of gravity variations between several water level stages were related to the sudden water level fluctuations and reservoir inflow. Moreover, these signals were also related to the surrounding earthquakes. Thus, the observation of time-variable gravity is potentially useful and especially important to monitor tectonic activities and geologic hazards surrounding the Three Gorges Reservoir. If combined with the natural seismic data, the relationship between gravity disturbances caused by water level changes and earthquakes will be investigated in the near future.

  12. Enhanced Enzyme Kinetic Stability by Increasing Rigidity within the Active Site*

    PubMed Central

    Xie, Yuan; An, Jiao; Yang, Guangyu; Wu, Geng; Zhang, Yong; Cui, Li; Feng, Yan

    2014-01-01

    Enzyme stability is an important issue for protein engineers. Understanding how rigidity in the active site affects protein kinetic stability will provide new insight into enzyme stabilization. In this study, we demonstrated enhanced kinetic stability of Candida antarctica lipase B (CalB) by mutating the structurally flexible residues within the active site. Six residues within 10 Å of the catalytic Ser105 residue with a high B factor were selected for iterative saturation mutagenesis. After screening 2200 colonies, we obtained the D223G/L278M mutant, which exhibited a 13-fold increase in half-life at 48 °C and a 12 °C higher T5015, the temperature at which enzyme activity is reduced to 50% after a 15-min heat treatment. Further characterization showed that global unfolding resistance against both thermal and chemical denaturation also improved. Analysis of the crystal structures of wild-type CalB and the D223G/L278M mutant revealed that the latter formed an extra main chain hydrogen bond network with seven structurally coupled residues within the flexible α10 helix that are primarily involved in forming the active site. Further investigation of the relative B factor profile and molecular dynamics simulation confirmed that the enhanced rigidity decreased fluctuation of the active site residues at high temperature. These results indicate that enhancing the rigidity of the flexible segment within the active site may provide an efficient method for improving enzyme kinetic stability. PMID:24448805

  13. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes.

    PubMed

    Cockburn, Darrell; Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

  14. 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

  15. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... (20″×14″) upright format signs specified in 29 CFR 1910.145(d)(4) and this paragraph; and (iii... 40 Protection of Environment 8 2011-07-01 2011-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an...

  16. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... (20″×14″) upright format signs specified in 29 CFR 1910.145(d)(4) and this paragraph; and (iii... 40 Protection of Environment 8 2010-07-01 2010-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an...

  17. 40 CFR 61.154 - Standard for active waste disposal sites.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... (20″×14″) upright format signs specified in 29 CFR 1910.145(d)(4) and this paragraph; and (iii... 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...

  18. 77 FR 39508 - Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-03

    ... specific project proposals on those leases) in an identified Wind Energy Area (WEA) on the OCS offshore... Bureau of Ocean Energy Management Commercial Wind Lease Issuance and Site Assessment Activities on the... Activities on the Atlantic OCS Offshore RI and MA'' to: Program Manager, Office of Renewable Energy...

  19. Effects of resource activities upon repository siting and waste containment with reference to bedded salt

    SciTech Connect

    Ashby, J.; Rowe, J.

    1980-02-01

    The primary consideration for the suitability of a nuclear waste repository site is the overall ability of the repository to safely contain radioactive waste. This report is a discussion of the past, present, and future effects of resource activities on waste containment. Past and present resource activities which provide release pathways (i.e., leaky boreholes, adjacent mines) will receive initial evaluation during the early stages of any repository site study. However, other resource activities which may have subtle effects on containment (e.g., long-term pumping causing increased groundwater gradients, invasion of saline water causing lower retardation) and all potential future resource activities must also be considered during the site evaluation process. Resource activities will affect both the siting and the designing of repositories. Ideally, sites should be located in areas of low resource activity and low potential for future activity, and repository design should seek to eliminate or minimize the adverse effects of any resource activity. Buffer zones should be created to provide areas in which resource activities that might adversely affect containment can be restricted or curtailed. This could mean removing large areas of land from resource development. The impact of these frozen assets should be assessed in terms of their economic value and of their effect upon resource reserves. This step could require a major effort in data acquisition and analysis followed by extensive numerical modeling of regional fluid flow and mass transport. Numerical models should be used to assess the effects of resource activity upon containment and should include the cumulative effects of different resource activities. Analysis by other methods is probably not possible except for relatively simple cases.

  20. Computational approaches to the determination of active site structures and reaction mechanisms in heterogeneous catalysts.

    PubMed

    Catlow, C R A; French, S A; Sokol, A A; Thomas, J M

    2005-04-15

    We apply quantum chemical methods to the study of active site structures and reaction mechanisms in mesoporous silica and metal oxide catalysts. Our approach is based on the use of both molecular cluster and embedded cluster (QM/MM) techniques, where the active site and molecular complex are described using density functional theory (DFT) and the embedding matrix simulated by shell model potentials. We consider three case studies: alkene epoxidation over the microporous TS-1 catalyst; methanol synthesis on ZnO and Cu/ZnO and C-H bond activation over Li-doped MgO.

  1. Computational approaches to the determination of active site structures and reaction mechanisms in heterogeneous catalysts.

    PubMed

    Catlow, C R A; French, S A; Sokol, A A; Thomas, J M

    2005-04-15

    We apply quantum chemical methods to the study of active site structures and reaction mechanisms in mesoporous silica and metal oxide catalysts. Our approach is based on the use of both molecular cluster and embedded cluster (QM/MM) techniques, where the active site and molecular complex are described using density functional theory (DFT) and the embedding matrix simulated by shell model potentials. We consider three case studies: alkene epoxidation over the microporous TS-1 catalyst; methanol synthesis on ZnO and Cu/ZnO and C-H bond activation over Li-doped MgO. PMID:15901543

  2. 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.

  3. 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

  4. Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor

    PubMed Central

    Spatzal, Thomas; Perez, Kathryn A; Howard, James B; Rees, Douglas C

    2015-01-01

    Dinitrogen reduction in the biological nitrogen cycle is catalyzed by nitrogenase, a two-component metalloenzyme. Understanding of the transformation of the inert resting state of the active site FeMo-cofactor into an activated state capable of reducing dinitrogen remains elusive. Here we report the catalysis dependent, site-selective incorporation of selenium into the FeMo-cofactor from selenocyanate as a newly identified substrate and inhibitor. The 1.60 Å resolution structure reveals selenium occupying the S2B site of FeMo-cofactor in the Azotobacter vinelandii MoFe-protein, a position that was recently identified as the CO-binding site. The Se2B-labeled enzyme retains substrate reduction activity and marks the starting point for a crystallographic pulse-chase experiment of the active site during turnover. Through a series of crystal structures obtained at resolutions of 1.32–1.66 Å, including the CO-inhibited form of Av1-Se2B, the exchangeability of all three belt-sulfur sites is demonstrated, providing direct insights into unforeseen rearrangements of the metal center during catalysis. DOI: http://dx.doi.org/10.7554/eLife.11620.001 PMID:26673079

  5. Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor.

    PubMed

    Spatzal, Thomas; Perez, Kathryn A; Howard, James B; Rees, Douglas C

    2015-12-16

    Dinitrogen reduction in the biological nitrogen cycle is catalyzed by nitrogenase, a two-component metalloenzyme. Understanding of the transformation of the inert resting state of the active site FeMo-cofactor into an activated state capable of reducing dinitrogen remains elusive. Here we report the catalysis dependent, site-selective incorporation of selenium into the FeMo-cofactor from selenocyanate as a newly identified substrate and inhibitor. The 1.60 Å resolution structure reveals selenium occupying the S2B site of FeMo-cofactor in the Azotobacter vinelandii MoFe-protein, a position that was recently identified as the CO-binding site. The Se2B-labeled enzyme retains substrate reduction activity and marks the starting point for a crystallographic pulse-chase experiment of the active site during turnover. Through a series of crystal structures obtained at resolutions of 1.32-1.66 Å, including the CO-inhibited form of Av1-Se2B, the exchangeability of all three belt-sulfur sites is demonstrated, providing direct insights into unforeseen rearrangements of the metal center during catalysis.

  6. 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.

  7. 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.

  8. Evaluation of physical activity web sites for use of behavior change theories.

    PubMed

    Doshi, Amol; Patrick, Kevin; Sallis, James F; Calfas, Karen

    2003-01-01

    Physical activity (PA) Web sites were assessed for their use of behavior change theories, including constructs of the health belief model, Transtheoretical Model, social cognitive theory, and the theory of reasoned action and planned behavior. An evaluation template for assessing PA Web sites was developed, and content validity and interrater reliability were demonstrated. Two independent raters evaluated 24 PA Web sites. Web sites varied widely in application of theory-based constructs, ranging from 5 to 48 on a 100-point scale. The most common intervention strategies were general information, social support, and realistic goal areas. Coverage of theory-based strategies was low, varying from 26% for social cognitive theory to 39% for health belief model. Overall, PA Web sites provided little assessment, feedback, or individually tailored assistance for users. They were unable to substantially tailor the on-line experience for users at different stages of change or different demographic characteristics.

  9. A conformational change in the peripheral anionic site of Torpedo californica acetylcholinesterase induced by a bis-imidazolium oxime.

    PubMed

    Legler, Patricia M; Soojhawon, Iswarduth; Millard, Charles B

    2015-09-01

    As part of ongoing efforts to design improved nerve agent antidotes, two X-ray crystal structures of Torpedo californica acetylcholinesterase (TcAChE) bound to the bis-pyridinium oxime, Ortho-7, or its experimental bis-imidazolium analogue, 2BIM-7, were determined. Bis-oximes contain two oxime groups connected by a hydrophobic linker. One oxime group of Ortho-7 binds at the entrance to the active-site gorge near Trp279, and the second binds at the bottom near Trp84 and Phe330. In the Ortho-7-TcAChE complex the oxime at the bottom of the gorge was directed towards the nucleophilic Ser200. In contrast, the oxime group of 2BIM-7 was rotated away from Ser200 and the oxime at the entrance induced a significant conformational change in the peripheral anionic site (PAS) residue Trp279. The conformational change alters the surface of the PAS and positions the imidazolium oxime of 2BIM-7 further from Ser200. The relatively weaker binding and poorer reactivation of VX-inhibited, tabun-inhibited or sarin-inhibited human acetylcholinesterase by 2BIM-7 compared with Ortho-7 may in part be owing to the unproductively bound states caught in crystallo. Overall, the reactivation efficiency of 2BIM-7 was comparable to that of 2-pyridine aldoxime methyl chloride (2-PAM), but unlike 2-PAM the bis-imidazolium oxime lacks a fixed charge, which may affect its membrane permeability. PMID:26327369

  10. [Three-dimensional Fluorescence Spectral Characteristics of Different Molecular Weight Fractionations of Dissolved Organic Matter in the Water-level Fluctuation Zones of Three Gorges Reservoir Areas].

    PubMed

    Chen, Xue-shuang; Jiang, Tao; Lu, Song; Wei, Shi-qiang; Wang, Ding-yong; Yan, Jin-long

    2016-03-15

    The study of the molecular weight (MW) fractions of dissolved organic matter (DOM) in aquatic environment is of interests because the size plays an important role in deciding the biogeochemical characteristics of DOM. Thus, using ultrafiltration ( UF) technique combined with three-dimensional fluorescence spectroscopy, DOM samples from four sampling sites in typical water-level fluctuation zones of Three Gorge Reservoir areas were selected to investigate the differences of properties and sources of different DOM MW fractions. The results showed that in these areas, the distribution of MW fractions was highly dispersive, but the approximately equal contributions from colloidal (Mr 1 x 10³-0.22 µm) and true dissolved fraction (Mr < 1 x 10³) to the total DOC concentration were found. Four fluorescence signals (humic-like A and C; protein-like B and T) were observed in all MW fractions including bulk DOM, which showed the same distribution trend: true dissolved > low MW (Mr 1 x 10³-10 x 10³) > medium MW (Mr 10 x 10³-30 x 10³) > high MW (Mr 30 x 10³-0.22 µm). Additionally, with decreasing MW fraction, fluorescence index (FI) and freshness index (BIX) increased suggesting enhanced signals of autochthonous inputs, whereas humification index ( HIX) decreased indicating lowe humification degree. It strongly suggested that terrestrial input mainly affected the composition and property of higher MW fractions of DOM, as compared to lower MW and true dissolved fractions that were controlled by autochthonous sources such as microbial and alga activities, instead of allochthonous sources. Meanwhile, the riparian different land-use types also affected obviously on the characteristics of DOM. Therefore, higher diversity of land-use types, and also higher complexity of ecosystem and landscapes, induced higher heterogeneity of fluorescence components in different MW fraction of DOM. PMID:27337878

  11. [Three-dimensional Fluorescence Spectral Characteristics of Different Molecular Weight Fractionations of Dissolved Organic Matter in the Water-level Fluctuation Zones of Three Gorges Reservoir Areas].

    PubMed

    Chen, Xue-shuang; Jiang, Tao; Lu, Song; Wei, Shi-qiang; Wang, Ding-yong; Yan, Jin-long

    2016-03-15

    The study of the molecular weight (MW) fractions of dissolved organic matter (DOM) in aquatic environment is of interests because the size plays an important role in deciding the biogeochemical characteristics of DOM. Thus, using ultrafiltration ( UF) technique combined with three-dimensional fluorescence spectroscopy, DOM samples from four sampling sites in typical water-level fluctuation zones of Three Gorge Reservoir areas were selected to investigate the differences of properties and sources of different DOM MW fractions. The results showed that in these areas, the distribution of MW fractions was highly dispersive, but the approximately equal contributions from colloidal (Mr 1 x 10³-0.22 µm) and true dissolved fraction (Mr < 1 x 10³) to the total DOC concentration were found. Four fluorescence signals (humic-like A and C; protein-like B and T) were observed in all MW fractions including bulk DOM, which showed the same distribution trend: true dissolved > low MW (Mr 1 x 10³-10 x 10³) > medium MW (Mr 10 x 10³-30 x 10³) > high MW (Mr 30 x 10³-0.22 µm). Additionally, with decreasing MW fraction, fluorescence index (FI) and freshness index (BIX) increased suggesting enhanced signals of autochthonous inputs, whereas humification index ( HIX) decreased indicating lowe humification degree. It strongly suggested that terrestrial input mainly affected the composition and property of higher MW fractions of DOM, as compared to lower MW and true dissolved fractions that were controlled by autochthonous sources such as microbial and alga activities, instead of allochthonous sources. Meanwhile, the riparian different land-use types also affected obviously on the characteristics of DOM. Therefore, higher diversity of land-use types, and also higher complexity of ecosystem and landscapes, induced higher heterogeneity of fluorescence components in different MW fraction of DOM.

  12. 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.

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

    SciTech Connect

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

    2015-06-04

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

  14. Active site of tripeptidyl peptidase II from human erythrocytes is of the subtilisin type.

    PubMed Central

    Tomkinson, B; Wernstedt, C; Hellman, U; Zetterqvist, O

    1987-01-01

    The present report presents evidence that the amino acid sequence around the serine of the active site of human tripeptidyl peptidase II is of the subtilisin type. The enzyme from human erythrocytes was covalently labeled at its active site with [3H]diisopropyl fluorophosphate, and the protein was subsequently reduced, alkylated, and digested with trypsin. The labeled tryptic peptides were purified by gel filtration and repeated reversed-phase HPLC, and their amino-terminal sequences were determined. Residue 9 contained the radioactive label and was, therefore, considered to be the active serine residue. The primary structure of the part of the active site (residues 1-10) containing this residue was concluded to be Xaa-Thr-Gln-Leu-Met-Asx-Gly-Thr-Ser-Met. This amino acid sequence is homologous to the sequence surrounding the active serine of the microbial peptidases subtilisin and thermitase. These data demonstrate that human tripeptidyl peptidase II represents a potentially distinct class of human peptidases and raise the question of an evolutionary relationship between the active site of a mammalian peptidase and that of the subtilisin family of serine peptidases. PMID:3313395

  15. 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

  16. Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.

    PubMed

    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.

  17. Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin

    SciTech Connect

    Dey, A.; Francis, E.J.; Adams, M.W.W.; Babini, E.; Takahashi, Y.; Fukuyama, K.; Hodgson, K.O.; Hedman, B.; Solomon, E.I.; /Stanford U., Chem. Dept. /Georgia U. /Bologna U. /Osaka U. /SLAC, SSRL

    2009-04-29

    A persistent puzzle in the field of biological electron transfer is the conserved iron-sulfur cluster motif in both high potential iron-sulfur protein (HiPIP) and ferredoxin (Fd) active sites. Despite this structural similarity, HiPIPs react oxidatively at physiological potentials, whereas Fds are reduced. Sulfur K-edge x-ray absorption spectroscopy uncovers the substantial influence of hydration on this variation in reactivity. Fe-S covalency is much lower in natively hydrated Fd active sites than in HiPIPs but increases upon water removal; similarly, HiPIP covalency decreases when unfolding exposes an otherwise hydrophobically shielded active site to water. Studies on model compounds and accompanying density functional theory calculations support a correlation of Fe-S covalency with ease of oxidation and therefore suggest that hydration accounts for most of the difference between Fd and HiPIP reduction potentials.

  18. 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.

  19. Wasp recruitment to the T cell:APC contact site occurs independently of Cdc42 activation.

    PubMed

    Cannon, J L; Labno, C M; Bosco, G; Seth, A; McGavin, M H; Siminovitch, K A; Rosen, M K; Burkhardt, J K

    2001-08-01

    Cdc42 and WASP are critical regulators of actin polymerization whose function during T cell signaling is poorly understood. Using a novel reagent that specifically detects Cdc42-GTP in fixed cells, we found that activated Cdc42 localizes to the T cell:APC contact site in an antigen-dependent manner. TCR signaling alone was sufficient to induce localization of Cdc42-GTP, and functional Lck and Zap-70 kinases were required. WASP also localized to the T cell:APC contact site in an antigen-dependent manner. Surprisingly, WASP localization was independent of the Cdc42 binding domain but required the proline-rich domain. Our results indicate that localized WASP activation requires the integration of multiple signals: WASP is recruited via interaction with SH3 domain-containing proteins and is activated by Cdc42-GTP concentrated at the same site. PMID:11520460

  20. Influence of flocculation on sediment deposition process at the Three Gorges Reservoir.

    PubMed

    Wang, Dangwei; Liu, Xiaofang; Ji, Zuwen; Dong, Zhandi; Hu, Haihua

    2016-01-01

    By comparing the original particle gradation of sediment from the Three Gorges Reservoir with the single particle gradation, the differences in these two particle gradations showed that there is sediment flocculation in the Three Gorges Reservoir, which can accelerate the sediment deposition rate in the reservoir. In order to determine the influence of flocculation on the sediment settling velocity, sediment was collected at the Three Gorges Reservoir, and the indoor quiescent settling experiment was performed to study the mechanism of sediment flocculation. The experimental results showed that sediments aggregated from single particles into floccules in the settling processes. The single particles smaller than 0.022 mm will participate in the formation of floccules, which accounts for 83% of the total amount of sediment in the Three Gorges Reservoir. Moreover, the degree of sediment flocculation and the increase in sediment settling velocity were directly proportional to the sediment concentration. Taking the average particle size and the median particle size as the representative particle size, respectively, the maximum flocculation factors were calculated to be 3.4 and 5.0. Due to the sediment flocculation, the volume of sediment deposition will increase by 66% when the mass settling flux factor of total sediment had a maximum value of 1.66, suggesting that flocculation has a significant influence on the sediment deposition rate in the Three Gorges Reservoir. PMID:26901731

  1. Influence of flocculation on sediment deposition process at the Three Gorges Reservoir.

    PubMed

    Wang, Dangwei; Liu, Xiaofang; Ji, Zuwen; Dong, Zhandi; Hu, Haihua

    2016-01-01

    By comparing the original particle gradation of sediment from the Three Gorges Reservoir with the single particle gradation, the differences in these two particle gradations showed that there is sediment flocculation in the Three Gorges Reservoir, which can accelerate the sediment deposition rate in the reservoir. In order to determine the influence of flocculation on the sediment settling velocity, sediment was collected at the Three Gorges Reservoir, and the indoor quiescent settling experiment was performed to study the mechanism of sediment flocculation. The experimental results showed that sediments aggregated from single particles into floccules in the settling processes. The single particles smaller than 0.022 mm will participate in the formation of floccules, which accounts for 83% of the total amount of sediment in the Three Gorges Reservoir. Moreover, the degree of sediment flocculation and the increase in sediment settling velocity were directly proportional to the sediment concentration. Taking the average particle size and the median particle size as the representative particle size, respectively, the maximum flocculation factors were calculated to be 3.4 and 5.0. Due to the sediment flocculation, the volume of sediment deposition will increase by 66% when the mass settling flux factor of total sediment had a maximum value of 1.66, suggesting that flocculation has a significant influence on the sediment deposition rate in the Three Gorges Reservoir.

  2. Mutations Closer to the Active Site Improve the Promiscuous Aldolase Activity of 4-Oxalocrotonate Tautomerase More Effectively than Distant Mutations.

