bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photochromic crown‐containing molecular switches of chemosensor activity
Authors: Bren Vladimir A. , Dubonosov Alexander D. , Minkin Vladimir I. , Tsukanov Alexey V. , Gribanova Tatyana N. , Shepelenko Evgenii N. , Revinsky Yurii V. , Rybalkin Vladimir P. 
Published: September 2007

AbstractThe crown‐ether functionalized 2‐(N‐acetyl‐N‐arylaminomethylene)benzo[b]thiophene‐3(2H)‐ones exhibit photochromic behavior involving photoinitiated Z/E‐isomerization around the exocyclic CC bond followed by a fast thermal N → O acetyl migration and syn → anti isomerization of the resulting kinetically stable O‐acetyl isomers. The reverse rearrangement is an acid catalyzed reaction. The addition of alkali‐earth metal ions to solutions of N‐acyl isomers induces negligible changes in their UV/Vis spectra, which can be significantly enhanced after irradiation and conversion to the O‐acyl isomers. The compounds obtained may be used as sensitive photodynamic chemosensors with the ‘off‐on’ mechanism for alkali‐earth ions (Ca2+, Ba2+). Quantum‐chemical calculations using the DFT B3LYP/LanL2DZ method predict greater affinity of these sensors to Ca2+ ions (in the gas phase) and to Ba2+ ions (in acetonitrile). Copyright © 2007 John Wiley & Sons, Ltd.
Synthesis and thermal crosslinking of oxazolidine‐functionalized polyurethanes
Authors: Andreu Robert , Lligadas Gerard , Carles Ronda Joan , Galià Marina , Cádiz Virginia 
Published: September 2007

AbstractA new oxazolidine derivative was obtained from phenol, 2‐amino‐2‐methylpropane‐1,3‐diol and paraformaldehyde. The reaction of this novel oxazolidine diol with phenylisocyanate lead to a urethane model compound which can be polymerized thermally by oxazolidine ring opening to give a Mannich bridge structure. Linear segmented polyurethanes were prepared by reaction of different ratios of oxazolidine diol and commercial polyethylenglycol (Mw ∼ 400) with 4,4′‐methylenbis (cyclohexylisocyanate) (HMDI, 90% isomers mixture). The polyurethanes were thermally characterized and crosslinked by oxazolidine ring opening to obtain materials which showed improved thermal stability. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4965–4973, 2007
Sphingolipids and the sphingosine kinase inhibitor, SKI II, induce BCL‐2‐independent apoptosis in human prostatic adenocarcinoma cells
Authors: Leroux M.E. , Auzenne E. , Evans R. , Hail N. , Spohn W. , Ghosh S.C. , Farquhar D. , McDonnell T. , Klostergaard J. 
Published: September 2007

AbstractBACKGROUNDElevated BCL‐2 is one mechanism of therapeutic resistance in prostate cancer (PC), and new approaches are needed to overcome such resistance.METHODSWe evaluated the effects of BCL‐2 over‐expression in human prostatic adenocarcinoma cells on their susceptibility to sphingolipids (SLs) and to the sphingosine kinase (SpK) inhibitor, SKI II.RESULTSIn survival assays, no significant differences were observed in the responses to sphingosine or ceramide among parental PC‐3 cells lacking detectable BCL‐2 and BCL‐2 over‐expressing PC‐3 transfectants; similarly, the responses to dimethyl‐sphingosine (DMSP) of parental LNCaP cells and a BCL‐2 over‐expressing LNCaP transfectant were equivalent. SKI II induced protracted, BCL‐2‐independent survival loss in both PC‐3 and LNCaP parental/transfectant pairs; in contrast, DMSP induced rapid cell shrinkage, caspase activation and caspase‐dependent DNA fragmentation. DMSP‐induced DNA fragmentation and loss of mitochondrial membrane potential were equivalent in BCL‐2 transfectants and parental PC‐3 cells and were not associated with BCL‐2 downregulation. DMSP‐mediated cytotoxicity was not associated with the enhanced production of reactive oxygen intermediates. SL analyses of parental and transfectant PC‐3 cells did not reveal increased levels of sphingosine‐1‐phosphate in the BCL‐2 transfectants; further, there only a modest early shift, corresponding to apoptotic onset, in pro‐ versus anti‐apoptotic SLs in response to DMSP treatment.CONCLUSIONSThus, in contrast to the inhibitory effects of BCL‐2 on apoptosis induced by various agents in tumor cells, SKI II and selected pro‐apoptotic SLs appear atypical in their independence from such inhibition, and may have merits as new candidates for treatment of AI PC. Prostate 67: 1699–1717, 2007. © 2007 Wiley‐Liss, Inc.
Electrospray ionization mass spectrometry of soybean lipoxygenases: N‐terminal acetylation, chemical modification, and solution conformation
Authors: Peariso Amber M. , Nicholson Kellie M. , Benjamin Jones R. , Green‐Church Kari B. , Funk Max O. 
Published: September 2007

