bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soluble, saturated‐red‐light‐emitting poly(p‐phenylenevinylene) containing triphenylamine units and cyano groups
Authors: Li Hongchao , Hu Yufeng , Zhang Yanguang , Ma Dongge , Wang Lixiang , Jing Xiabin , Wang Fosong 
Published: July 2004

AbstractA conjugated poly(p‐CN‐phenylenevinylene) (PCNPV) containing both electron‐donating triphenylamine units and electron‐withdrawing cyano groups was prepared via Knoevenagel condensation in a good yield. Gel permeation chromatography suggested that the soluble polymer had a very high weight‐average molecular weight of 309,000. A bright and saturated red emission was observed under UV excitation in solution and film. Cyclic voltammetry showed that the polymer presented quasi‐reversible oxidation with a relatively low potential because of the triphenylamine unit. A single‐layer indium tin oxide/PCNPV/Mg–Ag device emitted a bright red light (633 nm). © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 3947–3953, 2004
FlexX‐Scan: Fast, structure‐based virtual screening
Authors: Schellhammer Ingo , Rarey Matthias 
Published: July 2004

AbstractWe present a new software module, FlexX‐Scan, for high‐throughput, structure‐based virtual screening. FlexX‐Scan was developed with the aim to further speed up the virtual screening process. Based on the incremental construction docking tool FlexX (Rarey et al., J Mol Biol 1996;261:470–489), a compact descriptor for representing favorable protein interaction spots within the protein binding site has been developed. The descriptor is calculated using special‐purpose clustering techniques applied to the usual interaction points created by FlexX. The algorithm automatically detects a small set of interaction spots in the binding site for positioning ligand functional groups. The parametrizations of the base placement and incremental construction algorithms have been adapted to the new interaction model. We tested the software tool on a diverse set of 200 protein–ligand complexes from the protein database (PDB) (Kramer et al., Proteins 1999;37:228–241). On average, the algorithm proposes about 90 interaction spots per binding site compared to about 1000 interaction dots in FlexX. We observe that the docking solutions of FlexX‐Scan have a root‐mean‐square deviation from the crystal structure similar to the deviation of docking solutions of standard FlexX. For further validation we also performed virtual screening experiments for cyclin‐dependent kinase 2, thrombin, angiotensin‐converting enzyme, and dihydrofolat reductase. In these experiments, we screened a set of 34,000 random compounds and a number of known actives for each target. With FlexX‐Scan, we achieved comparable enrichments to standard FlexX, with an averaged computing time of 5–10 s per compound, depending on parametrization. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Escherichia coli adenylate kinase dynamics: Comparison of elastic network model modes with mode‐coupling 15N‐NMR relaxation data
Authors: Temiz N. Alpay , Meirovitch Eva , Bahar Ivet 
Published: July 2004

AbstractThe dynamics of adenylate kinase of Escherichia coli (AKeco) and its complex with the inhibitor AP5A, are characterized by correlating the theoretical results obtained with the Gaussian Network Model (GNM) and the anisotropic network model (ANM) with the order parameters and correlation times obtained with Slowly Relaxing Local Structure (SRLS) analysis of 15N‐NMR relaxation data. The AMPbd and LID domains of AKeco execute in solution large amplitude motions associated with the catalytic reaction Mg+2*ATP + AMP → Mg+2*ADP + ADP. Two sets of correlation times and order parameters were determined by NMR/SRLS for AKeco, attributed to slow (nanoseconds) motions with correlation time τ⟂ and low order parameters, and fast (picoseconds) motions with correlation time τ∥ and high order parameters. The structural connotation of these patterns is examined herein by subjecting AKeco and AKeco*AP5A to GNM analysis, which yields the dynamic spectrum in terms of slow and fast modes. The low/high NMR order parameters correlate with the slow/fast modes of the backbone elucidated with GNM. Likewise, τ∥ and τ⟂ are associated with fast and slow GNM modes, respectively. Catalysis‐related domain motion of AMPbd and LID in AKeco, occurring per NMR with correlation time τ⟂, is associated with the first and second collective slow (global) GNM modes. The ANM‐predicted deformations of the unliganded enzyme conform to the functional reconfiguration induced by ligand‐binding, indicating the structural disposition (or potential) of the enzyme to bind its substrates. It is shown that NMR/SRLS and GNM/ANM analyses can be advantageously synthesized to provide insights into the molecular mechanisms that control biological function. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Experimental indication for the existence of multiple Trp rotamers in von Willebrand Factor A3 domain
Authors: Hellings Mario , Engelborghs Yves , Deckmyn Hans , Vanhoorelbeke Karen , Schiphorst Marion E. , Akkerman Jan Willem N. , De Maeyer Marc 
Published: July 2004

