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https://www.readbyqxmd.com/read/28820312/architecture-of-the-atg2b-wdr45-complex-and-an-aromatic-y-hf-motif-crucial-for-complex-formation
#1
Jing-Xiang Zheng, Yan Li, Yue-He Ding, Jun-Jie Liu, Mei-Jun Zhang, Meng-Qiu Dong, Hong-Wei Wang, Li Yu
PtdIns3P signaling is critical for dynamic membrane remodeling during autophagosome formation. Proteins in the Atg18/WIPI family are PtdIns3P-binding effectors which can form complexes with proteins in the Atg2 family, and both families are essential for macroautophagy/autophagy. However, little is known about the biophysical properties and biological functions of the Atg2-Atg18/WIPI complex as a whole. Here, we demonstrate that an ortholog of yeast Atg18, mammalian WDR45/WIPI4 has a stronger binding capacity for mammalian ATG2A or ATG2B than the other 3 WIPIs...
August 18, 2017: Autophagy
https://www.readbyqxmd.com/read/28819924/dynamic-imaging-of-mitochondrial-membrane-proteins-in-specific-sub-organelle-membrane-locations
#2
REVIEW
Timo Appelhans, Karin B Busch
Mitochondria are cellular organelles with multifaceted tasks and thus composed of different sub-compartments. The inner mitochondrial membrane especially has a complex nano-architecture with cristae protruding into the matrix. Related to their function, the localization of mitochondrial membrane proteins is more or less restricted to specific sub-compartments. In contrast, it can be assumed that membrane proteins per se diffuse unimpeded through continuous membranes. Fluorescence recovery after photobleaching is a versatile technology used in mobility analyses to determine the mobile fraction of proteins, but it cannot provide data on subpopulations or on confined diffusion behavior...
August 17, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28819229/cryo-em-analysis-of-homodimeric-full-length-lrrk2-and-lrrk1-protein-complexes
#3
Kushal Sejwal, Mohamed Chami, Hervé Rémigy, Renée Vancraenenbroeck, William Sibran, Rosmarie Sütterlin, Paul Baumgartner, Robert McLeod, Marie-Christine Chartier-Harlin, Veerle Baekelandt, Henning Stahlberg, Jean-Marc Taymans
Leucine-rich repeat kinase 2 (LRRK2) is a large multidomain protein implicated in the pathogenesis of both familial and sporadic Parkinson's disease (PD), and currently one of the most promising therapeutic targets for drug design in Parkinson's disease. In contrast, LRRK1, the closest homologue to LRRK2, does not play any role in PD. Here, we use cryo-electron microscopy (cryo-EM) and single particle analysis to gain structural insight into the full-length dimeric structures of LRRK2 and LRRK1. Differential scanning fluorimetry-based screening of purification buffers showed that elution of the purified LRRK2 protein in a high pH buffer is beneficial in obtaining high quality cryo-EM images...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28815280/overcoming-challenges-in-single-particle-inductively-coupled-plasma-mass-spectrometry-measurement-of-silver-nanoparticles
#4
Jingyu Liu, Karen E Murphy, Michael R Winchester, Vincent A Hackley
Single particle ICP-MS has evolved rapidly as a quantitative method for determining nanoparticle size and number concentration at environmentally relevant exposure levels. Central to the application of spICP-MS is a commonly used, but not rigorously validated, calibration approach based on the measured transport efficiency and the response of ionic standards. In this work, we present a comprehensive and systematic study of the accuracy, precision and robustness of spICP-MS using the rigorously characterized reference material (RM) 8017 (Polyvinylpyrrolidone Coated Nominal 75 nm Silver Nanoparticles), recently issued by the National Institute of Standards and Technology (NIST)...
August 16, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28813142/atomic-force-microscopy-infrared-spectroscopy-of-individual-atmospheric-aerosol-particles-sub-diffraction-limit-vibrational-spectroscopy-and-morphological-analysis
#5
Amy Lynne Bondy, Rachel M Kirpes, Rachel Leah Merzel, Kerri A Pratt, Mark M Banaszak Holl, Andrew P Ault
Chemical analysis of atmospheric aerosols is an analytical challenge, as aerosol particles are complex chemical mixtures that can contain hundreds to thousands of species in attoliter volumes at the most abundant sizes in the atmosphere (~100 nm). These particles have global impacts on climate and health, but there are few methods available that combine imaging and the detailed molecular information from vibrational spectroscopy for individual particles <500 nm. Herein, we show the first application of atomic force microscopy with infrared spectroscopy (AFM-IR) to detect trace organic and inorganic species and probe intraparticle chemical variation in individual particles down to 150 nm...
