bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intrinsically disordered regions in autophagy proteins
Authors: Mei Yang , Su Minfei , Soni Gaurav , Salem Saeed , Colbert Christopher L. , Sinha Sangita C. 
Published: October 2013

ABSTRACTAutophagy is an essential eukaryotic pathway required for cellular homeostasis. Numerous key autophagy effectors and regulators have been identified, but the mechanism by which they carry out their function in autophagy is not fully understood. Our rigorous bioinformatic analysis shows that the majority of key human autophagy proteins include intrinsically disordered regions (IDRs), which are sequences lacking stable secondary and tertiary structure; suggesting that IDRs play an important, yet hitherto uninvestigated, role in autophagy. Available crystal structures corroborate the absence of structure in some of these predicted IDRs. Regions of orthologs equivalent to the IDRs predicted in the human autophagy proteins are poorly conserved, indicating that these regions may have diverse functions in different homologs. We also show that IDRs predicted in human proteins contain several regions predicted to facilitate protein–protein interactions, and delineate the network of proteins that interact with each predicted IDR‐containing autophagy protein, suggesting that many of these interactions may involve IDRs. Lastly, we experimentally show that a BCL2 homology 3 domain (BH3D), within the key autophagy effector BECN1 is an IDR. This BH3D undergoes a dramatic conformational change from coil to α‐helix upon binding to BCL2s, with the C‐terminal half of this BH3D constituting a binding motif, which serves to anchor the interaction of the BH3D to BCL2s. The information presented here will help inform future in‐depth investigations of the biological role and mechanism of IDRs in autophagy proteins. Proteins 2014; 82:565–578. © 2013 Wiley Periodicals, Inc.
Elastic network normal mode dynamics reveal the GPCR activation mechanism
Authors: Kolan Dikla , Fonar Gennadiy , Samson Abraham O. 
Published: October 2013

ABSTRACTG‐protein‐coupled receptors (GPCR) are a family of membrane‐embedded metabotropic receptors which translate extracellular ligand binding into an intracellular response. Here, we calculate the motion of several GPCR family members such as the M2 and M3 muscarinic acetylcholine receptors, the A2A adenosine receptor, the β2‐adrenergic receptor, and the CXCR4 chemokine receptor using elastic network normal modes. The normal modes reveal a dilation and a contraction of the GPCR vestibule associated with ligand passage, and activation, respectively. Contraction of the vestibule on the extracellular side is correlated with cavity formation of the G‐protein binding pocket on the intracellular side, which initiates intracellular signaling. Interestingly, the normal modes of rhodopsin do not correlate well with the motion of other GPCR family members. Electrostatic potential calculation of the GPCRs reveal a negatively charged field around the ligand binding site acting as a siphon to draw‐in positively charged ligands on the membrane surface. Altogether, these results expose the GPCR activation mechanism and show how conformational changes on the cell surface side of the receptor are allosterically translated into structural changes on the inside. Proteins 2014; 82:579–586. © 2013 Wiley Periodicals, Inc.
Docking, scoring, and affinity prediction in CAPRI
Authors: Lensink Marc F. , Wodak Shoshana J. 
Published: October 2013

ABSTRACTWe present the fifth evaluation of docking and related scoring methods used in the community‐wide experiment on the Critical Assessment of Predicted Interactions (CAPRI). The evaluation examined predictions submitted for a total of 15 targets in eight CAPRI rounds held during the years 2010–2012. The targets represented one the most diverse set tackled by the CAPRI community so far. They included only 10 “classical” docking and scoring problems. In one of the classical targets, the new challenge was to predict the position of water molecules in the protein–protein interface. The remaining five targets represented other new challenges that involved estimating the relative binding affinity and the effect of point mutations on the stability of designed and natural protein–protein complexes. Although the 10 classical CAPRI targets included two difficult multicomponent systems, and a protein–oligosaccharide complex with which CAPRI participants had little experience, this evaluation indicates that the performance of docking and scoring methods has remained quite robust. More remarkably, we find that automatic docking servers exhibit a significantly improved performance, with some servers now performing on par with predictions done by humans. The performance of CAPRI participants in the new challenges, briefly reviewed here, was mediocre overall, but some groups did relatively well and their approaches suggested ways of improving methods for designing binders and for estimating the free energies of protein assemblies, which should impact the field of protein modeling and design as a whole. Proteins 2013; 81:2082–2095. © 2013 Wiley Periodicals, Inc.
Secondary sugar binding site identified for LecA lectin from Pseudomonas aeruginosa
Authors: Blanchard Bertrand , Imberty Anne , Varrot Annabelle 
Published: October 2013

