bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein thermal stabilization by charged compatible solutes: Computational studies in rubredoxin from Desulfovibrio gigas
Authors: Micaelo Nuno M. , Victor Bruno L. , Soares Cláudio M. 
Published: February 2008

AbstractMolecular dynamics simulation studies of rubredoxin from Desulfovibrio gigas (RDG) were used to characterize the molecular mechanism of thermal stabilization by the compatible solute (CS) diglycerol‐phospate (DGP). DGP is a negatively charged CS that accumulates under salt stress in Archaeoglobus fulgidus. Experimental results show that a 100 mM DGP solution exerts a strong protection effect in the half‐life of RDG at 363 K (Lamosa et al., Appl Environ Microbiol 2000;66:1974–1979). RDG was simulated in four aqueous solutions at 300 and 363 K: pure aqueous media, 100 mM DGP, 100 mM NaCl, and 500 mM DGP. Our work shows that the 100 mM DGP solution is able to maintain the average protein structure when the temperature is increased, preventing the occurrence of large‐scale deviation of a mobile loop involved in the first steps of RDG unfolding. The molecular mechanism of thermal denaturation protection by DGP seems to involve the direct interaction between the protein and the CS by hydrogen bond interactions near the mobile loop. Several clusters of DGP molecules are formed and preferentially localized at neutral electrostatic regions of the surface. The increase of DGP concentration to 500 mM did not yield better stabilization of the protein suggesting that the thermal protective role of this charged CS is achieved at low concentrations, as shown experimentally. Proteins 2008. © 2008 Wiley‐Liss, Inc.
The peroxidase–cyclooxygenase superfamily: Reconstructed evolution of critical enzymes of the innate immune system
Authors: Zamocky Marcel , Jakopitsch Christa , Furtmüller Paul G. , Dunand Christophe , Obinger Christian 
Published: February 2008

AbstractThe authors have reconstructed the phylogenetic relationships of the main evolutionary lines of mammalian heme containing peroxidases. The sequences of intensively investigated human myeloperoxidase, eosinophil peroxidase, and lactoperoxidase, which participate in host defence against infections, were aligned together with newly found open reading frames coding for highly similar putative peroxidase domains in all kingdoms of life. The evolutionary relationships were reconstructed using neighbor‐joining, maximum parsimony, and maximum likelihood methods. It is demonstrated that this enzyme superfamily obeys the rules of birth‐and‐death model of multigene family evolution and contains proteins with a variety of function that could be grouped in seven subfamilies. On the basis of occurrence and the fact that two main enzymatic activities are related with these metalloproteins, they propose the name peroxidase–cyclooxygenase superfamily for this widely spread group of heme‐containing oxidoreductases. Well known structure–function relationships in mammalian peroxidases formed the basis for the critical inspection of all subfamilies. The presented data unequivocally suggest that predecessor genes of mammalian heme peroxidases have segregated very early in evolution. Before organisms developed an acquired immunity, their antimicrobial defence depended on enzymes that were recruited upon pathogen invasion and could produce antimicrobial reaction products. Thus, these peroxidatic heme proteins evolved to important components in the innate immune defence system. This work shows that even in certain prokaryotic organisms, genes encoding putative antimicrobial enzymes are found providing a group of bacteria with an evolutionary advantage over the others. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Biotinoyl domain of human acetyl‐CoA carboxylase: Structural insights into the carboxyl transfer mechanism
Authors: Lee Chung‐Kyung , Cheong Hae‐Kap , Ryu Kyoung‐Seok , Lee Jae Il , Lee Weontae , Jeon Young Ho , Cheong Chaejoon 
Published: February 2008

