bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphoinositide 3‐kinase acts through RAC and Cdc42 during agrin‐induced acetylcholine receptor clustering
Authors: Nizhynska Viktoria , Neumueller Ralph , Herbst Ruth 
Published: March 2007

AbstractThe formation of the neuromuscular junction (NMJ) is regulated by the nerve‐derived heparan sulfate proteoglycan agrin and the muscle‐specific kinase MuSK. Agrin induces a signal transduction pathway via MuSK, which promotes the reorganization of the postsynaptic muscle membrane. Activation of MuSK leads to the phosphorylation and redistribution of acetylcholine receptors (AChRs) and other postsynaptic proteins to synaptic sites. The accumulation of high densities of AChRs at postsynaptic regions represents a hallmark of NMJ formation and is required for proper NMJ function. Here we show that phosphoinositide 3‐kinase (PI3‐K) represents a component of the agrin/MuSK signaling pathway. Muscle cells treated with specific PI3‐K inhibitors are unable to form full‐size AChR clusters in response to agrin and AChR phosphorylation is reduced. Moreover, agrin‐induced activation of Rac and Cdc42 is impaired in the presence of PI3‐K inhibitors. PI3‐K is localized to the postsynaptic muscle membrane consistent with a role during agrin/MuSK signaling. These results put PI3‐K downstream of MuSK as regulator of AChR phosphorylation and clustering. Its role during agrin‐stimulated Rac and Cdc42 activation suggests a critical function during cytoskeletal reorganizations, which lead to the redistribution of actin‐anchored AChRs. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007.
Protein synthesis in distal axons is not required for axon growth in the embryonic spinal cord
Authors: Blackmore Murray , Letourneau Paul C. 
Published: March 2007

AbstractIt is now well established that new proteins are synthesized in the distal segments of elongating axons, where they may play an essential role in some guidance decisions. It remains unclear, however, whether distal protein synthesis also plays an essential role in axon growth per se. Previous in vitro experiments have shown that blocking protein synthesis in distal axons has no effect on the rate of axonal advance. However, because these experiments were performed in vitro and over a relatively short time period, the role of distal protein synthesis over longer periods and in a native tissue environment remained untested. Here, we tested whether protein synthesis in distal axons plays an essential role in the elongation of descending axons in the embryonic spinal cord. We developed an in situ model of the brainstem‐spinal projection of the embryonic chick, and developed a split‐chamber method in which inhibitors of proteins synthesis could be applied independently to cell bodies in the brainstem or to distal axons in the spinal cord. When protein synthesis was blocked in distal axons, axon growth remained robust for 2 days, which is the length of the experiment. However, when protein synthesis was blocked only in the brainstem, axonal elongation in the spinal cord ceased within 6 h. These data showed that protein synthesis in the distal axon is not essential to continue the advance of axons. Rather, essential proteins are synthesized more proximally and then transported rapidly to the distal axon. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007.
Supramolecular Helical Architectures Dictated by Folded and Extended Conformations of the Amino Acid in Ternary CuII/Diamine/Racemic Amino Acid Complexes
Authors: Subramanian Palani Sivagnana , Suresh Eringathodi , Casella Luigi 
Published: March 2007

AbstractThe ternary CuII complexes [Cu(D,L‐phe)(bpy)]·(ClO4) (1), [Cu(D,L‐phe)(phen)(H2O)]·ClO4·H2O (2), and [Cu(L‐phe)(bpy)(H2O)]·ClO4·H2O (3) (bpy = 2,2′‐bipyridine, phen = 1,10‐phenanthroline) adopt helical structures in the crystal state, as determined by an X‐ray structural analysis. The supramolecular helical assembly of these complexes was also investigated by single‐crystal X‐ray crystallography. The complexes derived from racemic amino acids (1 and 2) undergo spontaneous resolution in the solid state to form separate helical chains of the ternary complex that carry a single enantiomer of the amino acid. In the case of complex 1, the two helical chains resulting from the L‐ and D‐phe complexes bear opposite chirality, which means that the bulk crystalline sample is racemic. In contrast, the two helical chains generated by L‐ and D‐phe complexes in 2 have the same twist and pack together in a right‐handed assembly. The (P)/(M) handedness of the helical chains is dictated by the conformational chirality (λ/δ) of the chelate rings of the D/L‐aminoacids.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
Purines Bearing Phenanthroline or Bipyridine Ligands and Their RuII Complexes in Position 8 as Model Compounds for Electrochemical DNA Labeling – Synthesis, Crystal Structure, Electrochemistry, Quantum Chemical Calculations, Cytostatic and Antiviral Activity
Authors: Vrábel Milan , Hocek Michal , Havran Luděk , Fojta Miroslav , Votruba Ivan , Klepetářová Blanka , Pohl Radek , Rulíšek Lubomír , Zendlová Lucie , Hobza Pavel , Shih I‐hung , Mabery Eric , Mackman Richard 
Published: March 2007