ABSTRACTThe galactose‐specific lectin LecA from Pseudomonas aeruginosa is a target for the development of new anti‐infectious compounds. Sugar based molecules with anti‐adhesive properties present great potential in the fight against bacterial infection and biofilm formation. LecA is specific for oligosaccharides with terminal α‐galactoside residues and displays strong affinity for melibiose (αGal1‐6Glc) with a Kd of 38.8 µM. The crystal structure of LecA/melibiose complex shows classical calcium‐bridged binding of αGal in the primary binding site but also revealed a secondary sugar binding site with glucose bound. This sugar binding site is in close proximity to the galactose binding one, is independent of calcium and mainly involves interactions with a symmetry‐related protein. This discovery would help to the design of new potent inhibitors targeting both binding sites. Proteins 2014; 82:1060–1065. © 2013 Wiley Periodicals, Inc.
Performance of ZDOCK in CAPRI rounds 20–26
Authors: Vreven Thom , Pierce Brian G. , Hwang Howook , Weng Zhiping 
Published: October 2013

ABSTRACTWe report the performance of our approaches for protein–protein docking and interface analysis in CAPRI Rounds 20–26. At the core of our pipeline was the ZDOCK program for rigid‐body protein–protein docking. We then reranked the ZDOCK predictions using the ZRANK or IRAD scoring functions, pruned and analyzed energy landscapes using clustering, and analyzed the docking results using our interface prediction approach RCF. When possible, we used biological information from the literature to apply constraints to the search space during or after the ZDOCK runs. For approximately half of the standard docking challenges, we made at least one prediction that was acceptable or better. For the scoring challenges, we made acceptable or better predictions for all but one target. This indicates that our scoring functions are generally able to select the correct binding mode. Proteins 2013; 81:2175–2182. © 2013 Wiley Periodicals, Inc.
A novel twist on molecular interactions between thioredoxin and nicotinamide adenine dinucleotide phosphate‐dependent thioredoxin reductase
Authors: Kirkensgaard Kristine G. , Hägglund Per , Shahpiri Azar , Finnie Christine , Henriksen Anette , Svensson Birte 
Published: October 2013

AbstractThe ubiquitous disulfide reductase thioredoxin (Trx) regulates several important biological processes such as seed germination in plants. Oxidized cytosolic Trx is regenerated by nicotinamide adenine dinucleotide phosphate (NADPH)‐dependent thioredoxin reductase (NTR) in a multistep transfer of reducing equivalents from NADPH to Trx via a tightly NTR‐bound flavin. Here, interactions between NTR and Trx are predicted by molecular modelling of the barley NTR:Trx complex (HvNTR2:HvTrxh2) and probed by site directed mutagenesis. Enzyme kinetics analysis reveals mutants in a loop of the flavin adenine dinucleotide (FAD)‐binding domain of HvNTR2 to strongly affect the interaction with Trx. In particular, Trp42 and Met43 play key roles for recognition of the endogenous HvTrxh2. Trx from Arabidopsis thaliana is also efficiently recycled by HvNTR2 but turnover in this case appears to be less dependent on these two residues, suggesting a distinct mode for NTR:Trx recognition. Comparison between the HvNTR2:HvTrxh2 model and the crystal structure of the Escherichia coli NTR:Trx complex reveals major differences in interactions involving the FAD‐ and NADPH‐binding domains as supported by our experiments. Overall, the findings suggest that NTR:Trx interactions in different biological systems are fine‐tuned by multiple intermolecular contacts. Proteins 2014; 82:607–619. © 2013 Wiley Periodicals, Inc.
Prediction and validation of the unexplored RNA‐binding protein atlas of the human proteome
Authors: Zhao Huiying , Yang Yuedong , Janga Sarath Chandra , Kao C. Cheng , Zhou Yaoqi 
Published: October 2013

