bluuebunny/crossref_metadata_2025 huggingface dataset:
Alignment of Magnetic Nanorods in Solidifying Films
Authors: Gu Yu , Kornev Konstantin G.
Published: October 2013

In this paper, the kinetics of ordering of an assembly of non‐interacting nanorods suspended in a solidifying liquid film is studied theoretically. Assuming random orientation of nanorods at the initial moment of time, the time needed for nanorods to align along the direction of an external magnetic field is estimated. In the solidifying films with exponentially increasing viscosity, the viscous drag significantly resists the nanorod alignment. Therefore, some nanorods might be quenched halfway to the equilibrium orientation even before complete solidification of the film. Different regimes of ordering have been revealed and classified and the criterion for the alignment of nanorods prior to the film solidification has been introduced.
High‐Capacity Anode Materials for Lithium‐Ion Batteries: Choice of Elements and Structures for Active Particles
Authors: Nitta Naoki , Yushin Gleb
Published: October 2013

Growing market demand for portable energy storage has triggered significant research on high‐capacity lithium‐ion (Li‐ion) battery anodes. Various elements have been utilized in innovative structures to enable these anodes, which can potentially increase the energy density and decrease the cost of Li‐ion batteries. In this review, electrode and material parameters are considered in anode fabrication. The periodic table is then used to explore how the choice of anode material affects rate performance, cycle stability, Li‐ion insertion/extraction potentials, voltage hysteresis, volumetric and specific capacities, and other critical parameters. Silicon (Si), germanium (Ge), and tin (Sn) anodes receive more attention in literature and in this review, but other elements, such as antimony (Sb), lead (Pb), magnesium (Mg), aluminum (Al), gallium (Ga), phosphorus (P), arsenic (As), bismuth (Bi), and zinc (Zn) are also discussed. Among conversion anodes focus is placed on oxides, nitrides, phosphides, and hydrides. Nanostructured carbon (C) receives separate consideration. Issues in high‐ capacity research, such as volume change, insufficient coulombic efficiency, and solid electrolyte interphase (SEI) layer stability are elucidated. Finally, advanced carbon composites utilizing carbon nanotubes (CNT), graphene, and size preserving external shells are discussed, including high mass loading (thick) electrodes and electrodes capable of providing load‐bearing properties.
Silica‐Coating of Hematite Nanoparticles Using Reactive Water‐Soluble Polyalkoxysiloxanes
Authors: Doermbach Karla , Agrawal Garima , Servos Mark , Schipmann Susanne , Thies Sabrina , Klemradt Uwe , Pich Andrij
Published: October 2013

In this article, we report on a new one‐step synthetic route to obtain multi‐functional silica‐coated hematite particles using a water‐based surfactant‐free technology. The synthesis and properties of uniform silica‐coated hematite particles with adjustable size, morphology, and silica shell thickness are discussed in detail. The developed method allows simultaneous formation of the silica shell around hematite core and incorporation of reactive groups on the surface of core–shell nanoparticles. Vinyl groups are introduced to the silica surface at once by pre‐functionalization of a water‐soluble hyperbranched polyalkoxysiloxanes with active double bonds. The reactivity of these surface‐immobilized vinyl groups is demonstrated by covalent attachment of rhodamine B using a thiol‐en click reaction.
Ten‐year follow up of hydroxychloroquine treatment for ABCA3 deficiency
Authors: Williamson Michael , Wallis Colin
Published: October 2013

We present a child with interstitial lung disease (ILD) who was diagnosed with desquamative interstitial pneumonitis following CT thorax and open lung biopsy aged 2 years. Subsequently, surfactant protein gene analysis revealed mutations in the ABCA3 gene. This case of ABCA3 deficient ILD describes a stable clinical course over 10 years and highlights the potential benefit of hydroxychloroquine for this condition. Pediatr Pulmonol. 2014; 49:299–301. © 2013 Wiley Periodicals, Inc.
A case for early bronchoscopic airway assessment after disc battery ingestion
Authors: Wurzel Danielle F. , Masters I. Brent , Choo Kelvin L. , Isles Alan F.
Published: October 2013

Disc battery ingestion in children is becoming increasingly common with the proliferation of small battery‐powered electronic devices. In the case of esophageal impaction, the likelihood and severity of complications are proportionate to the time between ingestion and removal. Tracheo‐esophageal fistulae (TOF) are a recognized complication and can be life‐threatening. We describe an interesting case of disc battery ingestion with delayed recognition of a TOF. We document the tracheal mucosal healing process of a large airway defect and describe the role of bronchoscopy in guiding the timing of surgical intervention. This case highlights the important role of early bronchoscopic assessment in management of these patients. Pediatr Pulmonol. 2014; 49:E72–E74. © 2013 Wiley Periodicals, Inc.
Effect of Homolog Doping on Surface Morphology and Mass‐Loss Rates from PETN Crystals: Studies using Atomic Force Microscope and Thermogravimetric Analysis
Authors: Bhattacharia Sanjoy K. , Maiti Amitesh , Gee Richard H. , Nunley Jay , Weeks Brandon L.
Published: October 2013

