bluuebunny/crossref_metadata_2025_split huggingface dataset:
One‐pot synthesis of polyrotaxane by clipping and cyclopolymerization of α,ω‐diethynyl isophthalamide with pyridiniumdicarboxamide chloride
Authors: Isono Takuya , Satoh Toshifumi , Kakuchi Toyoji 
Published: May 2011

AbstractThe one‐pot synthesis of a main chain‐type polyrotaxane composed of axle molecules threaded through the macrocyclic units on the polymer main chain was achieved via the combination of cyclopolymerization and clipping procedures. The cyclopolymerization of an α,ω‐diethynyl monomer bearing an isophthalamide moiety (1), which clips onto an axle component bearing a pyridiniumdicarboxamide moiety (2·Cl) through a chloride anion was carried out in chloroform with the monomer concentration of 0.06 mol L−1 at 40 °C using [Rh(nbd)Cl]2/Et3N as a catalyst to afford a gel‐free polymer. The resulting polymer was assigned to the main chain‐type polyrotaxane with a poly(phenylacetylene) backbone (poly‐3·Cl) based on size exclusion chromatography and 1H NMR measurements. The diffusion‐order two‐dimensional NMR and circular dichroism spectra provided definitive proof of the rotaxaned architecture in the polymer. The mole fraction of the rotaxane unit in the total cyclic repeating unit was determined to be 26.3%. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
Preparation of porous crosslinked polymers with different surface morphologies via chemically induced phase separation
Authors: Luo Yu‐Shun , Cheng Kuo‐Chung , Huang Nan‐Du , Chiang Wen‐Pang , Li Shun‐Fu 
Published: May 2011

AbstractA novel and simple method for producing crosslinked polymers with controlled surface morphology is demonstrated in this study. The porous crosslinked polymers were made via stepwise polymerization of a mixture of epoxy resin, D.E.R. 331, and diethylene triamine in diisobutyl ketone (DIBK). Both the surface and bulk morphology of the cured polymers are dependent on the solvent fraction of the reactive solution. When the concentration of DIBK was more than about 30 vol %, chemically induced phase separation (CIPS) occurred during cure at 30 °C, and closed spherical pores, about 4 μm in diameter, appeared in the bulk of the crosslinked polymers, whose diameter increased to about 4.5 and 9 μm when the solvent was increased to 40% and 50%, respectively. The surface morphology of the epoxy networks is different from that of the bulk. Smaller pore size or dense skin was formed via the CIPS process, which can be tailored by covering the reactive solution with different contacting films during cure. The competition between the solvent‐rich and polymer‐rich phase absorbed onto the surface of contacting film could change the surface morphology. Therefore, the porous crosslinked polymers having similar bulk morphology could be prepared with a variety of surface structures. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Interactions of hydrophilic plasticizer molecules with amorphous starch biopolymer—an investigation into the glass transition and the water activity behavior
Authors: Liu Huihua , Chaudhary Deeptangshu , Ingram Gordon , John Joseph 
Published: May 2011

AbstractIn this article, we demonstrated that within a hydrophilic biopolymer–plasticizer system, the molecular “activity” of the plasticizer also influenced the extent of these interactions. We demonstrated through an analysis of crystallinity and calorimetry results that the equilibrium moisture content within the starch matrix can preferentially interact with the hydrophilic plasticizers and modify the polymer recrystallization process to an extent that the commonly acknowledged relationship between the crystallinity and the glass transition behavior is disrupted. Two plasticizers, glycerol (three OH groups) and xylitol (five OH groups), were selected. The water sorption isotherm of polymer samples with 5–20 wt % (dry basis) plasticizers were examined across a water activity range from ∼0.11 to ∼0.95 and using Guggenheim‐Anderson‐de Boer analysis, we compared the molar sorption enthalpies of various starch–plasticizer mixtures. Finally, the competitive plasticization between water and plasticizer molecules at different water activities was also discussed using known glass transition models. The analyses validated the antiplasticization limit for glycerol to be ∼10–15 wt %, but for xylitol, its antiplasticization behavior did not manifest till 20 wt %. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011
Trifluoperazine regulation of calmodulin binding to Fas: A computational study
Authors: Pan Di , Yan Qi , Chen Yabing , McDonald Jay M. , Song Yuhua 
Published: May 2011

