bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo ligand design to an ensemble of protein structures
Authors: Todorov N.P. , Buenemann C.L. , Alberts I.L. 
Published: March 2006

AbstractWe describe a combinatorial method for de novo ligand design to an ensemble of receptor structures. Receptor conformations, protonation states, and structural water molecules are considered consistently within the framework of de novo ligand design. The method relies on Monte Carlo optimization to search the space of ligand structures, conformations, and rigid‐body movements as well as receptor models. The method is applied to an ensemble of HIV protease and human collagenase receptor models. Ligand structures generated de novo exhibit the correct hydrogen‐bonding pattern in the core of the active site, with hydrophobic groups extending into the receptor S1 and S1′ pocket space. Furthermore, it is shown that known ligands are recovered in the correct binding mode and in the native, most tightly binding receptor model. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Analysis and prediction of helix–helix interactions in membrane channels and transporters
Authors: Hildebrand Peter Werner , Lorenzen Stephan , Goede Andrean , Preissner Robert 
Published: March 2006

AbstractMembrane proteins span a large variety of different functions such as cell‐surface receptors, redox proteins, ion channels, and transporters. Proteins with functional pores show different characteristics of helix–helix packing as other helical membrane proteins. We found that the helix–helix contacts of 13 nonhomologous high‐resolution structures of membrane channels and transporters are mainly accomplished by weakly polar amino acids (G > S > T > F) that preferably create contacts every fourth residue, typical for right‐handed helix crossings. There is a strong correlation between the now available biological hydrophobicity scale and the propensities of the weakly polar and hydrophobic residues to be buried at helix–helix interfaces or to be exposed to the lipids in membrane channels and transporters. The polar residues, however, make no major contribution towards the packing of their transmembrane helices, and are therefore subsumed to be primarily exposed to the polar milieu during the folding process. The contact formation of membrane channels and transporters is therefore ruled by the solubility of the residues, which we suppose to be the driving force for the assembly of their transmembrane helices. By contrast, in 14 nonhomologous high‐resolution structures of other membrane protein coils, also large and polar amino acids (D > S > M > Q) create characteristic contacts every 3.5th residues, which is a signature for left‐handed helix crossings. Accordingly, it seems that dependent on the function, different concepts of folding and stabilization are realized for helical membrane proteins. Using a sequence‐based matrix prediction method these differences are exploited to improve the prediction of buried and exposed residues of transmembrane helices significantly. When the sequence motifs typical for membrane channels and transporters were applied for the prediction of helix–helix contacts the quality of prediction rises by 16% to an average value of 76%, compared to the same approach when only single amino acid positions are taken into account. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Specific DNA binding by the homeodomain Nkx2.5(C56S): Detection of impaired DNA or unfolded protein by isothermal titration calorimetry
Authors: Fodor Elfrieda , Ginsburg Ann 
Published: March 2006

AbstractTitrations of specific 18‐bp duplex DNA with the cardiac‐specific homeodomain Nkx2.5(C56S) have utilized an ultrasensitive isothermal titration calorimeter (ITC). As the free DNA nears depletion, we observe large apparent decreases in the binding enthalpy when the DNA is impaired or when the temperature is sufficiently high to produce some unfolding of the free protein. Either effect can be attributed to refolding of the biopolymer that occurs as a result of stabilization due to the large favorable change in free energy on the homeodomain binding to DNA (−49.4 kJ/mol at 298 K). In either case, thermodynamic parameters obtained in such ITC experiments are unreliable. By using a lower temperature (85 vs. 95°C) during the annealing of complementary DNA strands, damage of the 18‐bp duplex DNA (Tm = 72°C) is avoided, and titrations with the homeodomain are normal at temperatures from 10 to 40°C when >95% of the protein is folded. Under the latter conditions, the heat capacity plot is linear with a ΔCp value of −0.80 ± 0.03 kJ K−1 mol−1, which is more negative than that calculated from the burial of solvent accessible surface areas (−0.64 ± 0.05 kJ K−1 mol−1), consistent with water structures being at the protein–DNA interfaces. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Accessibility of tobacco lipid transfer protein cavity revealed by15N NMR relaxation studies and molecular dynamics simulations
Authors: Da Silva Pedro , Landon Céline , Beltoise Romain , Ponchet Michel , Vovelle Françoise 
Published: March 2006

