bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing the electroluminescent efficiency of poly{5‐methoxy‐2‐[(2′‐ethyl‐hexyl)‐oxy]‐p‐phenylenevinylene}/poly(2,3‐diphenyl‐5‐octyl‐p‐phenylenevinylene) polyblends by the introduction of chemical bonding through a thermal treatment
Authors: Chow Hsuan‐Liang , Lin King‐Fu , Wang Ding‐Chang 
Published: November 2005

AbstractA significant improvement in the electroluminescence (EL) properties was observed for a poly{5‐methoxy‐2‐[(2′‐ethyl‐hexyl)‐oxy]‐p‐phenylenevinylene} (MEH–PPV)/poly(2,3‐diphenyl‐5‐octyl‐p‐phenylenevinylene) (DPO–PPV) blend after a thermal treatment at 200 °C for 2 h in vacuo to furnish the chemical bonding between polymer chains. 1H NMR spectroscopy and two‐photon excitation microscopy revealed that the chemical bonding turned the immiscible polyblend into a system more like a block copolymer with a vertically segregated morphology. Because both the lowest unoccupied molecular orbital and highest occupied molecular orbital levels of MEH–PPV in the wetting layer were higher than those of DPO–PPV in the upper layer, the heterojunction between the two layers of the polymers fit the category of so‐called type II heterojunctions. As a result, the turn‐on voltage of the polymer light‐emitting diode prepared with the thermally treated polyblend decreased to ∼0.6 V, and the EL emission intensities and quantum efficiencies increased to about 4 times those of the untreated polyblend. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 62–69, 2006
Damage effects of 120‐keV electron radiation on AG‐80 resin
Authors: Yu Gao , Shangli Dong , Dezhuang Yang , Shiyu He , Zhijun Li 
Published: November 2005

AbstractAG‐80 epoxy resin, namely tetraglycidyl diaminodiphenyl methane (TGDDM), was irradiated with electrons of 120 keV. The results show that the irradiation leads to four major damage effects on the surface layer of the AG‐80 resin, including the discharging, mass loss, degradation, and carbon enrichment. With increasing fluence to 1.05 × 1016 cm−2, the mass loss ratio increases gradually, and then tends to level off. The mass loss behavior can be attributed to a combined effect of the formation of gaseous radiolytic products and a degraded layer, the surface ablation due to discharging, and the skin carbon enrichment. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 177–184, 2006
Novel temperature‐responsive water‐soluble copolymers based on 2‐hydroxyethylacrylate and vinyl butyl ether and their interactions with poly(carboxylic acids)
Authors: Mun Grigoriy A. , Nurkeeva Zauresh S. , Akhmetkalieva Gulnara T. , Shmakov Sergey N. , Khutoryanskiy Vitaliy V. , Cheon Lee Sang , Park Kinam 
Published: November 2005

AbstractNovel water‐soluble amphiphilic copolymers have been synthesized by free radical copolymerization of 2‐hydroxyethylacrylate with vinyl butyl ether. In water these copolymers exhibit lower critical solution temperature, which depends on the content of hydrophobic vinyl butyl ether units. The interaction between these copolymers and poly(acrylic acid) or poly(methacrylic acid) in aqueous solutions results in formation of interpolymer complexes stabilized by hydrogen bonds and hydrophobic interactions. An increase in hydrophobicity of the copolymers leads to the enhancement of their complex formation ability with respect to poly(acrylic acid) and poly(methacrylic acid). Poly(methacrylic acid) forms stronger complexes with the copolymers when compared with poly(acrylic acid). The complexes exhibit dual sensitivity to pH‐ and temperature and this property may be easily adjusted regulating the strength of interaction. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 195–204, 2006
Chemical Vapor Deposition of Organosilicon Thin Films from Methylmethoxysilanes
Authors: Casserly Thomas B. , Gleason Karen K. 
Published: November 2005

