bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast evaluation of scaled opposite spin second‐order Møller–Plesset correlation energies using auxiliary basis expansions and exploiting sparsity
Authors: Jung Yousung , Shao Yihan , Head‐Gordon Martin 
Published: April 2007

AbstractThe scaled opposite spin Møller–Plesset method (SOS‐MP2) is an economical way of obtaining correlation energies that are computationally cheaper, and yet, in a statistical sense, of higher quality than standard MP2 theory, by introducing one empirical parameter. But SOS‐MP2 still has a fourth‐order scaling step that makes the method inapplicable to very large molecular systems. We reduce the scaling of SOS‐MP2 by exploiting the sparsity of expansion coefficients and local integral matrices, by performing local auxiliary basis expansions for the occupied‐virtual product distributions. To exploit sparsity of 3‐index local quantities, we use a blocking scheme in which entire zero‐rows and columns, for a given third global index, are deleted by comparison against a numerical threshold. This approach minimizes sparse matrix book‐keeping overhead, and also provides sufficiently large submatrices after blocking, to allow efficient matrix–matrix multiplies. The resulting algorithm is formally cubic scaling, and requires only moderate computational resources (quadratic memory and disk space) and, in favorable cases, is shown to yield effective quadratic scaling behavior in the size regime we can apply it to. Errors associated with local fitting using the attenuated Coulomb metric and numerical thresholds in the blocking procedure are found to be insignificant in terms of the predicted relative energies. A diverse set of test calculations shows that the size of system where significant computational savings can be achieved depends strongly on the dimensionality of the system, and the extent of localizability of the molecular orbitals. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007
Beiträge zur Theorie des mit einer euklidischen Schraubung verknüpften kubischen Nullsystems
Authors: Bereis Rudolf , Brauner Heinrich 
Published: April 2007

AbstractMit jeder euklidischen Schraubung ist eine gewisse Punkt‐Ebenenverwandtschaft 3. Grades verknüpft, deren allgemeine Theorie schon vielfach betrachtet wurde. Dieser Beitrag zur Theorie dieser Verwandtschaft, in dem vor allem Methoden der konstruktiven Geometrie Verwendung finden, liefert eine genaue Untersuchung der einer geraden Punktreihe bzw. einem Ebenenbüschel sowie gewissen Strahlmannigfaltigkeiten entsprechenden Gebilde.
Solvent effects on one‐bond BLi coupling constants in boryllithium compounds
Authors: Del Bene Janet E. , Elguero José 
Published: April 2007

AbstractEOM‐CCSD 11B7Li coupling constants and B chemical shifts have been computed for Li‐diazaborole and its complexes with one H2O or FLi molecule. BLi coupling constants for a model compound H2BLi and its complexes with up to 4 H2O or FLi molecules have also been obtained in an attempt to resolve discrepancies between the computed values of these properties for isolated Li‐diazaborole and experimentally determined values for boryllithium in a THF solution. The presence of solvent molecules increases the ion‐pair character of the BLi bond, with the result that 1J(BLi) decreases systematically as the basicity and the number of solvent molecules increases. In the presence of even a single solvent molecule, the boron chemical shift for Li‐diazaborole increases, and approaches the experimental value. The computed results emphasize the role of the solvent in determining these NMR properties. Copyright © 2007 John Wiley & Sons, Ltd.
Structural determination of seven new triterpenoids from Kadsura heteroclita by NMR techniques
Authors: Wang Wei , Xu Zhengren , Yang Min , Liu Rongxia , Wang Weixing , Liu Peng , Guo Dean 
Published: April 2007

AbstractSeven new triterpenoids, namely heteroclitalactones G–M (1–7), were isolated from the ethanol extract of the stems of Kadsura heteroclita. Structures of these compounds were characterized by extensive 1D and 2D NMR spectroscopic analyses. Copyright © 2007 John Wiley & Sons, Ltd.
Structural determination of a new 2(3 → 20)abeotaxane with an unusual 13β‐substitution pattern and a new 6/8/6‐ring taxane from Taxus cuspidata
Authors: Huo Changhong , Su Xiaohui , Li Xing , Zhang Xiping , Li Cunfang , Wang Yufang , Shi Qingwen , Kiyota Hiromasa 
Published: April 2007