AbstractElectrospray ionization mass spectrometry was used to examine both the covalent structure and solution conformation of the soybean lipoxygenases. The post‐translational modifications of two lipoxgyenases were identified as N‐terminal acetylations by tandem mass spectrometry of peptides generated by trypsin digestion. The N‐terminal sequence suggests that the proteins were substrates for the plant homolog of the N‐terminal acetyltransferase complex C in yeast. Analysis of samples of native lipoxygenase‐3 produced ions corresponding within experimental error to the mass of the N‐acetylated polypeptide and one iron atom. The precision of the measurements was within roughly 100 ppm for the 96,856 Da protein. This made it possible to detect the addition of a single oxygen atom to the enzyme in a chemical modification reaction with cumene hydroperoxide. The acid‐induced denaturation of lipoxygenase‐3, which was accompanied by nearly complete loss of catalytic activity, was observed below pH 3.5 with the appearance of ions in the mass spectrum derived from the apoprotein. There was no evidence for the loss of iron in the absence of unfolding. Solutions of lipoxygenase‐3 incubated in 0.1M acetic acid produced ions with a novel charge state distribution suggesting a unique conformation. Circular dichroism measurements showed that the secondary structure features of the native protein were retained in the new conformation. Dynamic light scattering revealed that the new conformation was not a consequence of protein aggregation as the hydrodynamic radius of lipoxygenase‐3 was significantly smaller in acetic acid solution than at pH 7.0. Remarkably, the enzyme incubated in acetic acid retained full catalytic activity. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Dynamics of group II chaperonin and prefoldin probed by 13C NMR spectroscopy
Authors: Kurimoto Eiji , Nishi Yohei , Yamaguchi Yoshiki , Zako Tamotsu , Iizuka Ryo , Ide Naoki , Yohda Masafumi , Kato Koichi 
Published: September 2007

AbstractGroup II chaperonin (CPN) cooperates with prefoldin (PFD), which forms a jellyfish‐shaped heterohexameric complex with a molecular mass of 87 kDa. PFD captures an unfolded protein with the tentacles and transfers it to the cavity of CPN. Although X‐ray crystal structures of CPN and PFD have been reported, no structural information has been so far available for the terminal regions of the PFD tentacles nor for the C‐terminal segments of CPNs, which were regarded to be functionally significant in the previous studies. Here we report 13C NMR analyses on archaeal PFD, CPN, and their complex, focusing on those structurally uncharacterized regions. The PFD and CPN complexes selectively labeled with 13C at methionyl carbonyl carbons were separately and jointly subjected to NMR measurements. 13C NMR spectral data demonstrated that the N‐terminal segment of the α and β subunits of PFD as well as the C‐terminal segments of the CPN hexadecamer retain significant degrees of freedom in internal motion even in the complex with a molecular mass of 1.1 MDa. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Discrimination of mesophilic and thermophilic proteins using machine learning algorithms
Authors: Gromiha M. Michael , Suresh M. Xavier 
Published: September 2007

