bluuebunny/crossref_metadata_2025_split huggingface dataset:
Goal‐Oriented Adaptivity for Optimization of Elliptic Systems subject to Pointwise Inequality Constraints: Application to Free Material Optimization
Authors: Wollner Winnifried 
Published: November 2010

AbstractWe are concerned with the derivation of goal‐oriented error estimates in the context of free material optimization. We will discuss the derivation of an error representation with respect to the cost functional of the optimization problem. Then we will use this representation in order to obtain a computable error estimator. The efficiency of the estimator is shown on a model problem in free material optimization. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A Regularized Sharp Interface Model for Phase Transformation Accounting for Prescribed Sharp Interface Kinetics
Authors: Hildebrand Felix , Miehe Christian 
Published: November 2010

AbstractThe macroscopic mechanical behavior of multi‐phasic materials depends on the formation and evolution of their microstructure by means of phase transformation. In case of martensitic transformations, the resulting phase boundaries are sharp interfaces. We carry out a geometrically motivated discussion of the regularization of such sharp interfaces by use of an order parameter/phase‐field and exploit the results for a regularized sharp interface model for two‐phase elastic materials with evolving phase boundaries. To account for the dissipative effects during phase transition, we model the material as a generalized standard medium with energy storage and a dissipation function that determines the evolution of the regularized interface. Making use of the level‐set equation, we are thereby able to directly translate prescribed sharp interface kinetic relations to the constitutive model in the regularized setting. We develop a suitable incremental variational three‐field framework for the dissipative phase transformation problem. Finally, the modeling capability and the associated numerical solution techniques are demonstrated by means of a representative numerical example. (© 2010 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Structures of the first and second double‐stranded RNA‐binding domains of human TAR RNA‐binding protein
Authors: Yamashita Seisuke , Nagata Takashi , Kawazoe Masahito , Takemoto Chie , Kigawa Takanori , Güntert Peter , Kobayashi Naohiro , Terada Takaho , Shirouzu Mikako , Wakiyama Motoaki , Muto Yutaka , Yokoyama Shigeyuki 
Published: November 2010

AbstractThe TAR RNA‐binding Protein (TRBP) is a double‐stranded RNA (dsRNA)‐binding protein, which binds to Dicer and is required for the RNA interference pathway. TRBP consists of three dsRNA‐binding domains (dsRBDs). The first and second dsRBDs (dsRBD1 and dsRBD2, respectively) have affinities for dsRNA, whereas the third dsRBD (dsRBD3) binds to Dicer. In this study, we prepared the single domain fragments of human TRBP corresponding to dsRBD1 and dsRBD2 and solved the crystal structure of dsRBD1 and the solution structure of dsRBD2. The two structures contain an α−β−β−β−α fold, which is common to the dsRBDs. The overall structures of dsRBD1 and dsRBD2 are similar to each other, except for a slight shift of the first α helix. The residues involved in dsRNA binding are conserved. We examined the small interfering RNA (siRNA)‐binding properties of these dsRBDs by isothermal titration colorimetry measurements. The dsRBD1 and dsRBD2 fragments both bound to siRNA, with dissociation constants of 220 and 113 nM, respectively. In contrast, the full‐length TRBP and its fragment with dsRBD1 and dsRBD2 exhibited much smaller dissociation constants (0.24 and 0.25 nM, respectively), indicating that the tandem dsRBDs bind simultaneously to one siRNA molecule. On the other hand, the loop between the first α helix and the first β strand of dsRBD2, but not dsRBD1, has a Trp residue, which forms hydrophobic and cation‐π interactions with the surrounding residues. A circular dichroism analysis revealed that the thermal stability of dsRBD2 is higher than that of dsRBD1 and depends on the Trp residue.
Structure of Sir2Tm bound to a propionylated peptide
Authors: Bheda Poonam , Wang Jennifer T. , Escalante‐Semerena Jorge C. , Wolberger Cynthia 
Published: November 2010