AbstractSummary: Plasma enhanced chemical vapor deposition was used to deposit organosilicate glass (OSG) thin films from trimethylmethoxysilane, dimethyldimethoxysilane, and methyltrimethoxysilane. Depositions were performed from the pure OSG precursor, as well as from mixtures where either oxygen or hydrogen was added to the gas feed. These films were analyzed via Fourier transform infrared spectroscopy (FTIR), variable angle spectroscopic ellipsometry (VASE), and electrical measurements. Reactions involved in the deposition of OSG thin films from methylmethoxysilanes with oxygen are not selective and lead to the undesirable loss of methyl functionality. Reducing chemistry achieved with hydrogen addition is selective, with hydrogen atoms reacting preferentially with the methoxy groups creating silanol or siloxyl radicals. This selectively forms bonds networking through condensation reactions without sacrificing the “built‐in” alkyl content of the precursor. Low‐k OSG thin films from methylmethoxysilanes and hydrogen were deposited via a low power, W/FM from 10.0 to 10.5 J/g dependent upon OSG precursor, PECVD process resulting in material dielectric constants ranging from 2.84 to 3.18.Dielectric constant as a function of increasing methyl substitution in the silicon precursor (n) shown for discharges the pure precursor, and for the cases of gas mixtures with H2 and O2 (OMe≡methoxy, Me≡methyl).magnified imageDielectric constant as a function of increasing methyl substitution in the silicon precursor (n) shown for discharges the pure precursor, and for the cases of gas mixtures with H2 and O2 (OMe≡methoxy, Me≡methyl).
Prediction of transporter family from protein sequence by support vector machine approach
Authors: Lin H. H. , Han L. Y. , Cai C. Z. , Ji Z. L. , Chen Y. Z. 
Published: November 2005

AbstractTransporters play key roles in cellular transport and metabolic processes, and in facilitating drug delivery and excretion. These proteins are classified into families based on the transporter classification (TC) system. Determination of the TC family of transporters facilitates the study of their cellular and pharmacological functions. Methods for predicting TC family without sequence alignments or clustering are particularly useful for studying novel transporters whose function cannot be determined by sequence similarity. This work explores the use of a machine learning method, support vector machines (SVMs), for predicting the family of transporters from their sequence without the use of sequence similarity. A total of 10,636 transporters in 13 TC subclasses, 1914 transporters in eight TC families, and 168,341 nontransporter proteins are used to train and test the SVM prediction system. Testing results by using a separate set of 4351 transporters and 83,151 nontransporter proteins show that the overall accuracy for predicting members of these TC subclasses and families is 83.4% and 88.0%, respectively, and that of nonmembers is 99.3% and 96.6%, respectively. The accuracies for predicting members and nonmembers of individual TC subclasses are in the range of 70.7–96.1% and 97.6–99.9%, respectively, and those of individual TC families are in the range of 60.6–97.1% and 91.5–99.4%, respectively. A further test by using 26,139 transmembrane proteins outside each of the 13 TC subclasses shows that 90.4–99.6% of these are correctly predicted. Our study suggests that the SVM is potentially useful for facilitating functional study of transporters irrespective of sequence similarity. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Unique GMP‐binding site in Mycobacterium tuberculosis guanosine monophosphate kinase
Authors: Hible Guillaume , Christova Petya , Renault Louis , Seclaman Edward , Thompson Andrew , Girard Eric , Munier‐Lehmann Hélène , Cherfils Jacqueline 
Published: November 2005