AbstractDeath‐inducing signaling complex (DISC) formation is a critical step in Fas‐mediated signaling for apoptosis. Previous experiments have demonstrated that the calmodulin (CaM) antagonist, trifluoperazine (TFP) regulates CaM‐Fas binding and affects Fas‐mediated DISC formation. In this study, we investigated the anti‐cooperative characteristics of TFP binding to CaM and the effect of TFP on the CaM‐Fas interaction from both structural and thermodynamic perspectives using combined molecular dynamics simulations and binding free energy analyses. We studied the interactions of different numbers of TFP molecules with CaM and explored the effects of the resulting conformational changes in CaM on CaM‐Fas binding. Results from these analyses showed that the number of TFP molecules bound to CaM directly influenced α‐helix formation and hydrogen bond occupancy within the α‐helices of CaM, contributing to the conformational and motion changes in CaM. These changes affected CaM binding to Fas, resulting in secondary structural changes in Fas and conformational and motion changes of Fas in CaM‐Fas complexes, potentially perturbing the recruitment of Fas‐associated death domain for DISC formation. The computational results from this study reveal the structural and molecular mechanisms that underlie the role of the CaM antagonist, TFP, in regulation of CaM‐Fas binding and Fas‐mediated DISC formation in a concentration‐dependent manner. Proteins 2011; © 2011 Wiley‐Liss, Inc.
SymmRef: A flexible refinement method for symmetric multimers
Authors: Mashiach‐Farkash Efrat , Nussinov Ruth , Wolfson Haim J. 
Published: May 2011

AbstractSymmetric protein complexes are abundant in the living cell. Predicting their atomic structure can shed light on the mechanism of many important biological processes. Symmetric docking methods aim to predict the structure of these complexes given the unbound structure of a single monomer, or its model. Symmetry constraints reduce the search‐space of these methods and make the prediction easier compared to asymmetric protein‐protein docking. However, the challenge of modeling the conformational changes that the monomer might undergo is a major obstacle. In this article, we present SymmRef, a novel method for refinement and reranking of symmetric docking solutions. The method models backbone and side‐chain movements and optimizes the rigid‐body orientations of the monomers. The backbone movements are modeled by normal modes minimization and the conformations of the side‐chains are modeled by selecting optimal rotamers. Since solved structures of symmetric multimers show asymmetric side‐chain conformations, we do not use symmetry constraints in the side‐chain optimization procedure. The refined models are re‐ranked according to an energy score. We tested the method on a benchmark of unbound docking challenges. The results show that the method significantly improves the accuracy and the ranking of symmetric rigid docking solutions. SymmRef is available for download at http:// bioinfo3d.cs.tau.ac.il/SymmRef/download.html. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Molecular dynamics study of small molecule inhibitors of the Bcl‐2 family
Authors: Acoca Stéphane , Cui Qizhi , Shore Gordon C. , Purisima Enrico O. 
Published: May 2011

AbstractWe carried out docking and molecular dynamics simulations on ABT‐737 and obatoclax, which are inhibitors of the Bcl‐2 family of proteins. We modeled the binding mode of ABT‐737 with Bcl‐xL, Bcl‐2, and Mcl‐1 and examined their dynamical behavior. We found that the binding of the chlorobiphenyl end of ABT‐737 was quite stable across all three proteins. However, the phenylpiperazine linker group was dramatically more mobile in Mcl‐1 compared to either Bcl‐xL or Bcl‐2. The S‐phenyl group at the p4 binding site was well‐anchored in Bcl‐xL and Bcl‐2 but was somewhat more mobile in Mcl‐1 although the phenyl ring itself on average stayed close to the p4 binding site in Mcl‐1. This greater mobility is likely due to the greater openness of the p3 and p4 binding sites on Mcl‐1. The calculated binding free energies were consistent with the much weaker binding affinity of ABT‐737 for Mcl‐1. Obatoclax was predicted to bind at the p1 and p2 binding sites of Mcl‐1 and the binding mode was quite stable during the molecular dynamics simulation with Mcl‐1 wrapping around the molecule. The modeled binding mode suggests that obatoclax is able to inhibit all three proteins because it makes use of the p1 and p2 binding sites alone, which is a fairly narrow groove in all three proteins unlike the p4 binding site, which is much broader in Mcl‐1. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Cover and spacer insertions: Small nonhydrophobic accessories that assist protein oligomerization
Authors: Nishi Hafumi , Koike Ryotaro , Ota Motonori 
Published: May 2011