AbstractPlant LTP1 are small helical proteins stabilized by four disulfide bridges and are characterized by the presence of an internal cavity, in which various hydrophobic ligands can be inserted. Recently, we have determined the solution structure of the recombinant tobacco LTP1_1. Unexpectedly, despite a global fold very similar to the structures already known for cereal seed LTP1, its binding properties are different: Tobacco LTP1_1 is able to bind only one monoacylated lipid, whereas cereal LTP1 can bind either one or two. The 3D structure of tobacco LTP1_1 revealed the presence of a hydrophobic cluster, not observed on cereal LTP1 structures, which may hinder one of the two entrances of the cavity defined for wheat LTP1. To better understand the mechanism of lipid entrance for tobacco LTP1_1 and to define the regions of the protein monitoring the accessibility of the cavity, we have complemented our structural data by the study of the internal dynamics of tobacco LTP1_1, using15N magnetic relaxation rate data and MD simulations at room and high temperatures. This work allowed us to define two regions of the protein experiencing the largest motions. These two regions delineate a portal that opens up during the simulation constituting a unique entrance of the hydrophobic cavity, in contrast with wheat LTP1 where two routes were detected. The hydrophobic interactions resulting from a few point mutations are strong enough to completely block the second portal so that the accessibility of the cavity is restricted to one entrance, explaining why this particular LTP1 binds only one lipid molecule. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Influence of metal salts on the photodegradation of imazapyr, an imidazolinone pesticide
Authors: Quivet Etienne , Faure René , Georges Joseph , Paıssé Jean‐Olivier , Lantéri Pierre 
Published: March 2006

AbstractThe behaviour of imazapyr (2‐(4‐isopropyl‐4‐methyl‐5‐oxo‐2‐imidazolin‐2‐yl)nicotinic acid), a broad spectrum herbicide of the imidazolinone family, has been studied under UV radiation in the presence of metal salts. Complexation interactions between imazapyr and metal ions decreased imazapyr photolysis. A chemometric study compared the photodegradation of imazapyr in aqueous solutions in the presence of Na+, Ca2+ or Cu2+ and their concomitant anionic species (Cl−, NO3−) at various pesticide/metal ion molar ratios. The study showed the major role of metal ions in the degradation of imazapyr and its main photoproducts. The molecules were strongly stabilised on complexation with metal ions, leading to an increase in persistence of the pesticide. Copyright © 2006 Society of Chemical Industry
Effects of Lagrangian multipliers on SWCNT in real space
Authors: Sünel N. , RIzaoǧlu E. , Harigaya K. , Özsoy O. 
Published: March 2006

AbstractElectronic properties, band‐width, band gap, and van Hove singularities of (3,0), (4,0), and (9,0) zigzag nanotubes are investigated comparatively in the Harigaya model and a toy model, including the contributions of bonds of different types to the SSH Hamiltonian differently. Optical transition frequencies are calculated. In this way, an experimental correlation between the two models is achieved. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers
Authors: Liu Ying , Liu Wenqing , Yang Yong , Liu Jianguo 
Published: March 2006

AbstractAb initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the CH…O red‐shifted and NH…π blue‐shifted hydrogen bonds in HNOC2H2dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of NH…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (NH) is due to the significant electron density redistribution effect. The blue shifts of the NH stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
O deficiency in the rutile TiO2(110) surface: Ab initio quantum chemical investigation of the electronic properties
Authors: Von Oertzen G. U. , Gerson A. R. 
Published: March 2006

