bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zweirädrige Energiesparbüchse. Das Fahrrad als alltägliches Verkehrsmittel
Authors: Schlichting H. Joachim , Suhr Wilfried 
Published: February 2008

AbstractVergleicht man die energetischen Transportkosten von Laufen, Fahrrad‐ und Autofahren im Stadtverkehr, dann schneidet das Rad am besten ab. Im Vergleich zum Gehen ist Radfahren energetisch etwa fünfmal günstiger. Dabei erlaubt es eine mehr als doppelt so hohe Geschwindigkeit. Das Autofahren ist in der Stadt sogar rund 24‐mal ungünstiger als Radeln, falls es sich um eine Person in einem Kleinwagen handelt.
Kontrollierte Hohlräume in der Nanowelt
Authors: Zacharias Margit 
Published: February 2008

AbstractBeim Übergang vom Mikro‐ zum Nanobereich können altbekannte Effekte plötzlich ganz erstaunliche Auswirkungen haben. So verändert sich die Diffusion, wenn die diffundierenden Atome in Nanokugeln oder Nanodrähten eingeschlossen sind. Dieser Effekt hat es unserer Gruppe am Max‐Planck‐Institut für Mikrostukturphysik in Halle und der Universität Freiburg ermöglicht, mikrometerlange Hohlräume mit Durchmessern von 30 bis 100 nm in Nanodrähten definiert zu erzeugen.
Highly porous elastomer‐silsesquioxane nanocomposites synthesized within high internal phase emulsions
Authors: Normatov Jenny , Silverstein Michael S. 
Published: February 2008

AbstractHighly porous elastomeric nanocomposites were successfully synthesized through copolymerization of 2‐ethylhexyl acrylate (EHA), divinyl benzene (DVB), and up to 9 mol % of a polyhedral oligomeric silsesquioxane bearing one propylmethacryl group and seven cyclohexyl groups (MACH‐POSS) within the external phase of high internal phase emulsions (HIPE). The chemical structures, morphologies, thermal properties, and mechanical properties of the polyHIPE were investigated. The mechanical loss peak temperature and full width at half maximum increased with increasing MACH‐POSS content. These changes indicate that copolymerization with MACH‐POSS limits segmental mobility and produces compositional distributions on the nanometer scale. At 9 mol % MACH‐POSS, the reduction in segmental mobility produced a glass transition temperature above room temperature and a significant increase in modulus that can be ascribed to the relatively glassy nature of the polymer. Inorganic monoliths with porosities of around 86%, O/Si of about 1.6, and less than 10% carbon were produced on pyrolysis of the nanocomposite polyHIPE. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2357–2366, 2008
Emulsion synthesis of nanoparticles containing PEDOT using conducting polymeric surfactant: Synergy for colloid stability and intercalation doping
Authors: Dai Chi‐an , Chang Chun‐jie , Chi Hung‐yu , Chien Hung‐ta , Su Wei‐fang , Chiu Wen‐yen 
Published: February 2008

AbstractPoly(3,4‐ethylenedioxythiophene): poly(styrenesulfonate) (PEDOT:PSS) is a widely used conductive aqueous dispersion synthesized by using emulsion polymerization method. To further enhance its solution processability and conductivity of PEDOT derivatives, we proposed to replace the nonconductive PSS with conductive poly[2‐(3thienyl)‐ethoxy‐4‐butylsulfonate] (PTEB) as surfactant for the emulsion polymerization of PEDOT. The reaction involved colloid stabilization and doping in one step, and yielded PEDOT:PTEB composite nanoparticles with high electrical conductivity. Contrary to its counterpart containing nonconductive surfactant, PEDOT: PTEB showed increasing film conductivity with increasing PTEB concentration. The result demonstrates the formation of efficient electrical conduction network formed by the fully conductive latex nanoparticles. The addition of PTEB for EDOT polymerization significantly reduced the size of composite particles, formed stable spherical particles, enhanced thermal stability, crystallinity, and conductivity of PEDOT:PTEB composite. Evidence from UV–VIS and FTIR measurement showed that strong molecular interaction between PTEB and PEDOT resulted in the doping of PEDOT chains. X‐ray analysis further demonstrated that PTEB chains were intercalated in the layered crystal structure of PEDOT. The emulsion polymerization of EDOT using conducting surfactant, PTEB demonstrated the synergistic effect of PTEB on colloid stability and intercalation doping of PEDOT during polymerization resulting in significant conductivity improvement of PEDOT composite nanoparticles. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2536–2548, 2008
Microstructural evolution in polyacrylonitrile fibers during oxidative stabilization
Authors: Yu Meijie , Wang Chengguo , Bai Yujun , Zhu Bo , Ji Minxia , Xu Yong 
Published: February 2008