    PubMed

    Rahimi, Mehran; van der Meer, Jan-Ytzen; Geertsema, Edzard M; Poddar, Harshwardhan; Baas, Bert-Jan; Poelarends, Gerrit J

    2016-07-01

    The enzyme 4-oxalocrotonate tautomerase (4-OT), which catalyzes enol-keto tautomerization as part of a degradative pathway for aromatic hydrocarbons, promiscuously catalyzes various carbon-carbon bond-forming reactions. These include the aldol condensation of acetaldehyde with benzaldehyde to yield cinnamaldehyde. Here, we demonstrate that 4-OT can be engineered into a more efficient aldolase for this condensation reaction, with a >5000-fold improvement in catalytic efficiency (kcat /Km ) and a >10(7) -fold change in reaction specificity, by exploring small libraries in which only "hotspots" are varied. The hotspots were identified by systematic mutagenesis (covering each residue), followed by a screen for single mutations that give a strong improvement in the desired aldolase activity. All beneficial mutations were near the active site of 4-OT, thus underpinning the notion that new catalytic activities of a promiscuous enzyme are more effectively enhanced by mutations close to the active site. PMID:27238293

  3. 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

  4. Kokanee Stock Status and Contribution of Cabinet Gorge Hatchery, Lake Pend Oreille, Idaho, 1987 Annual Progress Report.

    SciTech Connect

    Bowles, Edward C.

    1988-05-01

    Estimated kokanee Oncorhynchus nerka abundance in Lake Pend Oreille was 6.01 million during late summer 1987. This estimate is 40% higher than the 1986 estimate and is the second largest population estimate since 1977. Higher abundance is predominantly a result of enhanced fry survival and recruitment. Hatchery-reared fry contribution was 22% of total fry recruitment in 1987, compared to 8% in 1986, and resulted from a fivefold increase in survival. Much of this improvement can be attributed to the large (52 mm) fry produced at Cabinet Gorge Hatchery in 1987 and represents the first measurable contribution of the new hatchery to the kokanee rehabilitation program. Survival of hatchery-reared fry released into Clark Fork River was nearly one-half that of fry released into Sullivan Springs due to poor flow conditions and potentially high predation during migration from Cabinet Gorge Hatchery to Lake Pend Oreille. Wild fry survival was enhanced by early availability of forage (cladocern zooplankton) during fry emergence in late spring. Cladoceran production began three weeks earlier in 1987 than 1986, which resulted from reduced Mysis abundance and earlier thermal stratification of Lake Pend Oreille, which helped segregate cladocerans from mysid predation. Kokanee dry otolith coding was evaluated to provide a reliable long-term mark. Analysis of daily growth increments on otoliths was used successfully in 1987 to differentiate fry from various release sites. The technique will be refined during 1988 to include coding fry otoliths with water temperature fluctuations during hatchery residence. 23 refs., 20 figs., 2 tabs.

  5. 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.

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

    PubMed

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

    2016-08-18

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

  7. 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.

  8. A Tale of Two Isomerases: Compact versus Extended Active Sites in Ketosteroid Isomerase and Phosphoglucose Isomerase

    SciTech Connect

    Somarowthu, Srinivas; Brodkin, Heather R.; D’Aquino, J. Alejandro; Ringe, Dagmar; Ondrechen, Mary Jo; Beuning, Penny J.

    2012-07-11

    Understanding the catalytic efficiency and specificity of enzymes is a fundamental question of major practical and conceptual importance in biochemistry. Although progress in biochemical and structural studies has enriched our knowledge of enzymes, the role in enzyme catalysis of residues that are not nearest neighbors of the reacting substrate molecule is largely unexplored experimentally. Here computational active site predictors, THEMATICS and POOL, were employed to identify functionally important residues that are not in direct contact with the reacting substrate molecule. These predictions then guided experiments to explore the active sites of two isomerases, Pseudomonas putida ketosteroid isomerase (KSI) and human phosphoglucose isomerase (PGI), as prototypes for very different types of predicted active sites. Both KSI and PGI are members of EC 5.3 and catalyze similar reactions, but they represent significantly different degrees of remote residue participation, as predicted by THEMATICS and POOL. For KSI, a compact active site of mostly first-shell residues is predicted, but for PGI, an extended active site in which residues in the first, second, and third layers around the reacting substrate are predicted. Predicted residues that have not been previously tested experimentally were investigated by site-directed mutagenesis and kinetic analysis. In human PGI, single-point mutations of the predicted second- and third-shell residues K362, H100, E495, D511, H396, and Q388 show significant decreases in catalytic activity relative to that of the wild type. The results of these experiments demonstrate that, as predicted, remote residues are very important in PGI catalysis but make only small contributions to catalysis in KSI.

  9. SABER: A computational method for identifying active sites for new reactions

    PubMed Central

    Nosrati, Geoffrey R; Houk, K N

    2012-01-01

    A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644–1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were l-Ala d/l-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397

  10. SABER: a computational method for identifying active sites for new reactions.

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-05-01

    A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. PMID:22492397

  11. Preliminary examination of the impacts of repository site characterization activities and facility construction and operation activities on Hanford air quality

    SciTech Connect

    Glantz, C.S.; Ramsdell, J.V.

    1986-04-01

    Air quality impacts that would result from site characterization activities and from the construction and operation of a high-level nuclear wste repository at Hanford are estimated using two simple atmospheric dispersion models, HANCHI and CHISHORT. Model results indicate that pollutant concentrations would not exceed ambient air quality standards at any point outside the Hanford fenceline or at any publicly accessible location within the Hanford Site. The increase in pollutant concentrations in nearby communities due to site activities would be minimal. HANCHI and CHISHORT are documented in the appendices of this document. Further study of the repository's impact on air quality will be conducted when more detailed project plans and work schedules are available.

  12. Amphitheater-headed canyons formed by megaflooding at Malad Gorge, Idaho.

    PubMed

    Lamb, Michael P; Mackey, Benjamin H; Farley, Kenneth A

    2014-01-01

    Many bedrock canyons on Earth and Mars were eroded by upstream propagating headwalls, and a prominent goal in geomorphology and planetary science is to determine formation processes from canyon morphology. A diagnostic link between process and form remains highly controversial, however, and field investigations that isolate controls on canyon morphology are needed. Here we investigate the origin of Malad Gorge, Idaho, a canyon system cut into basalt with three remarkably distinct heads: two with amphitheater headwalls and the third housing the active Wood River and ending in a 7% grade knickzone. Scoured rims of the headwalls, relict plunge pools, sediment-transport constraints, and cosmogenic ((3)He) exposure ages indicate formation of the amphitheater-headed canyons by large-scale flooding ∼46 ka, coeval with formation of Box Canyon 18 km to the south as well as the eruption of McKinney Butte Basalt, suggesting widespread canyon formation following lava-flow diversion of the paleo-Wood River. Exposure ages within the knickzone-headed canyon indicate progressive upstream younging of strath terraces and a knickzone propagation rate of 2.5 cm/y over at least the past 33 ka. Results point to a potential diagnostic link between vertical amphitheater headwalls in basalt and rapid erosion during megaflooding due to the onset of block toppling, rather than previous interpretations of seepage erosion, with implications for quantifying the early hydrosphere of Mars. PMID:24344293

  13. Amphitheater-headed canyons formed by megaflooding at Malad Gorge, Idaho

    PubMed Central

    Lamb, Michael P.; Mackey, Benjamin H.; Farley, Kenneth A.

    2014-01-01

    Many bedrock canyons on Earth and Mars were eroded by upstream propagating headwalls, and a prominent goal in geomorphology and planetary science is to determine formation processes from canyon morphology. A diagnostic link between process and form remains highly controversial, however, and field investigations that isolate controls on canyon morphology are needed. Here we investigate the origin of Malad Gorge, Idaho, a canyon system cut into basalt with three remarkably distinct heads: two with amphitheater headwalls and the third housing the active Wood River and ending in a 7% grade knickzone. Scoured rims of the headwalls, relict plunge pools, sediment-transport constraints, and cosmogenic (3He) exposure ages indicate formation of the amphitheater-headed canyons by large-scale flooding ∼46 ka, coeval with formation of Box Canyon 18 km to the south as well as the eruption of McKinney Butte Basalt, suggesting widespread canyon formation following lava-flow diversion of the paleo-Wood River. Exposure ages within the knickzone-headed canyon indicate progressive upstream younging of strath terraces and a knickzone propagation rate of 2.5 cm/y over at least the past 33 ka. Results point to a potential diagnostic link between vertical amphitheater headwalls in basalt and rapid erosion during megaflooding due to the onset of block toppling, rather than previous interpretations of seepage erosion, with implications for quantifying the early hydrosphere of Mars. PMID:24344293

  14. Mathematical model for interactions and transport of phosphorus and sediment in the Three Gorges Reservoir.

    PubMed

    Huang, Lei; Fang, Hongwei; Reible, Danny

    2015-11-15

    Phosphorus fate and transport in natural waters plays a crucial role in the ecology of rivers and reservoirs. In this paper, a coupled model of hydrodynamics, sediment transport, and phosphorus transport is established, in which the effects of sediment on phosphorus transport are considered in detail. Phosphorus adsorption is estimated using a mechanistic surface complexation model which is capable of simulating the adsorption characteristics under various aquatic chemistry conditions. The sediment dynamics are analyzed to evaluate the deposition and release of phosphorus at the bed surface. In addition, the aerobic layer and anaerobic layer of the sediments are distinguished to study the distribution of phosphorus between dissolved and particulate phases in the active sediment layer. The proposed model is applied to evaluate the effects of various operating rules on sediment and phosphorus retention in the Three Gorges Reservoir (TGR). Results show that the proposed model can reasonably reflect the phosphorus transport with sediment, and management scenarios that influence sediment retention will also influence the phosphorus balance in the TGR. However, modest operational changes which have only minor effects on sediment retention also have limited influence on the phosphorous balance.

  15. [Distribution of Mercury in Plants at Water-Level-Fluctuating Zone in the Three Gorges Reservoir].

    PubMed

    Liang, Li; Wang, Yong-min; Li, Xian-yuan; Tang, Zhen-ya; Zhang, Xiang; Zhang, Cheng; WANG, Ding-yong

    2015-11-01

    The mercury (Hg) distribution and storage in plants at water-level-fluctuating zone (WLFZ) in the Three Gorges Reservoir were investigated by analyzing the total mercury(THg) and methylmercury ( MeHg) levels in different parts of plants collected from three typical sites including Shibaozhai, Zhenxi and Hanfeng Lake in WLFZ. The results indicated that THg and MeHg concentrations in plants ranged from (1.62 ± 0.57) to (49.42 ± 3.93) μg x kg(-1) and from (15.27 ± 7.09) to (1 974.67 ± 946.10) ng x kg(-1), respectively. In addition, THg levels in different plant parts followed the trend: root > leaf > stem, and similar trend for MeHg was observed with the highest level in root. An obvious spatial distribution was also found with the THg and MeHg levels in plants in Hanfeng higher than those in the same plants in the other two sampling sites (Shibaozhai and Zhenxi), and there was a difference of THg and MeHg storage in plants in various attitudes. The corresponding THg and MeHg storages were 145.3, 166.4, 124.3 and 88.2 mg x hm(-2), and 1.9, 2.7, 3.6 and 3.2 mg x hm(-2) in 145-150, 150-160, 160-170 and 170-175 m attitudes. The accumulation ability of dominant plants in WLFZ for THg (bioaccumulation factor, BAF < 1) was weaker than that for MeHg (BAF > 1).

  16. Contamination status of dioxins in sediment cores from the Three Gorges Dam area, China.

    PubMed

    Chen, Lei; Bi, Yonghong; Zhu, Kongxian; Hu, Zhengyu; Zhao, Wei; Henkelmann, Bernhard; Bernhöft, Silke; Temoka, Cedrique; Schramm, Karl-Werner

    2013-06-01

    In order to screen dioxin pollution in sediment of Three Gorges Dam (TGD) area, three sediment cores were obtained from two sites in 2010~2011; each core was divided into different samples with every 10 cm depth. Sediment dating determined by radiometry ((137)Cs, (210)Pb) and concentrations of dioxins were analyzed by high-resolution gas chromatography/mass spectrometry. The results indicated: Sediment dating showed no significant difference among all the samples from the same core and the two locations (ANOVA, p>0.05). The total amount of polychlorinated dibenzo-p-dioxins (PCDD)/Fs in all sample ranged from 30.7 to 371 pg/g dry weight (d.w.), with the mean value of 66.2 pg/g d.w. PCDDs occupied 60.33~85.22 % of dioxins in each sample, and PCDFs contributed to a very small extend. There was no significant difference in the dioxin concentration between 2010 and 2011 and in the two locations (t test, p>0.05), but the vertical distribution of dioxins showed significant different in different depths. Toxic equivalent (TEQ) (WHO 2005, Humans) of samples ranged from 0.15 to 1.60 pg/g d.w.; the mean was 0.41 pg/g d.w. No significant difference was found in TEQ between 2010 and 2011(t test, p>0.05). It could be concluded that the distribution of dioxins showed the spatial heterogeneous which resulted from the strong mixing and sediment deposition characteristics. Dioxin concentration in sediment cores was low with very low environmental risk potential. Dioxins at the two sites had the same origin, and exogenous input was the main source. It is the first report on the dioxins concentrations in sediment cores in the TGD area.

  17. Contamination status of dioxins in sediment cores from the Three Gorges Dam area, China.

    PubMed

    Chen, Lei; Bi, Yonghong; Zhu, Kongxian; Hu, Zhengyu; Zhao, Wei; Henkelmann, Bernhard; Bernhöft, Silke; Temoka, Cedrique; Schramm, Karl-Werner

    2013-06-01

    In order to screen dioxin pollution in sediment of Three Gorges Dam (TGD) area, three sediment cores were obtained from two sites in 2010~2011; each core was divided into different samples with every 10 cm depth. Sediment dating determined by radiometry ((137)Cs, (210)Pb) and concentrations of dioxins were analyzed by high-resolution gas chromatography/mass spectrometry. The results indicated: Sediment dating showed no significant difference among all the samples from the same core and the two locations (ANOVA, p>0.05). The total amount of polychlorinated dibenzo-p-dioxins (PCDD)/Fs in all sample ranged from 30.7 to 371 pg/g dry weight (d.w.), with the mean value of 66.2 pg/g d.w. PCDDs occupied 60.33~85.22 % of dioxins in each sample, and PCDFs contributed to a very small extend. There was no significant difference in the dioxin concentration between 2010 and 2011 and in the two locations (t test, p>0.05), but the vertical distribution of dioxins showed significant different in different depths. Toxic equivalent (TEQ) (WHO 2005, Humans) of samples ranged from 0.15 to 1.60 pg/g d.w.; the mean was 0.41 pg/g d.w. No significant difference was found in TEQ between 2010 and 2011(t test, p>0.05). It could be concluded that the distribution of dioxins showed the spatial heterogeneous which resulted from the strong mixing and sediment deposition characteristics. Dioxin concentration in sediment cores was low with very low environmental risk potential. Dioxins at the two sites had the same origin, and exogenous input was the main source. It is the first report on the dioxins concentrations in sediment cores in the TGD area. PMID:23296975

  18. Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity.

    PubMed

    Hartmann, Jens; Linke, Dennis; Bönniger, Christine; Tholey, Andreas; Sauter, Margret

    2015-12-15

    PSK (phytosulfokine) is a plant peptide hormone perceived by a leucine-rich repeat receptor kinase. Phosphosite mapping of epitope-tagged PSKR1 (phytosulfokine receptor 1) from Arabidopsis thaliana plants identified Ser(696) and Ser(698) in the JM (juxtamembrane) region and probably Ser(886) and/or Ser(893) in the AL (activation loop) as in planta phosphorylation sites. In vitro-expressed kinase was autophosphorylated at Ser(717) in the JM, and at Ser(733), Thr(752), Ser(783), Ser(864), Ser(911), Ser(958) and Thr(998) in the kinase domain. The LC-ESI-MS/MS spectra provided support that up to three sites (Thr(890), Ser(893) and Thr(894)) in the AL were likely to be phosphorylated in vitro. These sites are evolutionarily highly conserved in PSK receptors, indicative of a conserved function. Site-directed mutagenesis of the four conserved residues in the activation segment, Thr(890), Ser(893), Thr(894) and Thr(899), differentially altered kinase activity in vitro and growth-promoting activity in planta. The T899A and the quadruple-mutated TSTT-A (T890A/S893A/T894A/T899A) mutants were both kinase-inactive, but PSKR1(T899A) retained growth-promoting activity. The T890A and S893A/T894A substitutions diminished kinase activity and growth promotion. We hypothesize that phosphorylation within the AL activates kinase activity and receptor function in a gradual and distinctive manner that may be a means to modulate the PSK response.

  19. Conserved phosphorylation sites in the activation loop of the Arabidopsis phytosulfokine receptor PSKR1 differentially affect kinase and receptor activity

    PubMed Central

    Hartmann, Jens; Linke, Dennis; Bönniger, Christine; Tholey, Andreas; Sauter, Margret

    2015-01-01

    PSK (phytosulfokine) is a plant peptide hormone perceived by a leucine-rich repeat receptor kinase. Phosphosite mapping of epitope-tagged PSKR1 (phytosulfokine receptor 1) from Arabidopsis thaliana plants identified Ser696 and Ser698 in the JM (juxtamembrane) region and probably Ser886 and/or Ser893 in the AL (activation loop) as in planta phosphorylation sites. In vitro-expressed kinase was autophosphorylated at Ser717 in the JM, and at Ser733, Thr752, Ser783, Ser864, Ser911, Ser958 and Thr998 in the kinase domain. The LC–ESI–MS/MS spectra provided support that up to three sites (Thr890, Ser893 and Thr894) in the AL were likely to be phosphorylated in vitro. These sites are evolutionarily highly conserved in PSK receptors, indicative of a conserved function. Site-directed mutagenesis of the four conserved residues in the activation segment, Thr890, Ser893, Thr894 and Thr899, differentially altered kinase activity in vitro and growth-promoting activity in planta. The T899A and the quadruple-mutated TSTT-A (T890A/S893A/T894A/T899A) mutants were both kinase-inactive, but PSKR1(T899A) retained growth-promoting activity. The T890A and S893A/T894A substitutions diminished kinase activity and growth promotion. We hypothesize that phosphorylation within the AL activates kinase activity and receptor function in a gradual and distinctive manner that may be a means to modulate the PSK response. PMID:26472115

  20. Three Gorges Reservoir Area: soil erosion under natural condition vs. soil erosion under current land use

    NASA Astrophysics Data System (ADS)

    Schönbrodt, Sarah; Behrens, Thorsten; Scholten, Thomas

    2010-05-01

    Apparently, the current most prominent human-induced example for large scale environmental impact is the Three Gorges Dam in China. The flooding alongside the Yangtze River, and its tributaries results in a vast loss of settlement and farmland area with productive, fertile valley soils. Due to the associated high land use dynamic on uphill-sites, the soil resources are underlying high land use pressure. Within our study, the soil erosion under natural conditions is compared to the soil erosion under current land use after the impoundment. Both were modeled using the empirical Universal Soil Loss Equation (USLE) which is able to predict long-term annual soil loss with limited data. The database consists of digital terrain data (45 m resolution DEM, erosive slope length based on Monte-Carlo-Aggregation according to Behrens et al. (2008)), field investigations of recent erosion forms, and literature studies. The natural disposition to soil erosion was calculated considering the USLE factors R, S, and K. The soil erosion under current land use was calculated taking into account all USLE factors. The study area is the catchment of the Xiangxi River in the Three Gorges Reservoir area. Within the Xiangxi Catchment (3,200 km²) the highly dynamic backwater area (580 km²), and two micro-scale study sites (Xiangjiaba with 2.8 km², and Quyuan with 88 km²) are considered more detailed as they are directly affected by the river impoundment. Central features of the Xiangxi Catchment are the subtropical monsoon climate, an extremely steep sloping relief (mean slope angle 39°, SD 22.8°) artificially fractured by farmland terraces, and a high soil erodibility (mean K factor 0.37, SD 0.13). On the catchment scale the natural disposition to soil erosion makes up to mean 518.0 t ha-1 a-1. The maximum potential soil loss of 1,730.1 t ha-1 a-1 under natural conditions is reached in the Quyuan site (mean 635.8 t ha-1 a-1) within the backwater area (mean 582.9 t ha-1 a-1). In the

  1. 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

  2. Tuned by metals: the TET peptidase activity is controlled by 3 metal binding sites

    PubMed Central

    Colombo, Matteo; Girard, Eric; Franzetti, Bruno

    2016-01-01

    TET aminopeptidases are dodecameric particles shared in the three life domains involved in various biological processes, from carbon source provider in archaea to eye-pressure regulation in humans. Each subunit contains a dinuclear metal site (M1 and M2) responsible for the enzyme catalytic activity. However, the role of each metal ion is still uncharacterized. Noteworthy, while mesophilic TETs are activated by Mn2+, hyperthermophilic TETs prefers Co2+. Here, by means of anomalous x-ray crystallography and enzyme kinetics measurements of the TET3 aminopeptidase from the hyperthermophilic organism Pyrococcus furiosus (PfTET3), we show that M2 hosts the catalytic activity of the enzyme, while M1 stabilizes the TET3 quaternary structure and controls the active site flexibility in a temperature dependent manner. A new third metal site (M3) was found in the substrate binding pocket, modulating the PfTET3 substrate preferences. These data show that TET activity is tuned by the molecular interplay among three metal sites. PMID:26853450

  3. Human Activities in Natura 2000 Sites: A Highly Diversified Conservation Network

    NASA Astrophysics Data System (ADS)

    Tsiafouli, Maria A.; Apostolopoulou, Evangelia; Mazaris, Antonios D.; Kallimanis, Athanasios S.; Drakou, Evangelia G.; Pantis, John D.

