bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly trans‐1,4‐specific polymerization of 1,3‐butadiene catalyzed by [2,6‐bis{(4S)‐ (−)‐isopropyl‐2‐oxazolin‐2‐yl}pyridine] chromium complex activated with modified methylaluminoxane
Authors: Nakayama Yuushou , Sogo Kenji , Cai Zhengguo , Yasuda Hajime , Shiono Takeshi 
Published: January 2011

AbstractChromium complexes with N,N,N‐tridentate ligands, LCrCl3 (L = 2,6‐bis{(4S)‐(−)‐isopropyl‐2‐oxazolin‐2‐yl}pyridine (1), 2,2′:6′,2″‐terpyridine (2), and 4,4′,4″‐tri‐tert‐butyl‐2,2′:6′,2″‐terpyridine (3)), were prepared. The structures of 1 and 2 were determined by X‐ray crystallography. Upon activation with modified methylaluminoxane (MMAO), 1 catalyzed the polymerization of 1,3‐butadiene, while 2 and 3 was inactive. The obtained poly(1,3‐butadiene) obtained with 1‐MMAO was found to have completely trans‐1,4 structure. The 1‐MMAO system also showed catalytic activity for the polymerization of isoprene to give polyisoprene with trans‐1,4 (68%) and cis‐1,4 (32%) structure. Copyright © 2011 Society of Chemical Industry
Electrospinning formaldehyde‐crosslinked zein solutions
Authors: Selling Gordon W , Woods Kristen Kruger , Biswas Atanu 
Published: January 2011

AbstractIn order to develop zein fibers with improved physical properties and solvent resistance, formaldehyde was used as a crosslinking reagent before spinning. The crosslinking reaction was carried out in either acetic acid or ethanolic HCl where the amount of crosslinking reagent was between 1 and 6%. Reactions were carried out at various times and temperatures. When carried out in acetic acid, the maximum amount of formaldehyde that could be used was 1.5% as gelation occurred at higher levels. In ethanolic HCl, 6% formaldehyde could be incorporated into zein. All solutions were successfully electrospun, producing predominantly ribbon and round fibers; the morphology was strongly dependent on solvent and spinning solids. The formaldehyde‐crosslinked zein fabrics had double the tensile strength of control fabrics. SDS‐PAGE analysis clearly showed crosslinking had occurred. Electrospun fabrics from all formaldehyde‐treated zein solutions required an additional heating step in order to be resistant to dissolution in acetic acid, a known very good solvent for zein. Copyright © 2011 Society of Chemical Industry
Fracture behaviour of controlled‐rheology ethylene–propylene block copolymers
Authors: Salazar Alicia , Martín Tamara , Navarro José M , Rodríguez Jesús 
Published: January 2011

AbstractThe evolution of the molecular weight distribution and the thermal, mechanical and fracture behaviour of controlled‐rheology ethylene‐propylene block copolymers (ca 8 wt% ethylene content) has been analysed. Various concentrations of di‐tert‐butylperoxide were utilized. The melt flow index increased with the peroxide content due to the reduction of the molecular weight and the narrowing of the molecular weight distribution. However, the thermal behaviour and degree of crystallinity were not improved and some mechanical properties, such as the tensile strength and elongation at break, presented an anomalous behaviour. This trend can be explained by the presence of the elastomeric phase. The addition of peroxide influenced strongly the J–R curves obtained via the elastic–plastic fracture mechanics approach. The slope of these curves was markedly reduced with addition of peroxide to almost being flat for the highest concentration. This loss of ductility and the sudden decrease of the fracture toughness values with an increasing amount of peroxide were mainly due to the reduction in the molecular weight. Copyright © 2011 Society of Chemical Industry
Morphology and properties of stearate‐intercalated layered double hydroxide nanoplatelet‐reinforced thermoplastic polyurethane
Authors: Kotal Moumita , Srivastava Suneel Kumar , Bhowmick Anil Kumar , Chakraborty Sunity Kumar 
Published: January 2011