AbstractWe investigated fragmental sequences that were inserted into proteins during long molecular evolution and relevant to the association of homo‐oligomers. Seventeen insertions in 12 SCOP (structure classification of proteins) families were examined and were classified into large and small insertions. The large insertions are composed of interface‐like residues and effectively increase the interface area. In contrast, small insertions are composed of the residues that are not commonly found at the interfaces and have a small interface area: their roles in the oligomerization process are unclear. We found that the small insertions were located in the middle of protein sequences and therefore must involve residues with strong turn and less interface‐like propensities. From a structural viewpoint, small insertions were found to mask hydrophobic patches or act as spacers to fill cavities present at interfaces. The presence or absence of small insertions coincides with the annotated oligomeric states for homologs in the SwissProt database, and the calculation of the association scores predicts that small insertions contribute to the stability of oligomers. These results support the significant role of small, nonhydrophobic insertions in protein oligomerization. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Statistical mechanics‐based method to extract atomic distance‐dependent potentials from protein structures
Authors: Huang Sheng‐You , Zou Xiaoqin 
Published: May 2011

AbstractIn this study, we have developed a statistical mechanics‐based iterative method to extract statistical atomic interaction potentials from known, nonredundant protein structures. Our method circumvents the long‐standing reference state problem in deriving traditional knowledge‐based scoring functions, by using rapid iterations through a physical, global convergence function. The rapid convergence of this physics‐based method, unlike other parameter optimization methods, warrants the feasibility of deriving distance‐dependent, all‐atom statistical potentials to keep the scoring accuracy. The derived potentials, referred to as ITScore/Pro, have been validated using three diverse benchmarks: the high‐resolution decoy set, the AMBER benchmark decoy set, and the CASP8 decoy set. Significant improvement in performance has been achieved. Finally, comparisons between the potentials of our model and potentials of a knowledge‐based scoring function with a randomized reference state have revealed the reason for the better performance of our scoring function, which could provide useful insight into the development of other physical scoring functions. The potentials developed in this study are generally applicable for structural selection in protein structure prediction. © 2011 Wiley‐Liss, Inc.
Estimating the pKa values of basic and acidic side chains in ion channels using electrophysiological recordings: A robust approach to an elusive problem
Authors: Cymes Gisela D. , Grosman Claudio 
Published: May 2011

AbstractAs a step toward gaining a better understanding of the physicochemical bases of pKa‐value shifts in ion channels, we have previously proposed a method for estimating the proton affinities of systematically engineered ionizable side chains from the kinetic analysis of single‐channel current recordings. We reported that the open‐channel current flowing through mutants of the (cation‐selective) muscle nicotinic acetylcholine receptor (AChR) engineered to bear single basic residues in the transmembrane portion of the pore domain fluctuates between two levels of conductance. Our observations were consistent with the idea that these fluctuations track directly the alternate protonation–deprotonation of basic side chains: protonation of the introduced basic group would attenuate the single‐channel conductance, whereas its deprotonation would restore the wild‐type‐like level. Thus, analysis of the kinetics of these transitions was interpreted to yield the pKa values of the substituted side chains. However, other mechanisms can be postulated that would also be consistent with some of our findings but according to which the kinetic analysis of the fluctuations would not yield true pKas. Such mechanisms include the pH‐dependent interconversion between two conformations of the channel that, while both ion permeable, would support different cation‐conduction rates. In this article, we present experimental evidence for the notion that the fluctuations of the open‐channel current observed for the muscle AChR result from the electrostatic interaction between fixed charges and the passing cations rather than from a change in conformation. Hence, we conclude that bona fide pKa values can be obtained from single‐channel recordings. Proteins 2011; © 2011 Wiley‐Liss, Inc.
An NMR study of the N‐terminal domain of wild‐type hERG and a T65P trafficking deficient hERG mutant
Authors: Gayen Shovanlal , Li Qingxin , Chen Angela Shuyi , Nguyen Thi Hanh Thuy , Huang Qiwei , Hill Jeffrey , Kang CongBao 
Published: May 2011