AbstractThe first step in both normal haemostasis and arterial thrombosis is the interaction between collagen, von Willebrand factor (vWF), and glycoprotein Ib. The A3 domain of vWF forms the principal binding site for collagen type I and type III. Inhibition of the vWF‐collagen interaction by an anti‐human vWF monoclonal antibody (MoAb) 82D6A3 can be a potential way to prevent arterial thrombosis. Identification of the epitope of MoAb 82D6A3 showed recently that the consensus sequence SPWR obtained by phage display could adopt the conformation of the discontinuous epitope. Modelling showed that Trp982 in the vWF had to obtain a more solvent accessible conformation. We performed a detailed fluorescence study of Trp982 in the vWF A3. Using the method described by Hellings et al. (Biophys J 2003;85:1894–1902), we were able to identify two different low‐energy Trp982 rotamers and to link them with their experimentally derived fluorescence lifetimes. Fluorescence anisotropy showed no interconversion in the nanosecond timescale between the two different rotameric states. With these experiments, we gather strong indications for the existence of an exposed rotamer conformation and a rotamer that corresponds to the one observed in the X‐ray structure. These results strongly support the modeling work (Vanhoorelbeke et al., J Biol Chem 2003;278:37815‐37821). Proteins 2004. © 2004 Wiley‐Liss, Inc.
Novel scoring function for modeling structures of oligomers of transmembrane α‐helices
Authors: Park Yungki , Elsner Markus , Staritzbichler Rene , Helms Volkhard 
Published: July 2004

AbstractSpecific non‐covalent interactions between transmembrane (TM) α‐helices are important in a variety of biological processes. Experimental and computational studies have shown that van der Waals interactions play an important role in the tight packing between TM α‐helices, although polar interactions can also be important in some instances. Based on the assumption that van der Waals interaction alone is sufficient for a meso‐scale (residue‐scale) description of the interaction between TM α‐helices, we have designed a novel residue‐scale scoring function for modeling structures of oligomers of TM α‐helices. We first calculated atomistic van der Waals interaction energies between two amino acids, X and Y, of a pair of parallel α‐helices, glycine‐X‐glycine and glycine‐Y‐glycine and compiled them according to three variables, the distance between the two Cα atoms and the rotational angles of X and Y about their helical axes. Upon averaging over the rotational angles, we obtained one‐dimensional interaction energy profiles that are functions of the distance between Cα atoms only. Each of the interaction energy profiles was fitted with a generic fitting function of the distance between Cα atoms, yielding analytical scoring functions for all possible amino acid pairs. For glycophorin A, neu/erbB‐2, and phospholamban, lowest‐energy conformations obtained through exhaustive scanning of the entire conformational space using the scoring functions were compatible with available experimental data. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Relationship between chaperone activity and oligomeric size of recombinant human αA‐ and αB‐crystallin: A tryptic digestion study
Authors: Saha S. , Das K. P. 
Published: July 2004

Abstractα‐Crystallin, the major eye lens protein, exists as a large oligomer of two subunits, αA‐ and αB‐crystallin. The individual subunits assemble into the oligomer in vitro. It is generally believed that oligomerization is pre‐requisite for chaperone function, although there is no hard data available on this subject. We therefore undertook a study using limited tryptic digestion as a tool for examining the relationship between oligomeric size and chaperone activity of recombinant αA‐ and αB‐crystallin. We showed that tryptic digested fragments of both αA‐ and αB‐crystallin much smaller than the original subunits retain considerable chaperone activity. Our results indicate that chaperone activity depends more on the sequence of the reduced peptide than on its oligomeric size. The results also suggest that the presence of the α‐crystallin domain and hydrophobic clefts on the protein surface, which correlate poorly with oligomeric size, are important for chaperone function. Proteins 2004. © 2004 Wiley‐Liss, Inc.
A portable allosteric mechanism
Authors: Gryczynski Urszula , Schleif Robert 
Published: July 2004