August 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28811473/plant-made-polio-type-3-stabilized-vlps-a-candidate-synthetic-polio-vaccine
#6
Johanna Marsian, Helen Fox, Mohammad W Bahar, Abhay Kotecha, Elizabeth E Fry, David I Stuart, Andrew J Macadam, David J Rowlands, George P Lomonossoff
Poliovirus (PV) is the causative agent of poliomyelitis, a crippling human disease known since antiquity. PV occurs in two distinct antigenic forms, D and C, of which only the D form elicits a robust neutralizing response. Developing a synthetically produced stabilized virus-like particle (sVLP)-based vaccine with D antigenicity, without the drawbacks of current vaccines, will be a major step towards the final eradication of poliovirus. Such a sVLP would retain the native antigenic conformation and the repetitive structure of the original virus particle, but lack infectious genomic material...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28811371/angular-reconstitution-based-3d-reconstructions-of-nanomolecular-structures-from-superresolution-light-microscopy-images
#7
Desirée Salas, Antoine Le Gall, Jean-Bernard Fiche, Alessandro Valeri, Yonggang Ke, Patrick Bron, Gaetan Bellot, Marcelo Nollmann
Superresolution light microscopy allows the imaging of labeled supramolecular assemblies at a resolution surpassing the classical diffraction limit. A serious limitation of the superresolution approach is sample heterogeneity and the stochastic character of the labeling procedure. To increase the reproducibility and the resolution of the superresolution results, we apply multivariate statistical analysis methods and 3D reconstruction approaches originally developed for cryogenic electron microscopy of single particles...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28809982/coordination-polymer-derived-nano-sized-zinc-ferrite-with-excellent-performance-in-nitro-explosive-detection
#8
Debal Kanti Singha, Partha Mahata
Herein, a mixed metal coordination polymer, {(H2pip)[Zn1/3Fe2/3(pydc-2,5)2(H2O)]·2H2O} 1 {where H2pip = piperazinediium and pydc-2,5 = pyridine-2,5-dicarboxylate}, was successfully synthesized using a hydrothermal technique. To confirm the structure and phase purity of 1, single crystals of an isomorphous pure Fe compound, {(H2pip)[Fe(pydc-2,5)2(H2O)]·2H2O} 1a, were synthesized based on similar synthetic conditions. Single crystal X-ray data of 1a confirmed the one-dimensional anionic metal-organic coordination polymer hydrogen bonded with protonated piprazine (piperazinediium) and lattice water molecules...
August 15, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28809003/preparation-of-disease-related-protein-assemblies-for-single-particle-electron-microscopy
#9
A Cameron Varano, Naoe Harafuji, William Dearnaley, Lisa Guay-Woodford, Deborah F Kelly
Electron microscopy (EM) is a rapidly growing area of structural biology that permits us to decode biological assemblies at the nanoscale. To examine biological materials for single particle EM analysis, purified assemblies must be obtained using biochemical separation techniques. Here, we describe effective methodologies for isolating histidine (his)-tagged protein assemblies from the nucleus of disease-relevant cell lines. We further demonstrate how isolated assemblies are visualized using single particle EM techniques and provide representative results for each step in the process...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28805793/conformational-landscape-of-a-virus-by-single-particle-x-ray-scattering
#10
Ahmad Hosseinizadeh, Ghoncheh Mashayekhi, Jeremy Copperman, Peter Schwander, Ali Dashti, Reyhaneh Sepehr, Russell Fung, Marius Schmidt, Chun Hong Yoon, Brenda G Hogue, Garth J Williams, Andrew Aquila, Abbas Ourmazd
Using a manifold-based analysis of experimental diffraction snapshots from an X-ray free electron laser, we determine the three-dimensional structure and conformational landscape of the PR772 virus to a detector-limited resolution of 9 nm. Our results indicate that a single conformational coordinate controls reorganization of the genome, growth of a tubular structure from a portal vertex and release of the genome. These results demonstrate that single-particle X-ray scattering has the potential to shed light on key biological processes...