AbstractA series of ethynyl‐ or (4‐boronophenyl)bipyridines and‐phenanthrolines were prepared as versatile building blocks for attachment of bidentate N‐ligands to other molecules via cross‐coupling reactions. Their complexation with Ru(bpy)2Cl2 gave the corresponding RuII complexes. 9‐Benzyladenine derivatives bearing the bipyridine or phenanthroline complexes in position 8, attached via a conjugate acetylene or phenylene linker were prepared by cross‐coupling reactions of the ethynyl‐ or 4‐boronophenylbipyridines and ‐phenanthrolines with 9‐benzyl‐8‐bromoadenine. Their complexation with Ru(bpy)2Cl2 afforded the corresponding Ru complexes as model compounds for electrochemical DNA labeling. The same compounds were also prepared directly by cross‐coupling of 9‐benzyl‐8‐bromoadenine with Ru complexes of the alkynes and boronic acids. Both approaches are compared in terms of potential applications for labeling of nucleic acids. The crystal structures of two Ru complexes were determined by X‐ray diffraction. The electrochemistry of the model purines bearing the phenanthroline or bipyridine ligands and the Ru complexes was studied by means of cyclic or square‐wave voltammetry with carbon paste and mercury electrodes. The experimental redox potentials of the title compounds were compared with quantum chemical calculations. A very good agreement between experiment and theory was obtained, with a standard deviation of 0.13 V. It was shown that theoretical calculations can be of a limited predictive power for new RuII complexes, though it was difficult to reproduce differences smaller than 0.05 V. Several compounds of this series exhibited a considerable cytostatic effect and activity against the hepatitis C virus (HCV). (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
Diastereoselective and Regioselective Synthesis of Conformationally Restricted Thio‐dioxa‐ and Oxo‐oxathiaphosphorinane Dinucleotides Featuring Noncanonical α/β Torsion Angle Combinations (α,β‐CNAs)
Authors: Le Clézio Ingrid , Vigroux Alain , Escudier Jean‐Marc 
Published: March 2007

AbstractControl of the regioselective cyclisation of a stereodefined 5′‐C‐tosyloxy phosphorothioate dinucleotide unit to provide conformationally restricted dinucleotides of either thio‐dioxa‐ or oxo‐oxathiaphosphorinane types is described. NMR structural analysis of the newly synthesized building units showed the α and β torsional angles to be constrained to noncanonical values {gauche(+), trans} or {anticlinal(–), trans}.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)
Thermoset polyester as an alternative material for microchip electrophoresis/electrochemistry
Authors: Vickers Jonathan A. , Dressen Brian M. , Weston Melissa C. , Boonsong Kanokporn , Chailapakul Orawan , Cropek Donald M. , Henry Charles S. 
Published: March 2007

