bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into activation and RNA binding of trp RNA‐binding attenuation protein (TRAP) through all‐atom simulations
Authors: Murtola Teemu , Vattulainen Ilpo , Falck Emma 
Published: January 2008

AbstractTryptophan biosynthesis in Bacillus stearothermophilus is regulated by a trp RNA binding attenuation protein (TRAP). It is a ring‐shaped 11‐mer of identical 74 residue subunits. Tryptophan binding pockets are located between adjacent subunits, and tryptophan binding activates TRAP to bind RNA. Here, we report results from all‐atom molecular dynamics simulations of the system, complementing existing extensive experimental studies. We focus on two questions. First, we look at the activation mechanism, of which relatively little is known experimentally. We find that the absence of tryptophan allows larger motions close to the tryptophan binding site, and we see indication of a conformational change in the BC loop. However, complete deactivation seems to occur on much longer time scales than the 40 ns studied here. Second, we study the TRAP–RNA interactions. We look at the relative flexibilities of the different bases in the complex and analyze the hydrogen bonds between the protein and RNA. We also study the role of Lys37, Lys56, and Arg58, which have been experimentally identified as essential for RNA binding. Hydrophobic stacking of Lys37 with the nearby RNA base is confirmed, but we do not see direct hydrogen bonding between RNA and the other two residues, in contrast to the crystal structure. Rather, these residues seem to stabilize the RNA‐binding surface, and their positive charge may also play a role in RNA binding. Simulations also indicate that TRAP is able to attract RNA nonspecifically, and the interactions are quantified in more detail using binding energy calculations. The formation of the final binding complex is a very slow process: within the simulation time scale of 40 ns, only two guanine bases become bound (and no others), indicating that the binding initiates at these positions. In general, our results are in good agreement with experimental studies, and provide atomic‐scale insights into the processes. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Effect of bivalent cations on the interaction of transketolase with its donor substrate
Authors: Sevostyanova Irina A. , Yurshev Vladimir A. , Solovjeva Olga N. , Zabrodskaya Svetlana V. , Kochetov German A. 
Published: January 2008

AbstractThe effect of the type of the cation cofactor of transketolase (i.e., Ca2+ or Mg2+) on its interaction with xylulose 5‐phosphate (donor substrate) has been studied. In the presence of magnesium, the active centers of the enzyme were functionally equivalent with respect to xylulose 5‐phosphate binding and exhibited identical affinities for the donor substrate. Substitution of Ca2+ for Mg2+ results in the loss of the equivalence. In particular, this becomes apparent on binding of xylulose 5‐phosphates to one of the two active centers of the enzyme, which caused the second center to undergo a several fold decrease in the affinity for the donor substrate. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Hydrophobic clusters in protein structures
Authors: Arunachalam J. , Gautham N. 
Published: January 2008

AbstractGlobular proteins fold such that the hydrophobic groups are packed inside forming hydrophobic clusters, and the hydrophilic groups are present on the surface. In this article we analyze clusters of hydrophobic groups of atoms in 781 protein structures selected from the PDB. Our analysis showed that every structure consists of two types of clusters: at least one large cluster that forms the hydrophobic core and probably dictates the protein fold; and numerous smaller clusters, which might be involved in the stabilization of the fold. We also analyzed the preference of the hydrophobic groups in each of the amino acids toward forming hydrophobic clusters. We find that hydrophobic groups from the hydrophilic amino acids also contribute toward cluster formation. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Lipid membrane templates the ordering and induces the fibrillogenesis of Alzheimer's disease amyloid‐β peptide
Authors: Chi Eva Y. , Ege Canay , Winans Amy , Majewski Jaroslaw , Wu Guohui , Kjaer Kristian , Lee Ka Yee C. 
Published: January 2008

