bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative structural analysis of the binding domain of follicle stimulating hormone receptor
Authors: Fan Qing R. , Hendrickson Wayne A. 
Published: January 2008

AbstractProteins with leucine‐rich repeats (LRRs) specialize in mediating protein–protein interactions. The hormone binding portion of the receptor for follicle stimulating hormone (FSH) is an LRR protein by sequence, and the crystal structure of this domain from human FSH receptor in a complex with FSH shows that it does indeed have an LRR structure. It differs from other LRR domains, however, in being an all‐β protein composed of highly irregular repeats and having only slight overall curvature. Despite these distinctions and a superficial resemblance to β‐helical proteins, the binding domain of FSH receptor clearly is an LRR protein. The structure does consist of two parts with distinctively different curvatures. Comparison with the structures of other LRR‐containing proteins shows a correlation between curvature and main‐chain hydrogen bonding pattern of the parallel β‐sheet. The hormone‐binding site is located at the concave surface of the receptor structure, a feature common to proteins with LRR motifs. Analysis of the ligand‐binding site of LRR‐containing proteins reveals that they generally utilize extensive interface area and a large number of charged residues to facilitate high‐affinity protein‐protein interactions. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Rigid body essential X‐ray crystallography: Distinguishing the bend and twist of glutamate receptor ligand binding domains
Authors: Bjerrum Esben J. , Biggin Philip C. 
Published: January 2008

AbstractThe ligand‐binding domain (LBD) from the ionotropic glutamate receptor subtype 2 (GluR2) has been shown to adopt a range of ligand‐dependent conformational states. These states have been described in terms of the rotation required to fit subdomain (lobe) 2 following superposition of subdomain (lobe) 1. The LBD has a closed‐cleft conformation for full agonists, but partial agonists induce a range of closure, which in turn controls the open probability of discrete subconductance states in the full‐length receptor. Although this description is useful, it may not account for all physiologically important motions that the receptor undergoes. We have used an approach that combines the methods of essential dynamics and rigid‐body dynamics to analyze 124 monomer domains from 55 crystal structures of the GluR2 LBD. We are able to show that partial agonists also induce a significant amount of twist that would not be anticipated using one rotational descriptor between apo and full‐agonist‐bound states. Furthermore, one of the crystal structures (chain B from 1P1U, the GluR2 L650T‐AMPA complex), which has been suggested to represent an agonist‐bound inactive form of the receptor, lies at the extreme of this twist motion. We suggest that partial agonists not only prevent full closure but also move the receptor closer to this inactive state. We demonstrate additionally how the method can be used to compare the results of molecular dynamics simulations with the crystallographic data and the extent to which the conformational space explored by both overlaps. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Protein kinase C isozymes and their selectivity towards ruboxistaurin
Authors: Tang Sishi , Xiao Victor , Wei Lianhu , Whiteside Catharine I. , Kotra Lakshmi P. 
Published: January 2008

AbstractProtein kinase C (PKC) isozymes are an important class of enzymes in cell signaling and as drug targets. They are involved in specific pathways and have selectivity towards certain ligands, despite their high sequence similarities. Ruboxistaurin is a specific inhibitor of PKC‐β. To understand the molecular determinants for the selectivity of ruboxistaurin, we derived the three‐dimensional structures of the kinase domains of PKC‐α, ‐βI, and ‐ζ using homology modeling. Several binding orientations of ruboxistaurin in the binding sites of these PKC catalytic domains were analyzed, and a putative alternative binding site for PKC‐ζ was identified in its kinase domain. The calculated free energy of binding correlates well with the IC50 of the inhibitor against each PKC isozyme. A residue‐based energy decomposition analysis attributed the binding free energy to several key residues in the catalytic sites of these enzymes, revealing potential protein–ligand interactions responsible for ligand binding. The contiguous binding site revealed in the catalytic domain of PKC‐ζ provides avenues for selective drug design. The details of structural nuances for specific inhibition of PKC isozymes are presented in the context of the three‐dimensional structures of this important class of enzymes. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Structural insight into the distinct properties of copper transport by the Helicobacter pylori CopP protein
Authors: Park Sung Jean , Jung Yu‐Sun , Kim Ji‐Sun , Seo Min‐Duk , Lee Bong Jin 
Published: January 2008