    2013-05-01

    The Natura 2000 network was established across the European Union's (EU) Member States with the aim to conserve biodiversity, while ensuring the sustainability of human activities. However, to what kind and to what extent Natura 2000 sites are subject to human activities and how this varies across Member States remains unspecified. Here, we analyzed 111,269 human activity records from 14,727 protected sites in 20 Member States. The frequency of occurrence of activities differs among countries, with more than 86 % of all sites being subjected to agriculture or forestry. Activities like hunting, fishing, urbanization, transportation, and tourism are more frequently recorded in south European sites than in northern or eastern ones. The observed variations indicate that Natura 2000 networks are highly heterogeneous among EU Member States. Our analysis highlights the importance of agriculture in European landscapes and indicates possible targets for policy interventions at national, European, or "sub-European" level. The strong human presence in the Natura 2000 network throughout Member States, shows that conservation initiatives could succeed only by combining social and ecological sustainability and by ensuring the integration of policies affecting biodiversity.

  4. 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

  5. Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site.

    PubMed

    Gajadeera, Chathurada S; Zhang, Xinyi; Wei, Yinan; Tsodikov, Oleg V

    2015-02-01

    Cytoplasmic inorganic pyrophosphatase (PPiase) is an enzyme essential for survival of organisms, from bacteria to human. PPiases are divided into two structurally distinct families: family I PPiases are Mg(2+)-dependent and present in most archaea, eukaryotes and prokaryotes, whereas the relatively less understood family II PPiases are Mn(2+)-dependent and present only in some archaea, bacteria and primitive eukaryotes. Staphylococcus aureus (SA), a dangerous pathogen and a frequent cause of hospital infections, contains a family II PPiase (PpaC), which is an attractive potential target for development of novel antibacterial agents. We determined a crystal structure of SA PpaC in complex with catalytic Mn(2+) at 2.1Å resolution. The active site contains two catalytic Mn(2+) binding sites, each half-occupied, reconciling the previously observed 1:1 Mn(2+):enzyme stoichiometry with the presence of two divalent metal ion sites in the apo-enzyme. Unexpectedly, despite the absence of the substrate or products in the active site, the two domains of SA PpaC form a closed active site, a conformation observed in structures of other family II PPiases only in complex with substrate or product mimics. A region spanning residues 295-298, which contains a conserved substrate binding RKK motif, is flipped out of the active site, an unprecedented conformation for a PPiase. Because the mutant of Arg295 to an alanine is devoid of activity, this loop likely undergoes an induced-fit conformational change upon substrate binding and product dissociation. This closed conformation of SA PPiase may serve as an attractive target for rational design of inhibitors of this enzyme. PMID:25576794

  6. Analysis of active site residues of the antiviral protein from summer leaves from Phytolacca americana by site-directed mutagenesis.

    PubMed

    Poyet, J L; Hoeveler, A; Jongeneel, C V

    1998-12-30

    The summer leaf isoform of the pokeweed (Phytolacca americana) antiviral protein, PAP II, was produced in high yields from inclusion bodies in recombinant E. coli. On the basis of its sequence similarity with the spring leaf isoform (PAP I) and with the A chain of ricin, a three-dimensional model of the protein was constructed as an aid in the design of active site mutants. PAP II variants mutated in residues Asp 88 (D88N), Tyr 117 (Y117S), Glu 172 (E172Q), Arg 175 (R175H) and a combination of Asp 88 and Arg 175 (D88N/R175H) were produced in E. coli and assayed for their ability to inhibit protein synthesis in a rabbit reticulocyte lysate. All of these mutations had effects deleterious to the enzymatic activity of PAP II. The results were interpreted in the light of three reaction mechanisms proposed for ribosome-inactivating proteins (RIPs). We conclude that none of the proposed mechanisms is entirely consistent with the data presented here.

  7. NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site

    PubMed Central

    Hoffmann, Bernd; Mitchell, G. Thomas; Gendron, Patrick; Major, François; Andersen, Angela A.; Collins, Richard A.; Legault, Pascale

    2003-01-01

    Substrate cleavage by the Neurospora Varkud satellite (VS) ribozyme involves a structural change in the stem-loop I substrate from an inactive to an active conformation. We have determined the NMR solution structure of a mutant stem-loop I that mimics the active conformation of the cleavage site internal loop. This structure shares many similarities, but also significant differences, with the previously determined structures of the inactive internal loop. The active internal loop displays different base-pairing interactions and forms a novel RNA fold composed exclusively of sheared G-A base pairs. From chemical-shift mapping we identified two Mg2+ binding sites in the active internal loop. One of the Mg2+ binding sites forms in the active but not the inactive conformation of the internal loop and is likely important for catalysis. Using the structure comparison program mc-search, we identified the active internal loop fold in other RNA structures. In Thermus thermophilus 16S rRNA, this RNA fold is directly involved in a long-range tertiary interaction. An analogous tertiary interaction may form between the active internal loop of the substrate and the catalytic domain of the VS ribozyme. The combination of NMR and bioinformatic approaches presented here has identified a novel RNA fold and provides insights into the structural basis of catalytic function in the Neurospora VS ribozyme. PMID:12782785

  8. Immobilized low-activity waste site borehole 299-E17-21

    SciTech Connect

    Reidel, S.P.; Reynolds, K.D.; Horton, D.G.

    1998-08-01

    The Tank Waste Remediation System (TWRS) is the group at the Hanford Site responsible for the safe underground storage of liquid waste from previous Hanford Site operations, the storage and disposal of immobilized tank waste, and closure of underground tanks. The current plan is to dispose of immobilized low-activity tank waste (ILAW) in new facilities in the southcentral part of 200-East Area and in four existing vaults along the east side of 200-East Area. Boreholes 299-E17-21, B8501, and B8502 were drilled at the southwest corner of the ILAW site in support of the Performance Assessment activities for the disposal options. This report summarizes the initial geologic findings, field tests conducted on those boreholes, and ongoing studies. One deep (480 feet) borehole and two shallow (50 feet) boreholes were drilled at the southwest corner of the ILAW site. The primary factor dictating the location of the boreholes was their characterization function with respect to developing the geohydrologic model for the site and satisfying associated Data Quality Objectives. The deep borehole was drilled to characterize subsurface conditions beneath the ILAW site, and two shallow boreholes were drilled to support an ongoing environmental tracer study. The tracer study will supply information to the Performance Assessment. All the boreholes provide data on the vadose zone and saturated zone in a previously uncharacterized area.

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

    PubMed Central

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

    2006-01-01

    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. PMID:16415790

  10. A facile reflux procedure to increase active surface sites form highly active and durable supported palladium@platinum bimetallic nanodendrites

    NASA Astrophysics Data System (ADS)

    Wang, Qin; Li, Yingjun; Liu, Baocang; Xu, Guangran; Zhang, Geng; Zhao, Qi; Zhang, Jun

    2015-11-01

    A series of well-dispersed bimetallic Pd@Pt nanodendrites uniformly supported on XC-72 carbon black are fabricated by using different capping agents. These capping agents are essential for the branched morphology control. However, the surfactant adsorbed on the nanodendrites surface blocks the access of reactant molecules to the active surface sites, and the catalytic activities of these bimetallic nanodendrites are significantly restricted. Herein, a facile reflux procedure to effectively remove the capping agent molecules without significantly affecting their sizes is reported for activating supported nanocatalysts. More significantly, the structure and morphology of the nanodendrites can also be retained, enhancing the numbers of active surface sites, catalytic activity and stability toward methanol and ethanol electro-oxidation reactions. The as-obtained hot water reflux-treated Pd@Pt/C catalyst manifests superior catalytic activity and stability both in terms of surface and mass specific activities, as compared to the untreated catalysts and the commercial Pt/C and Pd/C catalysts. We anticipate that this effective and facile removal method has more general applicability to highly active nanocatalysts prepared with various surfactants, and should lead to improvements in environmental protection and energy production.

  11. Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions

    PubMed Central

    Herter, Susanne; Kranz, David C; Turner, Nicholas J

    2015-01-01

    Summary Cytochrome P450 monooxygenases are useful biocatalysts for C–H activation, and there is a need to expand the range of these enzymes beyond what is naturally available. A panel of 93 variants of active self-sufficient P450cam[Tyr96Phe]-RhFRed fusion enzymes with a broad diversity in active site amino acids was developed by screening a large mutant library of 16,500 clones using a simple, highly sensitive colony-based colorimetric screen against indole. These mutants showed distinct fingerprints of activity not only when screened in oxidations of substituted indoles but also for unrelated oxidations such as benzylic hydroxylations. PMID:26664590

  12. Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions.

    PubMed

    Kelly, Paul P; Eichler, Anja; Herter, Susanne; Kranz, David C; Turner, Nicholas J; Flitsch, Sabine L

    2015-01-01

    Cytochrome P450 monooxygenases are useful biocatalysts for C-H activation, and there is a need to expand the range of these enzymes beyond what is naturally available. A panel of 93 variants of active self-sufficient P450cam[Tyr96Phe]-RhFRed fusion enzymes with a broad diversity in active site amino acids was developed by screening a large mutant library of 16,500 clones using a simple, highly sensitive colony-based colorimetric screen against indole. These mutants showed distinct fingerprints of activity not only when screened in oxidations of substituted indoles but also for unrelated oxidations such as benzylic hydroxylations.

  13. Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions.

    PubMed

    Kelly, Paul P; Eichler, Anja; Herter, Susanne; Kranz, David C; Turner, Nicholas J; Flitsch, Sabine L

    2015-01-01

    Cytochrome P450 monooxygenases are useful biocatalysts for C-H activation, and there is a need to expand the range of these enzymes beyond what is naturally available. A panel of 93 variants of active self-sufficient P450cam[Tyr96Phe]-RhFRed fusion enzymes with a broad diversity in active site amino acids was developed by screening a large mutant library of 16,500 clones using a simple, highly sensitive colony-based colorimetric screen against indole. These mutants showed distinct fingerprints of activity not only when screened in oxidations of substituted indoles but also for unrelated oxidations such as benzylic hydroxylations. PMID:26664590

  14. Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels.

    PubMed

    Saam, Jan; Ivanov, Igor; Walther, Matthias; Holzhütter, Hermann-Georg; Kuhn, Hartmut

    2007-08-14

    Cells contain numerous enzymes that use molecular oxygen for their reactions. Often, their active sites are buried deeply inside the protein, which raises the question whether there are specific access channels guiding oxygen to the site of catalysis. Choosing 12/15-lipoxygenase as a typical example for such oxygen-dependent enzymes, we determined the oxygen distribution within the protein and defined potential routes for oxygen access. For this purpose, we have applied an integrated strategy of structural modeling, molecular dynamics simulations, site-directed mutagenesis, and kinetic measurements. First, we computed the 3D free-energy distribution for oxygen, which led to identification of four oxygen channels in the protein. All channels connect the protein surface with a region of high oxygen affinity at the active site. This region is localized opposite to the nonheme iron providing a structural explanation for the reaction specificity of this lipoxygenase isoform. The catalytically most relevant path can be obstructed by L367F exchange, which leads to a strongly increased Michaelis constant for oxygen. The blocking mechanism is explained in detail by reordering the hydrogen-bonding network of water molecules. Our results provide strong evidence that the main route for oxygen access to the active site of the enzyme follows a channel formed by transiently interconnected cavities whereby the opening and closure are governed by side chain dynamics. PMID:17675410

  15. CO Oxidation on Au/TiO2: Condition-Dependent Active Sites and Mechanistic Pathways.

    PubMed

    Wang, Yang-Gang; Cantu, David C; Lee, Mal-Soon; Li, Jun; Glezakou, Vassiliki-Alexandra; Rousseau, Roger

    2016-08-24

    We present results of ab initio electronic structure and molecular dynamics simulations (AIMD), as well as a microkinetic model of CO oxidation catalyzed by TiO2 supported Au nanocatalysts. A coverage-dependent microkinetic analysis, based on energetics obtained with density functional methods, shows that the dominant kinetic pathway, activated oxygen species, and catalytic active sites are all strongly depended on both temperature and oxygen partial pressure. Under oxidizing conditions and T < 400 K, the prevalent pathway involves a dynamic single atom catalytic mechanism. This reaction is catalyzed by a transient Au-CO species that migrates from the Au-cluster onto a surface oxygen adatom. It subsequently reacts with the TiO2 support via a Mars van Krevelen mechanism to form CO2 and finally the Au atom reintegrates back into the gold cluster to complete the catalytic cycle. At 300 ≤ T ≤ 600 K, oxygen-bound single Oad-Au(+)-CO sites and the perimeter Au-sites of the nanoparticle work in tandem to optimally catalyze the reaction. Above 600 K, a variety of alternate pathways associated with both single-atom and the perimeter sites of the Au nanoparticle are found to be active. Under low oxygen pressures, Oad-Au(+)-CO species can be a source of catalyst deactivation and the dominant pathway involves only Au-perimeter sites. A detailed comparison of the current model and the existing literature resolves many apparent inconsistencies in the mechanistic interpretations. PMID:27480512

  16. Tectonic control of Yarlung Tsangpo Gorge revealed by a buried canyon in Southern Tibet.

    PubMed

    Wang, Ping; Scherler, Dirk; Liu-Zeng, Jing; Mey, Jürgen; Avouac, Jean-Philippe; Zhang, Yunda; Shi, Dingguo

    2014-11-21

    The Himalayan mountains are dissected by some of the deepest and most impressive gorges on Earth. Constraining the interplay between river incision and rock uplift is important for understanding tectonic deformation in this region. We report here the discovery of a deeply incised canyon of the Yarlung Tsangpo River, at the eastern end of the Himalaya, which is now buried under more than 500 meters of sediments. By reconstructing the former valley bottom and dating sediments at the base of the valley fill, we show that steepening of the Tsangpo Gorge started at about 2 million to 2.5 million years ago as a consequence of an increase in rock uplift rates. The high erosion rates within the gorge are therefore a direct consequence of rapid rock uplift.

  17. [Applicability study of CRI treating sewage in the Three-Gorges Reservoir Region].

    PubMed

    Guo, Jin-Song; Wang, Chun-Yan; Fang, Fang; Yin, Liang; Yao, Ruo-Xu

    2006-11-01

    The present domestic study on CRI mainly focuses on the cold and dry northern areas of water deficit. Aiming at the Three Gorges Reservoir Region featured with mild and wet climate and amethyst soil, We make a pilot study on the construction of CRI and its sewage disposal effects, and explores the applicability of CRI to the Three-Gorges Reservoir Region. The findings show that the infiltration coefficient of amethyst soil is small--0.1m(3) x (m2 x d)(-1) when converted into hydraulic loading rate, and the CRI can obtain preferable sewage disposal effects with the mentioned hydraulic loading rate and 1d:3d wet/dry (W/D) ratio. Climate and soil features are the main factors to W/D ratio and 1d:3d W/D ratio is applicable to the region, which indicates CRI is feasible in sewage disposal in the Three-Gorges Reservoir Region.

  18. A unique DNase activity shares the active site with ATPase activity of the RecA/Rad51 homologue (Pk-REC) from a hyperthermophilic archaeon.

    PubMed

    Rashid, N; Morikawa, M; Kanaya, S; Atomi, H; Imanaka, T

    1999-02-19

    A RecA/Rad51 homologue from Pyrococcus kodakaraensis KOD1 (Pk-REC) is the smallest protein among various RecA/Rad51 homologues. Nevertheless, Pk-Rec is a super multifunctional protein and shows a deoxyribonuclease activity. This deoxyribonuclease activity was inhibited by 3 mM or more ATP, suggesting that the catalytic centers of the ATPase and deoxyribonuclease activities are overlapped. To examine whether these two enzymatic activities share the same active site, a number of site-directed mutations were introduced into Pk-REC and the ATPase and deoxyribonuclease activities of the mutant proteins were determined. The mutant enzyme in which double mutations Lys-33 to Ala and Thr-34 to Ala were introduced, fully lost both of these activities, indicating that Lys-33 and/or Thr-34 are important for both ATPase and deoxyribonuclease activities. The mutation of Asp-112 to Ala slightly and almost equally reduced both ATPase and deoxyribonuclease activities. In addition, the mutation of Glu-54 to Gln did not seriously affect the ATPase, deoxyribonuclease, and UV tolerant activities. These results strongly suggest that the active sites of the ATPase and deoxyribonuclease activities of Pk-REC are common. It is noted that unlike Glu-96 in Escherichia coli RecA, which has been proposed to be a catalytic residue for the ATPase activity, the corresponding residual Glu-54 in Pk-REC is not involved in the catalytic function of the protein.

  19. 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.

  20. Active sites and mechanisms for direct oxidation of benzene to phenol over carbon catalysts.

    PubMed

    Wen, Guodong; Wu, Shuchang; Li, Bo; Dai, Chunli; Su, Dang Sheng

    2015-03-23

    The direct oxidation of benzene to phenol with H2 O2 as the oxidizer, which is regarded as an environmentally friendly process, can be efficiently catalyzed by carbon catalysts. However, the detailed roles of carbon catalysts, especially what is the active site, are still a topic of debate controversy. Herein, we present a fundamental consideration of possible mechanisms for this oxidation reaction by using small molecular model catalysts, Raman spectra, static secondary ion mass spectroscopy (SIMS), DFT calculations, quasi in situ ATR-IR and UV spectra. Our study indicates that the defects, being favorable for the formation of active oxygen species, are the active sites for this oxidation reaction. Furthermore, one type of active defect, namely the armchair configuration defect was successfully identified.

  1. China`s Three Gorges Dam: Mammoth opportunities - and risks

    SciTech Connect

    Maize, K.P.

    1996-05-01

    China is embarking on an infrastructure project of almost unimaginable proportions. If it succeeds, it will be one of the modern wonders of the world. If it fails, the Chinese government could be impoverished for a generation. The Three Gorges Dam represents an audacious gamble for infrastructure-starved China. Like some U.S. utilities in the 1970`s and 1980`s, China is taking a giant roll of the dice on a single generating project. If it succeeds, the dam will be one of the modern wonders of the world. If it fails, China`s government could be impoverished for a generation. The scope of the project is breathtaking. Designed for flood control, navigation and hydropower, the dam will rise 185 meters, spanning a two-kilometer gap and creating a reservoir that will reach 600 kilometers westward to Chongqing. Twin five stage ship locks will lift river boats with 10,000 tonnes of cargo capacity, tripling the size of the vessels that can reach Chongqing.

  2. Predictability of wind ramps in the Columbia River Gorge

    NASA Astrophysics Data System (ADS)

    Smith, C.

    2013-12-01

    Wind generation capacity in the Bonneville Power Administration (BPA) system, which stands at 4,500 MW currently, can at time account for 70% of total electricity demand. With 2,500 additional MW of wind generation capacity expected by 2015, increasingly accurate forecasts are required to avoid water quality issues associated with hydropower dam overspill. Wind ramps, or large increases or decreases in wind generation over a short period of time, are particularly difficult to accurately forecast in the Columbia River Gorge area. Industry standard computational resources, combined with turbulence grey-zone issues associated with planetary boundary (PBL) schemes, suggest a leveling off of numerical weather prediction (NWP) model skill score with respect to increasing grid resolution until eddy resolving scales are resolved. However, we show that dispersion errors, which associated with wind ramps, continue to decrease for locations and seasons in which meso-scale and topographically forced diurnal motions account for a significant portion of the power spectral density of hub-height wind speeds.

  3. Downstream Yangtze River levels impacted by Three Gorges Dam

    NASA Astrophysics Data System (ADS)

    Wang, Jida; Sheng, Yongwei; Gleason, Colin J.; Wada, Yoshihide

    2013-12-01

    Changes in the Yangtze River level induced by large-scale human water regulation have profound implications on the inundation dynamics of surrounding lakes/wetlands and the integrity of related ecosystems. Using in situ measurements and hydrological simulation, this study reveals an altered Yangtze level regime downstream from the Three Gorges Dam (TGD) to the Yangtze estuary in the East China Sea as a combined result of (i) TGD’s flow regulation and (ii) Yangtze channel erosion due to reduced sediment load. During the average annual cycle of TGD’s regular flow control in 2009-2012, downstream Yangtze level variations were estimated to have been reduced by 3.9-13.5% at 15 studied gauging stations, manifested as evident level decrease in fall and increase in winter and spring. The impacts on Yangtze levels generally diminished in a longitudinal direction from the TGD to the estuary, with a total time lag of ˜9-12 days. Chronic Yangtze channel erosion since the TGD closure has lowered water levels in relation to flows at most downstream stations, which in turn counteracts the anticipated level increase by nearly or over 50% in winter and spring while reinforcing the anticipated level decrease by over 20% in fall. Continuous downstream channel erosion in the near future may further counteract the benefit of increased Yangtze levels during TGD’s water supplement in winter and accelerate the receding of inundation areas/levels of downstream lakes in fall.