Pentaerythritol tetranitrate (PETN) is an important energetic material, whose performance as a secondary explosive depends strongly on the density as well as flow porosity of powdered material, which in turn is governed by the size and surface properties of the PETN crystallite particles. Historically there has been evidence that the surface properties of PETN particles can be strongly influenced by the presence of homolog impurities of PETN, in particular, dipentaerythritol hexanitrate (diPEHN) and tripentaerythritol octanitrate (triPEON), although not many systematic studies characterizing such influence exist. In this work we employ thermogravimetric analysis (TGA) to measure mass‐loss rates at elevated temperatures and show that doping with a small amount of diPEHN and triPEON can reduce the mass‐loss rate from PETN single‐crystal surfaces by as much as 35 % as compared to undoped crystals. Arrhenius plots of mass‐loss rates as a function of temperature suggest that the reduction in evaporation is not due to the change in activation barrier of the molecular evaporation process, but perhaps due to the impedance to the receding motion of the steps by the immobile impurities on the surface. Removal of surface impurities through gentle washing with ethanol leads to enhanced mass‐loss rate relative to pure PETN suggesting a roughened surface morphology. Some surface roughening in doped crystals is supported by Atomic force microscopy (AFM) images of growth layers that show evidences of growth layer stacking and rough edges. We also find that a larger amount of impurity added to the original solution does not necessarily lead to a more highly doped crystal, which could perhaps be interpreted as PETN crystals being able to accommodate only up to a certain weight percent of homolog impurities.
Recombinant human lecithin‐cholesterol acyltransferase Fc fusion: Analysis of N‐ and O‐linked glycans and identification and elimination of a xylose‐based O‐linked tetrasaccharide core in the linker region
Authors: Spahr Chris , Kim Justin J. , Deng Sihong , Kodama Paul , Xia Zhen , Tang Jay , Zhang Richard , Siu Sophia , Nuanmanee Noi , Estes Bram , Stevens Jennitte , Zhou Mingyue , Lu Hsieng S.
Published: October 2013

Recombinant human lecithin‐cholesterol acyltransferase Fc fusion (huLCAT‐Fc) is a chimeric protein produced by fusing human Fc to the C‐terminus of the human enzyme via a linker sequence. The huLCAT‐Fc homodimer contains five N‐linked glycosylation sites per monomer. The heterogeneity and site‐specific distribution of the various glycans were examined using enzymatic digestion and LC‐MS/MS, followed by automatic processing. Almost all of the N‐linked glycans in human LCAT are fucosylated and sialylated. The predominant LCAT N‐linked glycoforms are biantennary glycans, followed by triantennary sugars, whereas the level of tetraantennary glycans is much lower. Glycans at the Fc N‐linked site exclusively contain typical asialobiantennary structures. HuLCAT‐Fc was also confirmed to have mucin‐type glycans attached at T407 and S409. When LCAT‐Fc fusions were constructed using a G‐S‐G‐G‐G‐G linker, an unexpected +632 Da xylose‐based glycosaminoglycan (GAG) tetrasaccharide core of Xyl‐Gal‐Gal‐GlcA was attached to S418. Several minor intermediate species including Xyl, Xyl‐Gal, Xyl‐Gal‐Gal, and a phosphorylated GAG core were also present. The mucin‐type O‐linked glycans can be effectively released by sialidase and O‐glycanase; however, the GAG could only be removed and localized using chemical alkaline β‐elimination and targeted LC‐MS/MS. E416 (the C‐terminus of LCAT) combined with the linker sequence is likely serving as a substrate for peptide O‐xylosyltransferase. HuLCAT‐Fc shares some homology with the proposed consensus site near the linker sequence, in particular, the residues underlined PPPE416GS418GGGGDK. GAG incorporation can be eliminated through engineering by shifting the linker Ser residue downstream in the linker sequence.
Probing impact of active site residue mutations on stability and activity of Neisseria polysaccharea amylosucrase
Authors: Daudé David , Topham Christopher M. , Remaud‐Siméon Magali , André Isabelle
Published: October 2013

The amylosucrase from Neisseria polysaccharea is a transglucosidase from the GH13 family of glycoside‐hydrolases that naturally catalyzes the synthesis of α‐glucans from the widely available donor sucrose. Interestingly, natural molecular evolution has modeled a dense hydrogen bond network at subsite −1 responsible for the specific recognition of sucrose and conversely, it has loosened interactions at the subsite +1 creating a highly promiscuous subsite +1. The residues forming these subsites are considered to be likely involved in the activity as well as the overall stability of the enzyme. To assess their role, a structure‐based approach was followed to reshape the subsite −1. A strategy based on stability change predictions, using the FoldX algorithm, was considered to identify the best candidates for site‐directed mutagenesis and guide the construction of a small targeted library. A miniaturized purification protocol was developed and both mutant stability and substrate promiscuity were explored. A range of 8°C between extreme melting temperature values was observed and some variants were able to synthesize series of oligosaccharides with distributions differing from that of the parental enzyme. The crucial role of subsite −1 was thus highlighted and the biocatalysts generated can now be considered as starting points for further engineering purposes.
Selective CGRP and adrenomedullin peptide binding by tethered RAMP‐calcitonin receptor‐like receptor extracellular domain fusion proteins
Authors: Moad Heather E. , Pioszak Augen A.
Published: October 2013