AbstractThe human Ether‐à‐go‐go Related Gene (hERG) potassium channel plays an important role in the heart by controlling the rapid delayed rectifier current. The N‐terminal 135 residues (NTD) contain a Per‐Arnt‐Sim (PAS) domain and an N‐terminal amphipathic helix. NMR relaxation analysis and H/D exchange experiments on the NTD demonstrated that the amphipathic helix is rigid and solvent accessible. An NTD containing a T65P mutation, which causes a hERG channel trafficking deficiency, was purified from E.coli. The mutant protein did not aggregate in gel filtration analysis and the amide cross peaks of its residues disappeared in an HSQC spectrum indicating the possibility of structural changes. A carbon chemical shift comparison of the residues with cross peaks in the HSQC spectrum showed no clear difference between the purified wild‐type protein and the purified mutant. There were multiple conformations observed for the T65P mutant protein at high temperatures from HSQC experiments and a thermal stability assay showed that the T65P mutation reduced the thermal stability of NTD. This instability may affect protein folding or structural dynamics of other regions. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Quantitative use of chemical shifts for the modeling of protein complexes
Authors: Stratmann Dirk , Boelens Rolf , Bonvin Alexandre M. J. J. 
Published: May 2011

AbstractDespite recent advances in the modeling of protein‐protein complexes by docking, additional information is often required to identify the best solutions. For this purpose, NMR data deliver valuable restraints that can be used in the sampling and/or the scoring stage, like in the data‐driven docking approach HADDOCK that can make use of NMR chemical shift perturbation (CSP) data to define the binding site on each protein and drive the docking. We show here that a quantitative use of chemical shifts (CS) in the scoring stage can help to resolve ambiguities. A quantitative CS‐RMSD score based on 1Hα,13Cα, and 15N chemical shifts ranks the best solutions always at the top, as demonstrated on a small benchmark of four complexes. It is implemented in a new docking protocol, CS‐HADDOCK, which combines CSP data as ambiguous interaction restraints in the sampling stage with the CS‐RMSD score in the final scoring stage. This combination of qualitative and quantitative use of chemical shifts increases the reliability of data‐driven docking for the structure determination of complexes from limited NMR data. Proteins 2011; © 2011 Wiley‐Liss, Inc.
On the development of protein pKa calculation algorithms
Authors: Carstensen Tommy , Farrell Damien , Huang Yong , Baker Nathan A. , Nielsen Jens Erik 
Published: May 2011

AbstractProtein pKa calculation methods are developed partly to provide fast non‐experimental estimates of the ionization constants of protein side chains. However, the most significant reason for developing such methods is that a good pKa calculation method is presumed to provide an accurate physical model of protein electrostatics, which can be applied in methods for drug design, protein design, and other structure‐based energy calculation methods. We explore the validity of this presumption by simulating the development of a pKa calculation method using artificial experimental data derived from a human‐defined physical reality. We examine the ability of an RMSD‐guided development protocol to retrieve the correct (artificial) physical reality and find that a rugged optimization landscape and a huge parameter space prevent the identification of the correct physical reality. We examine the importance of the training set in developing pKa calculation methods and investigate the effect of experimental noise on our ability to identify the correct physical reality, and find that both effects have a significant and detrimental impact on the physical reality of the optimal model identified. Our findings are of relevance to all structure‐based methods for protein energy calculations and simulation, and have large implications for all types of current pKa calculation methods. Our analysis furthermore suggests that careful and extensive validation on many types of experimental data can go some way in making current models more realistic. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Electrostatic pKa computations in proteins: Role of internal cavities
Authors: Meyer Tim , Kieseritzky Gernot , Knapp Ernst‐Walter 
Published: May 2011