AbstractThe allosteric mechanism by which the gene expression regulatory protein AraC regulates its DNA‐binding activity is shown to be portable by grafting it to β‐galactosidase, generating an arabinose‐regulated β‐galactosidase. A portion of the α‐peptide sequence that complements the activity of α‐acceptor β‐galactosidase was inserted into a nonessential region of the regulatory peptidyl arm of AraC protein. Arabinose, which regulates the position of the arm in AraC protein now regulates the availability of the α‐peptide to α‐acceptor β‐galactosidase, thereby modulating its activity in response to arabinose. Proteins 2004. © 2004 Wiley‐Liss, Inc.
FRP strengthening of concrete structures: new inventions and applications
Authors: Täljsten Björn 
Published: July 2004

AbstractThe advantages of FRP strengthening have been shown time and again during the last decade. All over the world several thousand structures retrofitted with FRPs exist. There are various reasons why the retrofit is needed, but since buildings and civil structures usually have a very long life, it is not uncommon that the demands on the structure change with time. The structures may have to carry larger loads at a later date or fulfil new standards. In extreme cases, a structure may need repair, owing to an accident, or to errors made during the design or construction phase, such that the structure needs to be strengthened before it can be used. Over the past decade, the issue of deteriorating infrastructure has become a topic of critical importance in Europe, and to an equal extent in North America and Japan.The deterioration of bridge decks, superstructure elements and columns can be traced to reasons ranging from ageing and environmentally induced degradation, to poor initial construction and lack of maintenance. Added to the problems of deterioration are issues related to the need for higher load ratings and increased numbers of lanes to accommodate the ever‐increasing traffic flow on major arteries.As a result, a significant portion of our infrastructure is currently either structurally or functionally deficient. Beyond the costs and visible consequences associated with continuous retrofit and repair of such structural components are the real consequences related to losses in production and overall economic issues related to time and resources caused by delays and detours. As we move into the twenty‐first century, the renewal of our lifelines becomes critical. Here, FRP strengthening may be a tool in the overall toolbox to be used to overcome some of the problems related to repair and strengthening of structures.In this paper a short historical background to plate bonding is presented. The paper focuses on the possibility of improving the existing technology and how drawbacks can be overcome.
Base sequence dependence of charge transport via short DNA bridges
Authors: Matulewski J. , Baranovskii S. D. , Thomas P. 
Published: July 2004

AbstractCharge transfer in a donor – short bridge – acceptor system is studied within a simple model of a DNA molecule. A difference in transfer rates via two bridges containing similar bases though with opposite sequences is demonstrated. The result calls for experimental verification. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Determination of molecular formulas and structural regularities of low molecular weight fulvic acids by size‐exclusion chromatography with electrospray ionization quadrupole time‐of‐flight mass spectrometry
Authors: These Anja , Winkler Marcus , Thomas Christoph , Reemtsma Thorsten 
Published: July 2004

AbstractSize‐exclusion chromatography was coupled to a quadrupole time‐of‐flight mass spectrometer using electrospray ionization in the negative ion mode to analyze Suwannee River fulvic acid. About 220 exact masses of low molecular weight fulvic acids (FAs) were measured in the range from m/z 190 to 350, and molecular formulas could be deduced for all these molecular masses. All molecular formulas can be described by the superimposition of three homologous series in the FA mixture: (a) a series of hydrogen homologs constituted of five to six members for a given number of carbons and oxygens; (b) a series of alkyl chain homologs with stepwise addition of one methylene group; and (c) isobaric compounds that differ by the formal replacement of an oxygen atom by a methane group. Product ion spectra of the FA species reflect the repeated parallel losses of carbon dioxide and water. The minimum number of carboxylate groups and the maximum number of hydroxy moieties could be determined from the product ion spectra. Furthermore, it was obvious that the structural differences between homologs in the three series are located in the carbon backbone of the FA rather than in its extremities that are expelled as neutral fragments. These structural regularities reduce the complexity of FA mixtures to a certain set of yet unknown basic structures. Copyright © 2004 John Wiley & Sons, Ltd.
Formation of molecular radical cations of aliphatic tripeptides from their complexes with CuII(12‐crown‐4)
Authors: Chu Ivan K. , Siu S. O. , Lam Corey N. W. , Chan Jenny C. Y. , Rodriquez Christopher F. 
Published: July 2004