AbstractMicrostructural evolution in polyacrylonitrile fibers during oxidative stabilization was investigated by high‐resolution transmission electron microscopy and wide‐angle X‐ray diffraction. Nanocrystallites and two types of amorphous structures, that is, onion‐like spheres and maze‐like matrix, are observed not only in the precursor fibers but also in the fibers stabilized at 230, 255, and 275 °C. During oxidative stabilization, changes take place earlier in the amorphous onion‐like spheres than in the ordered regions. With increasing temperature, the outer layers of the onion‐like spheres gradually interlace with each other, microscopically demonstrating crosslinking reactions among neighboring macromolecules. The interplanar spacing in crystalline regions increases and the crystallite size decreases as a result of an order–disorder transition. The transition in large crystallites is not completed even in the fibers that are stabilized at 275 °C, suggesting that uniform microstructure and fine crystallites are conducive to homogenous stabilization. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 759–765, 2008
Critical behavior of brittle‐ductile transition of polymers
Authors: Jiang Wei , Hu Yuexin , Yin Jinghua 
Published: February 2008

AbstractWe report that the brittle‐ductile transition of polymers induced by temperature exhibits critical behavior. When t close to 0, the critical surface to surface interparticle distance (IDc) follows the scaling law: IDc ∝ t−v, where t = 1 − T/T (T and T are the test temperature and brittle‐ductile transition temperature of matrix polymer, respectively) and v = 2/D. It is clear that the scaling exponent v only depends on dimension (D). For 2, 3, and 4 dimension, v = 1, 2/3, and 1/2 respectively. The result indicates that the IDc follows the same scaling law as that of the correlation length (ξ), when t approach to zero. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 766–769, 2008
Solifluction processes in an area of seasonal ground freezing, Dovrefjell, Norway
Authors: Harris Charles , Kern‐Luetschg Martina , Smith Fraser , Isaksen Ketil 
Published: February 2008

AbstractContinuous monitoring of soil temperatures, frost heave, thaw consolidation, pore water pressures and downslope soil movements are reported from a turf‐banked solifluction lobe at Steinhøi, Dovrefjell, Norway from August 2002 to August 2006. Mean annual air temperatures over the monitored period were slightly below 0°C, but mean annual ground surface temperatures were around 2°C warmer, due to the insulating effects of snow cover. Seasonal frost penetration was highly dependent on snow thickness, and at the monitoring location varied from 30–38 cm over the four years. The shallow annual frost penetration suggests that the site may be close to the limit of active solifluction in this area. Surface solifluction rates over the period 2002–06 ranged from 0.5 cm yr−1 at the rear of the lobe tread to 1.6 cm yr−1 just behind the lobe front, with corresponding soil transport rates of 6 cm3 cm−1 yr−1 and 46 cm3 cm−1 yr−1. Pore water pressure measurements indicated seepage of snowmelt beneath seasonally frozen soil in spring with artesian pressures beneath the confining frozen layer. Soil thawing was associated with surface settlement and downslope soil displacements, but following clearance of the frozen ground, later soil surface settlement was accompanied by retrograde movement. Summer rainfall events caused brief increases in pore pressure, but no further soil movement. Surface displacements exceeded maximum potential frost creep values and it is concluded that gelifluction was an important component of slow near‐surface mass movements at this site. Temporal and spatial variations in solifluction rates across the area are likely to be considerable and strongly influenced by snow distribution. Copyright © 2008 John Wiley & Sons, Ltd.
V domain of RAGE interacts with AGEs on prostate carcinoma cells
Authors: Allmen Edith Uetz‐von , Koch Michael , Fritz Günter , Legler Daniel F. 
Published: February 2008