  4. Sphingosine-1-phosphate receptor 1 reporter mice reveal receptor activation sites in vivo

    PubMed Central

    Kono, Mari; Tucker, Ana E.; Tran, Jennifer; Bergner, Jennifer B.; Turner, Ewa M.; Proia, Richard L.

    2014-01-01

    Activation of the GPCR sphingosine-1-phosphate receptor 1 (S1P1) by sphingosine-1-phosphate (S1P) regulates key physiological processes. S1P1 activation also has been implicated in pathologic processes, including autoimmunity and inflammation; however, the in vivo sites of S1P1 activation under normal and disease conditions are unclear. Here, we describe the development of a mouse model that allows in vivo evaluation of S1P1 activation. These mice, known as S1P1 GFP signaling mice, produce a S1P1 fusion protein containing a transcription factor linked by a protease cleavage site at the C terminus as well as a β-arrestin/protease fusion protein. Activated S1P1 recruits the β-arrestin/protease, resulting in the release of the transcription factor, which stimulates the expression of a GFP reporter gene. Under normal conditions, S1P1 was activated in endothelial cells of lymphoid tissues and in cells in the marginal zone of the spleen, while administration of an S1P1 agonist promoted S1P1 activation in endothelial cells and hepatocytes. In S1P1 GFP signaling mice, LPS-mediated systemic inflammation activated S1P1 in endothelial cells and hepatocytes via hematopoietically derived S1P. These data demonstrate that S1P1 GFP signaling mice can be used to evaluate S1P1 activation and S1P1-active compounds in vivo. Furthermore, this strategy could be potentially applied to any GPCR to identify sites of receptor activation during normal physiology and disease. PMID:24667638

  5. A three-dimensional model of mammalian tyrosinase active site accounting for loss of function mutations.

    PubMed

    Schweikardt, Thorsten; Olivares, Concepción; Solano, Francisco; Jaenicke, Elmar; García-Borrón, José Carlos; Decker, Heinz

    2007-10-01

    Tyrosinases are the first and rate-limiting enzymes in the synthesis of melanin pigments responsible for colouring hair, skin and eyes. Mutation of tyrosinases often decreases melanin production resulting in albinism, but the effects are not always understood at the molecular level. Homology modelling of mouse tyrosinase based on recently published crystal structures of non-mammalian tyrosinases provides an active site model accounting for loss-of-function mutations. According to the model, the copper-binding histidines are located in a helix bundle comprising four densely packed helices. A loop containing residues M374, S375 and V377 connects the CuA and CuB centres, with the peptide oxygens of M374 and V377 serving as hydrogen acceptors for the NH-groups of the imidazole rings of the copper-binding His367 and His180. Therefore, this loop is essential for the stability of the active site architecture. A double substitution (374)MS(375) --> (374)GG(375) or a single M374G mutation lead to a local perturbation of the protein matrix at the active site affecting the orientation of the H367 side chain, that may be unable to bind CuB reliably, resulting in loss of activity. The model also accounts for loss of function in two naturally occurring albino mutations, S380P and V393F. The hydroxyl group in S380 contributes to the correct orientation of M374, and the substitution of V393 for a bulkier phenylalanine sterically impedes correct side chain packing at the active site. Therefore, our model explains the mechanistic necessity for conservation of not only active site histidines but also adjacent amino acids in tyrosinase. PMID:17850513

  6. Calorimetric studies of the interactions of metalloenzyme active site mimetics with zinc-binding inhibitors.

    PubMed

    Robinson, Sophia G; Burns, Philip T; Miceli, Amanda M; Grice, Kyle A; Karver, Caitlin E; Jin, Lihua

    2016-07-19

    The binding of drugs to metalloenzymes is an intricate process that involves several interactions, including binding of the drug to the enzyme active site metal, as well as multiple interactions between the drug and the enzyme residues. In order to determine the free energy contribution of Zn(2+) binding by known metalloenzyme inhibitors without the other interactions, valid active site zinc structural mimetics must be formed and binding studies need to be performed in biologically relevant conditions. The potential of each of five ligands to form a structural mimetic with Zn(2+) was investigated in buffer using Isothermal Titration Calorimetry (ITC). All five ligands formed strong 1 : 1 (ligand : Zn(2+)) binary complexes. The complexes were used in further ITC experiments to study their interaction with 8-hydroxyquinoline (8-HQ) and/or acetohydroxamic acid (AHA), two bidentate anionic zinc-chelating enzyme inhibitors. It was found that tetradentate ligands were not suitable for creating zinc structural mimetics for inhibitor binding in solution due to insufficient coordination sites remaining on Zn(2+). A stable binary complex, [Zn(BPA)](2+), which was formed by a tridentate ligand, bis(2-pyridylmethyl)amine (BPA), was found to bind one AHA in buffer or a methanol : buffer mixture (60 : 40 by volume) at pH 7.25 or one 8-HQ in the methanol : buffer mixture at pH 6.80, making it an effective structural mimetic for the active site of zinc metalloenzymes. These results are consistent with the observation that metalloenzyme active site zinc ions have three residues coordinated to them, leaving one or two sites open for inhibitors to bind. Our findings indicate that Zn(BPA)X2 can be used as an active site structural mimetic for zinc metalloenzymes for estimating the free energy contribution of zinc binding to the overall inhibitor active site interactions. Such use will help aid in the rational design of inhibitors to a variety of zinc metalloenzymes

  7. Geomorphic evolution of the Yangtze Gorges and the time of their formation

    NASA Astrophysics Data System (ADS)

    Li, Jijun; Xie, Shiyou; Kuang, Mingsheng

    2001-11-01

    The Three Gorges of the Yangtze link its upper rocky valley to downstream alluvial sections. A series of stepped landforms exist in the Three Gorges area, the Sichuan Basin upstream and the Jianghan Basin downstream. These landforms are characterized by two planation surfaces, one erosional surface, and up to seven terraces. The higher planation surface (named the Exi Surface, ~1800-2000 m a.s.l.) and the lower planation surface (1200-1500 m) were probably formed in the Tertiary (prior to 3.4-3.6 Ma B.P.). No correlation seems to exist between the drainage networks of earlier period with the present Yangtze system. It is suggested that the erosional surface found in the study area at 800-1200 m in elevation above sea level was formed in Late Pliocene of Early Pleistocene. During this period following the last planation event, the ancestral Yangtze might have begun to adjust its drainage network. The seven terraces, well developed along the eastern Sichuan Basin and the Three Gorges, date from Early to Late Pleistocene (1.16-0.01 Ma B.P). The chronostratigraphic evidence and diagnostic sediments are generally comparable in time and space from the Sichuan Basin, through the Three Gorges, to the Jianghan Basin. Therefore, the present study proposes that the Three Gorges were cut not later than the initiation of the earliest terrace. The fluvial landforms in the Yangtze Gorges are characterized also by valley-in-valley cross-sections, i.e. an older U-shaped valley cut by a younger V-shaped valley. A tectonic rise accompanied by a rapid downcutting of the river channels predominated in the region.

  8. Identification of active sites in gold-catalyzed hydrogenation of acrolein.

    PubMed

    Mohr, Christian; Hofmeister, Herbert; Radnik, Jörg; Claus, Peter

    2003-02-19

    The active sites of supported gold catalysts, favoring the adsorption of C=O groups of acrolein and subsequent reaction to allyl alcohol, have been identified as edges of gold nanoparticles. After our recent finding that this reaction preferentially occurs on single crystalline particles rather than multiply twinned ones, this paper reports on a new approach to distinguish different features of the gold particle morphology. Elucidation of the active site issue cannot be simply done by varying the size of gold particles, since the effects of faceting and multiply twinned particles may interfere. Therefore, modification of the gold particle surface by indium has been used to vary the active site characteristics of a suitable catalyst, and a selective decoration of gold particle faces has been observed, leaving edges free. This is in contradiction to theoretical predictions, suggesting a preferred occupation of the low-coordinated edges of the gold particles. On the bimetallic catalyst, the desired allyl alcohol is the main product (selectivity 63%; temperature 593 K, total pressure p(total) = 2 MPa). From the experimentally proven correlation between surface structure and catalytic behavior, the edges of single crystalline gold particles have been identified as active sites for the preferred C=O hydrogenation. PMID:12580618

  9. Evidence for surface Ag + complexes as the SERS-active sites on Ag electrodes

    NASA Astrophysics Data System (ADS)

    Watanabe, T.; Kawanami, O.; Honda, K.; Pettinger, B.

    1983-12-01

    Evidence is given that SERS-active sites at Ag electrodes are associated with Ag + ions, forming sparingly soluble surface complexes with ligands such as pyridine molecules and halide ions. Such surface Ag + complexes contribute a factor of >800 to the overall (10 7-fold) enhancement, possibly via a resonance Raman effect.

  10. Strategies and Activities for Using Local Communities as Environmental Education Sites.

    ERIC Educational Resources Information Center

    Roth, Charles E.; Lockwood, Linda G.

    Presented are over 100 environmental education activities which use the local community for a learning site and resource. These lessons are grouped under seven topical headings: (1) biological neighbors, (2) physical environs, (3) built environs, (4) social environs, (5) understanding ourselves, (6) influencing change, and (7) improvement and…

  11. 78 FR 18576 - Agency Information Collection Activities; Comment Request; Experimental Sites Data Collection...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-27

    ... Agency Information Collection Activities; Comment Request; Experimental Sites Data Collection Instrument... information collection requirements and provide the requested data in the desired format. ED is soliciting... collection instrument will be used to collect specific information/performance data for analysis of...

  12. Penicillin Use in Meningococcal Disease Management: Active Bacterial Core Surveillance Sites, 2009

    PubMed Central

    Blain, Amy E.; Mandal, Sema; Wu, Henry; MacNeil, Jessica R.; Harrison, Lee H.; Farley, Monica M.; Lynfield, Ruth; Miller, Lisa; Nichols, Megin; Petit, Sue; Reingold, Arthur; Schaffner, William; Thomas, Ann; Zansky, Shelley M.; Anderson, Raydel; Harcourt, Brian H.; Mayer, Leonard W.; Clark, Thomas A.; Cohn, Amanda C.

    2016-01-01

    In 2009, in the Active Bacterial Core surveillance sites, penicillin was not commonly used to treat meningococcal disease. This is likely because of inconsistent availability of antimicrobial susceptibility testing and ease of use of third-generation cephalosporins. Consideration of current practices may inform future meningococcal disease management guidelines. PMID:27704009

  13. The Thumbs Up Ecology Curriculum: A Fun Group of School Site Activities for Sixth Graders.

    ERIC Educational Resources Information Center

    Smith, John; And Others

    This guide is a collection of "fun" school site activities for sixth graders. Some of the topics covered are: animals, trees, energy and lifestyle, land use and you, energy conservation, and car-pooling. Each section offers both introductory information about the topic as well as questions to ponder such as what, so what, now what, and another way…

  14. 78 FR 33908 - Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-05

    ... identified Wind Energy Area (WEA) on the OCS offshore Rhode Island (RI) and Massachusetts (MA). The revised... Bureau of Ocean Energy Management Commercial Wind Lease Issuance and Site Assessment Activities on the.... BOEM may issue one or more commercial wind energy leases in the WEA. The competitive lease process...

  15. 77 FR 3460 - Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-24

    ... published a final rule under 10 CFR Part 765 in the Federal Register on May 23, 1994, (59 FR 26714) to carry... for reimbursement. DOE amended the final rule on June 3, 2003, (68 FR 32955) to adopt several... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department...

  16. 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

    ... published a final rule under 10 CFR Part 765 in the Federal Register on May 23, 1994, (59 FR 26714) to carry... for reimbursement. DOE amended the final rule on June 3, 2003, (68 FR 32955) to adopt several... Reimbursement for Costs of Remedial Action at Active Uranium and Thorium Processing Sites AGENCY: Department...

  17. Archaeological Activity Report: Post-Review Discoveries Within 45BN431 at Solid Waste Site 128-F-2

    SciTech Connect

    T. E. Marceau; J. J. Sharpe

    2006-12-21

    During monitoring of remedial activities at Solid Waste Site 128-F-2 on August 19, 2005, a concentration of mussel shell was discovered in the west wall of a trench in the northen section of the waste site.

  18. Conformational dynamics of the active site loop of S-adenosylmethionine synthetase illuminated by site-directed spin labeling.

    PubMed

    Taylor, John C; Markham, George D

    2003-07-15

    S-adenosylmethionine synthetase (ATP: L-methionine S-adenosyltransferase, methionine adenosyltransferase, a.k.a. MAT) is one of numerous enzymes that have a flexible polypeptide loop that moves to gate access to the active site in a motion that is closely coupled to catalysis. Crystallographic studies of this tetrameric enzyme have shown that the loop is closed in the absence of bound substrates. However, the loop must open to allow substrate binding and a variety of data indicate that the loop is closed during the catalytic steps. Previous kinetic studies indicate that during turnover loop motion occurs on a time scale of 10(-2)s, ca. 10-fold faster than chemical transformations and turnover. Site-directed spin labeling has been used to introduce nitroxide groups at two positions in the loop to illuminate how the motion of the loop is affected by substrate binding. The two loop mutants constructed, G105C and D107C, retain wild type levels of MAT activity; attachment of a methanethiosulfonate spin label to convert the cysteine to the "R1" residue reduced the k(cat) only for the labeled D107R1 form (7-fold). The K(m) value for methionine increased 2- to 4-fold for the cysteine mutants and 2- to 7-fold for the labeled proteins, whereas the K(m) for ATP was changed by at most 2-fold. EPR spectra for both labeled proteins are nearly identical and show the presence of two major spin label environments with rotational diffusion rates differing by approximately 10-fold; the slower rate is ca. 4-fold faster than the estimated protein rotational rate. The spectra are not altered by addition of substrates or products. At both positions the less mobile conformation constitutes ca. 65% of the total species, indicating an equilibrium that only slightly favors one form, that in which the label is more immobilized. The equilibrium constant that relates the two forms is comparable to the equilibrium constant of 1.5 for a conformational change that was previously deduced from the

  19. Geologic map of Gunnison Gorge National Conservation Area, Delta and Montrose Counties, Colorado

    USGS Publications Warehouse

    Kellogg, Karl; Hansen, Wallace R.; Tucker, Karen S.; VanSistine, D. Paco

    2004-01-01

    This publication consists of a geologic map database and printed map sheet. The map sheet has a geologic map as the center piece, and accompanying text describes (1) the various geological units, (2) the uplift history of the region and how it relates to canyon downcutting, (3) the ecology of the gorge, and (4) human history. The map is intended to be used by the general public as well as scientists and goes hand-in-hand with a separate geological guide to Gunnison Gorge.

  20. Spectroscopic studies of single and double variants of M ferritin: lack of conversion of a biferrous substrate site into a cofactor site for O2 activation.

    PubMed

    Kwak, Yeonju; Schwartz, Jennifer K; Haldar, Suranjana; Behera, Rabindra K; Tosha, Takehiko; Theil, Elizabeth C; Solomon, Edward I

    2014-01-28

    Ferritin has a binuclear non-heme iron active site that functions to oxidize iron as a substrate for formation of an iron mineral core. Other enzymes of this class have tightly bound diiron cofactor sites that activate O2 to react with substrate. Ferritin has an active site ligand set with 1-His/4-carboxylate/1-Gln rather than the 2-His/4-carboxylate set of the cofactor site. This ligand variation has been thought to make a major contribution to this biferrous substrate rather than cofactor site reactivity. However, the Q137E/D140H double variant of M ferritin, has a ligand set that is equivalent to most of the diiron cofactor sites, yet did not rapidly react with O2 or generate the peroxy intermediate observed in the cofactor sites. Therefore, in this study, a combined spectroscopic methodology of circular dichroism (CD)/magnetic CD (MCD)/variable temperature, variable field (VTVH) MCD has been applied to evaluate the factors required for the rapid O2 activation observed in cofactor sites. This methodology defines the coordination environment of each iron and the bridging ligation of the biferrous active sites in the double and corresponding single variants of frog M ferritin. Based on spectral changes, the D140H single variant has the new His ligand binding, and the Q137E variant has the new carboxylate forming a μ-1,3 bridge. The spectra for the Q137E/D140H double variant, which has the cofactor ligand set, however, reflects a site that is more coordinately saturated than the cofactor sites in other enzymes including ribonucleotide reductase, indicating the presence of additional water ligation. Correlation of this double variant and the cofactor sites to their O2 reactivities indicates that electrostatic and steric changes in the active site and, in particular, the hydrophobic nature of a cofactor site associated with its second sphere protein environment, make important contributions to the activation of O2 by the binuclear non-heme iron enzymes.

  1. Characterization of the active site properties of CYP4F12.

    PubMed

    Eksterowicz, John; Rock, Dan A; Rock, Brooke M; Wienkers, Larry C; Foti, Robert S

    2014-10-01

    Cytochrome P450 4F12 is a drug-metabolizing enzyme that is primarily expressed in the liver, kidney, colon, small intestine, and heart. The properties of CYP4F12 that may impart an increased catalytic selectivity (decreased promiscuity) were explored through in vitro metabolite elucidation, kinetic isotope effect experiments, and computational modeling of the CYP4F12 active site. By using astemizole as a probe substrate for CYP4F12 and CYP3A4, it was observed that although CYP4F12 favored astemizole O-demethylation as the primary route of metabolism, CYP3A4 was capable of metabolizing astemizole at multiple sites on the molecule. Deuteration of astemizole at the site of O-demethylation resulted in an isotope effect of 7.1 as well as an 8.3-fold decrease in the rate of clearance for astemizole by CYP4F12. Conversely, although an isotope effect of 3.8 was observed for the formation of the O-desmethyl metabolite when deuterated astemizole was metabolized by CYP3A4, there was no decrease in the clearance of astemizole. Development of a homology model of CYP4F12 based on the crystal structure of cytochrome P450 BM3 predicted an active site volume for CYP4F12 that was approximately 76% of the active site volume of CYP3A4. As predicted, multiple favorable binding orientations were available for astemizole docked into the active site of CYP3A4, but only a single binding orientation with the site of O-demethylation oriented toward the heme was identified for CYP4F12. Overall, it appears that although CYP4F12 may be capable of binding similar ligands to other cytochrome P450 enzymes such as CYP3A4, the ability to achieve catalytically favorable orientations may be inherently more difficult because of the increased steric constraints of the CYP4F12 active site. PMID:25074871

  2. Characterization and sequencing of the active site of 1-aminocyclopropane-1-carboxylate synthase

    SciTech Connect

    Yip, Wing-Kin; Dong, Jian-Guo; Yang, S.F. ); Kenny, J.W.; Thompson, G.A. )

    1990-10-01

    The pyridoxal phosphate (PLP)-dependent 1-aminocyclopropane-1-carboxylic acid (ACC) synthase the key enzyme in ethylene biosynthesis, is inactivated by its substrate S-adenosylmethionine (AdoMet). Apple ACC synthase was purified with an immunoaffinity gel, and its active site was probed with NaB{sup 3}H{sub 4} or Ado({sup 14}C)Met. Peptide sequencing of both {sup 3}H- and {sup 14}C-labeled peptides revealed a common dodecapeptide of Ser-Leu-Ser-Xaa-Asp-Leu-Gly-Leu-Pro-Gly-Phe-Arg, where Xaa was the modified, radioactive residue in each case. Acid hydrolysis of the {sup 3}H-labeled enzyme released radioactive N-pyridoxyllysine, indicating that the active-site peptide contained lysine at position 4. Mass spectrometry of the {sup 14}C-labeled peptide indicated a protonated molecular ion at m/z 1390.6, from which the mass of Xaa was calculated to be 229, a number that is equivalent to the mass of a lysine residue alkylated by the 2-aminobutyrate portion of AdoMet, as we previously proposed. These results indicate that the same active-site lysine binds the PLP and convalently links to the 2-aminobutyrate portion of AdoMet during inactivation. The active site of tomato ACC synthase was probed in the same manner with Ado ({sup 14}C)Met. Sequencing of the tomato active-site peptide revealed two highly conserved dodecapeptides; the minor peptide possessed a sequence identical to that of the apple enzyme, whereas the major peptide differed from the minor peptide in that methionine replaced leucine at position 6.

  3. Lymphokine-activated killer (LAK) cells can be focused at sites of tumor growth by products of macrophage activation

    SciTech Connect

    Migliori, R.J.; Gruber, S.A.; Sawyer, M.D.; Hoffman, R.; Ochoa, A.; Bach, F.H.; Simmons, R.L.