AbstractMolecular radical cations have proven to be difficult to generate from aliphatic peptides under electrospray ionization mass spectrometry (ESI‐MS) conditions. For a family of small aliphatic peptides GGX, where XG, A, P, I, L and V, these cations have been generated by electrospraying a mixture of Cu.2+, 12‐crown‐4 and GGX in methanol/water. GGX.+ is readily formed from the collision‐induced dissociation (CID) of [CuII(12‐crown‐4)(GGX)].2+. The formation of these aliphatic peptide radical ions from these complexes, in cases where it is not possible from the corresponding complexes involving a series of amine ligands instead of 12‐crown‐4, is likely due to the second ionization energy of the [CuI(12‐crown‐4)(GGX)]+ complex being higher than that of the corresponding [CuI(amine)(GGX)]+ complex. Using these 12‐crown‐4 complexes, GGI can be differentiated from the isomeric GGL by comparing the CID spectra of their [a3+H].+ ions. Copyright © 2004 John Wiley & Sons, Ltd.
Structural analysis of naphthoquinone protein adducts with liquid chromatography/tandem mass spectrometry and the scoring algorithm for spectral analysis (SALSA)
Authors: Zhang Fagen , Bartels Michael J. 
Published: July 2004

AbstractThe relative reactivities of various naphthoquinone isomers (1,4‐, 1,2‐ and 2‐methyl‐1,4‐naphthoquinone) to two test proteins, apomyoglobin and human hemoglobin, were evaluated via liquid chromatography/electrospray ionization mass spectrometry (LC/ESI‐MS). The structural characterization of the resulting adducts was also obtained by LC/ESI‐MS analysis of the intact proteins. The reactive sites of apomyoglobin and human hemoglobin with 1,4‐naphthoquinone and 1,2‐naphthoquinone were also identified through characterization of adducted tryptic peptides by use of high‐pressure liquid chromatography/electrospray ionization with tandem mass spectrometry (HPLC/ESI‐MS/MS), TurboSEQUEST®, and the scoring algorithm for spectral analysis (SALSA). Four adducted peptides, which were formed by nucleophilic addition of a lysine amino acid residue to 1,4‐naphthoquinone, were also identified, as was an adducted peptide from incubation of 1,2‐naphthoquinone with apomyoglobin. In the case of incubation of human hemoglobin with the two naphthoquinones, two adducted peptides were identified from the N‐terminal valine modification of the alpha and beta chains of human hemoglobin. The adducted protein formation may imply that naphthalene produces its in vivo toxicity through 1,2‐ and 1,4‐naphthoquinone metabolites reacting with biomolecular proteins. Copyright © 2004 John Wiley & Sons, Ltd.
Fragmentation study of diastereoisomeric 2‐methyltetrols, oxidation products of isoprene, as their trimethylsilyl ethers, using gas chromatography/ion trap mass spectrometry
Authors: Wang Wu , Vas Gyorgy , Dommisse Roger , Loones Kristof , Claeys Magda 
Published: July 2004

AbstractThe diastereoisomeric 2‐methyltetrols, 2‐methylthreitol and 2‐methylerythritol, were recently reported as major secondary aerosol components in natural forest aerosols and proposed as molecular markers for the photooxidation of isoprene. In this study, we examine the complex electron and methane chemical ionization behaviors of their trimethylsilyl ethers. In order to gain insight into their fragmentation behaviors, threitol and erythritol were studied as model compounds, and deuterium labeling of the trimethylsilyl groups and ion trap MS2 experiments were performed. Copyright © 2004 John Wiley & Sons, Ltd.
Thin‐layer chromatography combined with diode laser desorption/atmospheric pressure chemical ionization mass spectrometry
Authors: Peng Song , Ahlmann Norman , Kunze Kerstin , Nigge Walter , Edler Michael , Hoffmann Thorsten , Franzke Joachim 
Published: July 2004