AbstractIn the past few years, layered double hydroxides (LDHs) with monolayer structure have been much studied for the development of polymer nanocomposites. LDHs with intercalated stearate anions form a bilayer structure with increased interlayer spacing and are expected to be better nanofillers in polymers. In the work reported, thermoplastic polyurethane (PU)/stearate‐intercalated LDH nanocomposites were prepared by solution intercalation and characterized. X‐ray diffraction and transmission electron microscopy confirmed the exfoliation at lower filler loading followed by intercalation at higher filler loading in PU matrix. As regards mechanical properties, these nanocomposites showed maximum improvements in tensile strength (45%) and elongation at break (53%) at 1 and 3 wt% loadings. Maximum improvements in storage and loss moduli (20%) with a shift of glass transition temperature (15 °C) and an increase in thermal stability (32 °C) at 50% weight loss were observed at 8 wt% loading in PU. Differential scanning calorimetry showed a shift of melting temperature of the soft segment in the nanocomposites compared to neat PU, possibly due to the nucleating effect of stearate‐intercalated LDH on the crystal structure of PU. All these findings are promising for the development of mechanically improved, thermally stable novel PU nanocomposites. Copyright © 2011 Society of Chemical Industry
α‐Amino acids as initiators of ε‐caprolactone and L,L‐lactide polymerization
Authors: Oledzka Ewa , Sokolowski Kamil , Sobczak Marcin , Kolodziejski Waclaw 
Published: January 2011

AbstractBiodegradable polymers/oligomers were successfully synthesized through a ring‐opening polymerization of ε‐caprolactone and L,L‐lactide, initiated by L‐arginine and L‐citrulline. The α‐amino acid initiators are natural, operationally simple, inexpensive, environmentally friendly and safe for human health. The polymerizations were performed with no solvents and without introducing any metal impurities. The chemical structures of the polymers obtained were elucidated using 1H NMR, 13C NMR and Fourier transform infrared spectroscopies. In addition, incorporation of α‐amino acid molecules into the polymer chain was confirmed using matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry. Due to the significant biological activity of L‐arginine and L‐citrulline, these α‐amino acid initiators may open a new route for the synthesis of functional polymers especially for pharmaceutical applications. Copyright © 2011 Society of Chemical Industry
2‐Methyl‐2,4‐pentanediol induces spontaneous assembly of staphylococcal α‐hemolysin into heptameric pore structure
Authors: Tanaka Yoshikazu , Hirano Nagisa , Kaneko Jun , Kamio Yoshiyuki , Yao Min , Tanaka Isao 
Published: January 2011

AbstractStaphylococcal α‐hemolysin is expressed as a water‐soluble monomeric protein and assembles on membranes to form a heptameric pore structure. The heptameric pore structure of α‐hemolysin can be prepared from monomer in vitro only in the presence of deoxycholate detergent micelles, artificially constructed phospholipid bilayers, or erythrocytes. Here, we succeeded in preparing crystals of the heptameric form of α‐hemolysin without any detergent but with 2‐methyl‐2,4‐pentanediol (MPD), and determined its structure. The structure of the heptameric pore was similar to that reported previously. In the structure, two molecules of MPD were bound around Trp179, around which phospholipid head groups were bound in the heptameric pore structure reported previously. Size exclusion chromatography showed that α‐hemolysin did not assemble spontaneously even when stored for 1 year. SDS‐PAGE analysis revealed that, among the compounds in the crystallizing buffer, MPD could induce heptamer formation. The concentration of MPD that most efficiently induced oligomerization was between 10 and 30%. Based on these observations, we propose MPD as a reagent that can facilitate heptameric pore formation of α‐hemolysin without membrane binding.
A structure‐based benchmark for protein–protein binding affinity
Authors: Kastritis Panagiotis L. , Moal Iain H. , Hwang Howook , Weng Zhiping , Bates Paul A. , Bonvin Alexandre M. J. J. , Janin Joël 
Published: January 2011