AbstractHelicobacter pylori CopP (HpCopP) is a putative copper binding regulatory protein composed of 66 amino acid residues. The small HpCopP protein is homologous to CopZ, encoded by the E. hirae and B. subtilis cop operons. To clarify the role of HpCopP in copper metabolism in H. pylori, we studied the structural and copper binding characteristics by NMR spectroscopy. Based on the resonance assignments, the tertiary structure of HpCopP was determined. Unlike the βαββαβ fold of the homologous CopZ, HpCopP adopts the βαββα fold. The superposition with structures of other bacterial copper binding proteins showed that the global structure of HpCopP follows the general topology of the family, regardless of absence of the C‐terminal β‐strand. The Cu(I) binding property of HpCopP was well conserved like CopZs: the structural changes due to Cu(I) and Ag(I) bindings were primarily restricted to the metal binding motif (CXXC motif). On the other hand, the Cu(II) binding property of CopP was different with that of CopZ: in the absence of reducing agent, Cu(II) ion oxidized a mutant HpCopP, resulting in disulfide bond formation in the CXXC motif. The Cu(II) ion binding property was evaluated using the mutant HpCopP, in which two amino acids were artificially introduced at the C‐terminus, since the reduced state of the CXXC motif was more stabile in the mutant HpCopP without a reducing agent. Here, the structure and copper binding property of HpCopP are discussed in detail. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Synthesis and sst2 binding profiles of new [Tyr3]octreotate analogs
Authors: Petrou Christos , Magafa Vassiliki , Nikolopoulou Anastasia , Pairas George , Nock Berthold , Maina Theodosia , Cordopatis Paul 
Published: January 2008

AbstractOne of the main objectives of our current work is the development of new somatostatin analogs that would retain the general characteristics of [Tyr3]octreotate (Tate) while showing potential for clinical application. In this respect, study of their interaction with the sst2 is crucial in providing preliminary structure‐activity relationships data. In the present work we report on the synthesis and the preliminary biological evaluation of a total of 15 new structurally modified [Tyr3]octreotate analogs. The binding affinities were determined during competition binding assays in sst2‐positive rat acinar pancreatic AR4‐2J cell membranes using [125I‐Tyr3]octreotide as the radioligand. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Structure of cubic polytype indium nitride layers on top of modified sapphire substrates
Authors: Morales F. M. , Lozano J. G. , García R. , Lebedev V. , Wang Ch. Y. , Cimalla V. , Ambacher O. , González D. 
Published: January 2008

AbstractThe cover picture of this issue of physica status solidi (c) has been taken from the article [1].
Development and application of an autonomous unmanned aerial vehicle for precise aerobiological sampling above agricultural fields
Authors: Schmale III David G. , Dingus Benjamin R. , Reinholtz Charles 
Published: January 2008

AbstractRemote‐controlled (RC) unmanned aerial vehicles (UAVs) have been used to study the movement of agricultural threat agents (e.g., plant and animal pathogens, invasive weeds, and exotic insects) above crop fields, but these RC UAVs are operated entirely by a ground‐based pilot and often demonstrate large fluctuations in sampling height, sampling pattern, and sampling speed. In this paper, we describe the development and application of an autonomous UAV for precise aerobiological sampling tens to hundreds of meters above agricultural fields. We equipped a Senior Telemaster UAV with four aerobiological sampling devices and a MicroPilot‐based autonomous system, and we conducted 25 sampling flights for potential agricultural threat agents at Virginia Tech's Kentland Farm. To determine the most appropriate sampling path for aerobiological sampling above crop fields with an autonomous UAV, we explored five different sampling patterns, including multiple global positioning system (GPS) waypoints plotted over a variety of spatial scales. An orbital sampling pattern around a single GPS waypoint exhibited high positional accuracy and produced altitude standard deviations ranging from 1.6 to 2.8 m. Autonomous UAVs have the potential to extend the range of aerobiological sampling, improve positional accuracy of sampling paths, and enable coordinated flight with multiple UAVs sampling at different altitudes. © 2008 Wiley Periodicals, Inc.
Investigation of metal‐induced crystallization in amorphous Ge/crystalline Al bilayers by Auger microanalysis and selected‐area depth profiling
Authors: Wang Z. M. , Wang J. Y. , Jeurgens L. P. H. , Mittemeijer E. J. 
Published: January 2008