AbstractThe (110) surface of rutile TiO2(110) has been modeled using a density functional theory (DFT) plane‐wave pseudo‐potential method (CASTEP). In this study, 6 and 9 atomic‐layer slabs have been examined. The stoichiometric surface converges to a low‐spin solution in both cases with a density of states (DOS) similar to that for the bulk. O deficiencies are introduced by the removal of neutral O atoms thus leaving a neutral model with a surfeit of 2 e−per vacancy. This results in the partial filling of the Ti t2gconduction band orbitals and a compensatory shift in the Fermi level. The reduced surface converges to a high‐spin solution in all cases, with the excess spin located within the previously unoccupied Ti t2gorbitals. Removal of the bridging surface O atoms results in an excess spin of 2 electrons per unit cell with approximately one‐half that for removal of in‐plane surface O atoms and subsurface O atoms. The removal of O atoms from the surface leads to an increase of the band gap, with the largest increase due to the removal of in‐plane 3‐fold coordinated surface O atoms, and the smallest one due to the removal of subsurface O atoms. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006
High‐Speed Separation and Size Characterization of Wheat and Barley Starch Granules by Lift‐Hyperlayer Asymmetrical Flow Field‐Flow Fractionation in Synergy with SPLITT Fractionation
Authors: Contado Catia , Wahlund Karl‐Gustav 
Published: March 2006

AbstractThe complementary employment of two separation techniques, one analytical‐scale, the other preparative‐scale, i.e. the lift‐hyperlayer asymmetrical flow field‐flow fractionation (AsyFlFFF) and the split flow‐thin cell (SPLITT) is presented for the first time as a methodology to size‐separate and rapidly characterize starch granules of different botanical origins. Very rapid separation and size characterization is achieved by AsyFlFFF and the techniques are mutually used to characterize and confirm data produced by the other. Light microscopy (LM) was used to test the quality of the performed SPLITT separations and consequently to evaluate the AsyFlFFF results. The procedure was applied to wheat and barley starch.
Towards a tribological reference test – fretting test?
Authors: Klaffke D. 
Published: March 2006

AbstractReference materials are in vogue. Reference methods for tribotesting are not available on a broad scale. Meaningful test methods working with simple specimens are of great interest for the calibration of results of tribological laboratory tests and also for the comparison of results from different sources. Gross slip fretting tests were performed at room temperature with a ball‐on‐flat configuration, using bearing steel (100Cr6, AISI 52100) easily available world‐wide. The scatter of friction and wear quantities was evaluated for tests with three different stroke values. In order to determine the effect of relative humidity (RH) on friction and wear results additional tests were performed in dry air and in moist air. The different methods of describing fretting results are discussed and recommendations are derived for the meaningful quantitative description of friction and wear results. On the basis of influence of stroke and RH on friction and wear results, proposals are given for the use of a fretting test as a reference procedure. Copyright © 2006 John Wiley & Sons, Ltd.
Thermally activated phenomena in nanoscopic sliding friction
Authors: Gnecco E. , Riedo E. , Bennewitz R. , Meyer E. , Brune H. 
Published: March 2006

AbstractThe role of thermal activation for a nanoasperity sliding on a flat surface with low speed is discussed. If the asperity slides in a vacuum, thermal vibrations may excite slipping from an equilibrium position to the next one along the sliding path. This effect is reduced if the velocity increases and leads to a logarithmic increase of friction with the sliding velocity. This is not always the case in a humid environment, where the formation of capillaries between tip and surface acts as an obstacle for thermally activated jumps. Depending on the wettability of the surface, different behaviors are observed. Copyright © 2006 John Wiley & Sons, Ltd.
Microtribology of silicon, oxide, and carbide surfaces
Authors: Ahmed S.I.‐U. , Bregliozzi G. , Haefke H. 
Published: March 2006