AbstractLysine propionylation is a recently identified post‐translational modification that has been observed in proteins such as p53 and histones and is thought to play a role similar to acetylation in modulating protein activity. Members of the sirtuin family of deacetylases have been shown to have depropionylation activity, although the way in which the sirtuin catalytic site accommodates the bulkier propionyl group is not clear. We have determined the 1.8 Å structure of a Thermotoga maritima sirtuin, Sir2Tm, bound to a propionylated peptide derived from p53. A comparison with the structure of Sir2Tm bound to an acetylated peptide shows that hydrophobic residues in the active site shift to accommodate the bulkier propionyl group. Isothermal titration calorimetry data show that Sir2Tm binds propionylated substrates more tightly than acetylated substrates, but kinetic assays reveal that the catalytic rate of Sir2Tm deacylation of propionyl‐lysine is slightly reduced to acetyl‐lysine. These results serve to broaden our understanding of the newly identified propionyl‐lysine modification and the ability of sirtuins to depropionylate, as well as deacetylate, substrates.
Site‐specific 19F NMR chemical shift and side chain relaxation analysis of a membrane protein labeled with an unnatural amino acid
Authors: Shi Pan , Wang Hu , Xi Zhaoyong , Shi Chaowei , Xiong Ying , Tian Changlin 
Published: November 2010

AbstractSite‐specific 19F chemical shift and side chain relaxation analysis can be applied on large size proteins. Here, one‐dimensional 19F spectra and T1, T2 relaxation data were acquired on a SH3 domain in aqueous buffer containing 60% glycerol, and a nine‐transmembrane helices membrane protein diacyl‐glycerol kinase (DAGK) in dodecyl phosphochoine (DPC) micelles. The high quality of the data indicates that this method can be applied to site‐specifically analyze side chain internal mobility of membrane proteins or large size proteins.
Solution structure of the human HSPC280 protein
Authors: Lin Jinzhong , Zhou Tao , Wang Jinfeng 
Published: November 2010

AbstractThe human HSPC280 protein belongs to a new family of low molecular weight proteins, which is only present in eukaryotes, and is absent in fungi. The solution structure of HSPC280 was determined using multidimensional NMR spectroscopy. The overall structure consists of three α‐helices and four antiparallel β‐strands and has a winged helix‐like fold. However, HEPC280 is not a typical DNA‐binding winged helix protein in that it lacks DNA‐binding activity. Unlike most winged‐helix proteins, HSPC280 has an unusually long 13‐residue (P62–V74) wing 1 loop connecting the β3 and β4 strands of the protein. Molecules of HSPC280 have a positively charged surface on one side and a negatively charged surface on the other side of the protein structure. Comparisons with the C‐terminal 80‐residue domain of proteins in the Abra family reveal a conserved hydrophobic groove in the HSPC280 family, which may allow HSPC280 to interact with other proteins.
Idiosyncrasy and identity in the prokaryotic phe‐system: Crystal structure of E. coli phenylalanyl‐tRNA synthetase complexed with phenylalanine and AMP
Authors: Mermershtain Inbal , Finarov Igal , Klipcan Liron , Kessler Naama , Rozenberg Haim , Safro Mark G. 
Published: November 2010

AbstractThe crystal structure of Phenylalanyl‐tRNA synthetase from E. coli (EcPheRS), a class II aminoacyl‐tRNA synthetase, complexed with phenylalanine and AMP was determined at 3.05 Å resolution. EcPheRS is a (αβ)2 heterotetramer: the αβ heterodimer of EcPheRS consists of 11 structural domains. Three of them: the N‐terminus, A1 and A2 belong to the α‐subunit and B1‐B8 domains to the β subunit. The structure of EcPheRS revealed that architecture of four helix‐bundle interface, characteristic of class IIc heterotetrameric aaRSs, is changed: each of the two long helices belonging to CLM transformed into the coil‐short helix structural fragments. The N‐terminal domain of the α‐subunit in EcPheRS forms compact triple helix domain. This observation is contradictory to the structure of the apo form of TtPheRS, where N‐terminal domain was not detected in the electron density map. Comparison of EcPheRS structure with TtPheRS has uncovered significant rearrangements of the structural domains involved in tRNAPhe binding/translocation. As it follows from modeling experiments, to achieve a tighter fit with anticodon loop of tRNA, a shift of ∼5 Å is required for C‐terminal domain B8, and of ∼6 to 7 Å for the whole N terminus. EcPheRSs have emerged as an important target for the incorporation of novel amino acids into genetic code. Further progress in design of novel compounds is anticipated based on the structural data of EcPheRS.
Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima
Authors: Forse G. Jason , Ram Nina , Banatao D. Rey , Cascio Duilio , Sawaya Michael R. , Klock Heath E. , Lesley Scott A. , Yeates Todd O. 
Published: November 2010

