bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative study on water structures in polyHEMA and polyMEA by XRD‐DSC simultaneous measurement
Authors: Kishi Akira , Tanaka Masaru , Mochizuki Akira 
Published: October 2008

AbstractWe have found that poly(2‐methoxyethylacrylate) (polyMEA) has excellent blood compatibility and proposed that the property is due to freezing bound water in the polymer. This water is defined as that which cold‐crystallizes at around −45°C in the heating process of differential scanning calorimetry (DSC). In addition, we have already reported that the water in polyMEA is classified into three types, nonfreezing, freezing bound, and free waters, whereas the water in other polymers is just classified into two types: free and nonfreezing waters. (J Biomed Mater Res 68A, 2004, 684) However, the phenomenon observed by DSC is the enthalpy change and is not a direct evidence for crystallization. To confirm cold‐crystallization, a comparative investigation of the thermal and crystallographical properties of water in hydrated polyMEA and poly(2‐hydroxyethylmethacrylate) (polyHEMA) as a control was carried out using simultaneous measurements by X‐ray diffractometer (XRD) and DSC. In addition, the effect of the water content in the polymers on the properties was studied. As for polyMEA, the finding that XRD crystalline peaks appearing in the heating process were assigned to hexagonal ice indicated cold‐crystallization. On the other hand, in the case of polyHEMA, the crystal due to ice was formed only in the cooling process, and during the heating process, the growth of crystal ice was not observed. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Understanding the mechanism of β‐sheet folding from a chemical and biological perspective
Authors: Jager Marcus , Deechongkit Songpon , Koepf Edward K. , Nguyen Houbi , Gao Jianmin , Powers Evan T. , Gruebele Martin , Kelly Jeffery W. 
Published: October 2008

AbstractPerturbing the structure of the Pin1 WW domain, a 34‐residue protein comprised of three β‐strands and two intervening loops has provided significant insight into the structural and energetic basis of β‐sheet folding. We will review our current perspective on how structure acquisition is influenced by the sequence, which determines local conformational propensities and mediates the hydrophobic effect, hydrogen bonding, and analogous intramolecular interactions. We have utilized both traditional site‐directed mutagenesis and backbone mutagenesis approaches to alter the primary structure of this β‐sheet protein. Traditional site‐directed mutagenesis experiments are excellent for altering side‐chain structure, whereas amide‐to‐ester backbone mutagenesis experiments modify backbone‐backbone hydrogen bonding capacity. The transition state structure associated with the folding of the Pin1 WW domain features a partially H‐bonded, near‐native reverse turn secondary structure in loop 1 that has little influence on thermodynamic stability. The thermodynamic stability of the Pin1 WW domain is largely determined by the formation of a small hydrophobic core and by the formation of desolvated backbone‐backbone H‐bonds enveloped by this hydrophobic core. Loop 1 engineering to the consensus five‐residue β‐bulge‐turn found in most WW domains or a four‐residue β‐turn found in most β‐hairpins accelerates folding substantially relative to the six‐residue turn found in the wild type Pin1 WW domain. Furthermore, the more efficient five‐ and four‐residue reverse turns now contribute to the stability of the three‐stranded β‐sheet. These insights have allowed the design of Pin1 WW domains that fold at rates that approach the theoretical speed limit of folding. © 2008 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 90: 751–758, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Benzophenone semicarbazone protection strategy for synthesis of aza‐glycine containing aza‐peptides
Authors: Bourguet Carine B. , Sabatino David , Lubell William D. 
Published: October 2008

AbstractAza‐glycine has been incorporated into peptide mimics as a tool for studying the active conformation and characterizing structure‐function relationships for activity. Side reactions, such as intramolecular cyclizations to form hydantoins and oxadiazalones, have, however, inhibited efforts to make activated aza‐Gly residues in solution using carbamate protection. Herein, we describe efficient incorporation of aza‐glycine into aza‐peptides using diphenyl hydrazone protection. Hydrazone acylation with p‐nitrobenzyl chloroformate provided the protected aza‐Gly activated ester, which was used to acylate a set of amino ester and amino acids to provide aza‐Gly‐Xaa aza‐dipeptide fragments for peptide synthesis. Removal of the hydrazone protection was performed under acidic conditions to provide the hydrochloride salt of the aza‐Gly residue for subsequent elongation of the aza‐peptide chain using standard coupling conditions. A proof of concept for the use of benzophenone protection has been established by the synthesis of an aza‐peptide analog of a potent activator of caspase 9 in cancer cells. © 2008 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 90: 824–831, 2008.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Lipopolysaccharide bound structures of the active fragments of fowlicidin‐1, a cathelicidin family of antimicrobial and antiendotoxic peptide from chicken, determined by transferred nuclear overhauser effect spectroscopy
Authors: Bhunia Anirban , Mohanram Harini , Bhattacharjya Surajit 
Published: October 2008