AbstractThe lipid membrane has been shown to mediate the fibrillogenesis and toxicity of Alzheimer's disease (AD) amyloid‐β (Aβ) peptide. Electrostatic interactions between Aβ40 and the phospholipid headgroup have been found to control the association and insertion of monomeric Aβ into lipid monolayers, where Aβ exhibited enhanced interactions with charged lipids compared with zwitterionic lipids. To elucidate the molecular‐scale structural details of Aβ‐membrane association, we have used complementary X‐ray and neutron scattering techniques (grazing‐incidence X‐ray diffraction, X‐ray reflectivity, and neutron reflectivity) in this study to investigate in situ the association of Aβ with lipid monolayers composed of either the anionic lipid 1,2‐dipalmitoyl‐sn‐glycero‐3‐[phospho‐rac‐(1‐glycerol)] (DPPG), the zwitterionic lipid 1,2‐dipalmitoyl‐sn‐glycero‐3‐phosphocholine (DPPC), or the cationic lipid 1,2‐dipalmitoyl 3‐trimethylammonium propane (DPTAP) at the air‐buffer interface. We found that the anionic lipid DPPG uniquely induced crystalline ordering of Aβ at the membrane surface that closely mimicked the β‐sheet structure in fibrils, revealing an intriguing templated ordering effect of DPPG on Aβ. Furthermore, incubating Aβ with lipid vesicles containing the anionic lipid 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐[phospho‐rac‐(1‐glycerol)] (POPG) induced the formation of amyloid fibrils, confirming that the templated ordering of Aβ at the membrane surface seeded fibril formation. This study provides a detailed molecular‐scale characterization of the early structural fluctuation and assembly events that may trigger the misfolding and aggregation of Aβ in vivo. Our results implicate that the adsorption of Aβ to anionic lipids, which could become exposed to the outer membrane leaflet by cell injury, may serve as an in vivo mechanism of templated‐aggregation and drive the pathogenesis of AD. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Adiabatic decoupling of the reaction coordinate
Authors: Lorquet J. C. 
Published: January 2008

AbstractWhen the dynamics is constrained by adiabatic invariance, a reactive process can be described as a one‐dimensional motion along the reaction coordinate in an effective potential. This simplification is often valid for central potentials and for the curved harmonic valley studied in the reaction path Hamiltonian model. For an ion–molecule reaction, the action integral 〈Pθ〉 = (1/2π)∮Pθdθ is an adiabatic invariant. The Poisson bracket of 〈Pθ〉2with Hamiltonians corresponding to a great variety of long‐range electrostatic interactions is found to decrease with the separation coordinater, faster than the corresponding potential. This indicates that the validity of the adiabatic approximation is not directly related to the shape of the potential energy surface. The leading role played by the translational momentum is accounted for by Jacobi's form of the least action principle. However, although the identification of adiabatic regions by this procedure is limited to a specific range of coordinate configurations, equivalent constraints must persist all along the reaction coordinate and must operate during the entire reaction, as a result of entropy conservation. The study of the translational kinetic energy released on the fragments is particularly appropriate to detect restrictions on energy exchange between the reaction coordinate and the bath of internal degrees of freedom. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Interactions of metal‐encapsulated fullerenes with solvents
Authors: Jalbout Abraham F. , Jiménez‐Fabián Isaac , de Leon Aned 
Published: January 2008

AbstractThe present investigation reports on the interaction of M@C60(M = Be, Mg, Ca) with solvents (H2O, CH3OH, HF, NH3) using Density Functional Theory calculations. Our computations reveal that the interaction of the fullerene species increases when endohedral metal atoms are inserted into its cavity. The most profound interaction of the fullerene systems is with water and hydrogen fluoride. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Improvement of scale factors for harmonic vibrational frequency calculations using new polarization functions
Authors: Sierraalta Anibal , Martorell Guillermo , Ehrmann Elena , Añez Rafael 
Published: January 2008