AbstractProtein crystallization continues to be a major bottleneck in X‐ray crystallography. Previous studies suggest that symmetric proteins, such as homodimers, might crystallize more readily than monomeric proteins or asymmetric complexes. Proteins that are naturally monomeric can be made homodimeric artificially. Our approach is to create homodimeric proteins by introducing single cysteines into the protein of interest, which are then oxidized to form a disulfide bond between the two monomers. By introducing the single cysteine at different sequence positions, one can produce a variety of synthetically dimerized versions of a protein, with each construct expected to exhibit its own crystallization behavior. In earlier work, we demonstrated the potential utility of the approach using T4 lysozyme as a model system. Here we report the successful application of the method to Thermotoga maritima CelA, a thermophilic endoglucanase enzyme with low sequence identity to proteins with structures previously reported in the Protein Data Bank. This protein had resisted crystallization in its natural monomeric form, despite a broad survey of crystallization conditions. The synthetic dimerization of the CelA mutant D188C yielded well‐diffracting crystals with molecules in a packing arrangement that would not have occurred with native, monomeric CelA. A 2.4 Å crystal structure was determined by single anomalous dispersion using a seleno‐methionine derivatized protein. The results support the notion that synthetic symmetrization can be a useful approach for enlarging the search space for crystallizing monomeric proteins or asymmetric complexes.
N‐glycosylation efficiency is determined by the distance to the C‐terminus and the amino acid preceding an Asn‐Ser‐Thr sequon
Authors: Bañó‐Polo Manuel , Baldin Francesca , Tamborero Silvia , Marti‐Renom Marc A. , Mingarro Ismael 
Published: November 2010

AbstractN‐glycosylation is the most common and versatile protein modification. In eukaryotic cells, this modification is catalyzed cotranslationally by the enzyme oligosaccharyltransferase, which targets the β‐amide of the asparagine in an Asn‐Xaa‐Ser/Thr consensus sequon (where Xaa is any amino acid but proline) in nascent proteins as they enter the endoplasmic reticulum. Because modification of the glycosylation acceptor site on membrane proteins occurs in a compartment‐specific manner, the presence of glycosylation is used to indicate membrane protein topology. Moreover, glycosylation sites can be added to gain topological information. In this study, we explored the determinants of N‐glycosylation with the in vitro transcription/translation of a truncated model protein in the presence of microsomes and surveyed 25,488 glycoproteins, of which 2,533 glycosylation sites had been experimentally validated. We found that glycosylation efficiency was dependent on both the distance to the C‐terminus and the nature of the amino acid that preceded the consensus sequon. These findings establish a broadly applicable method for membrane protein tagging in topological studies.
Structural characterization reveals that a PilZ domain protein undergoes substantial conformational change upon binding to cyclic dimeric guanosine monophosphate
Authors: Shin Jae‐Sun , Ryu Kyoung‐Seok , Ko Junsang , Lee Arum , Choi Byong‐Seok 
Published: November 2010

AbstractPA4608 is a single PilZ domain protein from Pseudomonas aeruginosa that binds to cyclic dimeric guanosine monophosphate (c‐di‐GMP). Although the monomeric structure of unbound PA4608 has been studied in detail, the molecular details of c‐di‐GMP binding to this protein are still uncharacterized. Hence, we determined the solution structure of c‐di‐GMP bound PA4608. We found that PA4608 undergoes conformational changes to expose the c‐di‐GMP binding site by ejection of the C‐terminal 310 helix. A dislocation of the C‐terminal tail in the presence of c‐di‐GMP implies that this region acts as a lid that alternately covers and exposes the hydrophobic surface of the binding site. In addition, mutagenesis and NOE data for PA4608 revealed that conserved residues are in contact with the c‐di‐GMP molecule. The unique structural characteristics of PA4608, including its monomeric state and its ligand binding characteristics, yield insight into its function as a c‐di‐GMP receptor.
Optical and scintillation properties of Pr3+‐doped Ca3(BO3)2 single crystals
Authors: Fujimoto Y. , Yanagida T. , Yokota Y. , Kawaguchi N. , Fukuda K. , Totsuka D. , Watanabe K. , Yamazaki A. , Chani V. , Yoshikawa A. 
Published: November 2010