AbstractThe diffusion processes and accompanying microstructural changes occurring in amorphous Ge (a‐Ge)/crystalline Al bilayers upon annealing have been investigated by using a combined approach of Auger microanalysis, selected‐area depth profiling (SA‐DPR), scanning electron microscopy (SEM) and X‐ray diffraction. Upon annealing at 150 °C for 10 min, the partially crystallized Al/a‐Ge (with the Al layer at the top) and a‐Ge/Al (with the a‐Ge layer at the top) specimens show reacted and unreacted regions with a lateral size of ∼1–2 µm at their surfaces. SA‐DPR at the location of unreacted regions at the surface shows that at such locations the original Al/a‐Ge (or a‐Ge/Al) bilayer structure is almost preserved. On the other hand, depth profiling at the location of reacted regions shows that at such locations the original a‐Ge sublayer had fully crystallized and contains 10–20 at.% Al, and that in the original Al sublayer, crystalline Ge (c‐Ge) had formed at the Al grain boundaries (GBs). These observations could be explained in consequence of the initiation of crystallization of a‐Ge at the Al GBs followed by the nucleation of crystallization at the a‐Ge/Al interface, as supported by thermodynamic calculations of interface energetics. Copyright © 2008 John Wiley & Sons, Ltd.
Analysis of grain boundaries in an embrittled ancient silver necklace
Authors: Vaníčková Jaroslava , Děd Jiří , Bartuška Pavel , Drahokoupil Jan , Čerňanský Marian , Lejček Pavel 
Published: January 2008

AbstractArchaeological silver objects are often found to be embrittled to some extent. Using light and scanning electron microscopy techniques, X‐ray diffraction and AES, the causes of this embrittlement were studied on a silver artefact buried for more than 1000 years in soil. This investigation revealed the presence of chlorine, sulphur and carbon at grain boundaries of the Ag–Cu based object suggesting that most likely; the substantial embrittlement is caused by an inter‐crystalline corrosion attack. The role of copper enrichment at the grain boundaries as a possible path of preferential corrosion attack is discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Quantification of surface excitation effects on the EPES‐determined IMFPs for GaN and SiC
Authors: Krawczyk Miroslaw 
Published: January 2008

AbstractSurface electron inelastic excitations, a consequence of electron surface interaction, effect substantially the measured peak intensities, or peak areas, in surface‐sensitive electron spectroscopies, and distort the quantitative information. To obtain reliable quantitative information from the electron spectra, the measured intensities and/or peak areas should be corrected for these effects.In the present work, we investigated, quantitatively, the influence of surface excitations on electron inelastic mean free paths (IMFPs) determined by elastic peak electron spectroscopy (EPES). We used IMFPs obtained from the previous EPES measurements of the electron elastic backscattering probability for GaN, SiC, and the Ni standard in the energy range 200–2000 eV. Calculated surface excitation parameters (SEPs) of both incident and emitted electrons were evaluated using the formulae of Chen, Tu et al., and Werner et al., and applied for correcting the EPES IMFPs. These corrected values were compared with those predicted by the TPP‐2M formula.We found that implementation of the surface excitation correction improved agreement between the resulting IMFPs for selected wide‐band semiconductors and the TPP‐2M values. The extent to which the IMFPs measured by EPES differ from the corresponding bulk values (on account of surface excitations) was found to depend on the semiconductor material with finite surface. The results also clearly demonstrated the importance of accounting for surface excitations for accuracy of the measured IMFPs. Copyright © 2008 John Wiley & Sons, Ltd.
Investigation of thin oxide films on titanium for capacitor applications
Authors: Schroth S. , Schneider M. , Mayer ‐ Uhma T. , Michaelis A. , Klemm V. 
Published: January 2008