AbstractA new 2(3 → 20)abeotaxane with an unusual 13β‐substitution pattern and a new 6/8/6‐ring taxane were isolated from the methanol extract of the needles of Taxus cuspidata. The structures were established as 2α,7β‐diacetoxy‐5α,10β,13β‐trihydroxy‐2(3 → 20)abeotaxa‐4(20), 11‐dien‐9‐one (1) and 2α,5α,7β,9α,13α‐pentahydroxy‐10β‐acetoxytaxa‐4(20),11‐diene (2) on the basis of 1D and 2D NMR spectral data and high‐resolution FAB‐MS analyses. Copyright © 2007 John Wiley & Sons, Ltd.
A proteomic study of the major allergens from yellow jacket venoms
Authors: Kolarich Daniel , Loos Andreas , Léonard Renaud , Mach Lukas , Marzban Gorji , Hemmer Wolfgang , Altmann Friedrich 
Published: April 2007

AbstractThe venoms of stinging insects belong to the most dangerous allergen sources and can cause fatal anaphylactic reactions. Reliable prediction of a patient's risk to anaphylactic reactions is vital, and diagnosis requires the knowledge of the relevant allergens. Recently, a new hyaluronidase ‐like glycoprotein from Vespula vulgaris (Ves v 2b) was identified. This led us to investigate hyaluronidases and also other major allergens from V. germanica and four additional Vespula species. By MALDI‐Q‐TOF‐MS, the new hyaluronidase‐like protein was shown to be the major component of the 43‐kDa band in all Vespula species studied. LC‐ESI‐Q‐TOF‐MS/MS sequencing of Ves g 2a and Ves g 2b facilitated the cloning of their cDNA. Ves v 2b and Ves g 2b turned out to be essentially identical on protein level. Whereas the less abundant “a” form displayed enzymatic activity, the new “b” homologue did not. This is probably caused by amino acid exchanges in the active site, and it raises questions about the physiological role of this protein. Sequence comparisons by MS/MS of antigen 5 and phospholipases from V. vulgaris, germanica, maculifrons, pensylvanica, flavopilosa and squamosa revealed the latter as a taxonomic outlier and led to the discovery of several not previously reported amino acid differences.
The phosphorylation pattern of bovine heart complex I subunits
Authors: Palmisano Giuseppe , Sardanelli Anna Maria , Signorile Anna , Papa Sergio , Larsen Martin R. 
Published: April 2007

AbstractThe phosphoproteome of bovine heart complex I of the respiratory chain has been analysed with a procedure based on nondenaturing gel electrophoretic separation of complex I from small quantities of mitochondria samples, in‐gel digestion, in combination with phosphopeptide enrichment by titanium dioxide and MS. The results, complemented by analyses of purified samples of complex I, showed phosphorylation of five subunits of the complex, 42 kDa (human gene NDUFA10), ESSS, B14.5a (human gene NDUFA7), B14.5b (human gene NDUFC2) and B16.6 (GRIM‐19). MS also revealed the presence of phosphorylated programmed cell death protein 8(AIF) in native and purified samples of complex I analysed. The possible physiological relevance of these findings is discussed.
Proteomic analysis of pancreatic endocrine tumor cell lines treated with the histone deacetylase inhibitor trichostatin A
Authors: Cecconi Daniela , Donadelli Massimo , Rinalducci Sara , Zolla Lello , Scupoli Maria Teresa , Scarpa Aldo , Palmieri Marta , Righetti Pier Giorgio 
Published: April 2007

AbstractEffects of the histone‐deacetylases inhibitor trichostatin A (TSA) on the growth of three different human pancreatic endocrine carcinoma cell lines (CM, BON, and QGP‐1) have been assessed via dosage‐dependent growth inhibition curves. TSA determined strong inhibition of cell growth with similar IC50 values for the different cell lines: 80.5 nM (CM), 61.6 nM (BON), and 86 nM (QGP‐1), by arresting the cell cycle in G2/M phase and inducing apoptosis. 2DE and nano‐RP‐HPLC‐ESI‐MS/MS analysis revealed 34, 33, and 38 unique proteins differentially expressed after TSA treatment in the CM, BON, and QGP‐1 cell lines, respectively. The most important groups of modulated proteins belong to cell proliferation, cell cycle, and apoptosis classes (such as peroxiredoxins 1 and 2, the diablo protein, and HSP27). Other proteins pertain to processes such as regulation of gene expression (nucleophosmin, oncoprotein dek), signal transduction (calcium‐calmodulin), chromatin, and cytoskeleton organization (calgizzarin, dynein, and lamin), RNA splicing (nucleolin, HNRPC), and protein folding (HSP70). The present data are in agreement with previous proteomic analyses performed on pancreatic ductal carcinoma cell lines (Cecconi, D. et al.., Electrophoresis 2003; Cecconi, D. et al., J. Proteome Res. 2005) and place histone‐deacetylases inhibitors among the potentially most powerful drugs for the treatment of pancreatic tumors.
Proton‐conductive membranes based on blends of polyimides
Authors: Okazaki Yasuhide , Nagaoka Shoji , Kawakami Hiroyoshi 
Published: April 2007