    1987-08-01

    Successful adoptive cancer immunotherapy presumably depends on the accumulation of tumoricidal leukocytes at the sites of tumor growth. Large numbers of lymphokine-activated killer (LAK) cells can be generated in vitro by growth in high concentrations of interleukin-2 (IL-2), but relatively few arrive at the tumor site after intravenous injection. We hypothesize that the delivery of LAK cells to tumor sites may be augmented by previously demonstrated lymphocyte-recruiting factors, including activated macrophage products such as interleukin-1 (IL-1) and tumor necrosis factor. /sup 111/Indium-labeled LAK cells were injected intravenously into syngeneic mice bearing the macrophage activator endotoxin (LPS) in one hind footpad, and saline solution was injected into the contralateral footpad. Significantly more activity was recovered from the LPS-bearing footpad at all times during a 96-hour period. Recombinant IL-1 also attracted more LAK cells after injection into tumor-free hind footpads. Furthermore, LAK cells preferentially homed to hind footpads that were bearing 3-day established sarcomas after intralesional injections of LPS, IL-1, or tumor necrosis factor when compared with contralateral tumor-bearing footpads injected with saline solution alone. In preliminary experiments, mice with hind-footpad tumors appeared to survive longer after combined systemic IL-2 and LAK therapy if intralesional LPS was administered. These studies demonstrate that macrophage activation factors that have been shown capable of attracting circulating normal lymphocytes can also effectively attract LAK cells from the circulation. By the stimulation of macrophages at the sites of tumor growth, more LAK cells can be attracted. It is hoped that by focusing the migration of LAK cells to tumors, LAK cells and IL-2 would effect tumor regression more efficiently and with less toxicity.

  4. 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

  5. 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

  6. 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.

  7. Asymmetry of the active site loop conformation between subunits of glutamate-1-semialdehyde aminomutase in solution.

    PubMed

    Campanini, Barbara; Bettati, Stefano; di Salvo, Martino Luigi; Mozzarelli, Andrea; Contestabile, Roberto

    2013-01-01

    Glutamate-1-semialdehyde aminomutase (GSAM) is a dimeric, pyridoxal 5'-phosphate (PLP)- dependent enzyme catalysing in plants and some bacteria the isomerization of L-glutamate-1-semialdehyde to 5-aminolevulinate, a common precursor of chlorophyll, haem, coenzyme B12, and other tetrapyrrolic compounds. During the catalytic cycle, the coenzyme undergoes conversion from pyridoxamine 5'-phosphate (PMP) to PLP. The entrance of the catalytic site is protected by a loop that is believed to switch from an open to a closed conformation during catalysis. Crystallographic studies indicated that the structure of the mobile loop is related to the form of the cofactor bound to the active site, allowing for asymmetry within the dimer. Since no information on structural and functional asymmetry of the enzyme in solution is available in the literature, we investigated the active site accessibility by determining the cofactor fluorescence quenching of PMP- and PLP-GSAM forms. PLP-GSAM is partially quenched by potassium iodide, suggesting that at least one catalytic site is accessible to the anionic quencher and therefore confirming the asymmetry observed in the crystal structure. Iodide induces release of the cofactor from PMP-GSAM, apparently from only one catalytic site, therefore suggesting an asymmetry also in this form of the enzyme in solution, in contrast with the crystallographic data.

  8. Seasonal succession of phytoplankton in response to the variation of environmental factors in the Gaolan River, Three Gorges Reservoir, China

    NASA Astrophysics Data System (ADS)

    Peng, Chengrong; Zhang, Lang; Zheng, Yangzhong; Li, Dunhai

    2013-07-01

    To understand the responses of a freshwater ecosystem to the impoundment of the Three Gorges Reservoir (TGR), phytoplankton was monitored in the tributaries of the TGR area. From August 2010 to July 2011, algal species composition, abundance, chlorophyll a and other environmental parameters were investigated in the Gaolan River, which is a tributary of Xiangxi River. Thirty-one algal genera from seven phyla were identified. Results show that the lowest concentrations of total phosphorus (TP) and total nitrogen (TN) were 0.06 mg/L and 1.08 mg/L, respectively. The values of TP and TN exceeded the threshold concentration of the eutrophic state suggested for freshwater bodies. In the Gaolan River, the succession of phytoplankton showed clear seasonal characteristics. Different dominant species were observed among seasons under the control of environment factors. In spring and summer, the dominant species were Nitzschia sp. and Aphanizomenon flos-aquae (L.) Ralfs, the limiting nutrient was NO{3/-}-N, and the key environmental factor for phytoplankton population succession was water temperature (WT). In autumn and winter, the dominant species were A. flos-aquae and Chlorella sp., the limiting nutrient was PO{4/3-}-P, and the key environmental factors were transparency and WT. This study illustrates the influence of physical and chemical factors on phytoplankton seasonal succession in a tributary of TGR since the downstream regions of Xiangxi River and Gaolan River became reservoirs after impoundment of the Three Gorges Dam. We suggest that this activity has significantly affected water quality in the dam area.

  9. Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

    PubMed Central

    Schöne, Stefanie; Jurk, Marcel; Helabad, Mahdi Bagherpoor; Dror, Iris; Lebars, Isabelle; Kieffer, Bruno; Imhof, Petra; Rohs, Remo; Vingron, Martin; Thomas-Chollier, Morgane; Meijsing, Sebastiaan H.

    2016-01-01

    The glucocorticoid receptor (GR) binds as a homodimer to genomic response elements, which have particular sequence and shape characteristics. Here we show that the nucleotides directly flanking the core-binding site, differ depending on the strength of GR-dependent activation of nearby genes. Our study indicates that these flanking nucleotides change the three-dimensional structure of the DNA-binding site, the DNA-binding domain of GR and the quaternary structure of the dimeric complex. Functional studies in a defined genomic context show that sequence-induced changes in GR activity cannot be explained by differences in GR occupancy. Rather, mutating the dimerization interface mitigates DNA-induced changes in both activity and structure, arguing for a role of DNA-induced structural changes in modulating GR activity. Together, our study shows that DNA sequence identity of genomic binding sites modulates GR activity downstream of binding, which may play a role in achieving regulatory specificity towards individual target genes. PMID:27581526

  10. Alkyl isocyanates as active site-directed inactivators of guinea pig liver transglutaminase.

    PubMed

    Gross, M; Whetzel, N K; Folk, J E

    1975-10-10

    Alkyl isocyanates are effective inactivators of guinea pig liver transglutaminase. Based on the specificity of the reaction the protection against inactivation by glutamine substrate, and the essential nature of calcium for the inactivation reaction, it is concluded that these reagents act as amide substrate analogs and, thus function in an active site-specific manner. Support for the contention that inactivation results from alkyl thiocarbamate ester formation through the single active site sulfhydryl group of the enzyme is (a) the loss of one free--SH group and the incorporation of 1 mol of reagent/mol of enzyme in the reaction, (b) similarity in chemical properties of the inactive enzyme derivative formed to those previously reported for another alkyl thiocarbamoylenzyme and an alkyl thiocarbamoylcysteine derivative, and (c) the finding that labeled peptides from digests of [methyl-14C]thiocarbamoyltransglutaminase and those from digests of iodoacetamide-inactivated enzyme occupy similar positions on peptide maps. Transglutaminase was found to be inactivated neither by urethan anlogs of its active ester substrates nor by urea analogs of its amide substrates. It is concluded on the basis of these findings that inactive carbamoylenzyme derivatives are formed only by direct addition of the transglutaminase active--SH group to the isocyanate C--N double bond, and not, like several serine active site enzymes, by nucleophilic displacement with urethan analogs of substrate, or by nucleophilic displacement with urea analogs of substrate. PMID:240837

  11. Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.

    PubMed

    Schöne, Stefanie; Jurk, Marcel; Helabad, Mahdi Bagherpoor; Dror, Iris; Lebars, Isabelle; Kieffer, Bruno; Imhof, Petra; Rohs, Remo; Vingron, Martin; Thomas-Chollier, Morgane; Meijsing, Sebastiaan H

    2016-01-01

    The glucocorticoid receptor (GR) binds as a homodimer to genomic response elements, which have particular sequence and shape characteristics. Here we show that the nucleotides directly flanking the core-binding site, differ depending on the strength of GR-dependent activation of nearby genes. Our study indicates that these flanking nucleotides change the three-dimensional structure of the DNA-binding site, the DNA-binding domain of GR and the quaternary structure of the dimeric complex. Functional studies in a defined genomic context show that sequence-induced changes in GR activity cannot be explained by differences in GR occupancy. Rather, mutating the dimerization interface mitigates DNA-induced changes in both activity and structure, arguing for a role of DNA-induced structural changes in modulating GR activity. Together, our study shows that DNA sequence identity of genomic binding sites modulates GR activity downstream of binding, which may play a role in achieving regulatory specificity towards individual target genes. PMID:27581526

  12. Alternative poly(A) site utilization during adenovirus infection coincides with a decrease in the activity of a poly(A) site processing factor.

    PubMed Central

    Mann, K P; Weiss, E A; Nevins, J R

    1993-01-01

    The recognition and processing of a pre-mRNA to create a poly(A) addition site, a necessary step in mRNA biogenesis, can also be a regulatory event in instances in which the frequency of use of a poly(A) site varies. One such case is found during the course of an adenovirus infection. Five poly(A) sites are utilized within the major late transcription unit to produce more than 20 distinct mRNAs during the late phase of infection. The proximal half of the major late transcription unit is also expressed during the early phase of a viral infection. During this early phase of expression, the L1 poly(A) site is used three times more frequently than the L3 poly(A) site. In contrast, the L3 site is used three times more frequently than the L1 site during the late phase of infection. Recent experiments have suggested that the recognition of the poly(A) site GU-rich downstream element by the CF1 processing factor may be a rate-determining step in poly(A) site selection. We demonstrate that the interaction of CF1 with the L1 poly(A) site is less stable than the interaction of CF1 with the L3 poly(A) site. We also find that there is a substantial decrease in the level of CF1 activity when an adenovirus infection proceeds to the late phase. We suggest that this reduction in CF1 activity, coupled with the relative instability of the interaction with the L1 poly(A) site, contributes to the reduced use of the L1 poly(A) site during the late stage of an adenovirus infection. Images PMID:8384308

  13. Fibromodulin Interacts with Collagen Cross-linking Sites and Activates Lysyl Oxidase*

    PubMed Central

    Bihan, Dominique; Bonna, Arkadiusz; Rubin, Kristofer; Farndale, Richard W.

    2016-01-01

    The hallmark of fibrotic disorders is a highly cross-linked and dense collagen matrix, a property driven by the oxidative action of lysyl oxidase. Other fibrosis-associated proteins also contribute to the final collagen matrix properties, one of which is fibromodulin. Its interactions with collagen affect collagen cross-linking, packing, and fibril diameter. We investigated the possibility that a specific relationship exists between fibromodulin and lysyl oxidase, potentially imparting a specific collagen matrix phenotype. We mapped the fibromodulin-collagen interaction sites using the collagen II and III Toolkit peptide libraries. Fibromodulin interacted with the peptides containing the known collagen cross-linking sites and the MMP-1 cleavage site in collagens I and II. Interestingly, the interaction sites are closely aligned within the quarter-staggered collagen fibril, suggesting a multivalent interaction between fibromodulin and several collagen helices. Furthermore, we detected an interaction between fibromodulin and lysyl oxidase (a major collagen cross-linking enzyme) and mapped the interaction site to 12 N-terminal amino acids on fibromodulin. This interaction also increases the activity of lysyl oxidase. Together, the data suggest a fibromodulin-modulated collagen cross-linking mechanism where fibromodulin binds to a specific part of the collagen domain and also forms a complex with lysyl oxidase, targeting the enzyme toward specific cross-linking sites. PMID:26893379

  14. Fibromodulin Interacts with Collagen Cross-linking Sites and Activates Lysyl Oxidase.

    PubMed

    Kalamajski, Sebastian; Bihan, Dominique; Bonna, Arkadiusz; Rubin, Kristofer; Farndale, Richard W

    2016-04-01

    The hallmark of fibrotic disorders is a highly cross-linked and dense collagen matrix, a property driven by the oxidative action of lysyl oxidase. Other fibrosis-associated proteins also contribute to the final collagen matrix properties, one of which is fibromodulin. Its interactions with collagen affect collagen cross-linking, packing, and fibril diameter. We investigated the possibility that a specific relationship exists between fibromodulin and lysyl oxidase, potentially imparting a specific collagen matrix phenotype. We mapped the fibromodulin-collagen interaction sites using the collagen II and III Toolkit peptide libraries. Fibromodulin interacted with the peptides containing the known collagen cross-linking sites and the MMP-1 cleavage site in collagens I and II. Interestingly, the interaction sites are closely aligned within the quarter-staggered collagen fibril, suggesting a multivalent interaction between fibromodulin and several collagen helices. Furthermore, we detected an interaction between fibromodulin and lysyl oxidase (a major collagen cross-linking enzyme) and mapped the interaction site to 12 N-terminal amino acids on fibromodulin. This interaction also increases the activity of lysyl oxidase. Together, the data suggest a fibromodulin-modulated collagen cross-linking mechanism where fibromodulin binds to a specific part of the collagen domain and also forms a complex with lysyl oxidase, targeting the enzyme toward specific cross-linking sites.

  15. Tool-using strategies by early hominids at bed II, Olduvai Gorge, Tanzania.

    PubMed

    Kimura, Y

    1999-12-01

    This study examines the current prevailing model of Oldowan technology-the opportunistic, least-effort strategy of stone tool making and using by early hominids. The sample includes the MNK chert factory site and three contemporaneous assemblages from Olduvai Gorge, all dated between 1.65 and 1.53 m.y.a. The analysis suggests that early hominids at Olduvai may have been selective, applying distinctive strategies in making and using tools depending on the different types of raw materials available to them. The preponderance of lava cores and near absence of flakes associated with the cores suggest that lava cores at Olduvai did not provide a source of flakes. They were primarily heavy-duty core tools, despite the fact that the majority of Olduvai lava is of excellent quality for flaking. Contrary to this pattern, the abundance of chert flakes and the lack of large chert cores suggest that the production of flakes was the most important strategy applied to chert. Original forms and flaking mechanics of the raw materials may have been important factors in the simultaneous application of the different, complementary strategies. The Oldowan tool-using strategy was dynamic and flexible, in response to changes in raw material availability. The use of chert between 1.65 and 1.53 m.y.a. was apparently related to the drastic decrease in flake production in lava and quartz. Finally, lack of initial reduction episodes of lava material challenges the idea of the stone cache strategy at Olduvai between 1.65 to 1.53 m.y.a.

  16. Paleoenvironmental and paleoecological reconstruction of a freshwater oasis in savannah grassland at FLK North, Olduvai Gorge, Tanzania

    NASA Astrophysics Data System (ADS)

    Ashley, Gail M.; Barboni, Doris; Dominguez-Rodrigo, Manuel; Bunn, Henry T.; Mabulla, Audax Z. P.; Diez-Martin, Fernando; Barba, Rebeca; Baquedano, Enrique

    2010-11-01

    The records of early hominins are commonly localized both temporally and spatially even in archaeologically rich basins like Olduvai Gorge, Tanzania. The FLK North site was discovered in 1960, but the reason for the exact location of this dense concentration of fossils and stone tools on a lake-margin flat has not been explained. We present new geological and geochemical information from six excavations in upper Bed I, which revealed up to 1.4-m-thick carbonate deposits, attesting to the presence of freshwater springs in the area surrounding FLK North. The δ 18O signatures of the tufa are typical for meteoric water that has evolved during evaporation. Tuff IF that caps the sequence was deposited on uneven topography with the highest area a low-relief ridge between two faults at the archaeological site and lowest areas being sites of groundwater discharge. The model proposed here is that rainfall on adjacent highlands was transported to the basin where faults acted as conduits for water. Similar hydrogeological settings at modern lakes Manyara and Eyasi, currently support lush groundwater forest and woodland despite arid climate. FLK North may have been an "oasis" offering freshwater and shelter for consuming meat by both carnivores and hominins.

  17. Spatial and seasonal variability of CO2 flux at the air-water interface of the Three Gorges Reservoir.

    PubMed

    Le, Yang; Lu, Fei; Wang, Xiaoke; Duan, Xiaonan; Tong, Lei; Ouyang, Zhiyun; Li, Hepeng

    2013-11-01

    Diffusive carbon dioxide (CO2) emissions from the water surface of the Three Gorges Reservoir, currently the largest hydroelectric reservoir in the world, were measured using floating static chambers over the course of a yearlong survey. The results showed that the average annual CO2 flux was (163.3 +/- 117.4) mg CO2/(m2.hr) at the reservoir surface, which was larger than the CO2 flux in most boreal and temperate reservoirs but lower than that in tropical reservoirs. Significant spatial variations in CO2 flux were observed at four measured sites, with the largest flux measured at Wushan (221.9 mg CO2/(m2.hr)) and the smallest flux measured at Zigui (88.6 mg CO2/(m(2).hr)); these differences were probably related to the average water velocities at different sites. Seasonal variations in CO2 flux were also observed at four sites, starting to increase in January, continuously rising until peaking in the summer (June-August) and gradually decreasing thereafter. Seasonal variations in CO2 flux could reflect seasonal dynamics in pH, water velocity, and temperature. Since the spatial and temporal variations in CO2 flux were significant and dependent on multiple physical, chemical, and hydrological factors, it is suggested that long-term measurements should be made on a large spatial scale to assess the climatic influence of hydropower in China, as well as the rest of the world.

  18. 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.

  19. A Frontier Molecular Orbital determination of the active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.

    1992-11-01

    An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of catalyzed reactions take place on single atom active sites on the metal surface. Thus, these sites can be considered as surface complexes made up of the central active atom surrounded by near-neighbor metal atom ``ligands`` with localized surface orbitals perturbed only by these ``ligands``. These ``complexes`` are based on a twelve coordinate species with the ``ligands`` attached to the t{sub 2g} orbitals and the coordinate axes coincident with the direction of the e{sub g} orbitals on the central atom. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  20. A Frontier Molecular Orbital determination of the active sites on dispersed metal catalysts

    SciTech Connect

    Augustine, R.L.; Lahanas, K.M.

    1992-01-01

    An angular overlap calculation has been used to determine the s, p and d orbital energy levels of the different types of surface sites present on a dispersed metal catalysts. The basis for these calculations is the reported finding that a large number of catalyzed reactions take place on single atom active sites on the metal surface. Thus, these sites can be considered as surface complexes made up of the central active atom surrounded by near-neighbor metal atom ligands'' with localized surface orbitals perturbed only by these ligands''. These complexes'' are based on a twelve coordinate species with the ligands'' attached to the t{sub 2g} orbitals and the coordinate axes coincident with the direction of the e{sub g} orbitals on the central atom. These data can permit a Frontier Molecular Orbital treatment of specific site activities as long as the surface orbital availability for overlap with adsorbed substrates is considered along with its energy value and symmetry.

  1. Mapping Topoisomerase IV Binding and Activity Sites on the E. coli Genome

    PubMed Central

    Lebailly, Elise; Pages, Carine; Cornet, Francois; Cosentino Lagomarsino, Marco

    2016-01-01

    Catenation links between sister chromatids are formed progressively during DNA replication and are involved in the establishment of sister chromatid cohesion. Topo IV is a bacterial type II topoisomerase involved in the removal of catenation links both behind replication forks and after replication during the final separation of sister chromosomes. We have investigated the global DNA-binding and catalytic activity of Topo IV in E. coli using genomic and molecular biology approaches. ChIP-seq revealed that Topo IV interaction with the E. coli chromosome is controlled by DNA replication. During replication, Topo IV has access to most of the genome but only selects a few hundred specific sites for its activity. Local chromatin and gene expression context influence site selection. Moreover strong DNA-binding and catalytic activities are found at the chromosome dimer resolution site, dif, located opposite the origin of replication. We reveal a physical and functional interaction between Topo IV and the XerCD recombinases acting at the dif site. This interaction is modulated by MatP, a protein involved in the organization of the Ter macrodomain. These results show that Topo IV, XerCD/dif and MatP are part of a network dedicated to the final step of chromosome management during the cell cycle. PMID:27171414

  2. Functional mimicry of the active site of glutathione peroxidase by glutathione imprinted selenium-containing protein.

    PubMed

    Liu, Lei; Mao, Shi-zhong; Liu, Xiao-man; Huang, Xin; Xu, Jia-yun; Liu, Jun-qiu; Luo, Gui-min; Shen, Jia-cong

    2008-01-01

    For imitating the active site of antioxidant selenoenzyme glutathione peroxidase (GPx), an artificial enzyme selenosubtilisin was employed as a scaffold for reconstructing substrate glutathione (GSH) specific binding sites by a bioimprinting strategy. GSH was first covalently linked to selenosubtilisin to form a covalent complex GSH-selenosubtilisin through a Se-S bond, then the GSH molecule was used as a template to cast a complementary binding site for substrate GSH recognition. The bioimprinting procedure consists of unfolding the conformation of selenosubtilisin and fixing the new conformation of the complex GSH-selenosubtilisin. Thus a new specificity for naturally occurring GPx substrate GSH was obtained. This bioimprinting procedure facilitates the catalytic selenium moiety of the imprinted selenosubtilisin to match the reactive thiol group of GSH in the GSH binding site, which contributes to acceleration of the intramolecular catalysis. These imprinted selenium-containing proteins exhibited remarkable rate enhancement for the reduction of H2O2 by GSH. The average GPx activity was found to be 462 U/micromol, and it was approximately 100 times that for unimprinted selenosubtilisin. Compared with ebselen, a well-known GPx mimic, an activity enhancement of 500-fold was observed. Detailed steady-state kinetic studies demonstrated that the novel selenoenzyme followed a ping-pong mechanism similar to the naturally occurring GPx. PMID:18163571

  3. Evidence for Oxygen Binding at the Active Site of Particulate Methane Monooxygenase

    PubMed Central

    Culpepper, Megen A.; Cutsail, George E.; Hoffman, Brian M.; Rosenzweig, Amy C.