AbstractMicrochip CE coupled with electrochemical detection (MCE‐EC) is a good method for the direct detection of many small molecule analytes because the technique is sensitive and readily miniaturized. Polymer materials are being increasingly used with MCE due to their affordability and ease of fabrication. While PDMS has become arguably the most widely used material in MCE‐EC due to the simplicity of microelectrode incorporation, it suffers from a lack of separation efficiency, lower surface stability, and a tendency for analyte sorption. Other polymers, such as poly(methylmethacrylate) (PMMA) and poly(carbonate) (PC), have higher separation efficiencies but require more difficult fabrication techniques for electrode incorporation. In this report, thermoset polyester (TPE) was characterized as an alternative material for MCE‐EC. TPE microchips were characterized in their native and plasma oxidized forms and after coating with polyelectrolyte multilayers (PEMs). TPE provides higher separation efficiencies when compared to PDMS microchips, while still using simple fabrication protocols. In this work, separation efficiencies as high as 295 000 N/m were seen when using TPE MCE‐EC devices. Furthermore, the EOF was higher and more consistent as a function of pH for both native and plasma‐treated TPE than PDMS. Finally, TPE is amenable to modification using simple PEM coatings as another way to control surface chemistry and surface charge.
How important is the selection of computational analysis method to the accuracy of rainwater tank behaviour modelling?
Authors: Mitchell V. Grace 
Published: March 2007

AbstractAs the concept of sustainable urban water management is incorporated into the practice of urban water resource managers, actions, such as the utilization of roof runoff via rainwater tanks, which have multiple benefits, are increasingly being built into urban water systems. Modelling tools are frequently used to predict the yield from rainwater tanks and to estimate the storage capacity required to achieve a given potable supply reduction level, with these estimates used in both urban water resources policy development and engineering design. Therefore, it is important that the accuracy of commonly used models is understood. This paper investigates the impact of computational time step, computational operating rule, initial storage level, and the length of simulation period on the accuracy of the storage–yield–reliability relationship calculated using a simple rainwater tank behaviour model. Four time steps (ranging from 6 min to 24 h), two operational rules (supply before spillage and supply after spillage), two initial storage level states (empty and full), and three simulation periods (50 years, 10 years and 1 year) were applied to a wide range of rainwater tank system configurations and three different locations in Australia. It was found that the supply‐after‐spillage computational operating rule is preferable, while the ratio of the average demand volume in a single computational time step divided by the storage capacity (ΔD/S) can be used to assess whether a given combination of demand, storage, inflow, and computational time step will provide long‐term yield estimates that are within ± 5% of the values produced by a simulation that used a 50‐year time series of climate, 6‐min time step, and a supply‐after‐spillage operational rule (50‐6‐YAS). Copyright © 2007 John Wiley & Sons, Ltd.
Role of binding entropy in the refinement of protein–ligand docking predictions: Analysis based on the use of 11 scoring functions
Authors: Ruvinsky Anatoly M. 
Published: March 2007

AbstractWe present results of testing the ability of eleven popular scoring functions to predict native docked positions using a recently developed method (Ruvinsky and Kozintsev, J Comput Chem 2005, 26, 1089) for estimation the entropy contributions of relative motions to protein‐ligand binding affinity. The method is based on the integration of the configurational integral over clusters obtained from multiple docked positions. We use a test set of 100 PDB protein‐ligand complexes and ensembles of 101 docked positions generated by (Wang et al. J Med Chem 2003, 46, 2287) for each ligand in the test set. To test the suggested method we compared the averaged root‐mean square deviations (RMSD) of the top‐scored ligand docked positions, accounting and not accounting for entropy contributions, relative to the experimentally determined positions. We demonstrate that the method increases docking accuracy by 10–21% when used in conjunction with the AutoDock scoring function, by 2–25% with G‐Score, by 7–41% with D‐Score, by 0–8% with LigScore, by 1–6% with PLP, by 0–12% with LUDI, by 2–8% with F‐Score, by 7–29% with ChemScore, by 0–9% with X‐Score, by 2–19% with PMF, and by 1–7% with DrugScore. We also compared the performance of the suggested method with the method based on ranking by cluster occupancy only. We analyze how the choice of a clustering‐RMSD and a low bound of dense clusters impacts on docking accuracy of the scoring methods. We derive optimal intervals of the clustering‐RMSD for 11 scoring functions. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007
Structural and electronic properties of boron‐doped lithium clusters: Ab initio and DFT studies
Authors: Li Ying , Wu Di , Li Zhi‐Ru , Sun Chia‐Chung 
Published: March 2007