AbstractCathelicidins comprise a major family of host‐defense antimicrobial peptides in vertebrates. The C‐terminal part of the cathelicidins is bestowed with antimicrobial and lipopolysaccharide (LPS) neutralizing activities. In this work, we repot high resolution solution structures of two nontoxic active fragments, residues 1–16 or RG16 and residues 8–26 or LK19, of fowlicidin‐1, a cathelicidin family of peptide from chicken, as a complex with LPS using two‐dimensional transferred nuclear Overhauser effect (Tr‐NOE) spectroscopy. Both peptides are highly flexible and do not assume any preferred conformations in their free states. Upon complexation with endotoxin or LPS, peptides undergo structural transitions towards folded conformations. Structure calculations reveal that the LK19 peptide adopts a well defined helical structure with a bend at the middle. By contrast, the first seven amino acids of RG16 are found to be flexible followed by a helical conformation for the residues L8‐A15. In addition, a truncated version of LK19 encompassing residues A15‐K26 or AK12 displays an amphipathic helical structure in LPS. Saturation transfer difference (STD) NMR studies demonstrate that all peptides, RG16, LK19, and AK12, are in close proximity with LPS, whereby the aromatic residues showed the strongest STD effects. Fluorescence studies with fluorescein isothiocyanate (FITC) labeled LPS in the presence of full‐length fowlicidin‐1, LK19, RG16, and AK12 indicated that LPS‐neutralization property of these peptides may result from plausible dissociation of LPS aggregates. The helical structures of peptide fragments derived from fowlicidin‐1 in LPS could be utilized to develop nontoxic antiendotoxic compounds. © 2008 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 9–22, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Loop‐length‐dependent SVM prediction of domain linkers for high‐throughput structural proteomics
Authors: Ebina Teppei , Toh Hiroyuki , Kuroda Yutaka 
Published: October 2008

AbstractThe prediction of structural domains in novel protein sequences is becoming of practical importance. One important area of application is the development of computer‐aided techniques for identifying, at a low cost, novel protein domain targets for large‐scale functional and structural proteomics. Here, we report a loop‐length‐dependent support vector machine (SVM) prediction of domain linkers, which are loops separating two structural domains. (DLP‐SVM is freely available at: http://www.tuat.ac.jp/∼domserv/cgi‐bin/DLP‐SVM.cgi.) We constructed three loop‐length‐dependent SVM predictors of domain linkers (SVM‐All, SVM‐Long and SVM‐Short), and also built SVM‐Joint, which combines the results of SVM‐Short and SVM‐Long into a single consolidated prediction. The performances of SVM‐Joint were, in most aspects, the highest, with a sensitivity of 59.7% and a specificity of 43.6%, which indicated that the specificity and the sensitivity were improved by over 2 and 3% respectively, when loop‐length‐dependent characteristics were taken into account. Furthermore, the sensitivity and specificity of SVM‐Joint were, respectively, 37.6 and 17.4% higher than those of a random guess, and also superior to those of previously reported domain linker predictors. These results indicate that SVMs can be used to predict domain linkers, and that loop‐length‐dependent characteristics are useful for improving SVM prediction performances. © 2008 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 1–8, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Autonomic innervation of the developing heart: Origins and function
Authors: Hildreth Victoria , Anderson Robert H. , Henderson Deborah J. 
Published: October 2008