ABSTRACTDetecting protein‐RNA interactions is challenging both experimentally and computationally because RNAs are large in number, diverse in cellular location and function, and flexible in structure. As a result, many RNA‐binding proteins (RBPs) remain to be identified. Here, a template‐based, function‐prediction technique SPOT‐Seq for RBPs is applied to human proteome and its result is validated by a recent proteomic experimental discovery of 860 mRNA‐binding proteins (mRBPs). The coverage (or sensitivity) is 42.6% for 1217 known RBPs annotated in the Gene Ontology and 43.6% for 860 newly discovered human mRBPs. Consistent sensitivity indicates the robust performance of SPOT‐Seq for predicting RBPs. More importantly, SPOT‐Seq detects 2418 novel RBPs in human proteome, 291 of which were validated by the newly discovered mRBP set. Among 291 validated novel RBPs, 61 are not homologous to any known RBPs. Successful validation of predicted novel RBPs permits us to further analysis of their phenotypic roles in disease pathways. The dataset of 2418 predicted novel RBPs along with confidence levels and complex structures is available at http://sparks-lab.org (in publications) for experimental confirmations and hypothesis generation. Proteins 2014; 82:640–647. © 2013 Wiley Periodicals, Inc.
Effects of D‐amino acid oxidase inhibition on memory performance and long‐term potentiation in vivo
Authors: Hopkins Seth C. , Campbell Una C. , Heffernan Michele L. R. , Spear Kerry L. , Jeggo Ross D. , Spanswick David C. , Varney Mark A. , Large Thomas H. 
Published: October 2013

AbstractN‐methyl‐d‐aspartate receptor (NMDAR) activation can initiate changes in synaptic strength, evident as long‐term potentiation (LTP), and is a key molecular correlate of memory formation. Inhibition of d‐amino acid oxidase (DAAO) may increase NMDAR activity by regulating d‐serine concentrations, but which neuronal and behavioral effects are influenced by DAAO inhibition remain elusive. In anesthetized rats, extracellular field excitatory postsynaptic potentials (fEPSPs) were recorded before and after a theta frequency burst stimulation (TBS) of the Schaffer collateral pathway of the CA1 region in the hippocampus. Memory performance was assessed after training with tests of contextual fear conditioning (FC, mice) and novel object recognition (NOR, rats). Oral administration of 3, 10, and 30 mg/kg 4H‐furo[3,2‐b]pyrrole‐5‐carboxylic acid (SUN) produced dose‐related and steady increases of cerebellum d‐serine in rats and mice, indicative of lasting inhibition of central DAAO. SUN administered 2 h prior to training improved contextual fear conditioning in mice and novel object recognition memory in rats when tested 24 h after training. In anesthetized rats, LTP was established proportional to the number of TBS trains. d‐cycloserine (DCS) was used to identify a submaximal level of LTP (5× TBS) that responded to NMDA receptor activation; SUN administered at 10 mg/kg 3–4 h prior to testing similarly increased in vivo LTP levels compared to vehicle control animals. Interestingly, in vivo administration of DCS also increased brain d‐serine concentrations. These results indicate that DAAO inhibition increased NMDAR‐related synaptic plasticity during phases of post training memory consolidation to improve memory performance in hippocampal‐dependent behavioral tests.
Estimating the frequency of Cry1F resistance in field populations of the European corn borer (Lepidoptera: Crambidae)
Authors: Siegfried Blair D , Rangasamy Murugesan , Wang Haichuan , Spencer Terence , Haridas Chirakkal V , Tenhumberg Brigitte , Sumerford Douglas V , Storer Nicholas P 
Published: October 2013

AbstractBACKGROUNDTransgenic corn hybrids that express toxins from Bacillus thuringiensis (Bt) have suppressed European corn borer populations and reduced the pest status of this insect throughout much of the US corn belt. A major assumption of the high‐dose/refuge strategy proposed for insect resistance management and Bt corn is that the frequency of resistance alleles is low so that resistant pests surviving exposure to Bt corn will be rare.RESULTSThe frequency of resistance to the Cry1F Bt toxin was estimated using two different screening tools and compared with annual susceptibility monitoring based on diagnostic bioassays and LC50 and EC50 determinations. An F1 screening approach where field‐collected individuals were mated to a resistant laboratory strain and progeny were assayed to determine genotype revealed that resistance alleles could be recovered even during the first year of commercially available Cry1F corn (2003). Estimates of frequency from 2003–2005 and 2006–2008 indicated that, although allele frequency was higher than theoretical assumptions (0.0286 and 0.0253 respectively), there was no indication that the frequency was increasing. Similar estimates in 2008 and 2009 using an F2 screening approach confirmed the presence of non‐rare resistance alleles (frequency ≈ 0.0093 and 0.0142 for 2008 and 2009, respectively). The results of both screening methods were in general agreement with the observed mortality in diagnostic bioassays and LC50 and EC50 determinations.CONCLUSIONSThese results are consistent with previous modeling results, suggesting that the high‐dose/refuge strategy that is in place for Bt corn may be effective in delaying resistance evolution even when a relatively high frequency of resistance alleles exists. © 2013 Society of Chemical Industry
Two‐color lasing in a coupled multilayer cavity with InAs quantum dots by optical pumping
Authors: Kitada Takahiro , Harayama Chiho , Morita Ken , Isu Toshiro 
Published: October 2013