AbstractAcetyl‐CoA carboxylase (ACC) catalyzes the first step in fatty acid biosynthesis: the synthesis of malonyl‐CoA from acetyl‐CoA. As essential regulators of fatty acid biosynthesis and metabolism, ACCs are regarded as therapeutic targets for the treatment of metabolic diseases such as obesity. In ACC, the biotinoyl domain performs a critical function by transferring an activated carboxyl group from the biotin carboxylase domain to the carboxyl transferase domain, followed by carboxyl transfer to malonyl‐CoA. Despite the intensive research on this enzyme, only the bacterial and yeast ACC structures are currently available. To explore the mechanism of ACC holoenzyme function, we determined the structure of the biotinoyl domain of human ACC2 and analyzed its characteristics and interaction with the biotin ligase, BirA using NMR spectroscopy. The 3D structure of the hACC2 biotinoyl domain has a similar folding topology to the earlier determined domains from E. coli and P. shermanii. However, the local structures near the biotinylation sites have notable differences that include the geometry of the consensus “Met‐Lys‐Met” (MKM) motif and the absence of “thumb” structure in the hACC2 biotinoyl domain. Observations of the NMR signals upon the biotinylation indicate that the biotin group of hACC2 does not affect the structure of the biotinoyl domain, while the biotin group for E. coli ACC interacts directly with the thumb residues that are not present in the hACC2 structure. These results imply that, in the E. coli ACC reaction, the biotin moiety carrying the carboxyl group from BC to CT can pause at the thumb of the BCCP domain. The human biotinoyl domain, however, lacks the thumb structure and does not have additional noncovalent interactions with the biotin moiety; thus, the flexible motion of the biotinylated lysine residue must underlie the “swinging arm” motion. The chemical shift perturbation and the cross saturation experiments of the human ACC2 holo‐biotinoyl upon the addition of the biotin ligase (BirA) showed the interaction surface near the MKM motif, the two glutamic acids (Glu 926, Glu 953), and the positively charged residues (several lysine and arginine residues). This study provides insight into the mechanism of ACC holoenzyme function and supports the swinging arm model in human ACCs. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment
Authors: Bandyopadhyay Debashree , Mehler Ernest L. 
Published: February 2008

AbstractA general method has been developed to characterize the hydrophobicity or hydrophilicity of the microenvironment (MENV), in which a given amino acid side chain is immersed, by calculating a quantitative property descriptor (QPD) based on the relative (to water) hydrophobicity of the MENV. Values of the QPD were calculated for a test set of 733 proteins to analyze the modulating effects on amino acid residue properties by the MENV in which they are imbedded. The QPD values and solvent accessibility were used to derive a partitioning of residues based on the MENV hydrophobicities. From this partitioning, a new hydrophobicity scale was developed, entirely in the context of protein structure, where amino acid residues are immersed in one or more “MENVpockets.” Thus, the partitioning is based on the residues “sampling” a large number of “solvents” (MENVs) that represent a very large range of hydrophobicity values. It was found that the hydrophobicity of around 80% of amino acid side chains and their MENV are complementary to each other, but for about 20%, the MENV and their imbedded residue can be considered as mismatched. Many of these mismatches could be rationalized in terms of the structural stability of the protein and/or the involvement of the imbedded residue in function. The analysis also indicated a remarkable conservation of local environments around highly conserved active site residues that have similar functions across protein families, but where members have relatively low sequence homology. Thus, quantitative evaluation of this QPD is suggested, here, as a tool for structure–function prediction, analysis, and parameter development for the calculation of properties in proteins. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Insect growth regulator effects of azadirachtin and neem oil on survivorship, development and fecundity of Aphis glycines (Homoptera: Aphididae) and its predator, Harmonia axyridis (Coleoptera: Coccinellidae)
Authors: Kraiss Heidi , Cullen Eileen M 
Published: February 2008