Calcitonin gene‐related peptide (CGRP) and adrenomedullin (AM) are related peptides that are potent vasodilators. The CGRP and AM receptors are heteromeric protein complexes comprised of a shared calcitonin receptor‐like receptor (CLR) subunit and a variable receptor activity modifying protein (RAMP) subunit. RAMP1 enables CGRP binding whereas RAMP2 confers AM specificity. How RAMPs determine peptide selectivity is unclear and the receptor stoichiometries are a topic of debate with evidence for 1:1, 2:2, and 2:1 CLR:RAMP stoichiometries. Here, we describe bacterial production of recombinant tethered RAMP‐CLR extracellular domain (ECD) fusion proteins and biochemical characterization of their peptide binding properties. Tethering the two ECDs ensures complex stability and enforces defined stoichiometry. The RAMP1‐CLR ECD fusion purified as a monomer, whereas the RAMP2‐CLR ECD fusion purified as a dimer. Both proteins selectively bound their respective peptides with affinities in the low micromolar range. Truncated CGRP(27‐37) and AM(37‐52) fragments were identified as the minimal ECD complex binding regions. The CGRP C‐terminal amide group contributed to, but was not required for, ECD binding, whereas the AM C‐terminal amide group was essential for ECD binding. Alanine‐scan experiments identified CGRP residues T30, V32, and F37 and AM residues P43, K46, I47, and Y52 as critical for ECD binding. Our results identify CGRP and AM determinants for receptor ECD complex binding and suggest that the CGRP receptor functions as a 1:1 heterodimer. In contrast, the AM receptor may function as a 2:2 dimer of heterodimers, although our results cannot rule out 2:1 or 1:1 stoichiometries.
The interdomain interface in bifunctional enzyme protein 3/4A (NS3/4A) regulates protease and helicase activities
Authors: Aydin Cihan , Mukherjee Sourav , Hanson Alicia M. , Frick David N. , Schiffer Celia A.
Published: October 2013

Hepatitis C (HCV) protein 3/4A (NS3/4A) is a bifunctional enzyme comprising two separate domains with protease and helicase activities, which are essential for viral propagation. Both domains are stable and have enzymatic activity separately, and the relevance and implications of having protease and helicase together as a single protein remains to be explored. Altered in vitro activities of isolated domains compared with the full‐length NS3/4A protein suggest the existence of interdomain communication. The molecular mechanism and extent of this communication was investigated by probing the domain–domain interface observed in HCV NS3/4A crystal structures. We found in molecular dynamics simulations that the two domains of NS3/4A are dynamically coupled through the interface. Interestingly, mutations designed to disrupt this interface did not hinder the catalytic activities of either domain. In contrast, substrate cleavage and DNA unwinding by these mutants were mostly enhanced compared with the wild‐type protein. Disrupting the interface did not significantly alter RNA unwinding activity; however, the full‐length protein was more efficient in RNA unwinding than the isolated protease domain, suggesting a more direct role in RNA processing independent of the interface. Our findings suggest that HCV NS3/4A adopts an “extended” catalytically active conformation, and interface formation acts as a switch to regulate activity. We propose a unifying model connecting HCV NS3/4A conformational states and protease and helicase function, where interface formation and the dynamic interplay between the two enzymatic domains of HCV NS3/4A potentially modulate the protease and helicase activities in vivo.
Concerning the structure of apoE
Authors: Frieden Carl , Garai Kanchan
Published: October 2013

Apolipoprotein E (apoE), first described in 1973, is a truly fascinating protein. While studies initially focused on its role in cholesterol and lipid metabolism, one apoE isoform (apoE4) is a major risk factor for development of late onset Alzheimer's disease. Yet the difference between apoE3, the common form, and apoE4 is a single amino acid of the 299 in this 34 kDa protein. Structure determination of the two domain full length apoE3 protein was only accomplished in 2011 and supports the notion that mutations in the N‐terminal domain can be propagated through the structure to the C‐terminal domain. Understanding the structural differences between apoE3 and apoE4 is critical for finding ways to modulate the deleterious effect of apoE4.
Characterization of human paraoxonase 1 variants suggest that His residues at 115 and 134 positions are not always needed for the lactonase/arylesterase activities of the enzyme
Authors: Bajaj Priyanka , Tripathy Rajan K. , Aggarwal Geetika , Pande Abhay H.
Published: October 2013

Human paraoxonase 1 (h‐PON1) hydrolyzes variety of substrates and the hydrolytic activities of enzyme can be broadly grouped into three categories; arylesterase, phosphotriesterase, and lactonase. Current models of the catalytic mechanism of h‐PON1 suggest that catalytic residues H115 and H134 mediate the lactonase and arylesterase activities of the enzyme. H‐PON1 is a strong candidate for the development of catalytic bioscavenger for organophosphate poisoning in humans. Recently, Gupta et al. (Nat. Chem. Biol. 2011. 7, 120) identified amino acid substitutions that significantly increased the activity of chimeric‐PON1 variant (4E9) against some organophosphate nerve agents. In this study we have examined the effect of these (L69G/S111T/H115W/H134R/R192K/F222S/T332S) and other substitutions (H115W/H134R and H115W/H134R/R192K) on the hydrolytic activities of recombinant h‐PON1 (rh‐PON1) variants. Our results show that the substitutions resulted in a significant increase in the organophosphatase activity of all the three variants of rh‐PON1 enzyme while had a variable effect on the lactonase/arylesterase activities. The results suggest that H residues at positions 115 and 134 are not always needed for the lactonase/arylesterase activities of h‐PON1 and force a reconsideration of the current model(s) of the catalytic mechanism of h‐PON1.
Expression of the cancer‐testis antigen BORIS correlates with prostate cancer
Authors: Cheema Zubair , Hari‐Gupta Yukti , Kita Georgia‐Xanthi , Farrar Dawn , Seddon Ian , Corr John , Klenova Elena
Published: October 2013

BACKGROUND

BORIS, a paralogue of the transcription factor CTCF, is a member of the cancer‐testis antigen (CT) family. BORIS is normally present at high levels in the testis; however it is aberrantly expressed in various tumors and cancer cell lines. The main objectives of this study were to investigate BORIS expression together with sub‐cellular localization in both prostate cell lines and tumor tissues, and assess correlations between BORIS and clinical/pathological characteristics.