AbstractBacterial nucleoside monophosphate (NMP) kinases, which convert NMPs to nucleoside diphosphates (NDP), are investigated as potential antibacterial targets against pathogenic bacteria. Herein, we report the biochemical and structural characterization of GMP kinase from Mycobacterium tuberculosis (GMPKMt). GMPKMt is a monomer with an unusual specificity for ATP as a phosphate donor, a lower catalytic efficiency compared with eukaryotic GMPKs, and it carries two redox‐sensitive cysteines in the central CORE domain. These properties were analyzed in the light of the high‐resolution crystal structures of unbound, GMP‐bound, and GDP‐bound GMPKMt. The latter structure was obtained in both an oxidized form, in which the cysteines form a disulfide bridge, and a reduced form which is expected to correspond to the physiological enzyme. GMPKMt has a modular domain structure as most NMP kinases. However, it departs from eukaryotic GMPKs by the unusual conformation of its CORE domain, and by its partially open LID and GMP‐binding domains which are the same in the apo‐, GMP‐bound, and GDP‐bound forms. GMPKMt also features a unique GMP binding site which is less close‐packed than that of mammalian GMPKs, and in which the replacement of a critical tyrosine by a serine removes a catalytic interaction. In contrast, the specificity of GMPKMt for ATP may be a general feature of GMPKs because of an invariant structural motif that recognizes the adenine base. Altogether, differences in domain dynamics and GMP binding between GMPKMt and mammalian GMPKs should reveal clues for the design of GMPKMt‐specific inhibitors. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Target selection and deselection at the Berkeley Structural Genomics Center
Authors: Chandonia John‐Marc , Kim Sung‐Hou , Brenner Steven E. 
Published: November 2005

AbstractAt the Berkeley Structural Genomics Center (BSGC), our goal is to obtain a near‐complete structural complement of proteins in the minimal organisms Mycoplasma genitalium and M. pneumoniae, two closely related pathogens. Current targets for structure determination have been selected in six major stages, starting with those predicted to be most tractable to high throughput study and likely to yield new structural information. We report on the process used to select these proteins, as well as our target deselection procedure. Target deselection reduces experimental effort by eliminating targets similar to those recently solved by the structural biology community or other centers. We measure the impact of the 69 structures solved at the BSGC as of July 2004 on structure prediction coverage of the M. pneumoniae and M. genitalium proteomes. The number of Mycoplasma proteins for which the fold could first be reliably assigned based on structures solved at the BSGC (24 M. pneumoniae and 21 M. genitalium) is approximately 25% of the total resulting from work at all structural genomics centers and the worldwide structural biology community (94 M. pneumoniae and 86 M. genitalium) during the same period. As the number of structures contributed by the BSGC during that period is less than 1% of the total worldwide output, the benefits of a focused target selection strategy are apparent. If the structures of all current targets were solved, the percentage of M. pneumoniae proteins for which folds could be reliably assigned would increase from approximately 57% (391 of 687) at present to around 80% (550 of 687), and the percentage of the proteome that could be accurately modeled would increase from around 37% (254 of 687) to about 64% (438 of 687). In M. genitalium, the percentage of the proteome that could be structurally annotated based on structures of our remaining targets would rise from 72% (348 of 486) to around 76% (371 of 486), with the percentage of accurately modeled proteins would rise from 50% (243 of 486) to 58% (283 of 486). Sequences and data on experimental progress on our targets are available in the public databases TargetDB and PEPCdb. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Misfolding of the amyloid β‐protein: A molecular dynamics study
Authors: Flöck Dagmar , Colacino Stefano , Colombo Giorgio , Di Nola Alfredo 
Published: November 2005

AbstractAmyloid β‐proteins spontaneously aggregate and build plaques in the brains of Alzheimer's disease patients. The polypeptide has been the subject of extensive in vitro and computational research. Still, the pathway to aggregational forms and their exact conformations remain largely unclear. Here we present an extensive molecular dynamics approach simulating the protein in various temperatures, pH conditions, and with different charge states of the N‐ and C‐termini, thus exploring the conformational space of the protein at large. Our results show that the protein is able to sample different conformations, many of which are rich in β structure content, and all characterized by a rapid loss of helix 1 that converts into a π‐helix, while helix 2 samples random and β‐rich structures. Moreover, a hydrophobic cluster is observed involving Val18, Phe19, Ala21, and Gly25. The results are carefully compared with recent NMR and spectroscopic data, and are in global agreement with the experimental findings. Proteins 2006. © 2005 Wiley‐Liss, Inc.
B. subtilis ykuD protein at 2.0 Å resolution: Insights into the structure and function of a novel, ubiquitous family of bacterial enzymes
Authors: Bielnicki Jakub , Devedjiev Yancho , Derewenda Urszula , Dauter Zbigniew , Joachimiak Andrzej , Derewenda Zygmunt S. 
Published: November 2005