AbstractWe have assembled a nonredundant set of 144 protein–protein complexes that have high‐resolution structures available for both the complexes and their unbound components, and for which dissociation constants have been measured by biophysical methods. The set is diverse in terms of the biological functions it represents, with complexes that involve G‐proteins and receptor extracellular domains, as well as antigen/antibody, enzyme/inhibitor, and enzyme/substrate complexes. It is also diverse in terms of the partners' affinity for each other, with Kd ranging between 10−5 and 10−14M. Nine pairs of entries represent closely related complexes that have a similar structure, but a very different affinity, each pair comprising a cognate and a noncognate assembly. The unbound structures of the component proteins being available, conformation changes can be assessed. They are significant in most of the complexes, and large movements or disorder‐to‐order transitions are frequently observed. The set may be used to benchmark biophysical models aiming to relate affinity to structure in protein–protein interactions, taking into account the reactants and the conformation changes that accompany the association reaction, instead of just the final product.
Fic domain‐catalyzed adenylylation: Insight provided by the structural analysis of the type IV secretion system effector BepA
Authors: Palanivelu Dinesh V. , Goepfert Arnaud , Meury Marcel , Guye Patrick , Dehio Christoph , Schirmer Tilman 
Published: January 2011

AbstractNumerous bacterial pathogens subvert cellular functions of eukaryotic host cells by the injection of effector proteins via dedicated secretion systems. The type IV secretion system (T4SS) effector protein BepA from Bartonella henselae is composed of an N‐terminal Fic domain and a C‐terminal Bartonella intracellular delivery domain, the latter being responsible for T4SS‐mediated translocation into host cells. A proteolysis resistant fragment (residues 10–302) that includes the Fic domain shows autoadenylylation activity and adenylyl transfer onto Hela cell extract proteins as demonstrated by autoradiography on incubation with α‐[32P]‐ATP. Its crystal structure, determined to 2.9‐Å resolution by the SeMet‐SAD method, exhibits the canonical Fic fold including the HPFxxGNGRxxR signature motif with several elaborations in loop regions and an additional β‐rich domain at the C‐terminus. On crystal soaking with ATP/Mg2+, additional electron density indicated the presence of a PPi/Mg2+ moiety, the side product of the adenylylation reaction, in the anion binding nest of the signature motif. On the basis of this information and that of the recent structure of IbpA(Fic2) in complex with the eukaryotic target protein Cdc42, we present a detailed model for the ternary complex of Fic with the two substrates, ATP/Mg2+ and target tyrosine. The model is consistent with an in‐line nucleophilic attack of the deprotonated side‐chain hydroxyl group onto the α‐phosphorus of the nucleotide to accomplish AMP transfer. Furthermore, a general, sequence‐independent mechanism of target positioning through antiparallel β‐strand interactions between enzyme and target is suggested.
Measuring rapid hydrogen exchange in the homodimeric 36 kDa HIV‐1 integrase catalytic core domain
Authors: Fitzkee Nicholas C. , Torchia Dennis A. , Bax Ad 
Published: January 2011

AbstractMeasurements of rapid hydrogen exchange (HX) of water with protein amide sites contain valuable information on protein structure and function, but current NMR methods for measuring HX rates are limited in their applicability to large protein systems. An alternate method for measuring rapid HX is presented that is well‐suited for larger proteins, and we apply the method to the deuterated, homodimeric 36 kDa HIV‐1 integrase catalytic core domain (CCD). Using long mixing times for water‐amide magnetization exchange at multiple pH values, HX rates spanning more than four orders of magnitude were measured, as well as NOE cross‐relaxation rates to nearby exchangeable protons. HX protection factors for the CCD are found to be large (>104) for residues along the dimer interface, but much smaller in many other regions. Notably, the catalytic helix (residues 152‐167) exhibits low HX protection at both ends, indicative of fraying at both termini as opposed to just the N‐terminal end, as originally thought. Residues in the LEDGF/p75 binding pocket also show marginal stability, with protection factors in the 10–100 range (∼1.4–2.7 kcal/mol). Additionally, elevated NOE cross‐relaxation rates are identified and, as expected, correspond to proximity of the amide proton to a rapidly exchanging proton, typically from an OH side chain. Indirect NOE transfer between H2O and the amide proton of I141, a residue in the partially disordered active site of the enzyme, suggests its proximity to the side chain of S147, an interaction seen in the DNA‐bound form for a homologous integrase.
Contributions of aromatic pairs to the folding and stability of long‐lived human γD‐crystallin
Authors: Kong Fanrong , King Jonathan 
Published: January 2011