AbstractBACKGROUNDThe expression of the scavenger receptor for advanced glycation end products (RAGE) and various ligands of RAGE correlate significantly with cancer progression. However, the mechanism of RAGE/sRAGE‐induced cancer cell activation and ligand usage remain largely unknown.METHODSAndrogen‐independent, highly invasive, as well as androgen‐dependent, non‐invasive human prostate carcinoma (CaP) cells were investigated for their interaction with the soluble form of RAGE (sRAGE). Using neutralizing antibodies and soluble proteins, the ligand for RAGE was identified on CaP cells and ligand binding with sRAGE was biochemically characterized.RESULTSBoth androgen‐independent, highly invasive and androgen‐dependent, non‐invasive CaP cells interacted with immobilized sRAGE in a surprisingly strong manner. Using C‐terminal truncation variants of RAGE we identified the V domain being responsible for the adhesion of CaP cells to sRAGE. Moreover, we demonstrate that this adhesion cannot be blocked by S100B or neutralizing antibodies against β integrins, or amphoterin. However, the CaP cell–RAGE interaction was inhibited with either AGE‐modified proteins, or with neutralizing antibodies against AGE or RAGE. Despite similar binding kinetics between AGE‐modified BSA and different RAGE domains, only applying an excess of sRAGE, but not the VC1 or V domain of RAGE, was able to block the CaP cell–RAGE interaction.CONCLUSIONSWe identified AGEs as the ligand for RAGE on both invasive and non‐invasive prostate cancer cells. Prostate 68: 748–758, 2008. © 2008 Wiley‐Liss, Inc.
Deriving protein dynamical properties from weighted protein contact number
Authors: Lin Chih‐Peng , Huang Shao‐Wei , Lai Yan‐Long , Yen Shih‐Chung , Shih Chien‐Hua , Lu Chih‐Hao , Huang Cuen‐Chao , Hwang Jenn‐Kang 
Published: February 2008

AbstractIt has recently been shown that in proteins the atomic mean‐square displacement (or B‐factor) can be related to the number of the neighboring atoms (or protein contact number), and that this relationship allows one to compute the B‐factor profiles directly from protein contact number. This method, referred to as the protein contact model, is appealing, since it requires neither trajectory integration nor matrix diagonalization. As a result, the protein contact model can be applied to very large proteins and can be implemented as a high‐throughput computational tool to compute atomic fluctuations in proteins. Here, we show that this relationship can be further refined to that between the atomic mean‐square displacement and the weighted protein contact‐number, the weight being the square of the reciprocal distance between the contacting pair. In addition, we show that this relationship can be utilized to compute the cross‐correlation of atomic motion (the B‐factor is essentially the auto‐correlation of atomic motion). For a nonhomologous dataset comprising 972 high‐resolution X‐ray protein structures (resolution <2.0 Å and sequence identity <25%), the mean correlation coefficient between the X‐ray and computed B‐factors based on the weighted protein contact‐number model is 0.61, which is better than those of the original contact‐number model (0.51) and other methods. We also show that the computed correlation maps based on the weighted contact‐number model are globally similar to those computed through normal model analysis for some selected cases. Our results underscore the relationship between protein dynamics and protein packing. We believe that our method will be useful in the study of the protein structure‐dynamics relationship. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Glutathione reductase and thioredoxin reductase at the crossroad: The structure of Schistosoma mansoni thioredoxin glutathione reductase
Authors: Angelucci Francesco , Miele Adriana E. , Boumis Giovanna , Dimastrogiovanni Daniela , Brunori Maurizio , Bellelli Andrea 
Published: February 2008

AbstractThioredoxin glutathione reductase (TGR) is a key flavoenzyme expressed by schistosomes that bridges two detoxification pathways crucial for the parasite survival in the host's organism. In this article we report the crystal structure (at 2.2 Å resolution) of TGR from Schistosoma mansoni (SmTGR), deleted in the last two residues. The structure reveals the peculiar architecture of this chimeric enzyme: the small Glutaredoxin (Grx) domain at the N‐terminus is joined to the large thioredoxin reductase (TR) one via an extended complementary surface, involving residues not conserved in the Grx superfamily; the TR domain interacts with an identical partner via its C‐terminal domain, forming a dimer with a twisted “W” shape. Although lacking the penultimate Selenocysteine residue (Sec), the enzyme is still able to reduce oxidized glutathione. These data update the interpretation of the interdomain communication in TGR enzymes. The possible function of this enzyme in pathogenic parasites is discussed. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Structural properties of the human respiratory syncytial virus P protein: Evidence for an elongated homotetrameric molecule that is the smallest orthologue within the family of paramyxovirus polymerase cofactors
Authors: Llorente María T. , Taylor Ian A. , López‐Viñas Eduardo , Gomez‐Puertas Paulino , Calder Lesley J. , García‐Barreno Blanca , Melero José A. 
Published: February 2008

