bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Investigation of the Conformation of β-Carrageenan by Molecular Mechanics and Molecular Dynamics Simulations
Authors: Ueda Kazuyoshi , Ochiai Hiroshi , Imamura Akira , Nakagawa Setsuko 
Published: July 2006

Abstract
Carrageenan is known to change its conformation from coil to helix and to form a gel. However, the accurate conformation and the transition mechanism have not yet been detailed. In this work, the conformational behavior of β-carrageenan (a copolymer with a carrabiose repeating unit, 1,4-linked 3,6-anhydro-α-d-galactose (A) and 1,3-linked β-d-galactose (B)), was studied by using molecular mechanics and molecular dynamics simulation methods with the program CHARMM22. The energy maps of the carrabiose as a function of the dihedral angles of the glycosidic linkages between the A–B (1–3 linkage) and B–A (1–4 linkage) carrabiose units were calculated. Both carrabiose units were found to have five deep potential energy minima. Based on these carrabiose conformations, 25 conformers of the single helical chain carradodecaose were constructed and their minimum energy conformations were investigated by molecular mechanics and molecular dynamics simulations. From the results of these analyses, a possible single helical structure of β-carrageenan was elucidated. The stability of this helical conformation is discussed by comparing it with a double helical conformation, which was found from X-ray diffraction analyses of oriented fiber samples of κ-and ι-carrageenans, which are well-studied members of the carrageenan family.
Reaction of α,β‐unsaturated ketones with cerium(IV) salts in alcohol
Authors: Horiuchi C. Akira , Saitoh Yoshikazu , Utsukihara Takamitsu , Takahashi Shigeo , Matsushita Masatoshi , He Liangyou , Takahashi T. Tomoyoshi , Hashimoto Chikao , Sugiyama Takashi , Nozaki Sukekatsu 
Published: June 2006

AbstractReaction of α,β‐unsaturated ketones with cerium(IV) salts or lanthanide triflates in alcohols gave good yields of the corresponding β‐alkoxy compounds. In the case of 2‐cyclopentenone and 2‐cyclohexenone, the 1,1,3‐trialkoxy acetal derivatives were obtained preferentially accompanied by β‐alkoxyketone, except 2‐cycloheptenone. However, in the reaction of 2‐cycloheptenone with alcohol using cerium(IV) sulfate (CS)‐molecular sieve, 1,1,3‐trialkoxy derivatives were obtained. Also, in the cases of 1‐penten‐3‐one, 4‐hexen‐3‐one and 3‐hepten‐2‐one, 1,1,3‐trialkoxy derivatives were obtained preferentially. Copyright © 2006 John Wiley & Sons, Ltd.
Peptide‐Capped Gold Nanoparticles: Towards Artificial Proteins
Authors: Lévy Raphaël 
Published: June 2006

AbstractPeptides can be designed to form self‐assembled monolayers on gold nanoparticles to give nanomaterials with some chemical properties analogous to those of proteins. A variety of molecular‐recognition properties are readily integrated within the peptide monolayer. Monofunctionalized nanoparticles are obtained by using separation methods that have been optimized for proteins. Recent applications as artificial enzymes and artificial enzyme substrates are presented. The limitations and long‐term potential of peptide‐capped nanoparticles as artificial proteins are discussed.
Radiation following percutaneous balloon aortic valvuloplasty to prevent restenosis (RADAR pilot trial)
Authors: Pedersen Wes R. , Van Tassel Robert A. , Pierce Talia A. , Pence David M. , Monyak David J. , Kim Tae H. , Harris Kevin M. , Knickelbine Thomas , Lesser John R. , Madison James D. , Mooney Michael R. , Goldenberg Irvin F. , Longe Terrence F. , Poulose Anil K. , Graham Kevin J. , Nelson Richard R. , Pritzker Marc R. , Pagan‐Carlo Luis A. , Boisjolie Charlene R. , Zenovich Andrey G. , Schwartz Robert S. 
Published: June 2006