METHODS

We examined BORIS mRNA expression, protein levels and cellular localization in a panel of human prostate tissues, cancer and benign, together with a panel prostate cell lines. We also compared BORIS levels and localization with clinical/pathological characteristics in prostate tumors.

RESULTS

BORIS was detected in all inspected prostate cancer cell lines and tumors, but was absent in benign prostatic hyperplasia. Increased levels of BORIS protein positively correlated with Gleason score, T‐stage and androgen receptor (AR) protein levels in prostate tumors. The relationship between BORIS and AR was further highlighted in prostate cell lines by the ability of ectopically expressed BORIS to activate the endogenous AR mRNA and protein. BORIS localization in the nucleus plus cytoplasm was also associated with higher BORIS levels and Gleason score.

CONCLUSIONS

Detection of BORIS in prostate tumors suggests potential applications of BORIS as a biomarker for prostate cancer diagnosis, as an immunotherapy target and, potentially, a prognostic marker of more aggressive prostate cancer. The ability of BORIS to activate the AR gene indicates BORIS involvement in the growth and development of prostate tumors. Prostate 74:164–176, 2014. © 2013 Wiley Periodicals, Inc.
Folding 19 proteins to their native state and stability of large proteins from a coarse‐grained model
Authors: Kapoor Abhijeet , Travesset Alex
Published: October 2013

We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H‐RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B‐factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse‐grained models. Further implications are described. Proteins 2014; 82:505–516. © 2013 Wiley Periodicals, Inc.
Structural and functional characterization of a novel α/β hydrolase from cariogenic pathogen Streptococcus mutans
Authors: Wang Zixi , Li Lanfen , Su Xiao‐Dong
Published: October 2013

The protein Smu.1393c from Streptococcus mutans is annotated as a putative α/β hydrolase, but it has low sequence identity to the structure‐known α/β hydrolases. Here we present the crystal structure of Smu.1393c at 2.0 Å resolution. Smu.1393c has a fully open alkaline substrate pocket, whose conformation is unique among other similar hydrolase structures. Three residues, Ser101, His251, and Glu125, were identified as the active center of Smu.1393c. By screening a series of artificial hydrolase substrates, we demonstrated Smu.1393c had low carboxylesterase activity towards short‐chain carboxyl esters, which provided a clue for exploring the in vivo function of Smu.1393c. Proteins 2014; 82:695–700. © 2013 Wiley Periodicals, Inc.
SVR_CAF: An integrated score function for detecting native protein structures among decoys
Authors: Zhou Jianhong , Yan Wenying , Hu Guang , Shen Bairong
Published: October 2013

An accurate score function for detecting the most native‐like models among a huge number of decoy sets is essential to the protein structure prediction. In this work, we developed a novel integrated score function (SVR_CAF) to discriminate native structures from decoys, as well as to rank near‐native structures and select best decoys when native structures are absent. SVR_CAF is a machine learning score, which incorporates the contact energy based score (CE_score), amino acid network based score (AAN_score), and the fast Fourier transform based score (FFT_score). The score function was evaluated with four decoy sets for its discriminative ability and it shows higher overall performance than the state‐of‐the‐art score functions. Proteins 2014; 82:556–564. © 2013 Wiley Periodicals, Inc.
Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20–27
Authors: Kilambi Krishna Praneeth , Pacella Michael S. , Xu Jianqing , Labonte Jason W. , Porter Justin R. , Muthu Pravin , Drew Kevin , Kuroda Daisuke , Schueler‐Furman Ora , Bonneau Richard , Gray Jeffrey J.
Published: October 2013

Rounds 20–27 of the Critical Assessment of PRotein Interactions (CAPRI) provided a testing platform for computational methods designed to address a wide range of challenges. The diverse targets drove the creation of and new combinations of computational tools. In this study, RosettaDock and other novel Rosetta protocols were used to successfully predict four of the 10 blind targets. For example, for DNase domain of Colicin E2–Im2 immunity protein, RosettaDock and RosettaLigand were used to predict the positions of water molecules at the interface, recovering 46% of the native water‐mediated contacts. For α‐repeat Rep4–Rep2 and g‐type lysozyme–PliG inhibitor complexes, homology models were built and standard and pH‐sensitive docking algorithms were used to generate structures with interface RMSD values of 3.3 Å and 2.0 Å, respectively. A novel flexible sugar–protein docking protocol was also developed and used for structure prediction of the BT4661–heparin‐like saccharide complex, recovering 71% of the native contacts. Challenges remain in the generation of accurate homology models for protein mutants and sampling during global docking. On proteins designed to bind influenza hemagglutinin, only about half of the mutations were identified that affect binding (T55: 54%; T56: 48%). The prediction of the structure of the xylanase complex involving homology modeling and multidomain docking pushed the limits of global conformational sampling and did not result in any successful prediction. The diversity of problems at hand requires computational algorithms to be versatile; the recent additions to the Rosetta suite expand the capabilities to encompass more biologically realistic docking problems. Proteins 2013; 81:2201–2209. © 2013 Wiley Periodicals, Inc.
Fluorescence spectroscopy of soluble E. coli SPase I Δ2‐75 reveals conformational changes in response to ligand binding
Authors: Bhanu Meera K. , Kendall Debra A.
Published: October 2013