AbstractThin passive films on titanium formed by electrolytic oxidation show a high relative permittivity and could be a promising cost effective dielectric material for capacitor applications. In the present work, the films were formed in an acetate buffer solution by potentiodynamic polarisation up to various potentials. The film thickness was determined by coulometry and ellipsometry. The growth factor is 2.7 nm/V. Furthermore, by using an electrochemical micro‐capillary cell the anodising process was performed at high lateral resolution on different substrate grains with various crystallographic orientations. An influence of the Ti grain orientation on the TiO2 film thickness could not be observed under the used experimental conditions. By means of transmission electron microscope(TEM) investigation the oxide film structure could be determined as prevailing amorphous. Copyright © 2008 John Wiley & Sons, Ltd.
Exploiting Enzymatic (Reversed) Hydrolysis in Directed Self‐Assembly of Peptide Nanostructures
Authors: Das Apurba K. , Collins Richard , Ulijn Rein V. 
Published: January 2008

AbstractEnzyme‐catalyzed reactions can be exploited to control molecular self‐assembly under physiological conditions by converting nonassembling precursors into self‐assembly building blocks. Two complementary approaches based on aromatic short‐peptide derivatives that form molecular hydrogels are demonstrated. Firstly, it is shown that esterase‐directed self assembly via hydrolysis of hydrophobic N‐(fluorenyl‐9‐methoxycarbonyl) (Fmoc)‐peptide methyl esters give rise to formation of transparent hydrogels composed of defined peptide nanotubes. The internal and external diameters of these tubes are highly tunable, depending on the amino acid composition and chain length of the building blocks. Secondly, protease‐directed self‐assembly of Fmoc‐peptide esters is achieved via amide‐bond formation (reversed hydrolysis) for combinations of Fmoc‐threonine and leucine/phenylalanine methyl esters, producing fibrous hydrogels. Upon treatment with an esterase, these systems revert back to solution, thus providing a two‐stage solution–gel–solution transition.
Combined cytotoxicity and genotoxicity of a marine toxin and seafood contaminant metal ions (chromium and cadmium)
Authors: Souid‐Mensi Ghada , Moukha Serge , Maaroufi Khira , Creppy Edmond E. 
Published: January 2008

AbstractAlgal bloom with consequent production of marine toxins contaminating bivalves is increasing in costal regions worldwide because of sea water quality worsening. Contamination of seafood by diarrheic shellfish poisoning toxins (DSP) together with metals is frequently reported, a phenomenon not fully explained yet. In this context, metal ions were assayed in clams collected from the banned area of Boughrara, Tunisia, contaminated by Gymnodinium and other algae such as Dinophysis sp, accumulated by these bivalves. The presence of toxic metals ions such as Chromium (Cr) and Cadmium (Cd) in meat, shells, and water released by the clams prompted us to experiment in Caco‐2 intestinal cell line toxic effects of these heavy metals ions in combination with okadaic acid, one DSP present in clams to assess the potential global toxicity. Cr and Cd produce additive effects in (i) reactive oxygen species production, (ii) cytotoxicity as assessed by the mitochondrial activity testing method (MTT test), and (iii) DNA lesions evaluated by agarose gel electrophoresis and acridine orange staining. Exaggerated DNA fragmentation is observed, suggesting an overloading of repair capacity of Caco‐2 cells. The apoptosis suggested by a DNA fragment sizing (180–200 bp) in agarose gel and mechanisms underlying these additive effects in Caco‐2 cells still need to be more comprehensively explained. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2008.
Hepatic metabolism of contaminants in the terapontid fish, yellowtail trumpeter (Amniataba caudavittata Richardson)
Authors: Webb Diane , Gagnon Marthe Monique , Rose Tom 
Published: January 2008