AbstractThe solvent accessible surface area (SASA) algorithm is conventionally used to characterize protein surfaces in electrostatic energy computations of proteins. Unfortunately, it often fails to find narrow cavities inside a protein. As a consequence pKa computations based on this algorithm perform badly. In this study a new cavity‐algorithm is introduced, which solves this problem and provides improved pKa values. The procedure is applied to 20 pKa values of titratable groups introduced as point mutations in SNase variants, where crystal structures are available. The computations of these pKas are particular challenging, since they are placed in a rather hydrophobic environment. For nine mutants, where the titratable residue is in contact with a large cavity, the RMSD between computed and measured pKa values is 2.04, which is a considerable improvement as compared to the original results obtained with Karlsberg+ (http://agknapp.chemie.fu‐berlin.de/karlsberg/) that yielded an RMSD of 8.8. However, for 11 titratable residues the agreement with experiments remains poor (RMSD = 6.01). Considering 15 pKas of SNase, which are in a more conventional less hydrophobic protein environment, the RMSD is 2.1 using the SASA‐algorithm and 1.7 using the new cavity‐algorithm. The agreement is reasonable but less good than what one would expect from the general performance of Karlsberg+ indicating that SNase belongs to the more difficult proteins with respect to pKa computations. We discuss the possible reasons for the remaining discrepancies between computed and measured pKas. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Optimisation and fabrication of a calorimetric gas sensor built up on a polyimide substrate for H2O2 monitoring
Authors: Kirchner Patrick , Oberländer Jan , Friedrich Peter , Berger Jörg , Suso Henri‐Pierre , Kupyna Andriy , Keusgen Michael , Schöning Michael J. 
Published: May 2011

AbstractA calorimetric gas sensor for the detection of vapourised H2O2 in aseptic filling processes was built up on a polyimide foil instead of silicon as substrate material in order to optimise the sensor response behaviour. The sensor was catalytically activated with a dispersion of manganese(IV) oxide. The reaction mechanism of the exothermic H2O2 decomposition on the catalyst involves two pathways: an initial reaction with electron exchange between the catalyst surface and H2O2 creating free radicals, and a chain reaction of these radicals with H2O2, in which the final products, namely water and oxygen, are formed. The calorimetric gas sensor possesses a linear response behaviour with a sensitivity of 7.15 °C/(% v/v) in a H2O2 concentration range from 0 to 8% v/v. magnified imageCalorimetric gas sensor on polyimide foil for H2O2 monitoring in sterilisation processes.
Luminescence properties of Eu3+, Bi3+ coactivated CaLaNbWO8 red phosphors under near UV and blue excitations
Authors: Thomas Mariyam , Rao Padala Prabhakar , Mahesh Sundaresan Pillai Kamalam , Kumari Leela Sandhya , Koshy Peter 
Published: May 2011

AbstractScheelite type red phosphors CaLa1–xNbWO8: xEu3+ (x = 0.01, 0.03, 0.05, 0.1, 0.15, 0.2, and 0.25) and CaLa0.8–yNbWO8: 0.2Eu3+, yBi3+(y = 0.1, 0.15, and 0.2) were prepared by conventional solid state reaction route. The crystalline structure, morphology and absorbance of these phosphors were characterized by powder X‐ray diffraction (XRD), scanning electron microscope (SEM), Fourier transform infrared (FT‐IR), and UV–Visible absorption spectroscopy. Investigations on their photoluminescent properties indicated that both Eu3+ doped and Eu3+, Bi3+ coactivated samples emit strong red light at 615 nm under both near UV (394 nm) and blue (465 nm) excitations. Bi3+ codoped system showed broadened charge transfer band (CTB) and stronger excitation peaks at 394 and 465 nm. The red emission intensity of CaLa0.8NbWO8: 0.2Eu3+ phosphor is improved by a factor of 2 as 20 mol% Bi3+ is introduced into the system, and is four times stronger than that of the commercial Y2O3:Eu3+ red phosphor. These phosphors are characterized by sharp red emission with color coordinates closer to the standard red phosphors. Thus, the above phosphors could be a promising red candidate for the phosphor converted white light emitting diodes (pc‐WLEDs).