AbstractWe prepared novel proton‐conductivity membranes based on blends of sulfonated polyimides. The blend membranes were prepared from a sulfonated homopolyimide and a sulfonated copolyimide with a solvent‐casting method. The proton conductivities of the blend membranes were measured as functions of the temperature with four‐point‐probe electrochemical impedance spectroscopy. The conductivity of the membranes strongly depended on the sulfonated homopolyimide content and increased with an increase in the content. The proton conductivity of all the blended membranes indicated a higher value than that determined in Nafion at 80 °C, and this may mean that the proton transfer in the blend membranes is responsible for the ionic channels induced by the hydrophobic and hydrophilic domains. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 1325–1332, 2007
Elevated haptoglobin level of cerebrospinal fluid in Guillain‐Barré syndrome revealed by proteomics analysis
Authors: Chang Kuo‐Hsuan , Lyu Rong‐Kuo , Tseng Mu‐Yun , Ro Long‐Sun , Wu Yih‐Ru , Chang Hong‐Shiu , Hsu Wen‐Chuin , Kuo Hung‐Chou , Huang Chin‐Chang , Chu Chun‐Che , Hsieh Sen‐Yung , Chen Chiung‐Mei 
Published: April 2007

AbstractGuillain‐Barré Syndrome (GBS) is a rare autoimmune inflammatory polyneuropathy with a high risk of respiratory failure and unclear pathogenesis. Currently, there are no valid biomarkers for diagnosis of GBS. We used 2‐DE and MS to analyze the protein profiles of five pairs of cerebrospinal fluid (CSF) samples of the GBS patients and the patient controls. Three proteins (orosomucoid, haptoglobin and apolipoprotein A‐IV) were up‐regulated, and two proteins (prostaglandin D2 synthase and transthyretin) were down‐regulated in the CSF of the GBS patients. The CSF haptoglobin level, quantified by enzyme‐linked immunosorbent assay, was significantly higher in the GBS patients (12.44 ± 2.70 μg/mL) compared to the chronic inflammatory demyelinating polyradiculoneuropathy (2.82 ± 0.83 μg/mL), viral meningitis (3.57 ± 0.97 μg/mL) and control patients (1.44 ± 0.35 μg/mL, p<0.05). This study indicated that protein profile analysis using a combination of 2‐DE and MS provides an effective strategy for elucidating the pathogenesis and identifying potential CSF biomarkers for GBS. The raised intrathecal synthesis of haptoglobin specifically only in GBS patients, but not in patients with other neurological diseases examined, provides evidence of central nervous system involvement in GBS, and may be used as a potential diagnostic marker for GBS.
Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites
Authors: Kawabata Takeshi , Go Nobuhiro 
Published: April 2007

AbstractOne of the simplest ways to predict ligand binding sites is to identify pocket‐shaped regions on the protein surface. Many programs have already been proposed to identify these pocket regions. Examination of their algorithms revealed that a pocket intrinsically has two arbitrary properties, “size” and “depth”. We proposed a new definition for pockets using two explicit adjustable parameters that correspond to these two arbitrary properties. A pocket region is defined as a space into which a small probe can enter, but a large probe cannot. The radii of small and large probe spheres are the two parameters that correspond to the “size” and “depth” of the pockets, respectively. These values can be adjusted individual putative ligand molecule. To determine the optimal value of the large probe spheres radius, we generated pockets for thousands of protein structures in the database, using several size of large probe spheres, examined the correspondence of these pockets with known binding site positions. A new measure of shallowness, a minimum inaccessible radius, Rinaccess, indicated that binding sites of coenzymes are very deep, while those for adenine/guanine mononucleotide have only medium shallowness and those for short peptides and oligosaccharides are shallow. The optimal radius of large probe spheres was 3–4 Å for the coenzymes, 4 Å for adenine/guanine mononucleotides, and 5 Å or more for peptides/oligosaccharides. Comparison of our program with two other popular pocket‐finding programs showed that our program had a higher performance of detecting binding pockets, although it required more computational time. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A 1.55 Å resolution X‐ray crystal structure of HEF2/ERH and insights into its transcriptional and cell‐cycle interaction networks
Authors: Jin Tengchuan , Guo Feng , Serebriiskii Ilya G , Howard Andrew , Zhang Yu‐Zhu 
Published: April 2007