AbstractThe oligomeric state and the hydrodynamic properties of human respiratory syncytial virus (HRSV) phosphoprotein (P), a known cofactor of the viral RNA‐dependent RNA polymerase (L), and a trypsin‐resistant fragment (X) that includes its oligomerization domain were analyzed by sedimentation equilibrium and velocity using analytical ultracentrifugation. The results obtained demonstrate that both P and fragment X are homotetrameric with elongated shapes, consistent with electron micrographs of the purified P protein in which thin rod‐like molecules of ∼12.5 ± 1.0 nm in length were observed. A new chymotrypsin resistant fragment (Y*) included in fragment X has been identified and purified by gel filtration chromatography. Fragment Y* may represent a minimal version of the P oligomerization domain. Thermal denaturation curves based on circular dichroism data of P protein showed a complex behavior. In contrast, melting data generated for fragments X and particularly fragment Y* showed more homogeneous transitions indicative of simpler structures. A three‐dimensional model of X and Y* fragments was built based on the atomic structure of the P oligomerization domain of the related Sendai virus, which is in good agreement with the experimental data. This model will be an useful tool to make rational mutations and test the role of specific amino acids in the oligomerization and functional properties of the HRSV P protein. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Toward better refinement of comparative models: Predicting loops in inexact environments
Authors: Sellers Benjamin D. , Zhu Kai , Zhao Suwen , Friesner Richard A. , Jacobson Matthew P. 
Published: February 2008

AbstractAchieving atomic‐level accuracy in comparative protein models is limited by our ability to refine the initial, homolog‐derived model closer to the native state. Despite considerable effort, progress in developing a generalized refinement method has been limited. In contrast, methods have been described that can accurately reconstruct loop conformations in native protein structures. We hypothesize that loop refinement in homology models is much more difficult than loop reconstruction in crystal structures, in part, because side‐chain, backbone, and other structural inaccuracies surrounding the loop create a challenging sampling problem; the loop cannot be refined without simultaneously refining adjacent portions. In this work, we single out one sampling issue in an artificial but useful test set and examine how loop refinement accuracy is affected by errors in surrounding side‐chains. In 80 high‐resolution crystal structures, we first perturbed 6–12 residue loops away from the crystal conformation, and placed all protein side chains in non‐native but low energy conformations. Even these relatively small perturbations in the surroundings made the loop prediction problem much more challenging. Using a previously published loop prediction method, median backbone (N‐Cα‐C‐O) RMSD's for groups of 6, 8, 10, and 12 residue loops are 0.3/0.6/0.4/0.6 Å, respectively, on native structures and increase to 1.1/2.2/1.5/2.3 Å on the perturbed cases. We then augmented our previous loop prediction method to simultaneously optimize the rotamer states of side chains surrounding the loop. Our results show that this augmented loop prediction method can recover the native state in many perturbed structures where the previous method failed; the median RMSD's for the 6, 8, 10, and 12 residue perturbed loops improve to 0.4/0.8/1.1/1.2 Å. Finally, we highlight three comparative models from blind tests, in which our new method predicted loops closer to the native conformation than first modeled using the homolog template, a task generally understood to be difficult. Although many challenges remain in refining full comparative models to high accuracy, this work offers a methodical step toward that goal. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Prediction of interaction sites from apo 3D structures when the holo conformation is different
Authors: Murga Leonel F. , Ondrechen Mary Jo , Ringe Dagmar 
Published: February 2008