    2012-01-01

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that converts methane to methanol in methanotrophic bacteria. The enzyme consists of three subunits, pmoB, pmoA, and pmoC, organized in an α3β3γ3 trimer. Studies of intact pMMO and a recombinant soluble fragment of the pmoB subunit, denoted spmoB, indicate that the active site is located within the soluble region of pmoB at the site of a crystallographically modeled dicopper center. In this work, we have investigated the reactivity of pMMO and spmoB with oxidants. Upon reduction and treatment of spmoB with O2 and H2O2 or pMMO with H2O2, an absorbance feature at 345 nm is generated. The energy and intensity of this band are similar to that of the μ-η2:η2-peroxo CuII 2 species formed in several dicopper enzymes and model compounds. The feature is not observed in inactive spmoB variants in which the dicopper center is disrupted, consistent with O2 binding to the proposed active site. Reaction of the 345 nm species with CH4 results in disappearance of the spectroscopic feature, suggesting that this O2 intermediate is mechanistically relevant. Taken together, these observations provide strong new support for the identity and location of the pMMO active site. PMID:22540911

  4. The ribotoxin restrictocin recognizes its RNA substrate by selective engagement of active site residues.

    PubMed

    Plantinga, Matthew J; Korennykh, Alexei V; Piccirilli, Joseph A; Correll, Carl C

    2011-04-12

    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

  5. Activation of human 5-hydroxytryptamine type 3 receptors via an allosteric transmembrane site.

    PubMed

    Lansdell, Stuart J; Sathyaprakash, Chaitra; Doward, Anne; Millar, Neil S

    2015-01-01

    In common with other members of the Cys-loop family of pentameric ligand-gated ion channels, 5-hydroxytryptamine type 3 receptors (5-HT3Rs) are activated by the binding of a neurotransmitter to an extracellular orthosteric site, located at the interface of two adjacent receptor subunits. In addition, a variety of compounds have been identified that modulate agonist-evoked responses of 5-HT3Rs, and other Cys-loop receptors, by binding to distinct allosteric sites. In this study, we examined the pharmacological effects of a group of monoterpene compounds on recombinant 5-HT3Rs expressed in Xenopus oocytes. Two phenolic monoterpenes (carvacrol and thymol) display allosteric agonist activity on human homomeric 5-HT3ARs (64 ± 7% and 80 ± 4% of the maximum response evoked by the endogenous orthosteric agonist 5-HT, respectively). In addition, at lower concentrations, where agonist effects are less apparent, carvacrol and thymol act as potentiators of responses evoked by submaximal concentrations of 5-HT. By contrast, carvacrol and thymol have no agonist or potentiating activity on the closely related mouse 5-HT3ARs. Using subunit chimeras containing regions of the human and mouse 5-HT3A subunits, and by use of site-directed mutagenesis, we have identified transmembrane amino acids that either abolish the agonist activity of carvacrol and thymol on human 5-HT3ARs or are able to confer this property on mouse 5-HT3ARs. By contrast, these mutations have no significant effect on orthosteric activation of 5-HT3ARs by 5-HT. We conclude that 5-HT3ARs can be activated by the binding of ligands to an allosteric transmembrane site, a conclusion that is supported by computer docking studies. PMID:25338672

  6. Final Report - Independent Verification Survey Activities at the Seperations Process Research Unit Sites, Niskayuna, New York

    SciTech Connect

    Evan Harpenau

    2011-03-15

    The Separations Process Research Unit (SPRU) complex located on the Knolls Atomic Power Laboratory (KAPL) site in Niskayuna, New York, was constructed in the late 1940s to research the chemical separation of plutonium and uranium (Figure A-1). SPRU operated as a laboratory scale research facility between February 1950 and October 1953. The research activities ceased following the successful development of the reduction oxidation and plutonium/uranium extraction processes. The oxidation and extraction processes were subsequently developed for large scale use by the Hanford and Savannah River sites (aRc 2008a). Decommissioning of the SPRU facilities began in October 1953 and continued through the 1990s.

  7. Technical basis for classification of low-activity waste fraction from Hanford site tanks

    SciTech Connect

    Petersen, C.A.

    1996-09-20

    The overall objective of this report is to provide a technical basis to support a U.S. Nuclear Regulatory Commission determination to classify the low-activity waste from the Hanford Site single-shell and double-shell tanks as `incidental` wastes after removal of additional radionuclides and immobilization.The proposed processing method, in addition to the previous radionuclide removal efforts, will remove the largest practical amount of total site radioactivity, attributable to high-level waste, for disposal is a deep geologic repository. The remainder of the waste would be considered `incidental` waste and could be disposed onsite.

  8. Technical basis for classification of low-activity waste fraction from Hanford site tanks

    SciTech Connect

    Petersen, C.A., Westinghouse Hanford

    1996-07-17

    The overall objective of this report is to provide a technical basis to support a U.S. Nuclear Regulatory Commission determination to classify the low-activity waste from the Hanford Site single-shell and double-shell tanks as `incidental` wastes after removal of additional radionuclides and immobilization.The proposed processing method, in addition to the previous radionuclide removal efforts, will remove the largest practical amount of total site radioactivity, attributable to high-level wastes, for disposal in a deep geologic repository. The remainder of the waste would be considered `incidental` waste and could be disposed onsite.

  9. Three Gorges Dam and its impact on the potential transmission of schistosomiasis in regions along the Yangtze River.

    PubMed

    Zhu, Huai-Min; Xiang, Shuo; Yang, Kun; Wu, Xiao-Hua; Zhou, Xiao-Nong

    2008-06-01

    Large-scale hydroprojects have a propensity for incurring schistosomiasis epidemics by altering the environments of their vicinities. As the construction of the Three Gorges Dam, one of the world's largest hydroprojects to date, draws near its conclusion, an assessment of the dam's capacity in causing schistosomiasis becomes more urgent and pressing. This article reviews recent investigations into the possible effects of the dam on schistosomiasis in the Three Gorges region and areas along the Yangtze downstream from the dam. Data used in this article were extracted from peer-reviewed papers found in PubMed, Chinese Journal of Parasitology and Parasitic Diseases, and Chinese Journal of Schistosomiasis Control. Results indicate that the Three Gorges Dam is capable of inducing a wide variety of environmental and ecological changes both within the Three Gorges region and in downstream areas. These changes, however, carry ambivalent implications for the reproduction of Oncomelania snails and the spreading of schistosome infections. Furthermore, major changes in the demographics and agricultural practices of the Three Gorges and downstream Yangtze areas caused by the dam could also exert significant influence on the transmission of schistosomiasis in these regions. Major conclusions of this review include the need for further ecological simulations of the Three Gorges Dam and the need for deploying monitoring and intervention systems to provide successful prophylaxis of the Three Gorges Dam-associated schistosomiasis emergence.

  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. 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.

  12. 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.

  13. Impact of single-site axonal GABAergic synaptic events on cerebellar interneuron activity.

    PubMed

    de San Martin, Javier Zorrilla; Jalil, Abdelali; Trigo, Federico F

    2015-12-01

    Axonal ionotropic receptors are present in a variety of neuronal types, and their function has largely been associated with the modulation of axonal activity and synaptic release. It is usually assumed that activation of axonal GABA(A)Rs comes from spillover, but in cerebellar molecular layer interneurons (MLIs) the GABA source is different: in these cells, GABA release activates presynaptic GABA(A) autoreceptors (autoRs) together with postsynaptic targets, producing an autoR-mediated synaptic event. The frequency of presynaptic, autoR-mediated miniature currents is twice that of their somatodendritic counterparts, suggesting that autoR-mediated responses have an important effect on interneuron activity. Here, we used local Ca(2+) photolysis in MLI axons of juvenile rats to evoke GABA release from individual varicosities to study the activation of axonal autoRs in single release sites. Our data show that single-site autoR conductances are similar to postsynaptic dendritic conductances. In conditions of high [Cl(-)](i), autoR-mediated conductances range from 1 to 5 nS; this corresponds to ∼30-150 GABA(A) channels per presynaptic varicosity, a value close to the number of channels in postsynaptic densities. Voltage responses produced by the activation of autoRs in single varicosities are amplified by a Na(v)-dependent mechanism and propagate along the axon with a length constant of 91 µm. Immunolabeling determination of synapse location shows that on average, one third of the synapses produce autoR-mediated signals that are large enough to reach the axon initial segment. Finally, we show that single-site activation of presynaptic GABA(A) autoRs leads to an increase in MLI excitability and thus conveys a strong feedback signal that contributes to spiking activity.

  14. Function of the active site lysine autoacetylation in Tip60 catalysis.

    PubMed

    Yang, Chao; Wu, Jiang; Zheng, Y George

    2012-01-01

    The 60-kDa HIV-Tat interactive protein (Tip60) is a key member of the MYST family of histone acetyltransferases (HATs) that plays critical roles in multiple cellular processes. We report here that Tip60 undergoes autoacetylation at several lysine residues, including a key lysine residue (i.e. Lys-327) in the active site of the MYST domain. The mutation of K327 to arginine led to loss of both the autoacetylation activity and the cognate HAT activity. Interestingly, deacetylated Tip60 still kept a substantial degree of HAT activity. We also investigated the effect of cysteine 369 and glutamate 403 in Tip60 autoacetylation in order to understand the molecular pathway of the autoacetylation at K327. Together, we conclude that the acetylation of K327 which is located in the active site of Tip60 regulates but is not obligatory for the catalytic activity of Tip60. Since acetylation at this key residue appears to be evolutionarily conserved amongst all MYST proteins, our findings provide an interesting insight into the regulatory mechanism of MYST activities. PMID:22470428

  15. Phytoplankton variation and its relationship with the environment in Xiangxi Bay in spring after damming of the Three-Gorges, China.

    PubMed

    Zhou, Guangjie; Zhao, Xuemin; Bi, Yonghong; Liang, Yubin; Hu, Jianlin; Yang, Min; Mei, Yu; Zhu, Kongxian; Zhang, Lin; Hu, Zhengyu

    2011-05-01

    Following the completion of the Three-Gorges Dam, there was a strong spring phytoplankton bloom in Xiangxi Bay of Three-Gorges Reservoir. However, our knowledge of relationship between spring phytoplankton bloom and environmental factors was still limited. In this study, phytoplankton species composition, biomass, chlorophyll a concentration and environmental factors at two sampling sites in Xiangxi Bay were investigated during 25 March to 18 May 2007. The Xiangxi Bay was eutrophic with the lowest values of total nitrogen and total phosphorus being 0.80 and 0.07 mg/L, respectively. A total of 66 algal taxa belonging to seven phyla and 45 genera were identified. Peridiniopsis niei Liu was the most abundant species which preferred standing water. Canonical correspondence analysis and correlation analysis revealed that nitrate was significantly associated with phytoplankton growth. The phytoplankton chlorophyll a concentration was correlated significantly negatively with nitrate concentration, and nitrate concentration was very low during bloom periods. Heavy rainfall was the main reason of phytoplankton chlorophyll a concentration and biomass decreasing and blooms disappearing. In addition, heavy rainfall also brought more nitrate into the Bay which provided sufficient nitrogen source for blooms occurring again.

  16. Phytoplankton variation and its relationship with the environment in Xiangxi Bay in spring after damming of the Three-Gorges, China.

    PubMed

    Zhou, Guangjie; Zhao, Xuemin; Bi, Yonghong; Liang, Yubin; Hu, Jianlin; Yang, Min; Mei, Yu; Zhu, Kongxian; Zhang, Lin; Hu, Zhengyu

    2011-05-01

    Following the completion of the Three-Gorges Dam, there was a strong spring phytoplankton bloom in Xiangxi Bay of Three-Gorges Reservoir. However, our knowledge of relationship between spring phytoplankton bloom and environmental factors was still limited. In this study, phytoplankton species composition, biomass, chlorophyll a concentration and environmental factors at two sampling sites in Xiangxi Bay were investigated during 25 March to 18 May 2007. The Xiangxi Bay was eutrophic with the lowest values of total nitrogen and total phosphorus being 0.80 and 0.07 mg/L, respectively. A total of 66 algal taxa belonging to seven phyla and 45 genera were identified. Peridiniopsis niei Liu was the most abundant species which preferred standing water. Canonical correspondence analysis and correlation analysis revealed that nitrate was significantly associated with phytoplankton growth. The phytoplankton chlorophyll a concentration was correlated significantly negatively with nitrate concentration, and nitrate concentration was very low during bloom periods. Heavy rainfall was the main reason of phytoplankton chlorophyll a concentration and biomass decreasing and blooms disappearing. In addition, heavy rainfall also brought more nitrate into the Bay which provided sufficient nitrogen source for blooms occurring again. PMID:20563898

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

    PubMed

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

    2007-04-20

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

  18. Linde FUSRAP Site Remediation: Engineering Challenges and Solutions of Remedial Activities on an Active Industrial Facility - 13506

    SciTech Connect

    Beres, Christopher M.; Fort, E. Joseph; Boyle, James D.

    2013-07-01

    The Linde FUSRAP Site (Linde) is located in Tonawanda, New York at a major research and development facility for Praxair, Inc. (Praxair). Successful remediation activities at Linde combines meeting cleanup objectives of radiological contamination while minimizing impacts to Praxair business operations. The unique use of Praxair's property coupled with an array of active and abandoned utilities poses many engineering and operational challenges; each of which has been overcome during the remedial action at Linde. The U.S. Army Corps of Engineers - Buffalo District (USACE) and CABRERA SERVICES, INC. (CABRERA) have successfully faced engineering challenges such as relocation of an aboveground structure, structural protection of an active water line, and installation of active mechanical, electrical, and communication utilities to perform remediation. As remediation nears completion, continued success of engineering challenges is critical as remaining activities exist in the vicinity of infrastructure essential to business operations; an electrical substation and duct bank providing power throughout the Praxair facility. Emphasis on engineering and operations through final remediation and into site restoration will allow for the safe and successful completion of the project. (authors)

  19. Crystallographic Analysis of Active Site Contributions to Regiospecificity in the Diiron Enzyme Toluene 4-Monooxygenase

    SciTech Connect

    Bailey, Lucas J.; Acheson, Justin F.; McCoy, Jason G.; Elsen, Nathaniel L.; Phillips, Jr., George N.; Fox, Brian G.

    2014-10-02

    Crystal structures of toluene 4-monooxygenase hydroxylase in complex with reaction products and effector protein reveal active site interactions leading to regiospecificity. Complexes with phenolic products yield an asymmetric {mu}-phenoxo-bridged diiron center and a shift of diiron ligand E231 into a hydrogen bonding position with conserved T201. In contrast, complexes with inhibitors p-NH{sub 2}-benzoate and p-Br-benzoate showed a {mu}-1,1 coordination of carboxylate oxygen between the iron atoms and only a partial shift in the position of E231. Among active site residues, F176 trapped the aromatic ring of products against a surface of the active site cavity formed by G103, E104 and A107, while F196 positioned the aromatic ring against this surface via a {pi}-stacking interaction. The proximity of G103 and F176 to the para substituent of the substrate aromatic ring and the structure of G103L T4moHD suggest how changes in regiospecificity arise from mutations at G103. Although effector protein binding produced significant shifts in the positions of residues along the outer portion of the active site (T201, N202, and Q228) and in some iron ligands (E231 and E197), surprisingly minor shifts (<1 {angstrom}) were produced in F176, F196, and other interior residues of the active site. Likewise, products bound to the diiron center in either the presence or absence of effector protein did not significantly shift the position of the interior residues, suggesting that positioning of the cognate substrates will not be strongly influenced by effector protein binding. Thus, changes in product distributions in the absence of the effector protein are proposed to arise from differences in rates of chemical steps of the reaction relative to motion of substrates within the active site channel of the uncomplexed, less efficient enzyme, while structural changes in diiron ligand geometry associated with cycling between diferrous and diferric states are discussed for their potential

  20. Active Site Dependent Reaction Mechanism over Ru/CeO2 Catalyst toward CO2 Methanation.

    PubMed

    Wang, Fei; He, Shan; Chen, Hao; Wang, Bin; Zheng, Lirong; Wei, Min; Evans, David G; Duan, Xue

    2016-05-18

    Oxygen vacancy on the surface of metal oxides is one of the most important defects which acts as the reactive site in a variety of catalytic reactions. In this work, operando spectroscopy methodology was employed to study the CO2 methanation reaction catalyzed by Ru/CeO2 (with oxygen vacancy in CeO2) and Ru/α-Al2O3 (without oxygen vacancy), respectively, so as to give a thorough understanding on active site dependent reaction mechanism. In Ru/CeO2 catalyst, operando XANES, IR, and Raman were used to reveal the generation process of Ce(3+), surface hydroxyl, and oxygen vacancy as well as their structural evolvements under practical reaction conditions. The steady-state isotope transient kinetic analysis (SSITKA)-type in situ DRIFT infrared spectroscopy undoubtedly substantiates that CO2 methanation undergoes formate route over Ru/CeO2 catalyst, and the formate dissociation to methanol catalyzed by oxygen vacancy is the rate-determining step. In contrast, CO2 methanation undergoes CO route over Ru surface in Ru/α-Al2O3 with the absence of oxygen vacancy, demonstrating active site dependent catalytic mechanism toward CO2 methanation. In addition, the catalytic activity evaluation and the oscillating reaction over Ru/CeO2 catalyst further prove that the oxygen vacancy catalyzes the rate-determining step with a much lower activation temperature compared with Ru surface in Ru/α-Al2O3 (125 vs 250 °C).

  1. Progress report on decommissioning activities at the Fernald Environmental Management Project (FEMP) site

    SciTech Connect

    1998-07-01

    The Fernald Environmental Management Project (FEMP), is located about 18 miles northwest of Cincinnati, Ohio. Between 1953 and 1989, the facility, then called the Feed Material Production Center or FMPC, produced uranium metal products used in the eventual production of weapons grade material for use by other US Department of Energy (DOE) sites. In 1989, FMPC`s production was suspended by the federal government in order to focus resources on environmental restoration versus defense production. In 1992, Fluor Daniel Fernald assumed responsibility for managing all cleanup activities at the FEMP under contract to the DOE. In 1990, as part of the remediation effort, the site was divided into five operable units based on physical proximity of contaminated areas, similar amounts of types of contamination, or the potential for a similar technology to be used in cleanup activities. This report continues the outline of the decontamination and decommissioning (D and D) activities at the FEMP site Operable Unit 3 (OU3) and provides an update on the status of the decommissioning activities. OU3, the Facilities Closure and Demolition Project, involves the remediation of more than 200 uranium processing facilities. The mission of the project is to remove nuclear materials stored in these buildings, then perform the clean out of the buildings and equipment, and decontaminate and dismantle the facilities.

  2. Identification of essential histidine residues in the active site of Escherichia coli xylose (glucose) isomerase.

    PubMed

    Batt, C A; Jamieson, A C; Vandeyar, M A

    1990-01-01

    Two conserved histidine residues (His-101 and His-271) appear to be essential components in the active site of the enzyme xylose (glucose) isomerase (EC 5.3.1.5). These amino acid residues were targeted for mutagenesis on the basis of sequence homology among xylose isomerases isolated from Escherichia coli, Bacillus subtilis, Ampullariella sp. strain 3876, and Streptomyces violaceus-niger. Each residue was selectively replaced by site-directed mutagenesis and shown to be essential for activity. No measurable activity was observed for any mutations replacing either His-101 or His-271. Circular dichroism measurements revealed no significant change in the overall conformation of the mutant enzymes, and all formed dimers similar to the wild-type enzyme. Mutations at His-271 could be distinguished from those at His-101, since the former resulted in a thermolabile protein whereas no significant change in heat stability was observed for the latter. Based upon these results and structural data recently reported, we speculate that His-101 is the catalytic base mediating the reaction. Replacement of His-271 may render the enzyme thermolabile, since this residue appears to be a ligand for one of the metal ions in the active site of the enzyme. PMID:2405386

  3. Structural basis for the active site inhibition mechanism of human kidney-type glutaminase (KGA).

    PubMed

    Thangavelu, K; Chong, Qing Yun; Low, Boon Chuan; Sivaraman, J

    2014-01-01

    Glutaminase is a metabolic enzyme responsible for glutaminolysis, a process harnessed by cancer cells to feed their accelerated growth and proliferation. Among the glutaminase isoforms, human kidney-type glutaminase (KGA) is often upregulated in cancer and is thus touted as an attractive drug target. Here we report the active site inhibition mechanism of KGA through the crystal structure of the catalytic domain of KGA (cKGA) in complex with 6-diazo-5-oxo-L-norleucine (DON), a substrate analogue of glutamine. DON covalently binds with the active site Ser286 and interacts with residues such as Tyr249, Asn335, Glu381, Asn388, Tyr414, Tyr466 and Val484. The nucleophilic attack of Ser286 sidechain on DON releases the diazo group (N2) from the inhibitor and results in the formation of an enzyme-inhibitor complex. Mutational studies confirmed the key role of these residues in the activity of KGA. This study will be important in the development of KGA active site inhibitors for therapeutic interventions.