AbstractThis paper presents an overview of the microtribological properties of silicon oxide, sapphire, and titanium carbide surfaces as well as a self‐assembled monolayer with respect to their application in microsystems. Testing was performed with a reciprocating microtribometer with normal loads in the micronewton to millinewton range. Silicon and titanium carbide balls were used as counterbodies. For silicon oxide, sapphire and a perfluorodecyltrichlorosilane self‐assembled monolayer (FDTS), the microfriction corresponds to the water contact angle when the smoother titanium carbide ball or the relatively rougher silicon ball was used as a counterbody. Microfriction measurements performed on tribopairs of the same material, but having different roughnesses, showed that the friction of the rougher tribopairs is lower than that of the smoother ones. Interestingly, in the microforce regime, reduction in friction was significant and almost as much as when hydrophobic self‐assembled monolayers are applied on smooth surfaces. This investigation showed that comparative microtribological investigations between different material systems can be very challenging due to the fact that comparable roughness values on samples and countersamples are difficult to realize. Copyright © 2006 John Wiley & Sons, Ltd.
Microtribological behaviour of thin DLC films using different testing methods
Authors: Bandorf R. , Lüthje H. , Staedler T. 
Published: March 2006

AbstractTo enhance the lifetime and reliability of microcomponents, thin microtribological films are applied to microparts. With reduction of the component size, investigation methods for tribological testing must be adapted. This paper studies the microtribological behaviour of thin diamond‐like carbon (DLC) films using different testing methods. To tie in with macroscopic results, to determine friction we used the well‐known pin‐on‐disc test with spherical surfaces of 10 mm diameter under a typical load of 3 N. For investigations of the behaviour under single asperity contact, Atomic Force Microscope (AFM) methods with applied loads of a few hundred micronewtons were used. Investigations on thin DLC films showed that the friction coefficient under single asperity contact is strongly dependent on the applied load and the resulting contact area. Especially for thin films (up to a few hundred nanometres) the friction coefficient is influenced by the substrate material. With decreasing substrate Young's modulus the friction coefficient also decreases. On the other hand, an increase in the abrasive wear resistance was observed using soft substrate materials. In this paper we show that the friction coefficient was also reduced by a simple surface structure. For investigations we used photolithography to create concentric circles in different substrates. This resulted in a behaviour like riding on rails for the pin‐on‐disc test. Depending on the tribological pairing the friction coefficient was reduced to more than 50% of the original value. Copyright © 2006 John Wiley & Sons, Ltd.
Robust multi‐model control of an autonomous wind power system
Authors: Cutululis Nicolas Antonio , Ceanga Emil , Hansen Anca Daniela , Sørensen Poul 
Published: March 2006

AbstractThis article presents a robust multi‐model control structure for a wind power system that uses a variable speed wind turbine (VSWT) driving a permanent magnet synchronous generator (PMSG) connected to a local grid. The control problem consists in maximizing the energy captured from the wind for varying wind speeds. The VSWT‐PMSG linearized model analysis reveals the resonant nature of its dynamic at points on the optimal regimes characteristic (ORC). The natural frequency of the system and the damping factor are strongly dependent on the operating point on the ORC. Under these circumstances a robust multi‐model control structure is designed. The simulation results prove the viability of the proposed control structure. Copyright © 2006 John Wiley & Sons, Ltd.
Using airborne and satellite SAR for wake mapping offshore
Authors: Christiansen Merete B. , Hasager Charlotte B. 
Published: March 2006

AbstractOffshore wind energy is progressing rapidly around Europe. One of the latest initiatives is the installation of multiple wind farms in clusters to share cables and maintenance costs and to fully exploit premium wind resource sites. For siting of multiple nearby wind farms, the wind turbine wake effect must be considered. Synthetic aperture radar (SAR) is an imaging remote sensing technique which offers a unique opportunity to describe spatial variations of wind speed offshore. For the first time an airborne SAR instrument was used for data acquisition over a large offshore wind farm. The aim was to identify the turbine wake effect from SAR‐derived wind speed maps as a downstream region of reduced wind speed. The aircraft SAR campaign was conducted on 12 October 2003 over the wind farm at Horns Rev in the North Sea. Nearly simultaneous measurements were acquired over the area by the SAR on board the ERS‐2 satellite. In addition, meteorological data were collected. Both aircraft and satellite SAR‐derived wind speed maps showed significant velocity deficits downstream of the wind farm. Wind speed maps retrieved from aircraft SAR suggested deficits of up to 20% downstream of the last turbine, whereas satellite SAR‐derived maps showed deficits of the order of 10%. The difference originated partly from the two different reference methods used for normalization of measured wind speeds. The detected region of reduced wind speed had the same width as the wind turbine array, indicating a low degree of horizontal wake dispersion. The downstream wake extent was approximately 10 km, which corresponds well with results from previous studies and with wake model predictions. Copyright © 2006 John Wiley & Sons, Ltd.
Intraoperative Jugular Venous Sampling Aids Detection of an Undescended Parathyroid Adenoma
Authors: Lee Lawrence S. , Canter Robert J. , Fraker Douglas L. 
Published: March 2006