AbstractMaintenance of homeostatic circulation in mammals and birds is reliant upon autonomic innervation of the heart. Neural branches of mixed cellular origin and function innervate the heart at the arterial and venous poles as it matures, eventually coupling autonomic output to the cardiac components, including the conduction system. The development of neural identity is controlled by specific networks of genes and growth factors, whereas functional properties are governed by the use of different neurotransmitters. In this review, we summarize briefly the anatomic arrangement of the vertebrate autonomic nervous system and describe, in detail, the innervation of the heart. We discuss the timing of cardiac innervation in the chick and mouse, emphasizing the relationship of the cardiac neural networks to the anatomical structures within the heart. We also discuss the variable contribution of the neural crest to vagal cardiac nerves, and summarize the main neurotransmitters secreted by the developing sympathetic and parasympathetic autonomic divisions. We provide an overview of the main growth factor and gene families involved in neural development, discussing how these factors may impact upon the development of cardiac abnormalities in congenital syndromes associated with autonomic dysfunction. Clin. Anat. 22:36–46, 2009. © 2008 Wiley‐Liss, Inc.
Identification of Additional Players in the Alternative Biosynthesis Pathway to Isovaleryl‐CoA in the Myxobacterium Myxococcus xanthus
Authors: Bode Helge B. , Ring Michael W. , Schwär Gertrud , Altmeyer Matthias O. , Kegler Carsten , Jose Ivy R. , Singer Mitchell , Müller Rolf 
Published: October 2008

AbstractIsovaleryl‐CoA (IV‐CoA) is usually derived from the degradation of leucine by using the Bkd (branched‐chain keto acid dehydrogenase) complex. We have previously identified an alternative pathway for IV‐CoA formation in myxobacteria that branches from the well‐known mevalonate‐dependent isoprenoid biosynthesis pathway. We identified 3‐hydroxy‐3‐methylglutaryl‐CoA (HMG‐CoA) synthase (MvaS) to be involved in this pathway in Myxococcus xanthus, which is induced in mutants with impaired leucine degradation (e.g., bkd−) or during myxobacterial fruiting‐body formation. Here, we show that the proteins required for leucine degradation are also involved in the alternative IV‐CoA biosynthesis pathway through the efficient catalysis of the reverse reactions. Moreover, we conducted a global gene‐expression experiment and compared vegetative wild‐type cells with bkd mutants, and identified a five‐gene operon that is highly up‐regulated in bkd mutants and contains mvaS and other genes that are directly involved in the alternative pathway. Based on our experiments, we assigned roles to the genes required for the formation of IV‐CoA from HMG‐CoA. Additionally, several genes involved in outer‐membrane biosynthesis and a plethora of genes encoding regulatory proteins were decreased in expression levels in the bkd− mutant; this explains the complex phenotype of bkd mutants including a lack of adhesion in developmental submerse culture.
Structure and Charge Control in Metal–Organic Frameworks Based on the Tetrahedral Ligand Tetrakis(4‐tetrazolylphenyl)methane
Authors: Dincǎ Mircea , Dailly Anne , Long Jeffrey R. 
Published: October 2008

AbstractUse of the tetrahedral ligand tetrakis(4‐tetrazolylphenyl)methane enabled isolation of two three‐dimensional metal–organic frameworks featuring 4,6‐ and 4,8‐connected nets related to the structures of garnet and fluorite with the formulae Mn6(ttpm)3⋅5 DMF⋅3 H2O (1) and Cu[(Cu4Cl)(ttpm)2]2⋅CuCl2⋅5 DMF⋅11 H2O (2) (H4ttpm=tetrakis(4‐tetrazolylphenyl)methane). The fluorite‐type solid 2 displays an unprecedented post‐synthetic transformation in which the negative charge of the framework is reduced by extraction of copper(II) chloride. Desolvation of this compound generates Cu4(ttpm)2⋅0.7 CuCl2 (2 d), a microporous material exhibiting a high surface area and significant hydrogen uptake.
Phosphorus‐Based Heteropentacenes: Efficiently Tunable Materials for Organic n‐Type Semiconductors
Authors: Dienes Yvonne , Eggenstein Matthias , Kárpáti Tamás , Sutherland Todd C. , Nyulászi László , Baumgartner Thomas 
Published: October 2008

AbstractBenzo‐condensed dithieno[3,2‐b:2′,3′‐d]phospholes have been synthesized that allow convenient tuning of properties that are essential for application as semiconductor materials in organic field‐effect transistor (OFET) devices. The versatile reactivity of the trivalent phosphorus atom in these heteropentacenes provides access to a series of materials that show different photophysical properties, significantly different organization in the solid state, and distinctly different electrochemical properties that can be achieved by simple chemical modifications. The materials show strong photoluminescence in solution and in the solid state that depends on the electronic nature of the phosphorus center. Electrochemical studies revealed that the phosphorus atom intrinsically furnishes materials with n‐channel or ambipolar behavior, also depending on its electronic nature. The experimental data were verified by DFT quantum chemical calculations and suggest that the phosphorus‐based heteropentacenes could be excellent candidates for n‐channel OFET semiconductor materials.
β′‐Hydroxy‐α,β‐unsaturated ketones: A new pharmacophore for the design of anticancer drugs. Part 2.
Authors: León Leticia G. , Carballo Rubén M. , Vega‐Hernández María C. , Miranda Pedro O. , Martín Víctor S. , Padrón Juan I. , Padrón José M. 
Published: October 2008