AbstractTwo‐color lasing in a GaAs/AlAs coupled multilayer cavity has been studied for a novel type of terahertz emitting devices. In the structure, two cavity layers based on GaAs were connected by the intermediate GaAs/AlAs distributed Bragg reflector multilayer and three layers of self‐assembled InAs quantum dots (QDs) were inserted only in the top‐side cavity layer as optical gain materials. The broadened QD emissions around 1.25 µm are very useful to realize the optical gain because they could cover the wide range of the mode frequency difference. Two mode emissions with an optical frequency difference of 3.2 THz were successfully demonstrated under room temperature cw operation by optical pumping. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fabrication and analysis of current confinement structure for photonic crystal laser
Authors: Yamauchi S. , Morifuji M. , Kondow M. 
Published: October 2013

AbstractWe recently proposed a laser structure with a circularly arranged cavity structure with AlOx with the aim of fabricating an electrically driven photonic crystal (PC) laser. Fabricating our proposed laser requires carrier injection to the cavity. In this study, we fabricated and investigated the current confinement structure for our proposed PC laser and established a process for fabricating the structure. We were able to apply current to a funnel and measure the current‐voltage characteristics of the structure. The electrical characteristics showed an ohmic feature, showing the possibility of fabricating our proposed PC laser. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Changing photoluminescence spectra of graphene oxide by centrifugation treatments
Authors: Kozawa Daichi , Miyauchi Yuhei , Mouri Shinichiro , Matsuda Kazunari 
Published: October 2013

AbstractWe conducted continuous‐wave photoluminescence (PL) measurements to study optical properties of graphene oxide (GO) before and after a centrifugation treatment. The pristine GOs show a PL peak around near‐infrared (NIR) region (∼1.7 eV). In contrast, the centrifuged GOs exhibit PL peaks at blue (∼2.8 eV) and UV (∼4.1 eV) region. The difference among the emission features in the pristine and centrifuged GOs originates from the change of major structure from the sp2 clusters to the quasi‐molecular structure. Our findings indicate tunability of PL from GOs in the range from NIR to UV region by the centrifugation treatment. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Enhancing carrier mobility of IGZO TFT fabricated by non‐vacuum mist CVD with O3 assistance
Authors: Kawaharamura Toshiyuki , Uchida Takayuki , Wang Dapeng , Sanada Masaru , Furuta Mamoru 
Published: October 2013

AbstractRecently, we succeeded in demonstrating an oxide TFT consisting of a channel layer (IGZO) and gate insulator (AlOx) continuously fabricated by non‐vacuum mist CVD. In this report, each thin film and the interfaces of the films have been improved with ozone (O3) assistance, as the initial oxide TFT had poor characteristics compared with those of the IGZO TFT fabricated by the conventional vacuum process. A superhydrophilic interface between AlOx and IGZO was obtained by removing the adhered organic matter from the film surface. The breakdown fields (EBD) and dielectric constant (κ) of the AlOx thin films were improved from 6 to 8 MV/cm and from 6 to 7, respectively, and the carrier concentration of the IGZO thin film decreased from 1019 to 1016 cm–3. The oxide TFT exhibited field effect mobility (μlin) of 8.7 cm2/(Vs), sub‐threshold slope (S) of around 0.3 V/dec. and hysteresis (ΔVH) of around 0.5 V. These values were obtained by improving each thin film and the interfaces of the films with O3 assistance. This result is an important first step toward non‐vacuum oxide TFT fabrication processes. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
First‐principles study of oxygen‐doping states in II‐VI semiconductors
Authors: Ishikawa Masato , Nakayama Takashi 
Published: October 2013