The bacterial Sec pathway is responsible for the translocation of secretory preproteins. During the later stages of transport, the membrane‐embedded signal peptidase I (SPase I) cleaves the signal peptide from a preprotein. We used tryptophan fluorescence spectroscopy of a soluble, catalytically active E. coli SPase I Δ2‐75 enzyme to study its dynamic conformational changes while in solution and when interacting with lipids and signal peptides. We generated four single Trp SPase I Δ2‐75 mutants, W261, W284, W300, and W310. Based on fluorescence quenching experiments, W300 and W310 were found to be more solvent accessible than W261 and W284 in the absence of ligands. W300 and W310 inserted into lipids, consistent with their location at the enzyme's proposed membrane‐interface region, while the solvent accessibilities of W261, W284, and W300 were modified in the presence of signal peptide, suggesting propagation of structural changes beyond the active site in response to peptide binding. The signal peptide binding affinity for the enzyme was measured via FRET experiments and the Kd determined to be 4.4 μM. The location of the peptide with respect to the enzyme was also established; this positioning is crucial for the peptide to gain access to the enzyme active site as it emerges from the translocon into the membrane bilayer. These studies reveal enzymatic structural changes required for preprotein proteolysis as it interacts with its two key partners, the signal peptide and membrane phospholipids. Proteins 2014; 82:596–606. © 2013 Wiley Periodicals, Inc.
Definition and classification of evaluation units for CASP10
Authors: Taylor Todd J. , Tai Chin‐Hsien , Huang Yuanpeng J. , Block Jeremy , Bai Hongjun , Kryshtafovych Andriy , Montelione Gaetano T. , Lee Byungkook
Published: October 2013

For the 10th experiment on Critical Assessment of the techniques of protein Structure Prediction (CASP), the prediction target proteins were broken into independent evaluation units (EUs), which were then classified into template‐based modeling (TBM) or free modeling (FM) categories. We describe here how the EUs were defined and classified, what issues arose in the process, and how we resolved them. EUs are frequently not the whole target proteins but the constituting structural domains. However, the assessors from CASP7 on combined more than one domain into 1 EU for some targets, which implied that the assessment also included evaluation of the prediction of the relative position and orientation of these domains. In CASP10, we followed and expanded this notion by defining multidomain EUs for a number of targets. These included 3 EUs, each made of two domains of familiar fold but arranged in a novel manner and for which the focus of evaluation was the interdomain arrangement. An EU was classified to the TBM category if a template could be found by sequence similarity searches and to FM if a structural template could not be found by structural similarity searches. The EUs that did not fall cleanly in either of these cases were classified case‐by‐case, often including consideration of the overall quality and characteristics of the predictions. Proteins 2014; 82(Suppl 2):14–25. © 2013 Wiley Periodicals, Inc.
Theoretical tests of the mechanical protection strategy in protein nanomechanics
Authors: Chwastyk Mateusz , Galera–Prat Albert , Sikora Mateusz , Gómez‐Sicilia Àngel , Carrión‐Vázquez Mariano , Cieplak Marek
Published: October 2013

We provide theoretical tests of a novel experimental technique to determine mechanostability of proteins based on stretching a mechanically protected protein by single‐molecule force spectroscopy. This technique involves stretching a homogeneous or heterogeneous chain of reference proteins (single‐molecule markers) in which one of them acts as host to the guest protein under study. The guest protein is grafted into the host through genetic engineering. It is expected that unraveling of the host precedes the unraveling of the guest removing ambiguities in the reading of the force‐extension patterns of the guest protein. We study examples of such systems within a coarse‐grained structure‐based model. We consider systems with various ratios of mechanostability for the host and guest molecules and compare them to experimental results involving cohesin I as the guest molecule. For a comparison, we also study the force‐displacement patterns in proteins that are linked in a serial fashion. We find that the mechanostability of the guest is similar to that of the isolated or serially linked protein. We also demonstrate that the ideal configuration of this strategy would be one in which the host is much more mechanostable than the single‐molecule markers. We finally show that it is troublesome to use the highly stable cystine knot proteins as a host to graft a guest in stretching studies because this would involve a cleaving procedure. Proteins 2014; 82:717–726. © 2014 Wiley Periodicals, Inc.
The maturation of HIV‐1 protease precursor studied by discrete molecular dynamics
Authors: Kimura Sachie , Caldarini Martina , Broglia Ricardo A. , Dokholyan Nikolay V. , Tiana Guido
Published: October 2013

The equilibrium properties of a HIV‐1‐protease precursor are studied by means of an efficient molecular dynamics scheme, which allows for the simulation of the folding of the protein monomers and their dimerization into an active form and compare them with those of the mature protein. The results of the model provide, with atomic detail, an overall account of several experimental findings, including the NMR conformation of the mature dimer, the calorimetric properties of the system, the effects of the precursor tail on the dimerization constant, the secondary chemical shifts of the monomer, and the paramagnetic relaxation enhancement data associated with the conformations of the precursor. It is found that although the mature protein can dimerize in a unique, single way, the precursor populates several dimeric conformations in which monomers are always native‐like, but their binding can be non‐native. Proteins 2014; 82:633–639. © 2013 Wiley Periodicals, Inc.
Green fluorescent protein fused to peptide agonists of two dissimilar G protein‐coupled receptors: novel ligands of the bradykinin B2 (rhodopsin family) receptor and parathyroid hormone PTH1 (secretin family) receptor
Authors: Charest‐Morin Xavier , Fortin Jean‐Philippe , Bawolak Marie‐Thérèse , Lodge Robert , Marceau François
Published: October 2013