AbstractNovel antiproliferative β′‐acyloxy‐α,β‐unsaturated ketones were obtained by means of an iron(III)‐catalyzed multicomponent domino process (ABB′ 3CR). The most active derivatives displayed GI50 values in the range of 0.5–3.9 μM against a panel of representative human solid tumor cell lines: A2780, SW1573, HBL‐100, T‐47D and WiDr. Analysis of cells following 24 h exposure to these drugs showed cell cycle arrest in the S and G2/M phase, in a dose‐dependent manner. Our data indicate that the β′‐acyloxy‐α,β‐unsaturated ketones cause permanent damage to the cells and induce apoptosis.
Synthesis and Properties of a Mitochondrial Peripheral Benzodiazepine Receptor Conjugate
Authors: El Alaoui Abdessamad , Schmidt Frédéric , Sarr Marianne , Decaudin Didier , Florent Jean‐Claude , Johannes Ludger 
Published: October 2008

AbstractPeripheral benzodiazepine receptors are potential targets for cancer therapeutics through the use of specific ligands such as the pro‐apoptotic benzodiazepine RO5‐4864. However, the poor water solubility of this compound has been a limitation to its application in vivo. Herein we describe an efficient synthesis for the conjugation, via a cleavable linker arm, of RO5‐4864 to a novel tumour‐delivery tool, the B‐subunit of Shiga toxin (STxB). The conjugate is water soluble and specifically targets cancer cells that overexpress the glycolipid Gb3, the cellular Shiga toxin receptor that is found on several human tumours. After internalisation via retrograde transport, the prodrug is cleaved inside cells to release the active principle. Delivery by STxB therefore increases the cytotoxic activity of RO5‐4864 and its tumour specificity.
Treatment of core‐binding‐factor in acute myelogenous leukemia with fludarabine, cytarabine, and granulocyte colony‐stimulating factor results in improved event‐free survival
Authors: Borthakur Gautam , Kantarjian Hagop , Wang Xuemei , Plunkett William K. , Gandhi Varsha V. , Faderl Stefan , Garcia‐Manero Guillermo , Ravandi Farhad , Pierce Sherry , Estey Elihu H. 
Published: October 2008

AbstractBACKGROUND.Acute myelogenous leukemia (AML) associated with core‐binding‐factor (CBF) abnormalities is the type of leukemia most responsive to cytarabine (ara‐C) therapy and is of relative favorable prognosis. In vitro and ex vivo observations suggest that increases in intracellular ara‐C levels influenced by administration of fludarabine and granulocyte colony‐stimulating factor (GCSF) increase the effect of ara‐C, prompting us to clinically evaluate the efficacy of such combinations.METHODS.We analyzed the event‐free survival of patients with newly diagnosed CBF AML treated with fludarabine and ara‐C (FA) (N = 45) or with FA and GCSF (FLAG) (N = 22) and compared results to patients treated with regimens consisting of idarubicin and ara‐C with or without GCSF (IA/IAG) (N = 47).RESULTS.After accounting for prognostic covariates other than treatment (including year in which treatment was administered), FA, and in particular FLAG, were associated with longer event‐free survival than IA/IAG.CONCLUSIONS.Thus, our data lends clinical credence to the observed modulation of ara‐C by fludarabine and GCSF. Cancer 2008. © 2008 American Cancer Society.
Intrinsic connections of the macaque monkey hippocampal formation: I. Dentate gyrus
Authors: Kondo Hideki , Lavenex Pierre , Amaral David G. 
Published: October 2008