AbstractDiscriminating thermophilic proteins from their mesophilic counterparts is a challenging task and it would help to design stable proteins. In this work, we have systematically analyzed the amino acid compositions of 3075 mesophilic and 1609 thermophilic proteins belonging to 9 and 15 families, respectively. We found that the charged residues Lys, Arg, and Glu as well as the hydrophobic residues, Val and Ile have higher occurrence in thermophiles than mesophiles. Further, we have analyzed the performance of different methods, based on Bayes rules, logistic functions, neural networks, support vector machines, decision trees and so forth for discriminating mesophilic and thermophilic proteins. We found that most of the machine learning techniques discriminate these classes of proteins with similar accuracy. The neural network‐based method could discriminate the thermophiles from mesophiles at the five‐fold cross‐validation accuracy of 89% in a dataset of 4684 proteins. Moreover, this method is tested with 325 mesophiles in Xylella fastidosa and 382 thermophiles in Aquifex aeolicus and it could successfully discriminate them with the accuracy of 91%. These accuracy levels are better than other methods in the literature and we suggest that this method could be effectively used to discriminate mesophilic and thermophilic proteins. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Dynamic property is a key determinant for protein–protein interactions
Authors: Bai Hongjun , Ma Wenzhe , Liu Shiyong , Lai Luhua 
Published: September 2007

AbstractDynamic property is highly correlated with the biological functions of macromolecules, such as the activity and specificity of enzymes and the allosteric regulation in the signal transduction process. Applications of the dynamic property to protein function researches have been discussed and encouraging progresses have been achieved, for example, in enzyme activity and protein–protein docking studies. However, how the global dynamic property contributes to protein–protein interaction was still unclear. We have studied the dynamic property in protein–protein interactions based on Gaussian Network Model and applied it to classify biological and nonbiological protein–protein complexes in crystal structures. The global motion correlation between residues from the two protomers was found to be remarkably different for biological and nonbiological complexes. This correlation has been used to discriminate biological and nonbiological complexes in crystal and gave a classification rate of 86.9% in the cross‐validation test. The innovation of this feature is that it is a global dynamic property which does not rely directly on the interfacial properties of the complex. In addition, the correlation of the global motions was found to be weakly correlated with the dissociation rate constant of protein complexes. We suggest that the dynamic property is a key determinant for protein–protein interaction, which can be used to discriminate native and crystal complexes and potentially be applied in protein–protein dynamic rate constants estimations. Proteins 2008. © 2007 Wiley‐Liss, Inc.
ClusPro: Performance in CAPRI rounds 6–11 and the new server
Authors: Comeau Stephen R. , Kozakov Dima , Brenke Ryan , Shen Yang , Beglov Dmitri , Vajda Sandor 
Published: September 2007

AbstractClusPro is the first fully automated, web‐based program for docking protein structures. Users may upload the coordinate files of two protein structures through ClusPro's web interface, or enter the PDB codes of the respective structures. The server performs rigid body docking, energy screening, and clustering to produce models. The program output is a short list of putative complexes ranked according to their clustering properties. ClusPro has been participating in CAPRI since January 2003, submitting predictions within 24 h after a target becomes available. In Rounds 6–11, ClusPro generated acceptable submissions for Targets 22, 25, and 27. In general, acceptable models were obtained for the relatively easy targets without substantial conformational changes upon binding. We also describe the new version of ClusPro that incorporates our recently developed docking program PIPER. PIPER is based on the fast Fourier transform correlation approach, but the method is extended to use pairwise interaction potentials, thereby increasing the number of near‐native docked structures. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Prediction and scoring of docking poses with pyDock
Authors: Grosdidier Solène , Pons Carles , Solernou Albert , Fernández‐Recio Juan 
Published: September 2007