AbstractBACKGROUND: Aphis glycines Matsumura, an invasive insect pest in North American soybeans, is fed upon by a key biological control agent, Harmonia axyridis Pallas. Although biological control is preferentially relied upon to suppress insect pests in organic agriculture, approved insecticides, such as neem, are periodically utilized to reduce damaging pest populations. The authors evaluated direct spray treatments of two neem formulations, azadirachtin and neem seed oil, under controlled conditions for effects on survivorship, development time and fecundity in A. glycines and H. axyridis.RESULTS: Both azadirachtin and neem seed oil significantly increased aphid nymphal mortality (80 and 77% respectively) while significantly increasing development time of those surviving to adulthood. First‐instar H. axyridis survival to adulthood was also significantly reduced by both neem formulations, while only azadirachtin reduced third‐instar survivorship. Azadirachtin increased H. axyridis development time to adult when applied to both instars, while neem oil only increased time to adult when applied to first instar. Neither neem formulation affected the fecundity of either insect.CONCLUSIONS: Results are discussed within the context of future laboratory and field studies aimed at clarifying if neem‐derived insecticides can be effectively integrated with biological control for soybean aphid management in organic soybeans. Copyright © 2008 Society of Chemical Industry
Pressure‐ and orientation‐dependent linear optical absorption spectra of radially deformed single‐walled carbon nanotubes
Authors: Liu Guogao , Wang Xiao , Chen Jiangwei , Lu Huaixian 
Published: February 2008

AbstractBased upon the Slater–Koster tight‐binding model and the gradient approximation, we investigate the linear optical properties of radially deformed single‐walled carbon nanotubes (SWNTs). It is found that, for the armchair tubes, the radial pressure may make the absorption peaks exhibited in the perfect tube shift to lower energy and eventually vanish, which is consistent with the experimental results observed in the optical spectra of squashed SWNT films. In addition, a lot of new and pressure‐ and orientation‐dependent absorption peaks emerge in the optical spectra of the radially deformed tubes. Finally, for comparison, the dependence of optical properties of deformed tubes on chirality is discussed simply. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Compton profiles of p‐Si and n‐Si in an external electric field
Authors: Demir D. , Sahin Y. 
Published: February 2008

AbstractThe Compton profiles of p‐Si and n‐Si have been measured in an external electric field with 59.54 keV gamma radiation from an Am‐241 source. The external electric field of intensities +167 kV/m and –167 kV/m were used to change the surface charge density of the samples. Comparison of the profiles of p‐Si and n‐Si in the same magnitude but opposite direction of the electric field gives information about the Compton scattering of gamma rays from holes. Furthermore, the Compton profile experiments in an external electric field can be used to identify the type of semiconductor. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Investigations of spin‐Hamiltonian parameters and defect structure for Mn4+ in Al2O3 from a two‐mechanism model
Authors: Wu Xiao‐Xuan , Feng Wen‐Lin , Fang Wang , Zheng Wen‐Chen 
Published: February 2008

AbstractThe complete high‐order perturbation formulas based on a two‐mechanism model for the spin‐Hamiltonian (SH) parameters (g ‐factors g||, g⊥, and zero‐field splitting D) of 3d3 ions in trigonal octahedral sites are derived. In the model, not only the conventional contribution to SH parameters from the crystal‐field (CF) mechanism, but also that from the charge‐transfer (CT) mechanism (which is omitted in the CF theory) are included. From these formulas, the SH parameters of Mn4+ replacing Al3+ in Al2O3 crystal are calculated by using the parameters related to the optical spectral data and the defect structure of the studied system. The results (including the relative importance of the CT mechanism on the SH parameters and the defect structure of Mn4+ impurity center) are discussed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Supramolecular structure of perylene tetracarboxdiimides
Authors: Marcon V. , Kirkpatrick J. , Pisula W. , Andrienko D. 
Published: February 2008

AbstractUsing atomistic molecular dynamics (MD) simulations we study the columnar phases of perylene tetracarboxdiimides (PDI) and establish correlations between the molecular structure, packing, and dynamical properties of these materials. Combining electronic structure calculations, MD and kinetic Monte Carlo simulations, a correlation is then established between molecular structure and charge mobility of columnar mesophases of perylene tetracarboxdiimide derivatives. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The low velocity impact response of auxetic carbon fibre laminates
Authors: Alderson K. L. , Coenen V. L. 
Published: February 2008