AbstractObjectives: We wished to determine the feasibility and early safety of external beam radiation therapy (EBRT) used following balloon aortic valvuloplasty (BAV) to prevent restenosis. Background: BAV for calcific aortic stenosis (AS) has been largely abandoned because of high restenosis rates, i.e., > 80% at 1 year. Radiation therapy is useful in preventing restenosis following vascular interventions and treating other benign noncardiovascular disorders. Methods: We conducted a 20‐patient, pilot study evaluating EBRT to prevent restenosis following BAV in elderly patients with calcific AS. Total doses ranging from 12–18 Gy were delivered in fractions over a 3–5 day post‐op period to the aortic valve. Echocardiography was performed pre and 2 days post‐op, 1, 6, and 12 months following BAV. Results: One‐year follow‐up is completed (age 89 ± 4). There were no complications related to EBRT. Eight patients died prior to 1 year; 5 of 10 (50%) in the low‐dose (12 Gy) group and 3 of 10 (30%) in the high‐dose (15–18 Gy) group. None of these 8 patients had restenosis, i.e., > 50% loss of the initial AVA gain, and only three deaths were cardiac in origin. One patient underwent aortic valve replacement and none repeated BAV. By 1 year, 3 of the initial 10 (30%) in the low‐dose group and 1 of 9 (11%) in the high‐dose group demonstrated restenosis (21% overall). Conclusions: EBRT following BAV in elderly patients with AS is feasible, free of early complications, and holds promise in reducing the 1 year restenosis rate in a dose‐dependent fashion. © 2006 Wiley‐Liss, Inc.
Rapid pacing to facilitate transcatheter prosthetic heart valve implantation
Authors: Webb John G. , Pasupati Sanjeevan , Achtem Leslie , Thompson Christopher R. 
Published: June 2006

AbstractObjectives: We describe the technique of, and our experience with, rapid ventricular burst pacing to facilitate transcatheter heart valve implantation. Background: Endovascular therapeutic procedures frequently require the precise placement of implantable devices. The precision of transcatheter device deployment may be hampered by cardiac motion or the effects of intravascular flow. Burst pacing is associated with a reduction in stroke volume, cardiac output, transvalvular flow, and cardiac motion. Methods: Rapid pacing was used in 40 consecutive patients with severe aortic stenosis undergoing implantation of catheter‐delivered prosthetic valves. Clinical, procedural, and hemodynamic records were reviewed. Results: A mean of 5 ± 2 burst pacing sequences at rates of 150–220 min−1 were used during balloon valvuloplasty and valve deployment. The duration of pacing required during valve deployment was 12 ± 3 sec. Pacing was relatively well tolerated when cautiously used with judicious recovery intervals and pressor support. Rapid pacing was associated with a rapid and effective reduction in systemic blood pressure, pulse pressure, transvalvular flow as well as cardiac and catheter motion. Conclusions: Rapid pacing is a relatively reliable technique to facilitate precise transcatheter deployment of prosthetic heart valves and other endovascular therapeutic devices. © 2006 Wiley‐Liss, Inc.
Asymmetric Allylic Substitution Catalyzed by C1‐Symmetrical Complexes of Molybdenum: Structural Requirements of the Ligand and the Stereochemical Course of the Reaction
Authors: Malkov Andrei V. , Gouriou Laure , Lloyd‐Jones Guy C. , Starý Ivo , Langer Vratislav , Spoor Paul , Vinader Victoria , Kočovský Pavel 
Published: June 2006