AbstractHuman γD‐crystallin (HγD‐Crys) is a highly stable protein that remains folded in the eye lens for the majority of an individual's lifetime. HγD‐Crys exhibits two homologous crystallin domains, each containing two Greek key motifs with eight β‐strands. Six aromatic pairs (four Tyr/Tyr, one Tyr/Phe and one Phe/Phe) are present in the β‐hairpin sequences of the Greek keys. Ultraviolet damage to the aromatic residues in lens crystallins may contribute to the genesis of cataract. Mutant proteins with these aromatic residues substituted with alanines were constructed and expressed inE. coli. All mutant proteins except F115A and F117A had lower thermal stability than the WT protein. In equilibrium experiments in guanidine hydrochloride (GuHCl), all mutant proteins had lower thermodynamic stability than the WT protein. N‐terminal domain (N‐td) substitutions shifted the N‐td transition to lower GuHCl concentration, but the C‐terminal domain (C‐td) transition remained unaffected. C‐td substitutions led to a more cooperative unfolding/refolding process, with both the N‐td and C‐td transitions shifted to lower GuHCl concentration. The aromatic pairs conserved for each Greek key motif (Greek key pairs) had larger contributions to both thermal stability and thermodynamic stability than the other pairs. Aromatic‐aromatic interaction was estimated as 1.5–2.0 kcal/mol. In kinetic experiments, N‐td substitutions accelerated the early phase of unfolding, while C‐td substitutions accelerated the late phase, suggesting independent domain unfolding. Only substitutions of the second Greek key pair of each crystallin domain slowed refolding. The second Greek keys may provide nucleation sites during the folding of the double‐Greek‐key crystallin domains.
The structure of human ubiquitin in 2‐methyl‐2,4‐pentanediol: A new conformational switch
Authors: Huang Kuo Ying , Amodeo Gabriele A. , Tong Liang , McDermott Ann 
Published: January 2011

AbstractA new crystal structure of human ubiquitin is reported at 1.8 Å resolution. Compared with the other known crystal structure or the solution NMR structure of monomeric human ubiquitin, this new structure is similar in its overall fold but differs with respect to the conformation of the backbone in a surface‐exposed region. The conformation reported here resembles conformations previously seen in complex with deubiquinating enzymes, wherein the Asp52/Gly53 main chain and Glu24 side chain move. This movement exposes the backbone carbonyl of Asp52 to the exterior of the molecule, making it possible to engage in hydrogen‐bond contacts with neighboring molecules, rather than in an internal hydrogen bond with the backbone of Glu24. This particular crystal form of ubiquitin has been used in a large number of solid state NMR studies. The structure described here elucidates the origin of many of the chemical shift differences comparing solution and solid state studies.
On the analysis of protein–protein interactions via knowledge‐based potentials for the prediction of protein–protein docking
Authors: Feliu Elisenda , Aloy Patrick , Oliva Baldo 
Published: January 2011

AbstractDevelopment of effective methods to screen binary interactions obtained by rigid‐body protein–protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein–protein binding. We have derived empirical knowledge‐based potential functions for selecting rigid‐body docking poses. These potentials include the energetic component that provides the residues with a particular secondary structure and surface accessibility. These scoring functions have been tested on a state‐of‐art benchmark dataset and on a decoy dataset of permanent interactions. Our results were compared with a residue‐pair potential scoring function (RPScore) and an atomic‐detailed scoring function (Zrank). We have combined knowledge‐based potentials to score protein–protein poses of decoys of complexes classified either as transient or as permanent protein–protein interactions. Being defined from residue‐pair statistical potentials and not requiring of an atomic level description, our method surpassed Zrank for scoring rigid‐docking decoys where the unbound partners of an interaction have to endure conformational changes upon binding. However, when only moderate conformational changes are required (in rigid docking) or when the right conformational changes are ensured (in flexible docking), Zrank is the most successful scoring function. Finally, our study suggests that the physicochemical properties necessary for the binding are allocated on the proteins previous to its binding and with independence of the partner. This information is encoded at the residue level and could be easily incorporated in the initial grid scoring for Fast Fourier Transform rigid‐body docking methods.
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures
Authors: Bernard Aymeric , Vranken Wim F. , Bardiaux Benjamin , Nilges Michael , Malliavin Thérèse E. 
Published: January 2011