AbstractThe two previous CAPRI experiments showed the success of our rigid‐body and refinement approach. For this third edition of CAPRI, we have used a new faster protocol called pyDock, which uses electrostatics and desolvation energy to score docking poses generated with FFT‐based algorithms. In target T24 (unbound/model), our best prediction had the highest value of fraction of native contacts (40%) among all participants, although it was not considered as acceptable by the CAPRI criteria. In target T25 (unbound/bound), we submitted a model with medium quality. In target T26 (unbound/unbound), we did not submit any acceptable model (but we would have submitted acceptable predictions if we had included available mutational information about the binding site). For targets T27 (unbound/unbound) and T28 (homo‐dimer using model), nobody (including us) submitted any acceptable model. Intriguingly, the crystal structure of target T27 shows an alternative interface that correlates with available biological data (we would have submitted acceptable predictions if we had included this). We also participated in all targets of the SCORERS experiment, with at least acceptable accuracy in all valid cases. We submitted two medium and four acceptable scoring models of T25. Using additional distance restraints (from mutational data), we had two medium and two acceptable scoring models of T26. For target T27, we submitted two acceptable scoring models of the alternative interface in the crystal structure. In summary, CAPRI showed the excellent capabilities of pyDock in identifying near‐native docking poses. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Toxicity of dimethoate and fenoxycarb to honey bee brood (Apis mellifera), using a new in vitro standardized feeding method
Authors: Aupinel Pierrick , Fortini Dominique , Michaud Bruno , Marolleau Franck , Tasei Jean‐Noël , Odoux Jean‐François 
Published: September 2007

AbstractA new in vitro method was devised to assess the effects of pesticides on honey bee brood. The method allowed the quantification of doses ingested by larvae and the assessment of larval and pupal mortality. Larval mortality in control samples was lower than 10%. Two active substances were tested: dimethoate and fenoxycarb. The LD50 of dimethoate was 1.9 µg larva−1 48 h after oral exposure of larvae at day 4. Additional dose‐related effects on pupal mortality were noted. After a chronic intoxication, the NOAEC (No Observed Adverse Effect Concentration) for larval mortality at day 7 was 2.5 mg kg−1, whereas a NOAEC of 5 mg kg−1 was found at day 22 for delayed effects on the reduction of adult emergence. Fenoxycarb applied at day 4 showed no effect on larvae, whereas emergence of adults was affected at doses higher than 6 ng larva−1. Copyright © 2007 Society of Chemical Industry
The relevance of sublethal effects in honey bee testing for pesticide risk assessment
Authors: Thompson Helen M , Maus Christian 
Published: September 2007

AbstractThe option of an evaluation and assessment of possible sublethal effects of pesticides on bees has been a subject of discussion by scientists and regulatory authorities. Effects considered included learning behaviour and orientation capacity. This discussion was enhanced by the French bee issue and allegations against systemic insecticides that were linked to the hypothesis that sublethal intoxication might even have led to reported colony losses. This paper considers whether and, if so, how sublethal effects should be incorporated into risk assessment, by addressing a number of questions: What is meant by a sublethal effect? Which sublethal effects should be measured, when and how? How are sublethal effects to be included in risk assessments? The authors conclude that sublethal studies may be helpful as an optional test to address particular, compound‐specific concerns, as a lower‐tier alternative to semi‐field or field testing, if the effects are shown to be ecologically relevant. However, available higher‐tier data (semi‐field, field tests) should make any additional sublethal testing unnecessary, and higher‐tier data should always override data of lower‐tier trials on sublethal effects. © Crown copyright 2007. Reproduced with the permission of Her Majesty's Stationery Office. Published by John Wiley & Sons, Ltd.
Ab initio electronic band structure calculations of half‐metallic c alcium pnictides
Authors: Jaiganesh G. , Eithiraj R. D. , Kalpana G. , Rajagopalan M. 
Published: September 2007

AbstractAb initio electronic structure calculations of hypothetical zinc‐blende CaX (X = P, As, Sb) were performed using tight‐binding linear muffin‐tin orbital method. It was found that, these compounds are ferromagnets exhibiting half‐metallicity. Total energy calculations show that the zinc blende ferromagnetic phase is more stable than the zinc‐blende non‐magnetic phase at equilibrium volume. Ground state properties such as equilibrium lattice constant, bulk modulus and cohesive energy were calculated. The calculated magnetic moment is found to be 1μB per formula unit for all these materials, which agrees well with the other theoretical results. On reducing the cell volume all these compounds are found to undergo a magnetic phase transition from zinc‐blende ferromagnetic phase to zinc‐blende non‐magnetic phase. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dispersion‐related theory for heat capacities of semiconductors
Authors: Pässler Roland 
Published: September 2007