AbstractThe lowest‐energy structures and electronic properties of the BLin (n = 1–7) clusters are reported using the B3LYP, MP2, and CCSD(T) methods with the aug‐cc‐pVDZ basis set. Though the results at the B3LYP level agree well with those at the CCSD(T) level, the MP2 method is rather unsatisfactory. The first three‐dimensional ground state in the BLin clusters occurs for BLi4, and the impurity B atom is seen to be trapped in a Li cage from the BLi6 cluster onwards. The evolution of the binding energies, vertical ionization potentials, and polarizability with size of cluster shows the BLi5 cluster to be most stable among the BLin clusters. Besides, the BLi5 cluster is also found to have the largest reaction enthalpy (49.8 kcal/mol) upon losing a Li atom, which is different from the previous prediction. The unique stability of the 8‐valence electron BLi5 can be understood from the cluster electronic shell model (CSM). However, in contradiction to the prediction of the CSM, the 2s level is filled prior to the 1d level in the BLin clusters. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Polarizable model potential function for nucleic acid bases
Authors: Nakagawa Setsuko 
Published: March 2007

AbstractA polarizable model potential (PMP) function for adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) is developed on the basis of ab initio molecular orbital calculations at the MP2/6‐31+G* level. The PMP function consists of Coulomb, van der Waals, and polarization terms. The permanent atomic charges of the Coulomb term are determined by using electrostatic potential (ESP) optimization. The multicenter polarizabilities of the polarization term are determined by using polarized one‐electron potential (POP) optimization in which the electron density changes induced by a test charge are target. Isotropic and anisotropic polarizabilities are adopted as the multicenter polarizabilities. In the PMP calculations using the optimized parameters, the interaction energies of Watson–Crick type A‐T and C‐G base pairs were −15.6 and −29.4 kcal/mol, respectively. The interaction energy of Hoogsteen type A‐T base pair was −17.8 kcal/mol. These results reproduce well the quantum chemistry calculations at the MP2/6‐311++G(3df,2pd) level within the differences of 0.6 kcal/mol. The stacking energies of A‐T and C‐G were −9.7 and −10.9 kcal/mol. These reproduce well the calculation results at the MP2/6‐311++G (2d,2p) level within the differences of 1.3 kcal/mol. The potential energy surfaces of the system in which a sodium ion or a chloride ion is adjacent to the nucleic acid base are calculated. The interaction energies of the PMP function reproduced well the calculation results at the MP2/6‐31+G* or MP2/6‐311++G(2d,2p) level. The reason why the PMP function reproduces well the high‐level quantum mechanical interaction energies is addressed from the viewpoint of each energy terms. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Protein structure prediction: Combining de novo modeling with sparse experimental data
Authors: Latek Dorota , Ekonomiuk Dariusz , Kolinski Andrzej 
Published: March 2007

AbstractRoutine structure prediction of new folds is still a challenging task for computational biology. The challenge is not only in the proper determination of overall fold but also in building models of acceptable resolution, useful for modeling the drug interactions and protein–protein complexes. In this work we propose and test a comprehensive approach to protein structure modeling supported by sparse, and relatively easy to obtain, experimental data. We focus on chemical shift‐based restraints from NMR, although other sparse restraints could be easily included. In particular, we demonstrate that combining the typical NMR software with artificial intelligence‐based prediction of secondary structure enhances significantly the accuracy of the restraints for molecular modeling. The computational procedure is based on the reduced representation approach implemented in the CABS modeling software, which proved to be a versatile tool for protein structure prediction during the CASP (CASP stands for critical assessment of techniques for protein structure prediction) experiments (see http://predictioncenter/CASP6/org). The method is successfully tested on a small set of representative globular proteins of different size and topology, including the two CASP6 targets, for which the required NMR data already exist. The method is implemented in a semi‐automated pipeline applicable to a large scale structural annotation of genomic data. Here, we limit the computations to relatively small set. This enabled, without a loss of generality, a detailed discussion of various factors determining accuracy of the proposed approach to the protein structure prediction. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Ultrafast shape recognition to search compound databases for similar molecular shapes
Authors: Ballester Pedro J. , Richards W. Graham 
Published: March 2007