  4. Structural Basis for the Active Site Inhibition Mechanism of Human Kidney-Type Glutaminase (KGA)

    PubMed Central

    Thangavelu, K.; Chong, Qing Yun; Low, Boon Chuan; Sivaraman, J.

    2014-01-01

    Glutaminase is a metabolic enzyme responsible for glutaminolysis, a process harnessed by cancer cells to feed their accelerated growth and proliferation. Among the glutaminase isoforms, human kidney-type glutaminase (KGA) is often upregulated in cancer and is thus touted as an attractive drug target. Here we report the active site inhibition mechanism of KGA through the crystal structure of the catalytic domain of KGA (cKGA) in complex with 6-diazo-5-oxo-L-norleucine (DON), a substrate analogue of glutamine. DON covalently binds with the active site Ser286 and interacts with residues such as Tyr249, Asn335, Glu381, Asn388, Tyr414, Tyr466 and Val484. The nucleophilic attack of Ser286 sidechain on DON releases the diazo group (N2) from the inhibitor and results in the formation of an enzyme-inhibitor complex. Mutational studies confirmed the key role of these residues in the activity of KGA. This study will be important in the development of KGA active site inhibitors for therapeutic interventions. PMID:24451979

  5. Site-dependent catalytic activity of graphene oxides towards oxidative dehydrogenation of propane.

    PubMed

    Tang, Shaobin; Cao, Zexing

    2012-12-28

    Graphene oxides (GOs) may offer extraordinary potential in the design of novel catalytic systems due to the presence of various oxygen functional groups and their unique electronic and structural properties. Using first-principles calculations, we explore the plausible mechanisms for the oxidative dehydrogenation (ODH) of propane to propene by GOs and the diffusion of the surface oxygen-containing groups under an external electric field. The present results show that GOs with modified oxygen-containing groups may afford high catalytic activity for the ODH of propane to propene. The presence of hydroxyl groups around the active sites provided by epoxides can remarkably enhance the C-H bond activation of propane and the activity enhancement exhibits strong site dependence. The sites of oxygen functional groups on the GO surface can be easily tuned by the diffusion of these groups under an external electric field, which increases the reactivity of GOs towards ODH of propane. The chemically modified GOs are thus quite promising in the design of metal-free catalysis. PMID:22801590

  6. How Force Might Activate Talin's Vinculin Binding Sites: SMD Reveals a Structural Mechanism

    PubMed Central

    Hytönen, Vesa P; Vogel, Viola

    2008-01-01

    Upon cell adhesion, talin physically couples the cytoskeleton via integrins to the extracellular matrix, and subsequent vinculin recruitment is enhanced by locally applied tensile force. Since the vinculin binding (VB) sites are buried in the talin rod under equilibrium conditions, the structural mechanism of how vinculin binding to talin is force-activated remains unknown. Taken together with experimental data, a biphasic vinculin binding model, as derived from steered molecular dynamics, provides high resolution structural insights how tensile mechanical force applied to the talin rod fragment (residues 486–889 constituting helices H1–H12) might activate the VB sites. Fragmentation of the rod into three helix subbundles is prerequisite to the sequential exposure of VB helices to water. Finally, unfolding of a VB helix into a completely stretched polypeptide might inhibit further binding of vinculin. The first events in fracturing the H1–H12 rods of talin1 and talin2 in subbundles are similar. The proposed force-activated α-helix swapping mechanism by which vinculin binding sites in talin rods are exposed works distinctly different from that of other force-activated bonds, including catch bonds. PMID:18282082

  7. From single crystal surfaces to single atoms: investigating active sites in electrocatalysis.

    PubMed

    O'Mullane, Anthony P

    2014-04-21

    Electrocatalytic processes will undoubtedly be at the heart of energising future transportation and technology with the added importance of being able to create the necessary fuels required to do so in an environmentally friendly and cost effective manner. For this to be successful two almost mutually exclusive surface properties need to be reconciled, namely producing highly active/reactive surface sites that exhibit long term stability. This article reviews the various approaches which have been undertaken to study the elusive nature of these active sites on metal surfaces which are considered as adatoms or clusters of adatoms with low coordination number. This includes the pioneering studies at extended well defined stepped single crystal surfaces using cyclic voltammetry up to the highly sophisticated in situ electrochemical imaging techniques used to study chemically synthesised nanomaterials. By combining the information attained from single crystal surfaces, individual nanoparticles of defined size and shape, density functional theory calculations and new concepts such as mesoporous multimetallic thin films and single atom electrocatalysts new insights into the design and fabrication of materials with highly active but stable active sites can be achieved. The area of electrocatalysis is therefore not only a fascinating and exciting field in terms of realistic technological and economical benefits but also from the fundamental understanding that can be acquired by studying such an array of interesting materials. PMID:24599277

  8. Targeting Large Kinase Active Site with Rigid, Bulky Octahedral Ruthenium Complexes

    SciTech Connect

    Maksimoska, Jasna; Feng, Li; Harms, Klaus; Yi, Chunling; Kissil, Joseph; Marmorstein, Ronen; Meggers, Eric

    2009-09-02

    A strategy for targeting protein kinases with large ATP-binding sites by using bulky and rigid octahedral ruthenium complexes as structural scaffolds is presented. A highly potent and selective GSK3 and Pim1 half-sandwich complex NP309 was successfully converted into a PAK1 inhibitor by making use of the large octahedral compounds {Lambda}-FL172 and {Lambda}-FL411 in which the cyclopentadienyl moiety of NP309 is replaced by a chloride and sterically demanding diimine ligands. A 1.65 {angstrom}cocrystal structure of PAK1 with {Lambda}-FL172 reveals how the large coordination sphere of the ruthenium complex matches the size of the active site and serves as a yardstick to discriminate between otherwise closely related binding sites.

  9. Novel active comb-shaped dry electrode for EEG measurement in hairy site.

    PubMed

    Huang, Yan-Jun; Wu, Chung-Yu; Wong, Alice May-Kuen; Lin, Bor-Shyh

    2015-01-01

    Electroencephalography (EEG) is an important biopotential, and has been widely applied in clinical applications. The conventional EEG electrode with conductive gels is usually used for measuring EEG. However, the use of conductive gel also encounters with the issue of drying and hardening. Recently, many dry EEG electrodes based on different conductive materials and techniques were proposed to solve the previous issue. However, measuring EEG in the hairy site is still a difficult challenge. In this study, a novel active comb-shaped dry electrode was proposed to measure EEG in hairy site. Different form other comb-shaped or spike-shaped dry electrodes, it can provide more excellent performance of avoiding the signal attenuation, phase distortion, and the reduction of common mode rejection ratio. Even under walking motion, it can effectively acquire EEG in hairy site. Finally, the experiments for alpha rhythm and steady-state visually evoked potential were also tested to validate the proposed electrode.

  10. Active-site titration analysis of surface influence on immobilized Candida antarctica Lipase B activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Matrix morphology and surface polarity effects were investigated for Candida antarctica lipase B immobilization. Measurements of the amount of lipase immobilized (bicinchoninic acid method) and the catalyst’s tributyrin hydrolysis activity, coupled with a determination of the lipase’s functional fr...

  11. Polyhalogenated aromatic hydrocarbons in surface sediments from Three Gorges Reservoir.

    PubMed

    Zhao, Gaofeng; Li, Kun; Zhou, Huaidong; Liu, Xiaoru; Zhang, Panwei; Wen, Wu; Yu, Yang; Yuan, Hao

    2013-01-01

    This study was conducted to investigate the current contamination status of polyhalogenated aromatic hydrocarbons (PHAHs) in sediments from the mainstream and 22 primary tributaries of the Yangtze River in the Three Gorges Reservoir region. To accomplish this, the concentrations of 22 polybrominated biphenyl (PBB) congeners, 27 polybrominated diphenyl ether (PBDE) congeners, and 27 polychlorinated biphenyl (PCB) congeners in sediment samples were measured by GC-MS/MS. The result showed that the observed values of PBBs and PBDEs were 22.41 and 35.24 pg g(-1) dw, respectively. PBB1, 31 and 103 were the predominant PBB congeners, while PBDE28, 47, 77 and 99 were the predominant PBDE congeners. PBB209 and BDE209 were detected in >39% of the samples, with geometric means 2.43 and 11.92 pg g(-1) dw, respectively. PCBs were found to be the predominant compounds in sediment samples among the three PHAH subfamilies, with a geometric mean of 1,231.11 pg g(-1) dw, and PCB8, 18, 28, 52 and 66 were the primary PCB congeners. The measured levels of PHAHs were compared with results recently reported in the literature and their respective sediment quality guidelines recommended by the USEPA. The levels of PHAHs in the present study were generally lower than their respective threshold-effect levels, or were comparable to those reported in relatively uncontaminated freshwater samples from other regions. Taken together, these results suggest that, in the reservoir, toxic biological effects on aquatic biota in response to PHAHs contamination of sediments can be expected to be negligible. PMID:23043334

  12. Wetland Diagenesis and Traces of Early Hominids, Olduvai Gorge, Tanzania

    NASA Astrophysics Data System (ADS)

    Deocampo, Daniel M.; Blumenschine, Robert J.; Ashley, Gail M.

    2002-03-01

    Lateral variations in whole-rock and clay geochemistry of basal Bed II claystones in Olduvai Gorge, Tanzania, reflect water quality differences across the Eastern Lacustrine Plain ∼1.75 myr ago. Bulk Ba/Sr and (Na2O+K2O+MgO)/Al2O3 range from 1.4 to 4.2 and from 0.7 to 1.4, respectively, and indicate leaching of lacustrine claystones beneath freshwater wetlands at times following lake retreat. Bulk MgO/Al2O3 (0.3-1.0) and molar Mg/Al (0.5-3.9) ratios of <0.2-μm clays reflect alteration of Mg-rich lacustrine clays. These indicators point to freshest conditions near Locality 43 of Hay (1976; HWK-East; Leakey, 1971), moderate conditions to the east (Locality 40-MCK), and high salinity and alkalinity to the west (Localities 85-VEK, 45-FLK). Clay geochemistry and artifact abundances are well correlated (r=-0.67, p<0.005), suggesting a relationship between paleo-water quality and hominid paleoecology. This pattern is consistent with predictions of greatest artifact discard/loss around freshwater sources where scavanging opportunities were greatest for hominids. This quantifies a relationship between artifact density distribution and a paleoecological proxy over landscape scales for the first time in Early Stone Age archaeology. In contrast, fossil bone abundance is uncorrelated (r=0.14, p=0.6), reflecting more complex taphonomic processes. Quantitative tests of landscape-scale land-use models are important for understanding early hominid behavior and its evolution.

  13. Mitochondrial nicotinamide nucleotide transhydrogenase: active site modification by 5'-(p-(fluorosulfonyl)benzoyl)adenosine

    SciTech Connect

    Phelps, D.C.; Hatefi, Y.

    1985-07-02

    Membrane-bound and purified mitochondrial energy-linked nicotinamide nucleotide transhydrogenase (TH) was inhibited by incubation with 5'-(p-(fluorosulfonyl)benzoyl)adenosine (FSBA), which is an analogue of TH substrates and their competitive inhibitors, namely, 5'-, 2'-, or 3'-AMP. NAD(H) and analogues, NADP, 5'-AMP, 5'-ADP, and 2'-AMP/3'-AMP mixed isomers protected TH against inhibition by FSBA, but NADPH accelerated the inhibition rate. In the absence of protective ligands or in the presence of NADP, FSBA appeared to modify the NAD(H) binding site of TH, because, unlike unmodified TH, the enzyme modified by FSBA under these conditions did not bind to an NAD-affinity column (NAD-agarose). However, when the NAD(H) binding site of TH was protected in the presence of 5'-AMP or NAD, then FSBA modification resulted in an inhibited enzyme that did bind to NAD-agarose, suggesting FSBA modification of the NADP(H) binding site or an essential residue outside the active site. (/sup 3/H)FSBA was covalently bound to TH, and complete inhibition corresponded to the binding of about 0.5 mol of (3H)FSBA/mol of TH. Since purified TH is known to be dimeric in the isolated state, this binding stoichiometry suggests half-of-the-sites reactivity. A similar binding stoichiometry was found earlier for complete inhibition of TH by (/sup 14/C)DCCD. The active site directed labeling of TH by radioactive FSBA should allow isolation of appropriate peptides for sequence analysis of the NAD(H) and possibly the NADP(H) binding domains.

  14. 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

  15. 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.

  16. Immobilization of alkaline phosphatase on solid surface through self-assembled monolayer and by active-site protection.

    PubMed

    Gao, En-Feng; Kang, Kyung Lhi; Kim, Jeong Hee

    2014-06-01

    Retaining biological activity of a protein after immobilization is an important issue and many studies reported to enhance the activity of proteins after immobilization. We recently developed a new immobilization method of enzyme using active-site protection and minimization of the cross-links between enzyme and surface with a DNA polymerase as a model system. In this study, we extended the new method to an enzyme with a small mono-substrate using alkaline phosphatase (AP) as another model system. A condition to apply the new method is that masking agents, in this case its own substrate needs to stay at the active-site of the enzyme to be immobilized in order to protect the active-site during the harsh immobilization process. This could be achieved by removal of essential divalent ion, Zn2+ that is required for full enzyme activity of AP from the masking solution while active-site of AP was protected with p-nitrophenyl phosphate (pNPP). Approximately 40% of the solution-phase activity was acquired with active-site protected immobilized AP. In addition to protection active-site of AP, the number of immobilization links was kinetically controlled. When the mole fraction of the activated carboxyl group of the linker molecule in self-assembled monolayer (SAM) of 12-mercaptododecanoic acid and 6-mercapto-1-ethanol was varied, 10% of 12-mercaptododecanoic acid gave the maximum enzyme activity. Approximately 51% increase in enzyme activity of the active-site protected AP was observed compared to that of the unprotected group. It was shown that the concept of active-site protection and kinetic control of the number of covalent immobilization bonds can be extended to enzymes with small mono-substrates. It opens the possibility of further extension of the new methods of active-site protection and kinetic control of immobilization bond to important enzymes used in research and industrial fields. PMID:24738440

  17. The effects of overwinter flowson the spring condition of rainbow and brown trout size classes in the Green River downstream of Flaming Gorge Dam, Utah.

    SciTech Connect

    Magnusson, A. K.; LaGory, K. E.; Hayse, J. W.; Environmental Science Division

    2010-06-25

    Flaming Gorge Dam, a hydroelectric facility operated by the Bureau of Reclamation (Reclamation), is located on the Green River in Daggett County, northeastern Utah. Until recently, and since the early 1990s, single daily peak releases or steady flows have been the operational pattern of the dam during the winter period. However, releases from Flaming Gorge Reservoir followed a double-peak pattern (two daily flow peaks) during the winters of 2006-2007 and 2008-2009. Because there is little recent long-term history of double-peaking at Flaming Gorge Dam, the potential effects of double-peaking operations on trout body condition in the dam's tailwater are not known. A study plan was developed that identified research activities to evaluate potential effects from winter double-peaking operations (Hayse et al. 2009). Along with other tasks, the study plan identified the need to conduct a statistical analysis of historical trout condition and macroinvertebrate abundance to evaluate the potential effects of hydropower operations. The results from analyses based on the combined size classes of trout (85-630 mm) were presented in Magnusson et al. (2008). The results of this earlier analysis suggested possible relationships between trout condition and flow, but concern that some of the relationships resulted from size-based effects (e.g., apparent changes in condition may have been related to concomitant changes in size distribution, because small trout may have responded differently to flow than large trout) prompted additional analysis of within-size class relationships. This report presents the results of analyses of three different size classes of trout (small: 200-299 mm, medium: 300-399 mm, and large: {ge}400 mm body length). We analyzed historical data to (1) describe temporal patterns and relationships among flows, benthic macroinvertebrate abundance, and condition of brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) in the tailwaters of Flaming

  18. Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces.

    PubMed

    Haider, Kamran; Wickstrom, Lauren; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

    2016-09-01

    The principles underlying water reorganization around simple nonpolar solutes are well understood and provide the framework for the classical hydrophobic effect, whereby water molecules structure themselves around solutes so that they maintain favorable energetic contacts with both the solute and the other water molecules. However, for certain solute surface topographies, water molecules, due to their geometry and size, are unable to simultaneously maintain favorable energetic contacts with both the surface and neighboring water molecules. In this study, we analyze the solvation of ligand-binding sites for six structurally diverse proteins using hydration site analysis and measures of local water structure, in order to identify surfaces at which water molecules are unable to structure themselves in a way that maintains favorable enthalpy relative to bulk water. These surfaces are characterized by a high degree of enclosure, weak solute-water interactions, and surface constraints that induce unfavorable pair interactions between neighboring water molecules. Additionally, we find that the solvation of charged side chains in an active site generally results in favorable enthalpy but can also lead to pair interactions between neighboring water molecules that are significantly unfavorable relative to bulk water. We find that frustrated local structure can occur not only in apolar and weakly polar pockets, where overall enthalpy tends to be unfavorable, but also in charged pockets, where overall water enthalpy tends to be favorable. The characterization of local water structure in these terms may prove useful for evaluating the displacement of water from diverse protein active-site environments.

  19. Den site activity patterns of adult male and female swift foxes, Vulpes velox, in Northwestern Texas

    USGS Publications Warehouse

    Lemons, P.R.; Ballard, W.B.; Sullivan, R.M.; Sovada, M.A.

    2003-01-01

    Activity of Swift Foxes (Vulpes velox) at den sites was studied in northwestern Texas during pup rearing seasons in 2000 and 2001 to determine role of males in parental care. Twenty-four percent of radio-collared females with a potential to breed successfully raised pups to eight weeks of age. We intensively monitored presence and absence of male and female Swift Foxes at two den sites each year. Females were present >2.6 times more at den sites than males during the pup rearing season. Female and male Swift Foxes largely stayed at dens during diurnal hours and were active away from dens during nocturnal and crepuscular hours. Females and males spent 12.4% and 3.0% more time at dens before pups emerged, than after pups emerged, respectively. Following depredation of one male parent, the female spent 29% less time at the den site. Decrease in time spent at the den by the female following loss of her mate suggested that loss of one parent might severely impact recruitment of Swift Foxes. Our observations indicated that intense Coyote (Canis latrans) depredation may severely impact pup-rearing success as well as the parental care within Swift Fox family groups.

  20. Hydrothermal alteration of the Ediacaran Doushantuo Formation in the Yangtze Gorges area (South China)

    NASA Astrophysics Data System (ADS)

    Derkowski, Arkadiusz; Bristow, Thomas F.; Wampler, J. M.; Środoń, Jan; Marynowski, Leszek; Elliott, W. Crawford; Chamberlain, C. Page

    2013-04-01

    The geochemical and fossil record preserved in the Ediacaran age (635-551 Ma) Doushantuo Formation of South China has been extensively examined to explore the impact of changing climate and the oxidation state of the oceans on the development and distribution of early multicellular life. In the Yangtze Gorges area, this formation shows many of the geochemical trends and features thought to typify global ocean chemistry in the Ediacaran Period, but there are indications that post-sedimentary processes modified these signals. This study of clay minerals and organic matter builds a more detailed picture of the type and degree of post-sedimentary alteration at different stratigraphic levels of the formation and focuses on how this alteration influenced stable carbon and oxygen isotope records. In the cratonward Jiulongwan and Huajipo sections of the Doushantuo Formation, its lower part (Members 1 and 2) consists largely of dolomitic shale, rich in authigenic saponite that crystallized in an alkaline sedimentary basin. Saponite has been altered to chlorite via corrensite across tens of meters of strata in lower Member 2, with increased alteration downward toward the cap dolostone. The greater chloritization is accompanied by lower δ18O and higher δD values of trioctahedral clays. This pattern of alteration of trioctahedral clays is likely due to hydrothermal fluid activity in the underlying, relatively permeable Nantuo Formation and cap dolostone. A concomitant increase of solid bitumen reflectance toward the base of the formation supports this idea. In the uppermost part of the formation in the Yangtze Gorges area (Member 4), a typical open water marine dolomitic shale rich in illite and organic matter, increases in the methylphenanthrenes ratio index and solid bitumen reflectance correlate with decrease of the bulk rock K/Al ratio upward, providing evidence for hot fluid migration above the nearly impermeable shale. Clay from the upper part of the formation is

  1. Large zinc cation occupancy of octahedral sites in mechanically activated zinc ferrite powders

    SciTech Connect

    Oliver, S. A.; Harris, V. G.; Hamdeh, H. H.; Ho, J. C.

    2000-05-08

    The cation site occupancy of a mechanically activated nanocrystalline zinc ferrite powder was determined as (Zn{sub 0.55}{sup 2+}Fe{sub 0.18}{sup 3+}){sub tet}[Zr{sub 0.45}{sup 2+}Fe{sub 1.82}{sup 3+}]{sub oct}O{sub 4} through analysis of extended x-ray absorption fine structure measurements, showing a large redistribution of cations between sites compared to normal zinc ferrite samples. The overpopulation of cations in the octahedral sites was attributed to the ascendance in importance of the ionic radii over the crystal energy and bonding coordination in determining which interstitial sites are occupied in this structurally disordered powder. Slight changes are observed in the local atomic environment about the zinc cations, but not the iron cations, with respect to the spinel structure. The presence of Fe{sup 3+} on both sites is consistent with the measured room temperature magnetic properties. (c) 2000 American Institute of Physics.