AbstractOxygen doping into zinc‐family II‐VI semiconductors is studied by the first‐principles calculation. We found that a large band‐gap reduction occurs for ZnS and ZnSe, while there is little reduction and appears a deep level of oxygen in the band gap for ZnTe. It is shown that such difference reflects the order of energy positions of host cation (Zn) 4s‐orbital and oxygen (O) 3s‐orbital states. We also study the electronic states and stability of oxy‐gen pair. By calculating the formation energy of O pair, we found that O dopants prefer to locate isolated. This is because O atom has so small radius that the pairing pro‐motes a large elastic strain in host system, which feature is in contrast to the case of N pair in III‐V systems.
Surface morphology of multilayer graphene synthesized directly on silicon dioxide
Authors: Katakura Kenta , Tomori Hikari , Ootuka Youiti , Kanda Akinobu 
Published: October 2013

AbstractWe report the surface morphology of multilayer graphene synthesized directly on a SiO2/Si substrate through graphitization of amorphous carbon with Ni catalyst. We demonstrate that the disorder‐induced Raman D peak is effectively suppressed when the Ni catalyst layer is covered with Au layer. Scanning electron microscope observation reveals that the Au layer prevents granulation of Ni after the annealing process, leading to the formation of continuous graphene with less holes. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Broadband emission centered at ∼1 µm with a Gaussian‐like spectrum by stacking In‐flushed QD layers
Authors: Ozaki Nobuhiko , Hino Yuji , Ohkouchi Shunsuke , Ikeda Naoki , Sugimoto Yoshimasa 
Published: October 2013

AbstractWe have grown a stack of In‐flushed InAs quantum dot (QD) layers to realize a broadband emission centered at ∼1 µm with a Gaussian‐like spectrum as a light source for optical coherence tomography (OCT). The In‐flush process, which enables control of the height of the QD, was optimized to control the emission wavelength and intensity of self‐assembled InAs/GaAs QDs. A partial capping layer of GaAs was deposited on as‐grown InAs/GaAs QDs with various thicknesses (dcap), and a rapid annealing of the sample was executed with the proper annealing temperature. By optimizing dcap and the annealing temperature for each QD layer, a broadband Gaussian‐like spectrum with a 102‐nm‐bandwidth was obtained. The coherence function of the emission spectrum exhibits a 4.5‐µm axial resolution for OCT images without distinct side lobes. These results demonstrate the effectiveness of the In‐flushed QDs as a light source to obtain high‐quality OCT images. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The influence of temperature on the recombination processes in blue and green InGaN LEDs
Authors: Crutchley Benjamin G. , Marko Igor P. , Sweeney Stephen J. 
Published: October 2013

AbstractA temperature dependent investigation into the efficiency droop effect in blue and green InGaN light‐emitting diodes (LEDs) is presented. The efficiency droop effect is observed to be the strongest at low temperatures in both blue and green LEDs. We show such behaviour is consistent with a reduced hole injection rate resulting in an increased concentration of electron leakage from the quantum wells. Spectral measurements demonstrate that the emission peak has an “s‐shape” dependence on tem‐perature and a full‐width at half‐maximum which increases with decreasing temperature below 100 K. Such observations indicate the importance of carrier localization in the InGaN LEDs. At temperatures where hole injection is not problematic the efficiency droop is the result of carrier delocalization and subsequent defect related recombination with increasing current injection. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Polymer‐free, low tension graphene mechanical resonators
Authors: Alemán Benjamín , Rousseas Michael , Yang Yisheng , Regan Will , Crommie Michael , Wang Feng , Zettl Alex 
Published: October 2013

AbstractGraphene resonators are fabricated using a polymer‐free, direct transfer method onto metal reinforced holey carbon grids. The resonators are distinguished by the absence of organic residues and excellent crystallinity. The normal mode frequencies are measured using a Fabry–Perot technique; resonance curves indicate highly linear behaviour but very little built‐in strain, which is consistent with device geometry examined by atomic force microscopy. We conclude that the oscillators' restoring force is due instead to graphene's intrinsic bending rigidity; our measurements indicate a value of approximately 1.0 eV, consistent with previous theoretical and experimental work. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)