AbstractDensity functional calculations were carried to improve the calculated CO vibrational frequencies for transition metal carbonyls. Two types of density functionals were studied, hybrid and generalized‐gradient methods. Using the simplex optimization method, new polarization functions for C and O atoms were obtained. With these new optimized functions, new scaling factors were obtained. The results reveal that, with the new polarization functions, the agreement between the calculated and the experimental values improves considerably. In general, the new scaling factors are very close to unit, with standard uncertainties close to ±0.006 cm−1. The use of the new polarization functions allows more precise calculations of the transition metal carbonyl CO vibrational frequencies. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Use of ab initio calculations to provide insights into the strength and nature of interfluorine interactions
Authors: Wang Yan‐Hua , Lu Yun‐Xiang , Zou Jian‐Wei , Yu Qing‐Sen 
Published: January 2008

AbstractShort interfluorine contacts (FF) are ubiquitous in crystal structures. This article presents a theoretical study of five dimeric complexes formed between fluorine‐containing molecules and hydrogen fluorine at the MP2 computational levels. The results derived from ab initio calculations show that in all cases, the intermolecular distances are less than the sum of van der Waals radii. Difluorine bond energies, computed at the MP2/aug‐cc‐pVTZ level of theory, span over a range from −0.71 to −3.77 kJ/mol, thus indicating that interfluorine interactions are relatively very weak but non‐negligible. The electrostatic force contributes dominantly to the stability of the systems under investigation, and as such the dispersion interaction makes energetic contributions to binding. As an NBO analysis suggested, the charge‐transfer force plays a minor role in the formation of the complexes. Finally, to gain more insights into the nature of interfluorine interactions, topological analysis of the electron density distribution and properties of bond critical points are determined by means of the quantum theory of atoms in molecules. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Bare silica nanoparticles as concentrating and affinity probes for rapid analysis of aminothiols, lysozyme and peptide mixtures using atmospheric‐pressure matrix‐assisted laser desorption/ionization ion trap and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Agrawal Kavita , Wu Hui‐Fen 
Published: January 2008

AbstractThe analysis of peptide mixtures from urine and plasma samples using bare (uncapped) SiO2 nanoparticles (NPs) with atmospheric‐pressure matrix‐assisted laser desorption/ionization mass spectrometry (AP‐MALDI‐MS) has been reported. The method was based on the adsorption of positively charged peptides on the surface of negatively charged SiO2 NPs through the electrostatic force of attraction. The adsorption on the surface of SiO2 NPs caused enhancement of ionization efficiency of analytes and subsequently increased the signal intensity of peptides. Maximum signal intensity was obtained at optimized concentration of SiO2 NPs and pH of the aqueous solution. The limits of detection (LODs) obtained for different peptides in deionized water with and without using SiO2 NPs were in the range 4.7–360 nM and 0.1–18.0 µM, respectively. The sensitivity of the proposed method was 21–53‐fold better than conventional use of AP‐MALDI‐MS. In addition, linearity in the range 9.5–95 nM was obtained for the peptide angiotensin‐II in deionized water with a correlation of estimation of 0.992 using an internal standard. The proposed method provided a simple way to facilitate the ionization of peptides, reduce sample complexity and increase the tolerance to salts and surfactants in the analysis of biological samples. The applicability of the present method was also demonstrated in the real‐world sample analysis of aminothiols and lysozyme using MALDI‐time‐of‐flight (TOF)‐MS. Copyright © 2008 John Wiley & Sons, Ltd.
Tandem mass spectrometry and hydrogen/deuterium exchange studies of protonated species of 1,1′‐bis(diphenylphosphino)‐ferrocene oxidative impurity generated during a Heck reaction
Authors: Wu Lianming , Hernandez‐Soto Heriberto , Liu David Q. , Vogt Frederick G. , O'Neill‐Slawecki Stacy A. , Su Qiaogong 
Published: January 2008