AbstractApplication of new chiral ligands (R)‐(−)‐12 a and (S)‐(+)‐12 c (VALDY), derived from amino acids, to the title reaction, involving cinnamyl (linear) and isocinnamyl (branched) type substrates (4 and 5 → 6), led to excellent regio‐ and enantioselectivities (>30:1, ≤98 % ee), showing that ligands with a single chiral center are capable of high asymmetric induction. The structural requirements of the ligand and the mechanism are discussed. The application of single enantiomers of deuterium‐labeled substrates (both linear 38 c and branched 37 c) and analysis of the products (41–43) by 2H{1H} NMR spectroscopy in a chiral liquid crystal matrix allowed the stereochemical pathways of the reaction to be distinguished. With ligand (S)‐(+)‐12 c, the matched enantiomer of branched substrate was found to be (S)‐5, which was converted into (R)‐6 with very high regio‐ and stereoselectivity via a process that involves net retention of stereochemistry. The mismatched enantiomer of the branched substrate was found to be (R)‐5, which was also converted into (R)‐6, that is, with apparent net inversion, but at a lower rate and with lower overall enantioselectivity. This latter feature, which may be termed a “memory effect”, reduced the global enantioselectivity in the reaction of the racemic substrate (±)‐5. The stereochemical pathway of the mismatched manifold has been shown also to be one of net retention, the apparent inversion occurring through equilibration via an Mo–allyl intermediate prior to nucleophilic attack. Incomplete equilibration leads to the memory effect and thus to lower enantioselectivity. Analysis of the mismatched manifold over the course of the reaction revealed that the memory effect is progressively attenuated with the nascent global selectivity increasing substantially as the reaction proceeds. The origin of this effect is suggested to be the depletion of CO sources in the reaction mixture, which attenuates turnover rate and thus facilitates greater equilibrium. The linear substrate was also converted into the branched product with net syn stereochemistry, as shown by isotopic labeling. An analogous process operates in the generation of small quantities of linear product from branched substrate.
An Alternative Approach to the g‐Matrix: Theory and Applications
Authors: Bolvin Hélène 
Published: June 2006

AbstractStarting from the formula proposed by Gerloch and McMeeking in 1975, the electronic g‐matrix is expressed as a sum of two matrices called Λ and Σ describing the orbital and spin contributions respectively. This approach is applied on benchmark diatomic and triatomic molecules, and on TiF3 and Cu(NH3)42+ using either CASPT2 or CCSD(T) methods to calculate the spin‐free states and SO‐RASSI to calculate spin–orbit coupling. Results compare very well to experimental data and to previous theoretical work; and, for each molecule, the anisotropy of the g‐matrix is modeled by the mean of a few parameters.
IL‐4 induces expression of TARC/CCL17 via two STAT6 binding sites
Authors: Wirnsberger Gerald , Hebenstreit Daniel , Posselt Gernot , Horejs‐Hoeck Jutta , Duschl Albert 
Published: June 2006

AbstractA cardinal feature of allergic disorders and immune responses is enhanced leukocyte trafficking. This is largely orchestrated by chemokines. The CC chemokine thymus‐ and activation‐regulated chemokine (TARC/CCL17) selectively attracts Th2 cells via the G protein‐coupled chemokine receptor CCR4. We show here that TARC/CCL17 is expressed by human T cells upon stimulation with IL‐4. Mapping of the transcriptional start site revealed the presence of two putative STAT6 binding motifs in proximity to the start position. EMSA and chromatin immunoprecipitation experiments demonstrated that STAT6 was able to bind to both motifs. A fragment of the TARC/CCL17 promoter containing both sites was tested in reporter gene assays for IL‐4 inducibility. The promoter was inducible in a STAT6‐deficient cell line only after introduction of functional STAT6. When mutations were inserted into one of the STAT6 motifs, IL‐4‐induced promoter activation was reduced. With both sites mutated, inducibility was completely abrogated. These data demonstrate collectively that T cells serve as a source of TARC/CCL17 when stimulated with IL‐4 and that STAT6 is essential for this.
Asymmetric Direct Aldol Reaction Catalysed by L‐Prolinethioamides
Authors: Gryko Dorota , Lipiński Radosław 
Published: June 2006

AbstractL‐Prolinethioamides have been found to be active catalysts for direct aldol reactions of acetone with aromatic aldehydes, affording aldol products in good yields and with good enantioselectivities. They were prepared from L‐proline and simple aliphatic and aromatic amines in optically pure form and in good overall yields. Studies employing ten catalysts allowed us to unequivocally establish the basic principles governing the outcome of the L‐prolinethioamide‐catalysed aldol reaction. In particular, the catalyst prepared from L‐proline and (S)‐phenylethylamine catalysed the reaction of acetone with 4‐cyanobenzaldehyde in 57 % yield and 93 % ee (100 % ee at –78 °C). Most importantly, we found that steric interaction between the catalyst and a donor or an acceptor is crucial for the stereoselectivity of the aldol addition, while the unwanted formation of imidazolidinethione (from the catalyst and acetone or an aldehyde) was shown to decrease both the ee and the yield. The influence of the amine moiety (–CSNHR), different solvents and temperatures were studied, and we also found that there is a linear correlation between the optical purity of the catalyst and the ee of the aldol product, which supports the hypothesis that the reaction proceeds by the enamine–imine mechanism, involving only one molecule of the catalyst in the transition state. For the first time, the formation of 1,5‐dihydroxypentan‐3‐one products (double addition products) was studied in detail. By precise optimisation we were able to show that the courses of the reactions of acetone with highly reactive aromatic aldehydes could be manipulated to give either the aldol products or 1,5‐dihydroxypentan‐3‐one derivatives as the major product in moderate ee. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Distribution of low‐density lipoprotein‐bound low‐molecular‐weight thiols: A new analytical approach
Authors: Zinellu Angelo , Sotgia Salvatore , Zinellu Elisabetta , Formato Marilena , Manca Salvatorica , Magliona Stefania , Ginanneschi Renzo , Deiana Luca , Carru Ciriaco 
Published: June 2006