AbstractIntroductionA missed parathyroid adenoma is an important cause of persistent or recurrent primary hyperparathyroidism. Despite the widespread use of preoperative localizing tests and the advent of the rapid intact blood parathyroid hormone assay (iPTH), difficult operative cases are encountered when abnormal parathyroid glands cannot be identified.MethodsOver a 5‐year period, 466 neck explorations were performed for primary hyperparathyroidism. This retrospective report describes the use of intraoperative jugular venous sampling to locate and remove successfully undescended parathyroid adenomas in three patients.ResultsIntraoperative jugular venous sampling for iPTH analysis was performed when a thorough neck exploration in combination with peripheral iPTH failed to reveal a source of hyperparathyroidism in patients with biochemically confirmed hyperparathyroidism. In all patients, a two‐ to fourfold iPTH gradient was observed between the affected and unaffected sides, and an undescended adenoma was located near the carotid bifurcation.ConclusionsIntraoperative jugular venous sampling with iPTH analysis may be a useful technique for successfully detecting an undescended adenoma when other, more routine measures have failed.
Islet Hyperplasia in Adults: Challenge to Preoperatively Diagnose Non‐Insulinoma Pancreatogenic Hypoglycemia Syndrome
Authors: Starke Achim , Saddig Christiane , Kirch Barbara , Tschahargane Cyrus , Goretzki Peter 
Published: March 2006

AbstractBackgroundPancreatic hyperfunctional islet hyperplasia in adults has been more and more frequently described in the literature. Postprandial neuroglycopenia, a negative normal fasting test, negative pancreatic imaging results, and positive intra‐arterial calcium stimulation of serum insulin are characteristic. In affected patients the term non‐insulinoma pancreatogenic hypoglycemia syndrome (NIPHS) was proposed.Materials and Methods/PatientsWe also encountered fasting hypoglycemia in such patients and therefore evaluated clinical and biochemical data in patients with NIPHS (n = 11), patients with insulinoma (n = 70), and patients in whom hypoglycemia was ruled out (n = 70).ResultsPatients with NIPHS were younger (median age: 41 years; range: 18–66) and mostly non‐obese (median body mass index/BMI: 22.2 kg/m2; range: 19–39) compared with patients with an insulinoma (median age: 50 years; median: BMI 26.1 kg/m2). During an oral glucose tolerance test (OGTT) followed by a standard fasting test, neuroglycopenia was observed postprandially with a mean minimal blood glucose level of 36 ± 9 mg/dl in 7 out of 11 patients. Spontaneous hypoglycemia during the fast was 38 ± 5 mg/dl in 8 out of 11 patients. The corresponding insulin levels were 9.2 ± 9.8 mU/l (OGTT) and 6.8 ± 5.4 mU/l (fasting), significantly lower than in patients with insulinoma (P < 0.001), but not different from patients without hypoglycemia (P = 0.05). After pancreatic resection 8 patients (73%) were cured with enduring euglycemia. Pathohistological islet abnormalities with hyperplasia, hypertrophy, and microadenomatosis were confirmed in all patients.ConclusionIn patients with postprandial and/or fasting neuroglycopenia NIPHS may be suspected when insulin levels are low but inadequately suppressed and localization studies failed to show a distinct pancreatic tumor.