AbstractThe desorption of an analyte by a continuous wave diode laser from a porous surface of a thin‐layer plate covered with a graphite suspension is presented. The thermally desorbed analyte molecules are ionized in the gas phase by a corona discharge at atmospheric pressure. Therefore, both essential processes—the desorption and the ionization of analyte molecules, which are often performed in one step—are separated. The target preparation is easy and fast since no additional extraction process is required. The mass spectrometric background signal was mostly limited to the low mass range showing no interference with typical compounds of interest. In this study, the calmative and antihypertensive drug reserpine was chosen as model analyte, which is often used for specification of mass spectrometers. No fragmentation was observed because of efficient collisional cooling under atmospheric pressure. The influence of diode laser power and the composition of the graphite suspension were investigated, and a primary optimization was performed. Copyright © 2004 John Wiley & Sons, Ltd.
Determination of halofuginone in eggs by liquid chromatography/tandem mass spectrometry after cleanup with immunoaffinity chromatography
Authors: Mortier L. , Daeseleire E. , Huet A.‐C. , Delahaut P. , Van Peteghem C. 
Published: July 2004

AbstractA sensitive and very selective high‐performance liquid chromatography/tandem mass spectrometric (LC/MS/MS) method for the detection of halofuginone in whole egg has been developed. After deproteinisation with acetonitrile and evaporation of the organic solvent, halofuginone was further isolated by applying immunoaffinity chromatography. The concentrated eluent was injected into the LC/MS/MS system on a C18 column. The precursor ion ([M+H]+) produced by positive electrospray ionisation was selected for fragmentation with argon. Validation parameters such as recovery, linearity and repeatability, decision limit (CCα) and detection capability (CCβ) were determined. Copyright © 2004 John Wiley & Sons, Ltd.
A parametric insensitive H2control design approach
Authors: Chevrel Philippe , Yagoubi Mohamed 
Published: July 2004

AbstractH2and H∞control design methodologies are known to be efficient to deal with multivariable control problems. However, most of them do not take explicitly the parametric uncertainties into account. This paper proposes a low parametric sensitivity H2control design method as an alternative toµ‐synthesis or robust H2control design. In addition to the standard H2criterion, the H2norm of the parametric sensitivity function is introduced in order to improve the robustness of the resulting controller. Unfortunately, this problem is a difficult one. Its equivalence to structured feedback H2control problem will be shown. The underlying BMI will be solved by making use of an iterative LMI procedure. Two examples will illustrate the interest of the approach. Copyright © 2004 John Wiley & Sons, Ltd.
Stability analysis and control of a class of differential‐algebraic nonlinear systems
Authors: Coutinho D. F. , Bazanella A. S. , Trofino A. , e Silva A. S. 
Published: July 2004

AbstractA new methodology based on the linear matrix inequality (LMI) framework is presented for the computation of polynomial Lyapunov functions for differential–algebraic nonlinear systems. The method is applied for estimating the domain of attraction of equilibria and also as a control design tool to increase the damping of the system. Numerical examples are used to demonstrate the approach. The results show the potential of the proposed approach as a tool for analysis and control design. Copyright © 2004 John Wiley & Sons, Ltd.
Robust stability of neutral systems: a Lyapunov‐Krasovskii constructive approach
Authors: Rodrìguez S.A. , Kharitonov V. , Dion J.‐M. , Dugard L. 
Published: July 2004

AbstractIn this paper, robust stability of uncertain linear neutral systems is analysed via a Lyapunov–Krasovskii constructive approach. This paper is the first attempt to compute the Lyapunov–Krasovskii functional for a given time derivative functional w(·) for the class of linear neutral type time delay systems. Copyright © 2004 John Wiley & Sons, Ltd.
Design of low‐order controllers satisfying sensitivity constraints for unstructured uncertain plants
Authors: Yaniv O. 
Published: July 2004

AbstractThis paper presents a simple analytically based algorithm for the design of reduced‐order controllers satisfying frequency‐dependent sensitivity specifications for SISO plants having unstructured uncertainty. The uncertainties can be additive as well as multiplicative, and can take the form of circles, polygons or sectors located around a nominal plant. Moreover, the circle radius and polygon and sector sizes may depend on the frequency. The proposed method is applicable to both continuous and discrete designs. Copyright © 2004 John Wiley & Sons, Ltd.