AbstractOptical and scintillation properties of Pr3+‐activated Ca3(BO3)2 (CBO) single crystals for neutron scintillator applications were examined. The crystals were grown by the micro‐pulling down (µ‐PD) method. In transmittance spectra, two absorption lines at 210 and 245 nm were observed and they were identified as Pr3+ transition from the ground state 3H to 5d state. The both of photo‐ and radio‐luminescence spectra of Pr3+‐doped CBO crystals demonstrated intense peak at 260 and 310 nm which was ascribed to the transition from the lowest 5d excited state to the 4f ground state levels of 3H. The main decay component was about 16–17 ns under 245 nm excitation wavelength. The relative scintillation light yield of 1.0% Pr3+‐doped CBO was about 90% when compared with that of reference Li‐glass scintillator (GS20) under 241Am 5.5 MeV α‐ray excitation, while that measured under 252Cf neutron irradiation was about 20%. It was concluded that this difference originated from the difference of energy released from the neutron reactions.
First‐principles calculation of vibrational properties of B12As2 crystal
Authors: Fan Zhaochuan , Wang Bin , Xu Xiaoxuan , Cao Xuewei , Wang Yufang 
Published: November 2010

AbstractWe use density functional perturbation theory (DFPT) to simulate the 26 vibrational modes of B12As2 crystal at the Γ point. All the 12 Raman‐active modes are in good agreement with experimental Raman spectra of B12As2. We explain several controversial modes of the past, such as the predicted Raman‐active mode with a low frequency and the Raman‐active mode at 503 cm−1. We also plot the dispersion curves of B12As2 from Brillouin zone center to Z (0.5, 0.5, 0.5) and to A (0.5, 0.0, 0.0). We determine the acoustic branch speeds to be in the range 9850–10 980 m/s for LA and 6940–7220 m/s for TA modes. Finally, we give the predicted physical properties, including the phonon entropy, the phonon heat capacity, elastic constants, and bulk modulus.
First‐principles study on the electronic structure of dilute magnetic semiconductor Ga1−xCrxP in zinc‐blende phase
Authors: Huang H. M. , Luo S. J. , Yao K. L. 
Published: November 2010

AbstractWe employ the full potential linearized augmented plane wave (FP‐LAPW) method based on spin‐polarized density functional theory (DFT) in order to investigate the structural, electronic, and magnetic properties of ordered dilute magnetic semiconductor (DMS) Ga1−xCrxP in zinc‐blende phase. The calculated electronic band structures and density of states of these DMSs are discussed. The results show that the ferromagnetic states are more favorable in energy than antiferromagnetic states. Ga1−xCrxP for x = 0.125, 0.25, and 0.50 exhibits half‐metallic (HM) characteristic with integral magnetic moment, and the sensitivity of half‐metallicity of Ga1−xCrxP as a function of lattice constant is also discussed.
Calculation of dissociation constants and chemical hardness of some biologically important molecules: A theoretical study
Authors: Vyas Nidhi , Ojha Animesh K. 
Published: November 2010

AbstractThe gas‐phase geometries of neutral, protonated, and deprotonated forms of some biologically important molecules, alanine (Ala), glycine (Gly), phenylalanine (Phe), and tyrosine (Tyr), were optimized using density functional theory at B3LYP/6‐311++G(d) and the ab initio HF/6‐311++G(d) level of theories. The neutral and different stable ionic states of Ala, Gly, Phe, and Tyr have also been solvated in aqueous medium using polarizable continuum model for the determination of solvation free energies in the aqueous solution. The gas‐phase acidity constants of above four molecules have been also calculated at both levels of theories and found that the values calculated at HF/6‐311++G(d) method are in good agreement with experimental results. A thermodynamic cycle was used to determine the solvation free energies for the proton dissociation process in aqueous solution and the corresponding pKa values of these molecules. The pKa values calculated at B3LYP/6‐311++G(d) method are well supported by the experimental data with a mean absolute deviation 0.12 pKa units. Additionally, the chemical hardness and the ionization potential (IP) for these molecules have been also explored at both the level of theories. The Tyr has less value of chemical hardness and IP at both levels of theories compared with other three molecules, Ala, Gly, and Phe. The calculated values of chemical hardness and IP are decreasing gradually with the substitution of the various functional groups in the side chain of the amino acids. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Prediction of microscopic protonation constants of polybasic molecules via computational methods: A complete microequilibrium analysis of spermine
Authors: Salehzadeh Sadegh , Gholiee Yasin , Bayat Mehdi 
Published: November 2010