AbstractThe classical procedure for nuclear magnetic resonance structure calculation allocates empirical distance ranges and uses historical values for weighting factors. However, Bayesian analysis suggests that there are more optimal choices for potential shape (bounds‐free log‐harmonic shape) and restraints weights. We compare the classical protocol with the Bayesian approach for more than 300 protein structures. We analyze the conformation similarity to the corresponding X‐ray crystal structure, the distribution of the conformations around their average, and independent validation criteria. On average, the log‐harmonic potential reduces the difference to the X‐ray crystal structure. If the log‐harmonic potential is used, the constant weighting tightens the distribution around the average conformation, with respect to the distributions obtained with Bayesian weighting. Conversely, the structure quality is improved by the Bayesian weighting over the classical procedure, whereas constant weighting worsens some criteria. The quality improvement obtained with the log‐harmonic potential coupled to Bayesian weighting validates this approach on a representative set of protein structures. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Rational design of new agrochemical fungicides using substructural descriptors
Authors: Speck‐Planche Alejandro , Guilarte‐Montero Lisvey , Yera‐Bueno Reider , Rojas‐Vargas Julio A , García‐López América , Uriarte Eugenio , Molina‐Pérez Enrique 
Published: January 2011

AbstractBACKGROUND:The increasing resistance of several phytopathogenic fungal species to existing agrochemical fungicides has alarmed the worldwide scientific community. In an attempt to overcome this problem, a discriminant model based on substructural descriptors was developed from a heterogeneous database of compounds for the design of, search for and prediction of agrochemical fungicides.RESULTS:The discriminant model classifies correctly 81.95% of the fungicides and 81.54% of the inactive compounds in the training series, with an accuracy of 81.72%. In the prediction series, the percentage of correct classification was 80.59 and 85.56% for fungicides and inactive compounds respectively, with an accuracy of 83.44%. Some fragments were extracted and their contributions were calculated. From the fragments that were determined to make positive contributions to the fungicidal activity, new molecules such as pyrrole derivatives were designed and the probabilities of their being fungicides were calculated. These molecules were correctly classified as potential fungicides.CONCLUSION:The discriminant model based on substructural descriptors provides a promising methodology for the development of molecular patterns to be used in the design of, search for and prediction of agrochemical fungicides of wide spectrum. This constitutes an alternative for the discovery of compounds that are able to decrease crop losses caused by phytopathogenic fungal species. Copyright © 2011 Society of Chemical Industry
Field control of Fusarium ear rot, Ostrinia nubilalis (Hübner), and fumonisins in maize kernels
Authors: Mazzoni Emanuele , Scandolara Andrea , Giorni Paola , Pietri Amedeo , Battilani Paola 
Published: January 2011

AbstractBACKGROUND: A 6 year study was conducted to evaluate the possible support of pesticides in mitigating mycotoxin contamination in maize grown in northern Italy. Different pesticides to control Ostrinia nubilalis (Hübner) (ECB), Fusarium verticillioides (Sacc.) Nirenb. and Aspergillus flavus Link were considered to check their efficacy and the best schedule to reduce fumonisin and aflatoxin contamination.RESULTS: Fumonisin B1 (FB1) contamination at harvest has been reduced by ECB control, while the addition of ingredients targeted to F. verticillioides gave a limited advantage, mainly with low FB1 contamination; nevertheless, fusaria control is relevant in high‐risk conditions, when FB1 is likely to exceed the legal limit. The combination of fungal and pest control in a single spray at silk browning stage (BBCH 67) is the best way of application. These results are robust because they were obtained in a 6 year trial, with relevant differences in meteorological conditions, ECB and fungal presence and mycotoxin contamination.CONCLUSION: Insecticides have been shown to give advantages in their application, while the low FB1 contamination in the final years of the study did not lead to conclusive data on the advantage of adding a fungicide. Chemicals applied did not modify A. flavus incidence or aflatoxin contamination (only detected in trace amounts). Copyright © 2011 Society of Chemical Industry