bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACTRounds 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

ABSTRACTThe 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

ABSTRACTFor 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

ABSTRACTWe 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

ABSTRACTThe 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

AbstractWe 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

AbstractCilostazol 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

AbstractMethamphetamine‐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.
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

AbstractBACKGROUNDLaboratory 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.RESULTSA 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.CONCLUSIONIn 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

AbstractBACKGROUNDSpodoptera 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.RESULTSAmong 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.CONCLUSIONOn 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

ABSTRACTOverall, 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.
(211) oriented ZnTe growth on m‐plane sapphire by MBE
Authors: Nakasu Taizo , Kobayashi Masakazu , Togo Hiroyoshi , Asahi Toshiaki 
Published: October 2013

AbstractSingle‐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

AbstractCrystalline 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

AbstractQuaternary 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)