We hypothesized that peptide hormone sequences that stimulate and internalize G protein‐coupled receptors (GPCRs) could be prolonged with a functional protein cargo. To verify this, we have selected two widely different pairs of peptide hormones and GPCRs that nevertheless share agonist‐induced arrestin‐mediated internalization. For the parathyroid hormone (PTH) PTH1 receptor (PTH1R) and the bradykinin (BK) B2 receptor (B2R), we have designed fusion proteins of the agonists PTH1‐34 and maximakinin (MK, a BK homologue) with the enhanced green fluorescent protein (EGFP), thus producing candidate high molecular weight ligands. According to docking models of each hormone to its receptor, EGFP was fused either at the N‐terminus (MK) or C‐terminus (PTH1‐34) of the ligand; the last construction is also secretable due to inclusion of the preproinsulin signal peptide and has been produced as a conditioned medium. EGFP‐MK has been produced as a lysate of transfected cells. Using an enzyme‐linked immunosorbent assay (ELISA) for GFP, average concentrations of 1.5 and 1670 nmol/L, respectively, of ligand were found in these preparations. The functional properties and potential of these analogs for imaging receptor‐expressing cells were examined. Microscopic and cytofluorometric evidence of specific binding and internalization of both fusion proteins was obtained using recipient HEK 293a cells that expressed the cognate recombinant receptor. Endosomal colocalization studies were conducted (Rab5, Rab7, β‐arrestin1). Evidence of agonist signaling was obtained (expression of c‐Fos, cyclic AMP responsive element (CRE) reporter gene for PTH1‐34‐EGFP). The constructs PTH1‐34‐EGFP and EGFP‐MK represent bona fide agonists that support the feasibility of transporting protein cargoes inside cells using GPCRs.
Cilostazol prevents retinal ischemic damage partly via inhibition of tumor necrosis factor‐α‐induced nuclear factor‐kappa B/activator protein‐1 signaling pathway
Authors: Ishizuka Fumiya , Shimazawa Masamitsu , Egashira Yusuke , Ogishima Hiromi , Nakamura Shinsuke , Tsuruma Kazuhiro , Hara Hideaki
Published: October 2013

Cilostazol is a specific inhibitor of phosphodiesterase III and is widely used to treat ischemic symptoms of peripheral vascular disease. We evaluated the protective effects of cilostazol in a murine model of ocular ischemic syndrome in which retinal ischemia was induced by 5‐h unilateral ligation of both the pterygopalatine artery (PPA) and the external carotid artery (ECA) in anesthetized mice. The effects of cilostazol (30 mg/kg, p.o.) on ischemia/reperfusion (I/R)‐induced retinal damage were examined by histological, retinal vascular permeability, and electrophysiological analyses. Using immunoblotting, the protective mechanism for cilostazol was evaluated by examining antiinflammatory effects of cilostazol on the expression of tumor necrosis factors‐α (TNF‐α) and tight junction proteins (ZO‐1 and claudin‐5), and the phosphorylations of nuclear factor‐kappa B (NF‐κB) and c‐Jun. The histological analysis revealed that I/R decreased the cell number in the ganglion cell layer (GCL) and the thicknesses of the inner plexiform layer (IPL) and inner nuclear layer (INL), and that cilostazol attenuated these decreases. Additionally, cilostazol prevented the hyperpermeability of blood vessels. Electroretinogram (ERG) measurements revealed that cilostazol prevented the I/R‐induced reductions in a‐, b‐, and oscillatory potential (OP) wave amplitudes seen at 5 days after I/R. Cilostazol inhibited the increased expression of TNF‐α and the phosphorylation levels of NF‐κB and c‐Jun in the retina after I/R. In addition, cilostazol prevented TNF‐α‐induced reduction of ZO‐1 and claudin‐5 expression in human retinal microvascular endothelial cells (HRMECs). These findings indicate that cilostazol may prevent I/R‐induced retinal damage partly through inhibition of TNF‐α‐induced NF‐κB/AP‐1 signaling pathway.
Methamphetamine causes acute hyperthermia‐dependent liver damage
Authors: Halpin Laura E. , Gunning William T. , Yamamoto Bryan K.
Published: October 2013

Methamphetamine‐induced neurotoxicity has been correlated with damage to the liver but this damage has not been extensively characterized. Moreover, the mechanism by which the drug contributes to liver damage is unknown. This study characterizes the hepatocellular toxicity of methamphetamine and examines if hyperthermia contributes to this liver damage. Livers from methamphetamine‐treated rats were examined using electron microscopy and hematoxylin and eosin staining. Methamphetamine increased glycogen stores, mitochondrial aggregation, microvesicular lipid, and hydropic change. These changes were diffuse throughout the hepatic lobule, as evidenced by a lack of hematoxylin and eosin staining. To confirm if these changes were indicative of damage, serum aspartate and alanine aminotransferase were measured. The functional significance of methamphetamine‐induced liver damage was also examined by measuring plasma ammonia. To examine the contribution of hyperthermia to this damage, methamphetamine‐treated rats were cooled during and after drug treatment by cooling their external environment. Serum aspartate and alanine aminotransferase, as well as plasma ammonia were increased concurrently with these morphologic changes and were prevented when methamphetamine‐induced hyperthermia was blocked. These findings support that methamphetamine produces changes in hepatocellular morphology and damage persisting for at least 24 h after drug exposure. At this same time point, methamphetamine treatment significantly increases plasma ammonia concentrations, consistent with impaired ammonia metabolism and functional liver damage. Methamphetamine‐induced hyperthermia contributes significantly to the persistent liver damage and increases in peripheral ammonia produced by the drug.
The interface of functional safety with process safety and risk analysis
Authors: Baybutt Paul
Published: October 2013