AbstractThe low velocity impact resistance of auxetic carbon fibre laminates has been compared to that of laminates with matched through‐the‐thickness modulus, but with Poisson's ratios of near zero and positive values. Four impact loads corresponding to major events in the static indentation response were examined and damage was assessed by ultrasonic C‐scans, detailed fractography and measurement of residual properties. It was found that enhancements were seen in resistance to low velocity for the auxetic laminates, but only at low energy levels, indicating some degree of rate dependency. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Estimates for the localised stiffness and heterogeneity of auxetic foams
Authors: Gaspar N. 
Published: February 2008

AbstractIn the task to accurately model auxetic foams, a number of details must be correctly accounted for. Firstly, the microstructure is not simple and can only be qualitatively described by traditional, regular, cellular models. Computed tomography (CT) data has been used to begin to describe the details of the complex geometry of the foams' microstructure and to describe it in a manner suitable for advanced models. Using these modelling techniques that are able to capture difficult geometries, values of the local and global mechanical properties are calculated. These mechanical calculations are based on a linear elastic core and global properties are a mean strain estimate. The latter is shown to be inadequate, highlighting the need for a heterogeneous basis for accurate modelling. The significant mechanical anisotropy of the material is reported and mechanical results are recast according to axis of major and minor principal stiffness demonstrating the elastic symmetry of the foam and a requirement of an objective methodology in modelling an inherently anisotropic material. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantitative chiral analysis of phthaloylglutamic acid and related analogs by a single ratio kinetic method using electrospray ionization and matrix‐assisted laser desorption techniques
Authors: Ramagiri Suma , Gupte Renuka , Rakov Igor , Yates Charles R. , Miller Duane D. 
Published: February 2008

AbstractA rapid method for quantitative chiral analysis of phthaloylglutamic acid and its dimethyl ester by Cook's kinetic method is demonstrated using electrospray ionization (ESI) and matrix‐assisted laser desorption techniques. Transition‐metal‐bound complex ions containing the chiral phthaloylglutamic acid and its dimethyl ester are generated by ESI mass spectrometry and subjected to collision‐induced dissociation. The ratio of the two competitive dissociation rates is related to the enantiomeric composition of the drug mixture. A seven‐point calibration curve, derived from the kinetic method, allowed rapid quantitation of the enantiomeric excess of drug mixtures. In this paper, matrix‐assisted laser desorption/ionization (MALDI) coupled with the linear ion trap (LIT) technique is evaluated for its applicability as a complementary technique to ESI for chiral discrimination and quantitation. Copyright © 2008 John Wiley & Sons, Ltd.
On the impacts of low rate DoS attacks on VoIP traffic
Authors: Shevtekar A. , Stille J. , Ansari N. 
Published: February 2008

AbstractLow rate TCP DoS (Shrew) and reduction of quality (RoQ) attacks have been proven to be detrimental to TCP traffic in the Internet. In this paper, we investigate the effect of these attacks on QoS sensitive, real time UDP traffic, like VoIP. Both of these attacks are difficult to detect, as the average attack traffic is low. These stealthy RoQ attacks are especially hard to detect as their periodicity is not well‐defined, and the attacks can contain spoofed source as well as destination IP addresses. Extensive ns2 simulations have been performed under realistic scenarios to validate the effects of these attacks on real time VoIP traffic using the G711 and G729a audio codecs. Forward Error Correction (FEC) is also considered in our analysis to recover packets from the packet loss caused by attacks. Without FEC, these attacks can drastically reduce the quality of VoIP traffic, leading to denial of service. To evaluate the perceptual quality of voice under attacks, the network losses are mapped to user's quality perception by using the ITU E‐model. The MOS range of the E‐model decreases frombesttomediumdue to the low rate TCP DoS and RoQ attacks even when FEC is deployed. In some of the attack scenarios, the packet losses are bursty, which can lead to dropped calls. In addition, the stealthy RoQ attacks with higher burst lengths are as effective as the shrew attack in impairing VoIP traffic. We have also evaluated the effects of the attack on the VoIP traffic on the DETERLAB testbed, which has specifically been built for conducting network security research, and the results are consistent with the ns2 simulation results. We believe our investigation is important to remove the misconception about low rate TCP DoS and RoQ attacks that they affect only TCP traffic in the Internet. Copyright © 2008 John Wiley & Sons, Ltd.
In situ structural analysis of corrosion products formed on the surfaces of iron‐based alloys
Authors: Suzuki Shigeru , Suzuki Shinya , Inoue Katsuya , Matsubara Eiichiro , Waseda Yoshio 
Published: February 2008