AbstractWe have carried out a detailed analysis of the intrinsic connectivity of the Macaca fascicularis monkey hippocampal formation. Here we report findings on the topographical organization of the major connections of the dentate gyrus. Localized anterograde tracer injections were made at various rostrocaudal levels of the dentate gyrus, and we investigated the three‐dimensional organization of the mossy fibers, the associational projection, and the local projections. The mossy fibers travel throughout the transverse extent of CA3 at the level of the cells of origin. Once the mossy fibers reach the distal portion of CA3, they change course and travel for 3–5 mm rostrally. The associational projection, originating from cells in the polymorphic layer, terminates in the inner one‐third of the molecular layer. The associational projection, though modest at the level of origin, travels both rostrally and caudally from the injection site for as much as 80% of the rostrocaudal extent of the dentate gyrus. The caudally directed projection is typically more extensive and denser than the rostrally directed projection. Cells in the polymorphic layer originate local projections that terminate in the outer two‐thirds of the molecular layer. These projections are densest at the level of the cells of origin but also extend several millimeters rostrocaudally. Overall, the topographic organization of the intrinsic connections of the monkey dentate gyrus is largely similar to that of the rat. Such extensive longitudinal connections have the potential for integrating information across much of the rostrocaudal extent of the dentate gyrus. J. Comp. Neurol. 511:497–520, 2008. © 2008 Wiley‐Liss, Inc.
An Investigation of Protonation Sites and Conformations of Protonated Amino Acids by IRMPD Spectroscopy
Authors: Wu Ronghu , McMahon Terry B. 
Published: October 2008

AbstractThe protonation sites and structures of a series of protonated amino acids (Gly, Ala, Pro, Phe, Lys and Ser) are investigated by means of infrared multiple‐photon dissociation (IRMPD) spectroscopy and electronic‐structure calculations. The IRMPD spectra of the protonated species are recorded using the combination of a free‐electron laser (FEL) and an electrospray‐ion‐trap mass spectrometer. The structures of different possible isomers of these protonated species are optimized at the B3LYP/6‐311+G(d, p) level of theory and the IR spectra calculated using the same computational method. For every amino acid studied herein, the current results indicate that a proton is bound to the α‐amino nitrogen, except for lysine, in which the protonation site is the amino nitrogen in the side chain. According to the calculated and experimental IRMPD results, the structures of the protonated amino acids may be assigned unambiguously. For Gly, Ala, and Pro, in each of the most stable isomers the protonated amino group forms an intramolecular hydrogen bond with the adjacent carbonyl oxygen. In the case of Gly, the isomer containing a proton bound to the carbonyl oxygen is theoretically possible. However, it does not exist under the experimental conditions because it has a significantly higher energy (i.e. 26.6 kcal mol−1) relative to the most stable isomer. For Ser and Phe, the protonated amino group forms two intramolecular hydrogen bonds with both the adjacent carbonyl oxygen and the side‐chain group in each of the most stable isomers. In protonated lysine, the protonated amino group in the side chain forms two hydrogen bonds with the α‐amino nitrogen and the carbonyl oxygen, which is a cyclic structure. Interestingly, for protonated lysine the zwitterionic structure is a local minimum energy isomer, but the experimental spectrum indicates that it does not exist under the experimental conditions. This is consistent with the fact that the zwitterionic isomer is 9.2 kcal mol−1 higher in free energy at 298 K than the most stable isomer. The carbonyl stretching vibration in the range of 1760–1800 cm−1 is especially sensitive to the structural change. In addition, IRMPD mechanisms for the protonated amino acids are also investigated.
Efficient Synthesis of Dimethyl Ether over HZSM‐5 Supported on Medium‐Surface‐Area β‐SiC Foam
Authors: Ivanova Svetlana , Vanhaecke Estelle , Louis Benoit , Libs Suzanne , Ledoux Marc‐Jacques , Rigolet Sévérine , Marichal Claire , Pham Charlotte , Luck Francis , Pham‐Huu Cuong 
Published: October 2008

AbstractIn this study, we aimed to produce a highly selective and stable catalyst for the production of dimethyl ether by methanol dehydration. The activities were compared of different active phases of the employed system, zeolite HZSM‐5 or γ‐alumina, supported on silicon carbide as foam, and it was found that the supported zeolite catalysts are more active than and as selective as the alumina‐based catalysts. The as‐prepared zeolite/SiC composites reveal good stability in long‐term tests in the presence or absence of steam. The high stability is attributed to the presence of highly dispersed micrometer‐sized zeolite particles, which make the active sites more accessible to the reactants and promote the quick transfer of the desired product, dimethyl ether, out of the catalyst bed, minimizing deactivation of the catalyst.