  2. The competition plot: a simple test of whether two reactions occur at the same active site.

    PubMed Central

    Chevillard, C; Cárdenas, M L; Cornish-Bowden, A

    1993-01-01

    The competition plot is a method for determining whether or not two enzyme-catalysed reactions occur at the same active site. It is a plot of total rate against p, where p varies from 0 to 1 and specifies the concentrations (1-p)a0 and pb0 of two substrates in terms of reference concentrations a0 and b0 chosen so as to give the same rates at p = 0 and p = 1. If the two substrates react at the same site, the competition plot gives a horizontal straight line, i.e. the total rate is independent of p. Independent reactions at two separate sites give a curve with a maximum; separate reactions with cross-inhibition generate curves with either maxima or minima according to whether the Michaelis constants of the two substrates are smaller or larger than their inhibition constants in the other reactions. Although ambiguous results can sometimes arise, experimental strategies exist for avoiding them, for example working as close as possible to the lower of the two limiting rates. When tested with yeast hexokinase, the plot indicated phosphorylation of glucose and fructose at the same site. Conversely, with a mixture of yeast hexokinase and galactokinase it indicated phosphorylation of glucose and galactose at different sites. In both cases the observed behaviour agreed with the known properties of the enzymes. A slight modification to the definition of this plot allows it to be applied also to enzymes that deviate from Michaelis-Menten kinetics. PMID:8424801

  3. 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

  4. A splice site mutant of maize activates cryptic splice sites, elicits intron inclusion and exon exclusion, and permits branch point elucidation.

    PubMed

    Lal, S; Choi, J H; Shaw, J R; Hannah, L C

    1999-10-01

    DNA sequence analysis of the bt2-7503 mutant allele of the maize brittle-2 gene revealed a point mutation in the 5' terminal sequence of intron 3 changing GT to AT. This lesion completely abolishes use of this splice site, activates two cryptic splice sites, and alters the splicing pattern from extant splice sites. One activated donor site, located nine nt 5' to the normal splice donor site, begins with the dinucleotide GC. While non-consensus, this sequence still permits both trans-esterification reactions of pre-mRNA splicing. A second cryptic site located 23 nt 5' to the normal splice site and beginning with GA, undergoes the first trans-esterification reaction leading to lariat formation, but lacks the ability to participate in the second reaction. Accumulation of this splicing intermediate and use of an innovative reverse transcriptase-polymerase chain reaction technique (J. Vogel, R.H. Wolfgang, T. Borner [1997] Nucleic Acids Res 25: 2030-2031) led to the identification of 3' intron sequences needed for lariat formation. In most splicing reactions, neither cryptic site is recognized. Most mature transcripts include intron 3, while the second most frequent class lacks exon 3. Traditionally, the former class of transcripts is taken as evidence for the intron definition of splicing, while the latter class has given credence to the exon definition of splicing. PMID:10517832

  5. Spatial forecast of landslides in three gorges based on spatial data mining.

    PubMed

    Wang, Xianmin; Niu, Ruiqing

    2009-01-01

    The Three Gorges is a region with a very high landslide distribution density and a concentrated population. In Three Gorges there are often landslide disasters, and the potential risk of landslides is tremendous. In this paper, focusing on Three Gorges, which has a complicated landform, spatial forecasting of landslides is studied by establishing 20 forecast factors (spectra, texture, vegetation coverage, water level of reservoir, slope structure, engineering rock group, elevation, slope, aspect, etc). China-Brazil Earth Resources Satellite (Cbers) images were adopted based on C4.5 decision tree to mine spatial forecast landslide criteria in Guojiaba Town (Zhigui County) in Three Gorges and based on this knowledge, perform intelligent spatial landslide forecasts for Guojiaba Town. All landslides lie in the dangerous and unstable regions, so the forecast result is good. The method proposed in the paper is compared with seven other methods: IsoData, K-Means, Mahalanobis Distance, Maximum Likelihood, Minimum Distance, Parallelepiped and Information Content Model. The experimental results show that the method proposed in this paper has a high forecast precision, noticeably higher than that of the other seven methods.

  6. The Three Gorges Dam of China: Technology to Bridge Two Centuries

    ERIC Educational Resources Information Center

    Wahby, Wafeek S.

    2003-01-01

    Some of the most sophisticated 20th-century technologies have been applied to build the largest hydroelectric dam in the world, the Three Gorges Dam Project (TGDP) of China. The author administered a study abroad course in China from May 27 to June 10, 2000, to study the massive project as it approached the halfway mark of its second and most…

  7. The Short-Term Impact of Involuntary Migration in China's Three Gorges: A Prospective Study

    ERIC Educational Resources Information Center

    Hwang, Sean-Shong; Cao, Yue; Xi, Juan

    2011-01-01

    The aim of this study is to measure the short-term impact of involuntary migration resulting from China's Three Gorges Dam project on the 1.3 million persons being displaced. We focus on the social, economic, and mental and physical health impact using three sets of indicators. Using a prospective research design, we gathered information about…

  8. Spatial and seasonal variability of diffusive methane emissions from the Three Gorges Reservoir

    NASA Astrophysics Data System (ADS)

    Yang, Le; Lu, Fei; Wang, Xiaoke; Duan, Xiaonan; Song, Wenzhi; Sun, Binfeng; Zhang, Qianqian; Zhou, Yongjuan

    2013-06-01

    investigate temporal and spatial variations in diffusive CH4 emission from the surface of the Three Gorges Reservoir, CH4 emissions were measured using the static chamber technique along the mainstream of the reservoir from January to December 2010. The overall average CH4 flux is 7.93 mg CH4 m-2 d-1, which is comparable to those from other temperate reservoirs but significantly lower than those from tropical reservoirs. Seasonal variations showed that CH4 emission reached the maximum in the summer and turned to the low levels in the other seasons; such variations reflected the seasonal dynamics of temperature, dissolved oxygen, and water velocity. Moreover, the yearly average CH4 flux decreased from upstream to downstream before the Three Gorges Dam, but CH4 emission from the surface of the downstream river was higher than that from the surface at Zigui, the upstream water before the Three Gorges Dam. The differences in water velocity and allochthonous input of organic matter probably caused the spatial variations in CH4 emission. These results indicate that systematic sampling is needed to better estimate CH4 emission through coverage of the temporal and spatial scales and to better assess the influence of CH4 emission from the Three Gorges Reservoir on climate change in China, as well as the rest of the world.

  9. 33 CFR 110.127b - Flaming Gorge Lake, Wyoming-Utah.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... following points, excluding a 150-foot-wide fairway, extending southeasterly from the launching ramp, as..., extending southeasterly from the launching ramp, as established by the Superintendent, Flaming Gorge... launching ramp to a point beyond the floating breakwater and then westerly, as established by...

  10. 33 CFR 110.127b - Flaming Gorge Lake, Wyoming-Utah.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... following points, excluding a 150-foot-wide fairway, extending southeasterly from the launching ramp, as..., extending southeasterly from the launching ramp, as established by the Superintendent, Flaming Gorge... launching ramp to a point beyond the floating breakwater and then westerly, as established by...

  11. 33 CFR 110.127b - Flaming Gorge Lake, Wyoming-Utah.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... following points, excluding a 150-foot-wide fairway, extending southeasterly from the launching ramp, as..., extending southeasterly from the launching ramp, as established by the Superintendent, Flaming Gorge... launching ramp to a point beyond the floating breakwater and then westerly, as established by...

  12. 33 CFR 110.127b - Flaming Gorge Lake, Wyoming-Utah.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... following points, excluding a 150-foot-wide fairway, extending southeasterly from the launching ramp, as..., extending southeasterly from the launching ramp, as established by the Superintendent, Flaming Gorge... launching ramp to a point beyond the floating breakwater and then westerly, as established by...

  13. 76 FR 62089 - General Management Plan/Abbreviated Final Environmental Impact Statement, New River Gorge...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-06

    ... Abbreviated Final Environmental Impact Statement for the General Management Plan (GMP/EIS) for New River Gorge... GMP/EIS includes an analysis of agency and public comments received on the Draft GMP/EIS with NPS responses, errata sheets detailing editorial corrections to the Draft GMP/EIS, and copies of agency...

  14. Characterizing Active Site Conformational Heterogeneity along the Trajectory of an Enzymatic Phosphoryl Transfer Reaction.

    PubMed

    Zeymer, Cathleen; Werbeck, Nicolas D; Zimmermann, Sabine; Reinstein, Jochen; Hansen, D Flemming

    2016-09-12

    States along the phosphoryl transfer reaction catalyzed by the nucleoside monophosphate kinase UmpK were captured and changes in the conformational heterogeneity of conserved active site arginine side-chains were quantified by NMR spin-relaxation methods. In addition to apo and ligand-bound UmpK, a transition state analog (TSA) complex was utilized to evaluate the extent to which active site conformational entropy contributes to the transition state free energy. The catalytically essential arginine side-chain guanidino groups were found to be remarkably rigid in the TSA complex, indicating that the enzyme has evolved to restrict the conformational freedom along its reaction path over the energy landscape, which in turn allows the phosphoryl transfer to occur selectively by avoiding side reactions. PMID:27534930

  15. 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).

  16. Twinning in fcc lattice creates low-coordinated catalytically active sites in porous gold.

    PubMed

    Krajčí, Marian; Kameoka, Satoshi; Tsai, An-Pang

    2016-08-28

    We describe a new mechanism for creation of catalytically active sites in porous gold. Samples of porous gold prepared by de-alloying Al2Au exhibit a clear correlation between the catalytic reactivity towards CO oxidation and structural defects in the fcc lattice of Au. We have found that on the stepped {211} surfaces quite common twin boundary defects in the bulk structure of porous gold can form long close-packed rows of atoms with the coordination number CN = 6. DFT calculations confirm that on these low-coordinated Au sites dioxygen chemisorbs and CO oxidation can proceed via the Langmuir-Hinshelwood mechanism with the activation energy of 37 kJ/mol or via the CO-OO intermediate with the energy barrier of 19 kJ/mol. The existence of the twins in porous gold is stabilized by the surface energy.

  17. 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.

  18. Twinning in fcc lattice creates low-coordinated catalytically active sites in porous gold

    NASA Astrophysics Data System (ADS)

    Krajčí, Marian; Kameoka, Satoshi; Tsai, An-Pang

    2016-08-01

    We describe a new mechanism for creation of catalytically active sites in porous gold. Samples of porous gold prepared by de-alloying Al2Au exhibit a clear correlation between the catalytic reactivity towards CO oxidation and structural defects in the fcc lattice of Au. We have found that on the stepped {211} surfaces quite common twin boundary defects in the bulk structure of porous gold can form long close-packed rows of atoms with the coordination number CN = 6. DFT calculations confirm that on these low-coordinated Au sites dioxygen chemisorbs and CO oxidation can proceed via the Langmuir-Hinshelwood mechanism with the activation energy of 37 kJ/mol or via the CO-OO intermediate with the energy barrier of 19 kJ/mol. The existence of the twins in porous gold is stabilized by the surface energy.

  19. Twinning in fcc lattice creates low-coordinated catalytically active sites in porous gold.

    PubMed

    Krajčí, Marian; Kameoka, Satoshi; Tsai, An-Pang

    2016-08-28

    We describe a new mechanism for creation of catalytically active sites in porous gold. Samples of porous gold prepared by de-alloying Al2Au exhibit a clear correlation between the catalytic reactivity towards CO oxidation and structural defects in the fcc lattice of Au. We have found that on the stepped {211} surfaces quite common twin boundary defects in the bulk structure of porous gold can form long close-packed rows of atoms with the coordination number CN = 6. DFT calculations confirm that on these low-coordinated Au sites dioxygen chemisorbs and CO oxidation can proceed via the Langmuir-Hinshelwood mechanism with the activation energy of 37 kJ/mol or via the CO-OO intermediate with the energy barrier of 19 kJ/mol. The existence of the twins in porous gold is stabilized by the surface energy. PMID:27586937

  20. Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites.

    PubMed

    Wang, P-H; De Sancho, D; Best, R B; Blumberger, J

    2016-01-01

    The diffusion of ligands to actives sites of proteins is essential to enzyme catalysis and many cellular signaling processes. In this contribution we review our recently developed methodology for calculation of rate constants for diffusion and binding of small molecules to buried protein active sites. The diffusive dynamics of the ligand obtained from molecular dynamics simulation is coarse grained and described by a Markov state model. Diffusion and binding rate constants are then obtained either from the reactive flux formalism or by fitting the time-dependent population of the Markov state model to a phenomenological rate law. The method is illustrated by applications to diffusion of substrate and inhibitors in [NiFe] hydrogenase, CO-dehydrogenase, and myoglobin. We also discuss a recently developed sensitivity analysis that allows one to identify hot spots in proteins, where mutations are expected to have the strongest effects on ligand diffusion rates.

  1. Characterizing Active Site Conformational Heterogeneity along the Trajectory of an Enzymatic Phosphoryl Transfer Reaction

    PubMed Central

    Zeymer, Cathleen; Werbeck, Nicolas D.; Zimmermann, Sabine

    2016-01-01

    Abstract States along the phosphoryl transfer reaction catalyzed by the nucleoside monophosphate kinase UmpK were captured and changes in the conformational heterogeneity of conserved active site arginine side‐chains were quantified by NMR spin‐relaxation methods. In addition to apo and ligand‐bound UmpK, a transition state analog (TSA) complex was utilized to evaluate the extent to which active site conformational entropy contributes to the transition state free energy. The catalytically essential arginine side‐chain guanidino groups were found to be remarkably rigid in the TSA complex, indicating that the enzyme has evolved to restrict the conformational freedom along its reaction path over the energy landscape, which in turn allows the phosphoryl transfer to occur selectively by avoiding side reactions. PMID:27534930

  2. Computation of Rate Constants for Diffusion of Small Ligands to and from Buried Protein Active Sites.

    PubMed

    Wang, P-H; De Sancho, D; Best, R B; Blumberger, J

    2016-01-01

    The diffusion of ligands to actives sites of proteins is essential to enzyme catalysis and many cellular signaling processes. In this contribution we review our recently developed methodology for calculation of rate constants for diffusion and binding of small molecules to buried protein active sites. The diffusive dynamics of the ligand obtained from molecular dynamics simulation is coarse grained and described by a Markov state model. Diffusion and binding rate constants are then obtained either from the reactive flux formalism or by fitting the time-dependent population of the Markov state model to a phenomenological rate law. The method is illustrated by applications to diffusion of substrate and inhibitors in [NiFe] hydrogenase, CO-dehydrogenase, and myoglobin. We also discuss a recently developed sensitivity analysis that allows one to identify hot spots in proteins, where mutations are expected to have the strongest effects on ligand diffusion rates. PMID:27497172

  3. The active site of RNA polymerase II participates in transcript cleavage within arrested ternary complexes.

    PubMed Central

    Rudd, M D; Izban, M G; Luse, D S

    1994-01-01

    RNA polymerase II may become arrested during transcript elongation, in which case the ternary complex remains intact but further RNA synthesis is blocked. To relieve arrest, the nascent transcript must be cleaved from the 3' end. RNAs of 7-17 nt are liberated and transcription continues from the newly exposed 3' end. Factor SII increases elongation efficiency by strongly stimulating the transcript cleavage reaction. We show here that arrest relief can also occur by the addition of pyrophosphate. This generates the same set of cleavage products as factor SII, but the fragments produced with pyrophosphate have 5'-triphosphate termini. Thus, the active site of RNA polymerase II, in the presence of pyrophosphate, appears to be capable of cleaving phosphodiester linkages as far as 17 nt upstream of the original site of polymerization, leaving the ternary complex intact and transcriptionally active. Images PMID:8058756

  4. Disposal Activities and the Unique Waste Streams at the Nevada National Security Site (NNSS)

    SciTech Connect

    Arnold, P.

    2012-10-31

    This slide show documents waste disposal at the Nevada National Security Site. Topics covered include: radionuclide requirements for waste disposal; approved performance assessment (PA) for depleted uranium disposal; requirements; program approval; the Waste Acceptance Review Panel (WARP); description of the Radioactive Waste Acceptance Program (RWAP); facility evaluation; recent program accomplishments, nuclear facility safety changes; higher-activity waste stream disposal; and, large volume bulk waste streams.

  5. Electron tunnelling through azurin is mediated by the active site Cu ion

    NASA Astrophysics Data System (ADS)

    Alessandrini, Andrea; Gerunda, Mimmo; Canters, G. W.; Verbeet, M. Ph.; Facci, Paolo

    2003-07-01

    Cu- and Zn-azurin chemisorbed on Au(1 1 1) have been comparatively investigated by electrochemical scanning tunnelling microscopy in buffer solution. Cu-azurin shows a marked tunnelling current resonance upon substrate potential at -0.21 V (vs SCE), whereas Zn counterparts do not. These data, discussed in terms of current theories on electron tunnelling through redox adsorbates, demonstrate the role of the electroactive metal ion present in the active site in assisting electron transfer via this metalloprotein.

  6. 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.

  7. Structural insight into the active site of a Bombyx mori unclassified glutathione transferase.

    PubMed

    Hossain, Md Tofazzal; Yamamoto, Kohji

    2015-01-01

    Glutathione transferases (GSTs) are major detoxification enzymes that play central roles in the defense against various environmental toxicants as well as oxidative stress. Here, we identify amino acid residues of an unclassified GST from Bombyx mori, bmGSTu-interacting glutathione (GSH). Site-directed mutagenesis of bmGSTu mutants indicated that amino acid residues Asp103, Ser162, and Ser166 contribute to catalytic activity.

  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. Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site.

    PubMed

    Debela, Mekdes; Magdolen, Viktor; Grimminger, Valerie; Sommerhoff, Christian; Messerschmidt, Albrecht; Huber, Robert; Friedrich, Rainer; Bode, Wolfram; Goettig, Peter

    2006-10-01

    Human tissue kallikrein 4 (hK4) belongs to a 15-member family of closely related serine proteinases. hK4 is predominantly expressed in prostate, activates hK3/PSA, and is up-regulated in prostate and ovarian cancer. We have identified active monomers of recombinant hK4 besides inactive oligomers in solution. hK4 crystallised in the presence of zinc, nickel, and cobalt ions in three crystal forms containing cyclic tetramers and octamers. These structures display a novel metal site between His25 and Glu77 that links the 70-80 loop with the N-terminal segment. Micromolar zinc as present in prostatic fluid inhibits the enzymatic activity of hK4 against fluorogenic substrates. In our measurements, wild-type hK4 exhibited a zinc inhibition constant (IC50) of 16 microM including a permanent residual activity, in contrast to the zinc-independent mutants H25A and E77A. Since the Ile16 N terminus of wild-type hK4 becomes more accessible for acetylating agents in the presence of zinc, we propose that zinc affects the hK4 active site via the salt-bridge formed between the N terminus and Asp194 required for a functional active site. hK4 possesses an unusual 99-loop that creates a groove-like acidic S2 subsite. These findings explain the observed specificity of hK4 for the P1 to P4 substrate residues. Moreover, hK4 shows a negatively charged surface patch, which may represent an exosite for prime-side substrate recognition. PMID:16950394

  10. 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.

  11. Crystal Structure of Albaflavenone Monooxygenase Containing a Moonlighting Terpene Synthase Active Site

    SciTech Connect

    Zhao, Bin; Lei, Li; Vassylyev, Dmitry G.; Lin, Xin; Cane, David E.; Kelly, Steven L.; Yuan, Hang; Lamb, David C.; Waterman, Michael R.

    2010-01-08

    Albaflavenone synthase (CYP170A1) is a monooxygenase catalyzing the final two steps in the biosynthesis of this antibiotic in the soil bacterium, Streptomyces coelicolor A3(2). Interestingly, CYP170A1 shows no stereo selection forming equal amounts of two albaflavenol epimers, each of which is oxidized in turn to albaflavenone. To explore the structural basis of the reaction mechanism, we have studied the crystal structures of both ligand-free CYP170A1 (2.6 {angstrom}) and complex of endogenous substrate (epi-isozizaene) with CYP170A1 (3.3 {angstrom}). The structure of the complex suggests that the proximal epi-isozizaene molecules may bind to the heme iron in two orientations. In addition, much to our surprise, we have found that albaflavenone synthase also has a second, completely distinct catalytic activity corresponding to the synthesis of farnesene isomers from farnesyl diphosphate. Within the cytochrome P450 {alpha}-helical domain both the primary sequence and x-ray structure indicate the presence of a novel terpene synthase active site that is moonlighting on the P450 structure. This includes signature sequences for divalent cation binding and an {alpha}-helical barrel. This barrel is unusual because it consists of only four helices rather than six found in all other terpene synthases. Mutagenesis establishes that this barrel is essential for the terpene synthase activity of CYP170A1 but not for the monooxygenase activity. This is the first bifunctional P450 discovered to have another active site moonlighting on it and the first time a terpene synthase active site is found moonlighting on another protein.

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

    PubMed

    Hassani, Sorour; Haghbeen, Kamahldin; Fazli, Mostafa

    2016-10-21