AbstractIn situ X‐ray diffraction measurements were performed for analyzing the constituent species of corrosion products freshly formed on the surfaces of pure iron and iron‐based alloys, namely, iron − 0.58 mass% phosphorus and iron − 3.2 mass% molybdenum. As these elements are often added into corrosion‐resistant steels, their influence on the constituent species of the corrosion products was studied. The sample surfaces were corroded by dropping an NaCl aqueous solution and cyclically exposing them to wet and dry atmospheres. The results revealed that γ‐FeOOH was formed as the main corrosion product on the surface of the iron‐based alloys, and small amounts of species such as green rust (GR), and magnetite were formed depending on the addition of the alloying elements. It is considered that the formation of different constituent species of the corrosion products is influenced by the alloying elements in the corrosion products. It was shown that in situ X‐ray diffraction measurements enable us to obtain information on different species in the corrosion products formed under various conditions. Copyright © 2008 John Wiley & Sons, Ltd.
Numerical modelling of the electrochemical behaviour of 316 stainless steel based upon static and dynamic experimental microcapillary‐based techniques: effect of electrolyte flow and capillary size
Authors: Krawiec Halina , Vignal Vincent , Akid Robert 
Published: February 2008

AbstractThe objective of this work was to determine the parameters that affect the mass transport and the distribution of species in microcapillaries close to the specimen surface. Local experiments were carried out under static and flow conditions on type 316L stainless steel in 1.7 M NaCl, pH = 3, by means of the electrochemical microcell and the scanning droplet cell technique. The polarisation behaviour of pure iron (used as a model system) in an aqueous environment was calculated adopting a finite element approach and was compared to the experimental results. The corrosion system consists of three parallel electrochemical reactions: the oxygen reduction reaction (ORR), the hydrogen evolution reaction (HER) and iron dissolution. Copyright © 2008 John Wiley & Sons, Ltd.
Fragmentation of molecular compounds on silicon wafers and low dielectric constant materials studied by time‐of‐flight secondary ion mass spectrometry using a polyatomic ion source
Authors: Ravanel X. , Trouiller C. , Juhel M. , Wyon C. , Kwakman L. F. T. , Léonard D. 
Published: February 2008

AbstractRecent time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) studies using primary cluster ion sources such as Aun+, SFn+, Bin+ or C60+ have shown polyatomic ions to be more appropriate for the detection of high mass molecular secondary ions than monoatomic ion sources like Ga+, thanks to secondary ion yield and ion formation efficiency enhancements.This work is part of a study aiming at improving molecular compound quantification at the surface of microelectronics industry substrates by taking advantage of a polyatomic ion source in ToF‐SIMS analysis. It focuses on the case of a phthalate‐related contamination. Fundamental parameters like secondary ion yield, damage cross section and secondary ion efficiency were studied as a function of the size and the energy of the primary ions. The substrate composition influence on the ToF‐SIMS results was also studied by comparing several substrates of interest in the microelectronics industry such as silicon wafers and low dielectric constant materials SiOxCyHz.Phthalate‐related secondary ions detected at the surface of the contaminated surfaces were compared and a fragmentation pathway of the di‐isononyl phthalate (DNP) molecule was determined. A drastic improvement of the secondary ion yield was provided when using a polyatomic ion source. Furthermore, a clear increase in damage cross section was observed as a function of the secondary ion size for a given Bin primary ion as well as an increase for a given fragment as a function of the number of Bi atoms in the Bin aggregate. This led to a lower static limit when taking into account higher phthalate fragments and primary ions of larger size. Copyright © 2008 John Wiley & Sons, Ltd.