AbstractThe predictability of catalytic and binding sites from apo structures is addressed for proteins that undergo significant conformational change upon binding. Theoretical microscopic titration curves (THEMATICS), an electrostatics‐based method for the prediction of functional sites, is performed on a test set of 24 proteins with both apo and holo structures available. For 23 of these 24 proteins (96%), THEMATICS predicts the correct catalytic or binding site for both the apo and holo forms. For only one of the 24 proteins, THEMATICS makes the correct prediction for the holo structure but fails for the apo structure. The metrics used by THEMATICS to identify functional residues generally are larger in absolute value for the functional residues in the holo forms compared to the corresponding residues in the apo forms. However, even in the apo forms, these identifying metrics are still statistically significantly larger for functional residues than for residues not involved in catalysis or binding. This indicates that some of the unusual electrostatic properties of functional residues are preserved in the apo conformation. Evidence is presented that certain residues immediately surrounding the active catalytic and binding residues impart functionally important chemical and electrostatic properties to the active residues. At least parts of these microenvironments exist in the unbound conformations, such that THEMATICS is able to distinguish the functional residues even in the apo structures. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Discrimination of near‐native structures in protein–protein docking by testing the stability of local minima
Authors: Kozakov Dima , Schueler‐Furman Ora , Vajda Sandor 
Published: February 2008

AbstractFast Fourier transform (FFT) correlation methods of protein–protein docking, combined with the clustering of low energy conformations, can find a number of local minima on the energy surface. For most complexes, the locations of the near‐native structures can be constrained to the 30 largest clusters, each surrounding a local minimum. However, no reliable further discrimination can be obtained by energy measures because the differences in the energy levels between the minima are comparable with the errors in the energy evaluation. In fact, no current scoring function accounts for the entropic contributions that relate to the width rather than the depth of the minima. Since structures at narrow minima loose more entropy, some of the nonnative states can be detected by determining whether or not a local minimum is surrounded by a broad region of attraction on the energy surface. The analysis is based on starting Monte Carlo Minimization (MCM) runs from random points around each minimum, and observing whether a certain fraction of trajectories converge to a small region within the cluster. The cluster is considered stable if such a strong attractor exists, has at least 10 convergent trajectories, is relatively close to the original cluster center, and contains a low energy structure. We studied the stability of clusters for enzyme–inhibitor and antibody–antigen complexes in the Protein Docking Benchmark. The analysis yields three main results. First, all clusters that are close to the native structure are stable. Second, restricting considerations to stable clusters eliminates around half of the false positives, that is, solutions that are low in energy but far from the native structure of the complex. Third, dividing the conformational space into clusters and determining the stability of each cluster, the combined approach is less dependent on a priori information than exploring the potential conformational space by Monte Carlo minimizations. Proteins 2008. © 2008 Wiley‐Liss, Inc.
NMR structure and dynamics of human ephrin‐B2 ectodomain: The functionally critical C‐D and G‐H loops are highly dynamic in solution
Authors: Ran Xiaoyuan , Qin Haina , Liu Jingxian , Fan Jing‐Song , Shi Jiahai , Song Jianxing 
Published: February 2008

AbstractEph receptors and ephrins constitute the largest family of receptor tyrosine kinases with 15 individual receptors and nine ligands. Its ectodomains represent attractive targets not only for understanding fundamental mechanisms underlying axon guidance, cell migration, segmentation, tumorigenesis, and bone remodeling, but also for drug screening/design to treat cancers, bone diseases and viral infection. So far no NMR study on the ephrin ectodomains is available and as such their properties in solution still remain unknown. In this study, we presented the first NMR structure and dynamics of the human ephrin‐B2 ectodomain as well as its interaction with the receptor EphB2. Strikingly, the NMR study reveals a picture different from those previously obtained by X‐ray crystallography. Although in solution it still adopts the same Greek key fold, with the central β‐barrel (∼30% of the molecule) highly similar to that in crystal structures, the other regions are highly dynamic and accessible to the bulk solvent. In particular, the functionally critical C‐D and G‐H loops of the ephrin‐B2 ectodomain are highly flexible as reflected by several NMR probes including hydrogen exchange and 15N backbone relaxation data. Nevertheless, as revealed by ITC and NMR, the ephrin‐B2 ectodomain binds to EphB2 with a Kd of 22.3 nM to form a tight complex in which the tip of the C‐D loop and the C‐terminus still remain largely flexible. The present results may bear critical implications in understanding the molecular details as well as designing antagonists of therapeutic interest for Eph‐ephrin interactions. Proteins 2008. © 2008 Wiley‐Liss, Inc.