AbstractFunctional complementation screens can identify known or novel proteins with important intracellular activities. We have isolated human enhancer of filamentation 2 (HEF2) in a screen to find human genes that promote pseudohyphal growth in budding yeast. HEF2 is identical to enhancer of rudimentary homolog (ERH), a highly conserved protein of 104 amino acids. In silico protein‐interaction mapping implies that HEF2/ERH interacts with transcription factors, cell‐cycle regulators, and other proteins shown to enhance filamentous growth in S. cerevisiae, suggesting a context for studies of HEF2/ERH function. To provide a mechanistic basis to study of HEF2/ERH, we have determined the crystal structure of HEF2/ERH at 1.55 Å. The crystal asymmetric unit contains a HEF2/ERH monomer. The two monomers of the physiological dimer are related by the y, x, –z crystal symmetric operation. The HEF2/ERH structure is characterized by a novel α + β fold, a four‐strand antiparallel β‐sheet with three α‐helixes on one side of the sheet. The β‐sheets from the two monomers together constitute a pseudo‐β‐barrel, and form the center of the functional HEF2/ERH dimer, with a cavity channel at the dimer interface. Docking of this structure to the HEF2/ERH partner protein DCOH/PCD suggests that HEF2/ERH may regulate the oligomeric state of this protein. These data suggest that HEF2/ERH may be an important transcription regulator that also functions in the control of cell‐cycle progression. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Benchmarking of TASSER in the ab initio limit
Authors: Borreguero Jose M. , Skolnick Jeffrey 
Published: April 2007

AbstractA significant number of protein sequences in a given proteome have no obvious evolutionarily related protein in the database of solved protein structures, the PDB. Under these conditions, ab initio or template‐free modeling methods are the sole means of predicting protein structure. To assess its expected performance on proteomes, the TASSER structure prediction algorithm is benchmarked in the ab initio limit on a representative set of 1129 nonhomologous sequences ranging from 40 to 200 residues that cover the PDB at 30% sequence identity and which adopt α, α + β, and β secondary structures. For sequences in the 40–100 (100–200) residue range, as assessed by their root mean square deviation from native, RMSD, the best of the top five ranked models of TASSER has a global fold that is significantly close to the native structure for 25% (16%) of the sequences, and with a correct identification of the structure of the protein core for 59% (36%). In the absence of a native structure, the structural similarity among the top five ranked models is a moderately reliable predictor of folding accuracy. If we classify the sequences according to their secondary structure content, then 64% (36%) of α, 43% (24%) of α + β, and 20% (12%) of β sequences in the 40–100 (100–200) residue range have a significant TM‐score (TM‐score ≥0.4). TASSER performs best on helical proteins because there are less secondary structural elements to arrange in a helical protein than in a beta protein of equal length, since the average length of a helix is longer than that of a strand. In addition, helical proteins have shorter loops and dangling tails. If we exclude these flexible fragments, then TASSER has similar accuracy for sequences containing the same number of secondary structural elements, irrespective of whether they are helices and/or strands. Thus, it is the effective configurational entropy of the protein that dictates the average likelihood of correctly arranging the secondary structure elements. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Drug block of the hERG potassium channel: Insight from modeling
Authors: Stansfeld Phillip J. , Gedeck Peter , Gosling Martin , Cox Brian , Mitcheson John S. , Sutcliffe Michael J. 
Published: April 2007