AbstractFinding a set of molecules, which closely resemble a given lead molecule, from a database containing potentially billions of chemical structures is an important but daunting problem. Similar molecular shapes are particularly important, given that in biology small organic molecules frequently act by binding into a defined and complex site on a macromolecule. Here, we present a new method for molecular shape comparison, named ultrafast shape recognition (USR), capable of screening billions of compounds for similar shapes using a single computer and without the need of aligning the molecules before testing for similarity. Despite its extremely fast comparison rate, USR will be shown to be highly accurate at describing, and hence comparing, molecular shapes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Molecular dynamics simulation of single wall carbon nanotubes polymerization under compression
Authors: Braga S. F. , Galvão D. S. 
Published: March 2007

AbstractSingle wall carbon nanotubes (SWCNTs) often aggregate into bundles of hundreds of weakly interacting tubes. Their cross‐polymerization opens new possibilities for the creation of new super‐hard materials. New mechanical and electronic properties are expected from these condensed structures, as well as novel potential applications. Previous theoretical results presented geometric modifications involving changes in the radial section of the compressed tubes as the explanation to the experimental measurements of structural changes during tube compression. We report here results from molecular dynamics simulations of the SWCNTs polymerization for small diameter arm chair tubes under compression. Hydrostatic and piston‐type compression of SWCNTs have been simulated for different temperatures and rates of compression. Our results indicate that large diameter tubes (10,10) are unlike to polymerize while small diameter ones (around 5 Å) polymerize even at room temperature. Other interesting results are the observation of the appearance of spontaneous scroll‐like structures and also the so‐called tubulane motifs, which were predicted in the literature more than a decade ago. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
Strategies to improve contrast in turboFLASH imaging: Reordered phase encoding and K‐space segmentation
Authors: Chien Daisy , Atkinson Dennis J. , Edelman Robert R. 
Published: March 2007

AbstractTurboFLASH (fast low‐angle shot) sequences enable the acquisition of an image in a fraction of a second. However, unique to T1‐weighted ultra‐fast imaging, the magnetization variation during image acquisition can produce artifacts along the phase‐encoding direction. In this study, the signal behavior and nature of these artifacts were analyzed with various acquisition schemes to improve image contrast. The magnetization variation during image acquisition and its filtering effect on the image were simulated for three different approaches to T1‐weighted turboFLASH imaging: standard turboFLASH with (a) mono‐tonically ascending phase‐encoding steps, (b) reordered phase encoding, and (c) k‐space segmentation. Each of the modified data acquisition schemes has advantages. However, for sub‐second imaging, reordered phase encoding produced improved image contrast over that of standard turboFLASH, and segmented k‐space imaging gave superior tissue contrast compared with that of both standard and reordered turboFLASH, with imaging time that permits breath‐hold studies.
MR microscopy at 7.0 T: Effects of brain iron
Authors: Malisch Timothy W. , Hedlund Laurence W. , Suddarth Steve A. , Johnson G. Allan 
Published: March 2007

AbstractThe T2 of brain tissue is known to be field dependent, decreasing as B0 increases. Previous studies have attributed reduced T2 in the structures of the extrapyramidal motor system (EPMS) to high iron concentrations. The present study was designed to manipulate physiologic iron concentrations and study the effects on T2 and on the field dependence of T2 at 7.0 T in whole formalin‐fixed brains. A rat model was devised in which iron concentrations in the structures of interest were altered by diet manipulation. Cerebral structures with different iron content were imaged and T2 measured with MR microscopy at both 2.0 and 7.0 T. T2 of all tissues was shorter by 40%–60% at 7.0 T. Although some dependence of T2 on iron concentration was evident, it was less than expected. The strongest correlation was in the substantia nigra. The highest‐resolution studies, at 30 × 30 × 50 μm, show the myelin bundles in many of the EPMS structures but not in the substantia nigra. From these data, it appears that T2 at greater field strengths depends more on susceptibility‐induced spin dephasing imposed by diffusion through the tissue micro‐structure than on the presence of iron.