AbstractThe yellowtail trumpeter (Amniataba caudavittata) is an estuarine‐dependent omnivorous fish found in the Swan‐Canning Estuary, Western Australia. Thirty five fish were injected with either the polycyclic aromatic hydrocarbon, benzo[a]pyrene (B[a]P), the synthetic flavenoid β‐naphthoflavone (BNF), or used as controls. The fish were then sampled at 3 and 7 days postinjection. Induction of the enzyme ethoxyresorufin O‐deethylase (EROD) activity was nonsignificant while ethoxycoumarin O‐deethylase (ECOD) activity induction differed amongst treatments. A high interindividual variability in the EROD activity was observed. The measurement of sorbitol dehydrogenase in the serum (s‐SDH) was elevated (BNF 2.2 times and B[a]P 3.2 times the control fish) demonstrating that liver cell damage had occurred. Increases in biliary metabolites of both B[a]P‐type and pyrene‐type (19 times and 3.4 times the controls respectively) indicated that detoxification of pyrene‐type compounds had taken place. Fish of the Terapontidae family, such as the yellowtail trumpeter, were found to be suitable for biomonitoring the health of the Swan‐Canning Estuary. A combination of ECOD activity, s‐SDH, and the measurement of biliary metabolites represents a suitable suite of biomarkers for environmental monitoring of the sublethal effects of PAH pollution in these fish. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2008.
Occurrence of azaarenes in sediments of the Danshuei River, Taiwan—The use of azaarenes as indicator of anthropogenic source to the estuarine system
Authors: Chen Hung‐Yu , Su Chih‐Chieh , Hung Chin‐Chang , Yeh Tzu‐Chi , Shen Ying‐Hung , Tsai Cheng‐Han , Chen Liang‐De , Gong Gwo‐Ching 
Published: January 2008

AbstractAzaarenes belong to the newly identified classes of anthropogenic pollutants. To our knowledge, this study presents the first result of pollution history of azaarenes and their controlling factors in estuary. To understand the transport mechanisms, surface sediment samples were collected from 18 sites of the Danshuei River during the summer and the winter of 2005. The highest concentrations of azaarene, 21.9 ng g−1 for 2‐ring, 9.89 ng g−1 for 3‐ring, and 9.17 ng g−1 for 4‐ring, were observed in midstream surface sediments near the Shi–Zi–Tou waste water pumping station. Therefore, this waste water pumping station not only provides a good sediment accumulation environment but also discharges small particle size sediments, which contain mass amounts of azaarenes into the Danshuei River. This research also finds highly significant covariations among 3‐ring and 4‐ring azaarenes, which suggests similar source strengths and transport mechanisms for these compounds. Additionally, core samples were collected from two sites of the Danshuei River and analyzed to determine the pollution history. Values found in the core sediments correspond to pollution events in recent history. Contaminant inputs via in situ burning of dumping field and wastewater discharge for the periods of 1975–1985 and 2004–2005, respectively, were two major sources of azaarenes to the Danshuei River. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2008.
Patulin influences the expression of Th1/Th2 cytokines by activated peripheral blood mononuclear cells and T cells through depletion of intracellular glutathione
Authors: Luft Petra , Oostingh Gertie Janneke , Gruijthuijsen Yvonne , Horejs‐Hoeck Jutta , Lehmann Irina , Duschl Albert 
Published: January 2008

AbstractPatulin is a mold toxin secreted mainly by fungi of the Penicillium species. Exposure generally results from consumption of moldy fruits and fruit products. Since recent studies identified mold exposure as a risk factor for allergic diseases, we examined the effects of patulin on human peripheral blood mononuclear cells (PBMC) prepared from buffy coats of healthy donors. Cells were stimulated with CD3‐ and CD28‐specific antibodies in the presence or absence of patulin. Effects of patulin on PBMCs were evaluated by proliferation, viability assays, and cytokine ELISAs. The presence of 50 ng/mL patulin strongly decreased the amounts of several cytokines in the supernatant of stimulated PBMCs. This decrease in cytokine secretion was not due to cytotoxic effects of patulin. Moreover, the extent of the reduction of cytokine amounts was cytokine specific, affecting some (IL‐4, IL‐13, IFNγ, and IL‐10), but not others (IL‐8, IL‐5). We show that all effects could be abolished by adding thiol containing compounds. A depletion of intracellular GSH could be measured after incubation of cells with patulin. Taken together, our data indicate that patulin modulates the functional activation of PBMCs with respect to proliferation and cytokine secretion patterns by depletion of intracellular GSH. The depletion of intracellular glutathione may influence the balance between Th1 and Th2 cells and have implications for allergic diseases. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2008.