AbstractThe crystal structure of the product of the Bacillus subtilis ykuD gene was solved by the multiwavelength anomalous dispersion (MAD) method and refined using data to 2.0 Å resolution. The ykuD protein is a representative of a distinctly prokaryotic and ubiquitous family found among both pathogenic and nonpathogenic Gram‐positive and Gram‐negative bacteria. The deduced amino acid sequence reveals the presence of an N‐terminal LysM domain, which occurs among enzymes involved in cell wall metabolism, and a novel, putative catalytic domain with a highly conserved His/Cys‐containing motif of hitherto unknown structure. As the wild‐type protein did not crystallize, a double mutant was designed (Lys117Ala/Gln118Ala) to reduce excess surface conformational entropy. As expected, the structure of the LysM domain is similar to the NMR structure reported for an analogous domain from Escherichia coli murein transglycosylase MltD. The molecular model also shows that the 112‐residue‐long C‐terminal domain has a novel tertiary fold consisting of a β‐sandwich with two mixed sheets, one containing five strands and the other, six strands. The two β‐sheets form a cradle capped by an α‐helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of the ykuD family may play an important role in cell wall biology. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Dynamics of the trimeric AcrB transporter protein inferred from a B‐factor analysis of the crystal structure
Authors: Lu W.C. , Wang C.Z. , Yu E.W. , Ho K.M. 
Published: November 2005

AbstractThe Escherichia coli AcrB multidrug transporter recognizes a wide range of toxic chemicals and actively extrudes them from cells. The molecular basis of multidrug transport in AcrB remains unknown. Herein, we describe normal mode analyses to study important regions for drug recognition and extrusion in this transporter. Based on the X‐ray structure of AcrB, an elastic network model has been able to correct errors arising from crystal imperfection in the experimental B‐factors. The results allow us to understand the functional dynamics of this membrane protein. It is expected that this technique can be applied to other membrane proteins with known structures. Proteins 2006. © 2005 Wiley‐Liss, Inc.
SimFold energy function for de novo protein structure prediction: Consensus with Rosetta
Authors: Fujitsuka Yoshimi , Chikenji George , Takada Shoji 
Published: November 2005

AbstractPredicting protein tertiary structures by in silico folding is still very difficult for proteins that have new folds. Here, we developed a coarse‐grained energy function, SimFold, for de novo structure prediction, performed a benchmark test of prediction with fragment assembly simulations for 38 test proteins, and proposed consensus prediction with Rosetta. The SimFold energy consists of many terms that take into account solvent‐induced effects on the basis of physicochemical consideration. In the benchmark test, SimFold succeeded in predicting native structures within 6.5 Å for 12 of 38 proteins; this success rate was the same as that by the publicly available version of Rosetta (ab initio version 1.2) run with default parameters. We investigated which energy terms in SimFold contribute to structure prediction performance, finding that the hydrophobic interaction is the most crucial for the prediction, whereas other sequence‐specific terms have weak but positive roles. In the benchmark, well‐predicted proteins by SimFold and by Rosetta were not the same for 5 of 12 proteins, which led us to introduce consensus prediction. With combined decoys, we succeeded in prediction for 16 proteins, four more than SimFold or Rosetta separately. For each of 38 proteins, structural ensembles generated by SimFold and by Rosetta were qualitatively compared by mapping sampled structural space onto two dimensions. For proteins of which one of the two methods succeeded and the other failed in prediction, the former had a less scattered ensemble located around the native. For proteins of which both methods succeeded in prediction, often two ensembles were mixed up. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Pressure effect on the stability and the conformational dynamics of the D‐Galactose/D‐Glucose‐binding protein from Escherichia coli
Authors: Marabotti Anna , Herman Petr , Staiano Maria , Varriale Antonio , de Champdoré Marcella , Rossi Mosè , Gryczynski Zygmunt , D'Auria Sabato 
Published: November 2005