AbstractA reasonable analytical basis for dispersion‐related descriptions of the temperature dependences of harmonic parts of isochoric heat capacities is given by a three‐oscillator model for phonon density of states (PDOS) spectra of semiconductors with a relatively large degree of phonon dispersion. Within this model, a combination of two lower‐energy oscillators substitutes the lower (acoustical) part, and a single higher‐energy oscillator represents the upper (optical) part of PDOS spectra. This model provides good simulations of T ‐dependences of harmonic parts of isochoric heat capacities from moderately low to high temperatures. The incorporation of continuous (quadratic and quartic) power function components into the low‐energy tail region enables a very fine description of temperature dependences also throughout the cryogenic region. Deviations of experimentally measured heat capacities from their harmonic parts are quantified by a conveniently designed low‐order anharmonicity term. The corresponding analytical model provides excellent numerical simulations of isobaric heat capacities of Si and Ge from absolute zero up to room temperature on the basis of least‐mean‐square fittings involving total sets of 6 model‐specific parameters in combination with known zero temperature values of Debye temperatures. As important by‐products of these fittings we obtain adequate values for the material‐specific PDOS spectra moments for all orders within the range –3 < n ≤ 10. The extended version of this dispersion‐related description, which involves a power series expansion for anharmonic components of heat capacities, represents an unprecedented analytical tool for adequate numerical representations of isobaric heat capacities of Si and Ge throughout the whole experimentally relevant temperature region, i.e. from absolute zero up to the respective melting points.Supporting information for this acticle (Appendices on “Self‐sufficient scheme for estimations of even moments” and “Direct use of heat capacity data for determinations of lower moments”) is provided online at www.pss‐b.com.(© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Strong photoacoustic oscillations in layered TlGaSe2 semiconductor
Authors: Grivickas Vytautas , Bikbajevas Vitalijus , Gulbinas Karolis , Gavryushin Vladimir , Linnros Jan 
Published: September 2007

AbstractPeriodic deflections of infrared probe are observed in TlGaSe2 after lateral excitation with optical pulse. The effect is explained by generation of photoacoustic dilatational wave, which propagates within the crystal. Low pulse fluence (0.01 mJ/cm2) is needed to induce such wave when the layer plane is excited. Acoustic wave is generated within a μm‐distance near the excited face, much shorter then the light penetration depth, 1/α, where α is the absorption coefficient. In the temperature range 105–120 K, where ferroelectric‐paraelectric phase transition occur in TlGaSe2, discontinuous changes of the longitudinal sound velocity have been detected. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantitative Structure‐Activity Relationship Modeling of Triaminotriazine Drugs Based on Heuristic Method
Authors: Liu Kunping , Xia Binbin , Ma Weiping , Zheng Bo , Zhang Xiaoyun , Fan Botao 
Published: September 2007

AbstractA quantitative structure‐activity relationship was developed by the Heuristic Method (HM) to study a series of triaminotriazine drugs. Five classes' descriptors were calculated by the software CODESSA in this study. HM was used both for pre‐selecting molecular descriptors and for developing the linear model. The in vitro cell growth inhibition activity of triaminotriazine drugs toward HT‐29, a Colorectal Cancer (CRC) cell line, was correlated with five descriptors, with a squared correlation coefficient (R2) of 0.8780 and squared cross‐validated correlation coefficient ($\rm{ R_{_{{\rm{cv}}} }^2 }$) of 0.8199, respectively. The stability and validity of the model were evaluated by validation. This paper provided a way to predict the in vitro cell growth inhibition activity of triaminotriazine drugs toward HT‐29 from their structures alone and gave some insight into structural features related to triaminotriazine drugs.
Coherent superposition of resonance wave function in terms of weighted orthogonalized natural localized configurations
Authors: Pakiari A. H. , Azami S. M. 
Published: September 2007

AbstractIn this research, the projection technique has been applied in order to decompose the electronic wave function into its weighted orthogonalized resonance components. These components have been constructed by determinants whose orbitals are selected among natural bond orbitals. However, the procedure is general and any other localized orbitals can be used as well. Both σ and π delocalize systems have been considered in order to check the reliability of the calculated resonance weights. For π‐systems, the presented procedure could predict significant decrease of weight of certain resonance structures when the molecular planarity was destroyed. Water cyclic clusters were also tested and the results confirmed the existence of strong σ‐delocalization in the clusters. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008