AbstractOxidation of 1,1′‐bis(diphenylphosphino)‐ferrocene (DPPF) was found to occur when it served as the ligand for Pd(II)(CH3COO)2 in a Heck reaction. This oxidative impurity of DPPF, referred to as DPPF(O), was identified by high‐performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) and exact mass measurements. Protonated DPPF(O) exhibited unique fragmentation pathways in the gas phase. Hydrogen/deuterium (H/D) exchange experiments provided important insights into the dissociation mechanisms of protonated DPPF(O), suggesting the existence of isomeric structures of the product ions by retaining or losing a proton (or deuteron) upon collision‐induced dissociation (CID). The specific fate of the proton (or deuteron) upon CID is postulated to be dependent on the distance between the exchangeable proton (or deuteron) and the sites of bond cleavage. Density functional theory (DFT) calculations at the B3LYP/LANL2DZ level of theory showed that oxygen in DPPF(O) plays a pivotal role in invoking π‐cation interactions between the p‐type lone pair electrons (nπ) in oxygen and the anti‐bonding orbital of Fe(II), accounting for the major fragmentation pathways of protonated DPPF(O). Facile formation of organometallic distonic ions in dissociation of protonated DPPF(O), and especially of protonated DPPF, could be useful for further exploration of their chemical properties by gas‐phase ion/molecule reactions. Copyright © 2008 John Wiley & Sons, Ltd.
Debt, income and mental disorder in the general population
Authors: Jenkins R. , Bhugra D. , Bebbington P. , Brugha T. , Farrell M. , Coid J. , Fryers T. , Weich S. , Singleton N. , Meltzer H. 
Published: January 2008

BackgroundThe association between poor mental health and poverty is well known but its mechanism is not fully understood. This study tests the hypothesis that the association between low income and mental disorder is mediated by debt and its attendant financial hardship.MethodThe study is a cross-sectional nationally representative survey of private households in England, Scotland and Wales, which assessed 8580 participants aged 16–74 years living in general households. Psychosis, neurosis, alcohol abuse and drug abuse were identified by the Clinical Interview Schedule – Revised, the Schedule for Assessment in Neuropsychiatry (SCAN), the Alcohol Use Disorder Identification Test (AUDIT) and other measures. Detailed questions were asked about income, debt and financial hardship.ResultsThose with low income were more likely to have mental disorder [odds ratio (OR) 2.09, 95% confidence interval (CI) 1.68–2.59] but this relationship was attenuated after adjustment for debt (OR 1.58, 95% CI 1.25–1.97) and vanished when other sociodemographic variables were also controlled (OR 1.07, 95% CI 0.77–1.48). Of those with mental disorder, 23% were in debt (compared with 8% of those without disorder), and 10% had had a utility disconnected (compared with 3%). The more debts people had, the more likely they were to have some form of mental disorder, even after adjustment for income and other sociodemographic variables. People with six or more separate debts had a six-fold increase in mental disorder after adjustment for income (OR 6.0, 95% CI 3.5–10.3).ConclusionsBoth low income and debt are associated with mental illness, but the effect of income appears to be mediated largely by debt.
Reclaiming the critical dimension of realism: Hans J. Morgenthau on the ethics of scholarship
Authors: COZETTE MURIELLE 
Published: January 2008

AbstractThis article investigates Morgenthau’s views on the ethics of scholarship and argues that all his works should be read in the light of his central goal: speaking truth to power. Doing so demonstrates that for Morgenthau, a realist theory of international politics includes two dimensions: it is supposed to explain international relations, but it is also, fundamentally, a critical project which questions the existing status quo. While the explanatory dimension of realism is debated at great length, its critical dimension is consistently overlooked by the more recent, self-named ‘critical’ approaches which tend to present the two adjectives ‘realist’ and ‘critical’ as mutually exclusive. This amounts to an insidious high-jacking of the very adjective critical, which in most cases merely signals one does not espouse a realist perspective. This is highly problematic as it obscures the fact that for Morgenthau, the founding father of realism, political science is by definition a subversive and revolutionary force critical of the existing order. Highlighting the critical dimension that lies at the core of the realist project as formulated by Morgenthau therefore challenges the current narrow use of the adjective ‘critical’ in the discipline and leads to reclaim it for the realist tradition.
Realism and the Left: the case of Hans J. Morgenthau
Authors: SCHEUERMAN WILLIAM E. 
Published: January 2008