AbstractWe have recently demonstrated that low‐density lipoprotein (LDL) apoprotein is able to bind the most concentrated plasma thiols such as cysteine, cysteinylglycine, and homocysteine by disulfide linkage. However, the LIF CE assay employed to measure linked thiols was not sensitive enough to verify whether low concentrated plasma thiols as glutathione and glutamylcysteine are also linked to apoprotein. By modifying sample treatment and electrophoretic parameters we set up a new method with an LOQ of about 1.5 nmol/L, by which we demonstrate that LDL apoprotein binds all physiological plasma thiols. The increased sensitivity was obtained by drying released apoB thiols after reduction treatment, dissolving them directly in a low volume of derivatization buffer and decreasing the dilution factor of derivatized sample before CE injection. Moreover, by increasing the concentration of the electrolyte buffer, we improved the selectivity of peaks, in particular between glutathione (GSH) and the impurity peak derived from unreacted 5‐iodoacetamidofluorescein, which in the previous electrophoretic conditions were overlapped. The method optimization, reached by searching the best combination between sample matrix and CE run buffer, is fully described. Given the potential pathologic significance of protein thiolation, the proposed method may be useful to understand the mechanisms and the balances that regulate the interaction between thiols and –SH free groups of proteins.
Comparison of oligonucleotide migration in a bicontinuous cubic phase of monoolein and water and in a fibrous agarose hydrogel
Authors: Sanandaji Nima , Carlsson Nils , Voinova Marina , Åkerman Björn 
Published: June 2006

AbstractPorous hydrogels such as agarose are commonly used to analyze DNA and water‐soluble proteins by electrophoresis. More recently lyotropic liquid crystals, such as the diamond cubic phase formed by the lipid monoolein and water, has become a new type of well‐defined porous structure of interest for both hydrophilic and amphiphilic analytes. Here we compare these two types of matrixes by investigating the nature of retardation they confer to an oligonucleotide that migrates in their respective aqueous phases. The retardation for a 25‐mer oligonucleotide was found to be about 35‐fold stronger in the cubic phase than in an agarose hydrogel modified to have the same average pore size. According to modelling, the strong retardation is primarily due to the fact that hydrodynamic interaction with the continuous monoolein membrane is a stronger source of friction than the steric interactions (collisions) with discrete gel fibres. A secondary effect is that the regular liquid crystal has a narrower pore‐size distribution than the random network of the agarose gel. In agreement with experiments, these two effects together predict that the retardation in the cubic phase is a 30‐fold stronger than in an agarose gel with the same average pore radius.
On‐chip chiral separation based on bovine serum albumin‐conjugated carbon nanotubes as stationary phase in a microchannel
Authors: Weng Xuexiang , Bi Hongyan , Liu Baohong , Kong Jilie 
Published: June 2006