The fundamental requirement of the IEC 61511/ISA 84 standard on Safety Instrumented Systems (SIS) is to establish the Safety Integrity Levels (SILs) required for Safety Instrumented Functions (SIFs) by evaluating process risks and comparing them to risk tolerance criteria. This article addresses issues that impact the determination of SILs for SIFs and their implications for use of the standard. The issues largely revolve around the interface of the standard with process safety and risk analysis. They include the justification for relative contributions to risk reduction from SIS and non‐SIS protection layers, use of appropriate risk tolerance criteria, difficulties with defining hazardous events consistently, the appropriateness of different SIL determination methods, the importance of fully considering common cause failures, the importance of addressing uncertainties, the need to verify risk reduction for non‐SIS as well as SIS protection layers, the role of systematic failures, and the need to ensure quality in supporting process hazard analysis studies. © 2013 American Institute of Chemical Engineers Process Saf Prog 32: 346–350, 2013
Process safety leading indicators—a perspective from Europe
Authors: Knijff Piet , Allford Lee , Schmelzer Peter
Published: October 2013

In 2012, the European Process Safety Centre (EPSC) published Making the case for leading indicators in process safety which is a pamphlet on the selection, development, and implementation of leading indicators for process safety. The document contains details on the type and spread of indicators which EPSC members have established within their own companies. In addition, EPSC provided several practical tips for the do's and don'ts of successful implementation including presentation of data and engagement of staff. This article is to develop these aspects further while exploring the relationship between leading indicators on a plant, business unit, and corporate level. Additionally, the interaction between leading and lagging indicators is to be highlighted alongside the management space which process safety indicators now inhabit with respect to monitoring and audit/review activities. © 2013 American Institute of Chemical Engineers Process Saf Prog 32: 332–336, 2013
Biochemical and molecular characterisation and cross‐resistance in field and laboratory chlorpyrifos‐resistant strains of Laodelphax striatellus (Hemiptera: Delphacidae) from eastern China
Authors: Xu Lu , Wu Min , Han Zhaojun
Published: October 2013

BACKGROUND

Laboratory selection is often employed in resistance mechanism studies because field‐derived populations commonly do not have high enough resistance for such studies. In the present study, a field‐collected Laodelphax striatellus population from eastern China was laboratory selected for chlorpyrifos resistance and susceptibility, and the developed strains, along with a field population, were studied for cross‐resistance and resistance mechanisms at biochemical and molecular levels.

RESULTS

A 158.58‐fold chlorpyrifos‐resistant strain (JH‐chl) and a chlorpyrifos‐susceptible strain (JHS) were established after laboratory selection of 25 generations. Cross‐resistance to deltamethrin, diazinon, methomyl, carbosulfan, acephate and imidacloprid were detected in JH‐chl and a field‐collected strain (JHF). Synergism and enzyme activity data suggested potential involvement of P450s and esterases in JH‐chl as well as AChE alteration. Furthermore, CYP6AY3v2, CYP306A2v2, CYP353D1v2 and LSCE36 genes were significantly overexpressed in JH‐chl (6.87–12.14‐fold). Feeding of dsRNAs reduced the expression of the four target genes (35.6–56.8%) and caused significant adult mortality (75.21–88.45%), implying resistance reduction. However, mechanism(s) conferring chlorpyrifos resistance in JHF were unclear.

CONCLUSION

In contrast to previous reports, multiple overexpressed detoxification genes were potentially associated with chlorpyrifos resistance, as confirmed by RNAi feeding tests. Chlorpyrifos resistance exhibits cross‐resistance with insecticides in the same and different classes. © 2013 Society of Chemical Industry
Selection and characterisation of an HD1‐like Bacillus thuringiensis isolate with a high insecticidal activity against Spodoptera littoralis (Lepidoptera: Noctuidae)
Authors: Azzouz Hichem , Kebaili‐Ghribi Jihene , ben Farhat‐Touzri Dalel , Daoud Fatma , Fakhfakh Ines , Tounsi Slim , Jaoua Samir
Published: October 2013

BACKGROUND

Spodoptera littoralis (Boisduval) larvae are known by their susceptibility to Bacillus thuringiensis subsp. aizawai strains. In order to prevent the appearance of B. thuringiensis (Bt) resistance and to develop economical Bt‐based biopesticides, the selection and the characterisation of a B. thuringiensis isolate toxic against S. littoralis larvae and overproducing δ‐endotoxins were investigated.

RESULTS

Among 124 Tunisian B. thuringiensis isolates assessed against S. littoralis larvae, four isolates showed toxicity similar to and higher than the toxicity of the aizawai strain HD133 and the kurstaki strain HD1 respectively. The plasmid pattern of the selected isolates was similar to that of HD1. Polymerase chain reaction (PCR) analysis using specific primers revealed that these isolates present different gene contents. The only detected gene encoding Spodoptera‐specific toxin was cry9. The selected isolates were found to produce bipyramidal and cubic crystals. The assessment of δ‐endotoxin production by these isolates showed that BUPM28 produced 43.71 and 80.81% more δ‐endotoxin than HD1 and HD133 respectively. The application of osmotic or heat shock stress on the BUPM28 isolate made it possible to enhance δ‐endotoxin production by 22 and 23% respectively.