AbstractThe commonplace view that the intellectual roots of Hans J. Morgenthau’s Realist theory lie in conservative central European political traditions (such as Bismarckian Realpolitik) requires modification. The young Morgenthau was a protégé of one of Weimar Germany’s most prominent left-wing legal thinkers and barristers, Hugo Sinzheimer, a committed Social Democrat who influenced many young jurists who hoped to pursue a peaceful, legally-based transition to democratic socialism. Although Morgenthau’s biographers have acknowledged his close personal ties to Sinzheimer, they have ignored the ways in which his early work was directly influenced by Sinzheimer’s left-wing legal sociology. Morgenthau’s initial rendition of Realism took the form of a critical-minded sociology of law, inspired by Sinzheimer, which aimed to bring about fundamental reforms to the international system. Only after the demise of the democratic Left did Morgenthau begin to shed his reformist faith in the possibility of legally based global reform. His mature version of Realism can be interpreted as a response to his disillusionment with the politically progressive and socially reformist vision of law championed by the interwar democratic Left.
The one coalition they craved to join: Turkey in the Korean War
Authors: BROWN CAMERON S. 
Published: January 2008

AbstractTwice since the Cold War ended in 1990, Turkey has been with roughly the same dilemma: a US-led multinational force requested Turkey’s cooperation in launching a military attack against Iraq, ostensibly to enforce UN resolutions. Public and elite opinion was largely against Turkish involvement in both 1990 and 2003, and when Turkey did cooperate with the US-led coalition during the former, it was almost entirely due to efforts of then Turkish President Turgut Özal. In many ways, the dilemma faced by Turkey during these two Gulf Wars finds a fascinating parallel to the situation it faced with the Korean War half a century before. At that time, Turkey had to decide whether to join the US-led multinational force that had been authorised by the UN to reverse North Korea’s unprovoked attack on its southern neighbour. Turkey in 1950, however, was much more eager to play an active role than in 1990 or 2003 – to the point where it eagerly committed significant ground forces, despite the fact that the war in question did not directly threaten Turkey’s security interests. This article examines the forces that motivated Turkey to send nearly 5,000 troops almost 5,000 miles away from home, and concludes with thoughts on the implications for alliance theory.
The life history of the plant pathogen Pseudomonas syringae is linked to the water cycle
Authors: Morris Cindy E , Sands David C , Vinatzer Boris A , Glaux Catherine , Guilbaud Caroline , Buffière Alain , Yan Shuangchun , Dominguez Hélène , Thompson Brian M 
Published: January 2008

Abstract
Pseudomonas syringae is a plant pathogen well known for its capacity to grow epiphytically on diverse plants and for its ice-nucleation activity. The ensemble of its known biology and ecology led us to postulate that this bacterium is also present in non-agricultural habitats, particularly those associated with water. Here, we report the abundance of P. syringae in rain, snow, alpine streams and lakes and in wild plants, in addition to the previously reported abundance in epilithic biofilms. Each of these substrates harbored strains that corresponded to P. syringae in terms of biochemical traits, pathogenicity and pathogenicity-related factors and that were ice-nucleation active. Phylogenetic comparisons of sequences of four housekeeping genes of the non-agricultural strains with strains of P. syringae from disease epidemics confirmed their identity as P. syringae. Moreover, strains belonging to the same clonal lineage were isolated from snow, irrigation water and a diseased crop plant. Our data suggest that the different substrates harboring P. syringae modify the structure of the associated populations. Here, we propose a comprehensive life cycle for P. syringae—in agricultural and non-agricultural habitats—driven by the environmental cycle of water. This cycle opens the opportunity to evaluate the importance of non-agricultural habitats in the evolution of a plant pathogen and the emergence of virulence. The ice-nucleation activity of all strains from snow, unlike from other substrates, strongly suggests that P. syringae plays an active role in the water cycle as an ice nucleus in clouds.