AbstractA novel method of chiral separation based on protein‐stationary phase immobilized in a poly(methyl methacrylate) microfluidic chip was developed. BSA conjugated with the shortened carboxylic single‐walled carbon nanotubes (SWNTs) was employed as the chiral selector. Successful separation of tryptophan enantiomers was achieved in less than 70 s with a resolution factor of 1.35 utilizing a separation length of 32 mm. This is the first example of chiral separation based on SWNTs‐BSA conjugates as stationary phase immobilized in microchip channel. The stability of the stationary phase in the channel was examined by microchip electrophoresis with laser‐induced fluorescence detection. Factors that influenced the chiral separation resolution were examined. Under the optimized conditions, the proposed modified chip revealed adequate repeatability concerning run‐to‐run. These results show that the use of SWNTs‐BSA conjugates within microfluidic channels hold great promise for a variety of analytical schemes.
A simple protocol for protein extraction of recalcitrant fruit tissues suitable for 2‐DE and MS analysis
Authors: Song Jun , Braun Gordon , Bevis Eric , Doncaster Kristen 
Published: June 2006

AbstractFruit tissues are considered recalcitrant plant tissue for proteomic analysis. Three phenol‐free protein extraction procedures for 2‐DE were compared and evaluated on apple fruit proteins. Incorporation of hot SDS buffer, extraction with TCA/acetone precipitation was found to be the most effective protocol. The results from SDS‐PAGE and 2‐DE analysis showed high quality proteins. More than 500 apple polypeptides were separated on a small scale 2‐DE gel. The successful protocol was further tested on banana fruit, in which 504 and 386 proteins were detected in peel and flesh tissues, respectively. To demonstrate the quality of the extracted proteins, several protein spots from apple and banana peels were cut from 2‐DE gels, analyzed by MS and have been tentatively identified. The protocol described in this study is a simple procedure which could be routinely used in proteomic studies of many types of recalcitrant fruit tissues.
Knowledge‐based proteome profiling: Considering identified proteins to evaluate separation efficiency by 2‐D PAGE
Authors: Gundacker Nina , Bayer Editha , Traxler Elisabeth , Zwickl Hannes , Kubicek Markus , Stöckl Johannes , Gerner Christopher 
Published: June 2006

AbstractProteome profiling techniques rely on the separation of proteins or peptides and their subsequent quantification. The reliability of this technique is still limited because a proteome profiling result does not necessarily represent the true protein composition of the analysed sample, thus seriously hampering proper data interpretation. Many experimentally observed proteome alterations are biologically not significant. It was the aim of this study to use the knowledge of the biological context of proteins in order to establish optimised proteome profiling protocols. While 2‐D spot patterns of total cell protein fractions were found to poorly represent the true protein composition, purified subcellular protein fractions were found to better represent the protein composition of the analysed sample. The application of a standardised protocol to different kinds of cells revealed several striking observations. Firstly, the protein composition of cultured cells of various origins is very similar. Secondly, proteome alterations observed with the described protocols do make sense from a biologic point of view and may thus be considered as truly representative for the analysed samples. Thirdly, primary white blood cells isolated from different donors were found to show minor, but reproducible and significant individual differences. We designate the consideration of known properties of identified proteins in proteome profiles as a knowledge‐based approach. The present data suggest that this approach may tremendously help to improve the applied techniques and assess the results. We demonstrate that the fulfilment of well‐defined criteria of proteome profiles eventually results in reliable and biologically relevant data.
Binding of Ca2+, Mg2+, and heparin by human serum amyloid P component in affinity capillary electrophoresis
Authors: Heegaard Niels H. H. , He Xinya , Blomberg Lars G. 
Published: June 2006

AbstractHuman serum amyloid P component (SAP) is a glycoprotein circulating in the blood and found in association with all types of amyloid (malfolded potein aggregates) examined so far. Despite uncertainties regarding the precise function of SAP in vivo, the lectin‐like properties of this Ca2+‐activated protein with affinity for anionic saccharides and malfolded proteins are well known. The propensity to form homomeric penta‐ or decamers in solution and the selfaggregation in the presence of Ca2+ as well as the tendency of SAP to attach to uncoated fused silica have precluded the analysis of SAP by microelectrophoretic methods. We now work out conditions to characterize the binding of Ca2+ and Mg2+ and the binding of heparin to SAP in the presence of divalent metal ions by ACE. The results show a strong binding of heparin (sub‐μM apparent dissociation constants) even in the abscence of Ca2+ at low ionic strength, pH 8.2. Also, a selective interaction with Ca2+ compared with Mg2+ is demonstrated. The approach will further the use of microelectrophoretic methods to examine the interactions of SAP with ligands of putative pathophysiological relevance such as lipopolysaccharides and misfolded proteins.