AbstractFor the first time, a simple methodology is reported for theoretical calculation of microscopic protonation constants of polybasic molecules in solution. Density functional theory study was used for complete microequilibrium analysis of spermine, H2N(CH2)3NH(CH2)4NH(CH2)3NH2, a linear tetraamine with 16 known microspecies. A general thermodynamic cycle is proposed to calculate protonation microconstants of polybasic molecules using calculated micro‐ΔG values in aqueous solution. The microscopic protonation constants were determined with considering both the most abundant and most stable conformers for all microspecies. The results show that the microscopic protonation constants derived from the most abundant conformers (i.e., linear conformers in which the intramolecular hydrogen bonding does not exist) are in good agreement with the corresponding available experimental data. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Theoretical investigations on the weak nonbonded CS···CH2 interactions: Chalcogen‐bonded complexes with singlet carbene as an electron donor
Authors: Zhao Qiang , Feng Dacheng , Sun Youmin , Hao Jingcheng , Cai Zhengting 
Published: November 2010

AbstractIn this article, we explored the noncovalent bonding interactions between OCS, SCS, F2CS, Cl2CS, and singlet carbene. Six chalcogen‐bonded complexes were obtained. It is found that all the vibrational frequencies of CS bond presented a red shift character. Interaction energy, topology property of the electron density and its Laplacian, and the donor–acceptor interaction have been investigated. All these results show that there exists a weak nonbonded interaction between the chalcogen bond donor and CH2. An energy decomposition analysis was performed to disclose that the electrostatic interaction is the main stabilized factor in these nonbonded complexes. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
In‐gel protein N‐ and C‐termini identification and its application for transgenic protein characterization
Authors: Xiang Bosong , Macisaac Susan , Lardizabal Kathryn , Li Bin 
Published: November 2010

AbstractA new method for the determination of N‐ and C‐termini of a protein isolated in a polyacrylamide gel is introduced. In‐gel partial protein hydrolysis by hydrochloric acid is used to generate N‐ and C‐terminal peptides for identification. This new method is complementary to existing techniques. The application of the in‐gel protein termini identification technique to the characterization of the transgenic protein diacylglycerol acyltransferase (UrDGAT2A) purified from soybean seeds is also reported here. Both N‐ and C‐termini of UrDGAT2A were successfully identified and the N‐terminus was found to be blocked by acetylation. The analysis results of UrDGAT2A and two commercial proteins (bovine serum albumin (BSA) and alcohol dehydrogenase) are used to demonstrate the effectiveness of the method in identifying actual N‐ and C‐termini, terminal truncation and blocking. Copyright © 2010 John Wiley & Sons, Ltd.
A suite of sensitive chemical methods to determine the δ15N of ammonium, nitrate and total dissolved N in soil extracts
Authors: Lachouani Petra , Frank Alexander H. , Wanek Wolfgang 
Published: November 2010

AbstractNatural 15N abundances (δ15N values) of different soil nitrogen pools deliver crucial information on the soil N cycle for the analysis of biogeochemical processes. Here we report on a complete suite of methods for sensitive δ15N analysis in soil extracts. A combined chemical reaction of vanadium(III) chloride (VCl3) and sodium azide under acidic conditions is used to convert nitrate into N2O, which is subsequently analyzed by purge‐and‐trap isotope ratio mass spectrometry (PTIRMS) with a cryo‐focusing unit. Coupled with preparation steps (microdiffusion for collection of ammonium, alkaline persulfate oxidation to convert total dissolved N (TDN) or ammonium into nitrate) this allows the determination of the δ15N values of nitrate, ammonium and total dissolved N (dissolved organic N, microbial biomass N) in soil extracts with the same basic protocol. The limits of quantification for δ15N analysis with a precision of 0.5‰ were 12.4 µM for ammonium, 23.7 µM for TDN, 16.5 µM for nitrate and 22.7 µM for nitrite. Copyright © 2010 John Wiley & Sons, Ltd.