CONCLUSION

On the basis of its potent insecticidal activity and its high level of δ‐endotoxin production, the BUPM28 isolate can be considered to be an effective alternative for the control of S. littoralis. © 2013 Society of Chemical Industry
Rural Migration, Agrarian Change, and Institutional Dynamics: Perspectives from the Majority World
Authors: Argent Neil , Tonts Matthew , Stockdale Aileen
Published: October 2013

Overall, this special issue provides insights into the mutually constitutive ways in which rapid economic development associated with industrialisation drives institutional change, migration and mobility, and, finally, altered relationships between – and conceptions of – rural and urban. The following papers pose important conceptual, normative as well as practical, policy‐relevant questions relating to the human consequences of these processes and point to the applications of population research – a central objective of this journal. Copyright © 2013 John Wiley & Sons, Ltd.
Atomic layer deposition of ZrO2 for graphene‐based multilayer structures: In situ and ex situ characterization of growth process
Authors: Tamm Aile , Kozlova Jekaterina , Aarik Lauri , Aidla Aleks , Lu Jun , Kiisler Alma‐Asta , Kasikov Aarne , Ritslaid Peeter , Mändar Hugo , Hultman Lars , Sammelselg Väino , Kukli Kaupo , Aarik Jaan
Published: October 2013

Real time monitoring of atomic layer deposition by quartz crystal microbalance (QCM) was used to follow the growth of ZrO2 thin films on graphene. The films were grown from ZrCl4 and H2O on graphene prepared by chemical vapor deposition method on 100‐nm thick nickel film or on Cu‐foil and transferred onto QCM sensor. The deposition was performed at a substrate temperature of 190 °C. The growth of the dielectric film on graphene was significantly retarded compared to the process carried out on QCM without graphene. After the deposition of dielectric films, the basic structure of graphene was retained.
(211) oriented ZnTe growth on m‐plane sapphire by MBE
Authors: Nakasu Taizo , Kobayashi Masakazu , Togo Hiroyoshi , Asahi Toshiaki
Published: October 2013

Single‐crystalline and single domain ZnTe thin films are sought for high‐performance terahertz wave detectors, and ZnTe/sapphire heterostructures were considered since the Electro‐Optical (EO) effect could be obtained only from epilayers. ZnTe epilayers were grown on m‐plane sapphire substrates by molecular beam epitaxy, and the potential of single domain epilayers was explored. Through the X‐ray diffraction pole figure measurement it was confirmed that one (100) oriented ZnTe domain along with two kinds of (211) oriented domains were formed on the m‐plane sapphire when the layer was grown at 340 °C. When the layer was grown at 350 °C, the (211) oriented domain dominated the film. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Investigation of the crystalline quality of a gallium oxide thick film grown by RF magnetron sputtering
Authors: Ishibashi Kazuya , Aida Ryohei , Takahara Motoki , Kudo Jyun , Tsunoda Isao , Takakura Kenichiro , Nakashima Toshiyuki , Shibuya Mutsuo , Murakami Katsuya
Published: October 2013

Crystalline quality and optical properties of gallium oxide films grown on SiO2substrates by RF magnetron sputtering were studied. After the post annealing, it could be confirmed growth of gallium oxide (Ga2O3) film changed in a β ‐Ga2O3 film. Estimated optical energy gap of as‐grown and post annealed films are the same from 4.85 to 4.90 eV. The energy gap for as‐deposited film corresponds to band gap of β ‐Ga2O3.It has a property of β ‐Ga2O3 nevertheless the as‐deposited Ga2O3 films. The integrated absorption coefficient under the energy gap decreases with increasing thickness of Ga2O3 film. These results indicate that crystalline quality of β ‐Ga2O3 film is improved by increment the film thickness. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Polyvinylpyrrolidone (PVP) assisted single‐step synthesis of kesterite Cu2ZnSnS4 nanoparticles by solvothermal process
Authors: Mali Sawanta S. , Kim Hyungjin , Shim Chang Su , Patil Pramod S. , Hong Chang Kook
Published: October 2013

Quaternary kesterite‐type Cu2ZnSnS4 (CZTS) nanoparticles (NPs) were successfully synthesized by a single‐step solvothermal process. Semiconductor CZTS nanoparticles were obtained from ethylene glycol (EG) and CZTS precursor after solvothermal process at 180 °C for 30 h in polyvinylpyrrolidone (PVP) medium. The synthesized CZTS NPs were further annealed at 450 °C in nitrogen atmosphere and used for further characterizations. The CZTS NPs were characterized using X‐ray powder diffraction (XRD), field emission scanning electron microscopy (FESEM), micro Raman spectroscopy, high resolution transmission electron microscopy (HRTEM) and X‐ray photoelectron spectroscopy (XPS). The optical properties of the CZTS NPs were recorded by UV–vis absorption spectroscopy. The results showed that the synthesized CZTS nanoparticles are kesterite‐type CZTS, with good crystallinity and a stoichiometric composition. Moreover, the prepared nanoparticles have a size ranging from 5–7 nm and a band gap of ∼1.5 eV.

magnified image

(© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)