AbstractThe effect of the pressure on the structure and stability of the D‐Galactose/D‐Glucose binding protein (GGBP) from Escherichia coli was studied by steady‐state and time‐resolved fluorescence spectroscopy, and the ability of glucose ligand to stabilize the GGBP structure was also investigated. Steady‐state fluorescence experiments showed a marked quenching of fluorescence emission of GGBP in the absence of glucose. Instead, the presence of glucose seems to stabilize the structure of GGBP at low and moderate pressure values. Time‐resolved fluorescence measurements showed that the GGBP τmean in the absence of glucose varies significantly up to 600 bar, while in the presence of the ligand it is almost unaffected by pressure increase up to 600 bar. The effect of the pressure on GGBP was also studied by molecular dynamics simulations. The simulation data support the spectroscopic results and confirm that the presence of glucose is able to contrast the negative effects of pressure on the protein structure. Taken together, the spectroscopic and computer simulation studies suggest that at pressure values up to 2000 bar the structure of GGBP in the absence of glucose remains folded, but a significant perturbation of the protein secondary structures can be detected. The binding of glucose reduces the negative effect of pressure on protein structure and confers protection from perturbation especially at moderate pressure values. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Structure and mechanism of the farnesyl diphosphate synthase from Trypanosoma cruzi: Implications for drug design
Authors: Gabelli Sandra B. , McLellan Jason S. , Montalvetti Andrea , Oldfield Eric , Docampo Roberto , Amzel L. Mario 
Published: November 2005

AbstractTypanosoma cruzi, the causative agent of Chagas disease, has recently been shown to be sensitive to the action of the bisphosphonates currently used in bone resorption therapy. These compounds target the mevalonate pathway by inhibiting farnesyl diphosphate synthase (farnesyl pyrophosphate synthase, FPPS), the enzyme that condenses the diphosphates of C5 alcohols (isopentenyl and dimethylallyl) to form C10 and C15 diphosphates (geranyl and farnesyl). The structures of the T. cruzi FPPS (TcFPPS) alone and in two complexes with substrates and inhibitors reveal that following binding of the two substrates and three Mg2+ ions, the enzyme undergoes a conformational change consisting of a hinge‐like closure of the binding site. In this conformation, it would be possible for the enzyme to bind a bisphosphonate inhibitor that spans the sites usually occupied by dimethylallyl diphosphate (DMAPP) and the homoallyl moiety of isopentenyl diphosphate. This observation may lead to the design of new, more potent anti‐trypanosomal bisphosphonates, because existing FPPS inhibitors occupy only the DMAPP site. In addition, the structures provide an important mechanistic insight: after its formation, geranyl diphosphate can swing without leaving the enzyme, from the product site to the substrate site to participate in the synthesis of farnesyl diphosphate. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Limited validity of group additivity for the folding energetics of the peptide group
Authors: Avbelj Franc , Baldwin Robert L. 
Published: November 2005

AbstractThe principle of group additivity is a standard feature of analyses of the energetics of protein folding, but it is known that it may not always be valid for the polar peptide group. The neighboring residue effect shows that group additivity is not strictly valid for a heteropeptide. We show here that group additivity fails seriously for peptide groups close to either peptide end, even for a homopeptide that has blocked end groups with no formal charges involved. The failure of group additivity is caused by the electrostatic character of the solvation of peptide polar groups and is illustrated with values of the electrostatic solvation free energy (ESF) calculated by DelPhi. Solvation free energies and enthalpies are known experimentally for monoamides and are often used to model the solvation of peptide groups, but ESF results show that monoamide values are very different from those of peptide groups. A main cause of the difference is that peptide solvation depends on the dipole–dipole interactions made between adjacent peptide groups, which vary with peptide conformation. Ligands that interact with the peptide backbone by an electrostatic mechanism could show a similar peptide end effect, and hydrogen exchange results from the literature confirm that exchange rates are position‐dependent close to peptide ends. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Natively unfolded regions of the vertebrate fibrinogen molecule
Authors: Doolittle Russell F. , Kollman Justin M. 
Published: November 2005

AbstractAlthough it has long been realized that a large portion of the fibrinogen α chain has little if any defined structure, the physiological significance of this flexible appendage remains mysterious. Proteins 2005. © 2005 Wiley‐Liss, Inc.