AbstractMany commonly used, structurally diverse, drugs block the human ether‐a‐go‐go‐related gene (hERG) K+channel to cause acquired long QT syndrome, which can lead to sudden death via lethal cardiac arrhythmias. This undesirable side effect is a major hurdle in the development of safe drugs. To gain insight about the structure of hERG and the nature of drug block we have produced structural models of the channel pore domain, into each of which we have docked a set of 20 hERG blockers. In the absence of an experimentally determined three‐dimensional structure of hERG, each of the models was validated against site‐directed mutagenesis data. First, hERG models were produced of the open and closed channel states, based on homology with the prokaryotic K+channel crystal structures. The modeled complexes were in partial agreement with the mutagenesis data. To improve agreement with mutagenesis data, a KcsA‐based model was refined by rotating the four copies of the S6 transmembrane helix half a residue position toward the C‐terminus, so as to place all residues known to be involved in drug binding in positions lining the central cavity. This model produces complexes that are consistent with mutagenesis data for smaller, but not larger, ligands. Larger ligands could be accommodated following refinement of this model by enlarging the cavity using the inherent flexibility about the glycine hinge (Gly648) in S6, to produce results consistent with the experimental data for the majority of ligands tested. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Structure networks of E. coli glutaminyl‐tRNA synthetase: Effects of ligand binding
Authors: Sathyapriya R. , Vishveshwara Saraswathi 
Published: April 2007

AbstractIt is well known that proteins undergo backbone as well as side chain conformational changes upon ligand binding, which is not necessarily confined to the active site. Both the local and the global conformational changes brought out by ligand‐binding have been extensively studied earlier. However, the global changes have been reported mainly at the protein backbone level. Here we present a method that explicitly takes into account the side chain interactions, yet providing a global view of the ligand‐induced conformational changes. This is achieved through the analysis of Protein Structure Networks (PSN), constructed from the noncovalent side chain interactions in the protein. Here, E. coli Glutaminyl‐tRNA synthetase (GlnRS) in the ligand‐free and different ligand‐bound states is used as a case study to assess the effect of binding of tRNA, ATP, and the amino acid Gln to GlnRS. The PSNs are constructed on the basis of the strength of noncovalent interactions existing between the side chains of amino acids. The parameters like the size of the largest cluster, edge to node ratio, and the total number of hubs are used to quantitatively assess the structure network changes. These network parameters have effectively captured the ligand‐induced structural changes at a global structure network level. Hubs, the highly connected amino acids, are also identified from these networks. Specifically, we are able to characterize different types of hubs based on the comparison of structure networks of the GlnRS system. The differences in the structure networks in both the presence and the absence of the ligands are reflected in these hubs. For instance, the characterization of hubs that are present in both the ligand‐free and all the ligand‐bound GlnRS (the invariant hubs) might implicate their role in structural integrity. On the other hand, identification of hubs unique to a particular ligand‐bound structure (the exclusive hubs) not only highlights the structural differences mediated by ligand‐binding at the structure network level, but also highlights significance of these amino acids hubs in binding to the ligand and catalyzing the biochemical function. Further, the hubs identified from this study could be ideal targets for mutational studies to ascertain the ligand‐induced structure–function relationships in E. coli GlnRS. The formalism used in this study is simple and can be applied to other protein‐ligands in general to understand the allosteric changes mediated by the binding of ligands. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Energy structure and micromechanism of photo‐electromotive force effect in V‐doped CdTe crystals
Authors: Gnatenko Yu. P. , Brodyn M. S. , Faryna I. O. , Bukivskij P. M. , Shigiltchoff O. A. , Furyer M. S. , Gamernyk R. V. , Kukhtarev N. , Kukhtareva T. 
Published: April 2007

AbstractFor the first time photo‐electromotive force (photo‐EMF) measurements were carried out for CdTe crystals doped with V atoms as a result of the photogeneration of carriers from deep impurity centers to the conduction band. Tilted geometry was applied that allowed two‐dimensional monitoring of the vi‐ bration source. The CdTe:V crystals were excited by a He–Ne laser with a wavelength of 1.15 μm (ħω = 1.08 eV) and P = 2 mW. The mechanism of the appearance of the holographic current in the CdTe:V crystals taking into account real defect structure was proposed. The frequency dependence of the ac photo‐EMF (holographic) current for the CdTe:V crystals was measured. It was shown that a low cut‐off frequency for a laser intensity I = 0.2 mW/mm2 equals 6.0 kHz, which corresponds to a response time of 26 μs. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)