August 14, 2017: Nature Methods
https://www.readbyqxmd.com/read/28799771/understanding-nonradiative-recombination-through-defect-induced-conical-intersections
#11
Yinan Shu, B Scott Fales, Wei-Tao Peng, Benjamin G Levine
Defects are known to introduce pathways for the nonradiative recombination of electronic excitations in semiconductors, but implicating a specific defect as a nonradiative center remains challenging for both experiment and theory. In this Perspective, we present recent progress toward this goal involving the identification and characterization of defect-induced conical intersections (DICIs), points of degeneracy between the ground and first excited electronic states of semiconductor materials that arise from the deformation of specific defects...
August 16, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28795793/an-unprecedented-case-a-low-specific-surface-area-anatase-n-doped-carbon-nanocomposite-derived-from-a-new-single-source-precursor-affords-fast-and-stable-lithium-storage
#12
Man Gao, Kaixiang Zou, Yuanfu Deng, Zhenxia Zhao, Yingwei Li, Guohua Chen
A nanocomposite of ultra-fine anatase nanoparticles (< 5 nm) embedded N-doped carbon (TiO2-NPs/NC) with a relatively low specific surface area was successfully synthesized by in-situ pyrolysis of a new and cheap single source precursor of (H2en)3[Ti4(O2)4(Hcit)2(cit)2]∙12H2O (en = ethylenediamine and H4cit = citric acid) under 550 oC and inert atmosphere. The precursor in crystalline state was isolated from an aqueous solution containing of titanium butoxide, citric acid, hydrogen peroxide and ethylenediamine and was characterized...
August 10, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28795512/single-particle-cryo-em-improved-ab-initio-3d-reconstruction-with-simple-prime
#13
Cyril F Reboul, Michael Eager, Dominika Elmlund, Hans Elmlund
Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. We developed the SIMPLE open-source image-processing suite for analysing cryo-EM images of single-particles. A core component of SIMPLE is the probabilistic PRIME algorithm for identifying clusters of images in 2D and determine relative orientations of single-particle projections in 3D. Here we extend our previous work on PRIME and introduce new stochastic optimisation algorithms that improve the robustness of the approach...
August 10, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28792742/sequential-release-of-proteins-from-structured-multishell-microcapsules
#14
Ulyana Shimanovich, Thomas C T Michaels, Erwin J de Genst, Dijana Matak-Vinkovic, Christopher M Dobson, Tuomas P J Knowles
In nature, a wide range of functional materials is based on proteins. Increasing attention is also turning to the use of proteins as artificial biomaterials in the form of films, gels, particles and fibrils that offer great potential for applications in areas ranging from molecular medicine to materials science. To date, however, most such applications have been limited to single component materials despite the fact that their natural analogues are composed of multiple types of proteins with a variety of functionalities that are co-assembled in a highly organized manner on the micron scale, a process which is currently challenging to achieve in the laboratory...
August 9, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28790980/exploring-microdiversity-in-novel-kordia-sp-bacteroidetes-with-proteorhodopsin-from-the-tropical-indian-ocean-via-single-amplified-genomes
#15
Marta Royo-Llonch, Isabel Ferrera, Francisco M Cornejo-Castillo, Pablo Sánchez, Guillem Salazar, Ramunas Stepanauskas, José M González, Michael E Sieracki, Sabrina Speich, Lars Stemmann, Carlos Pedrós-Alió, Silvia G Acinas
Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28790440/adenoviral-e4-34k-protein-interacts-with-virus-packaging-components-and-may-serve-as-the-putative-portal
#16
Yadvinder S Ahi, Ahmed O Hassan, Sai V Vemula, Kunpeng Li, Wen Jiang, Guang Jun Zhang, Suresh K Mittal
Studies on dsDNA bacteriophages have revealed that a DNA packaging complex assembles at a special vertex called the 'portal vertex' and consists of a portal, a DNA packaging ATPase and other components. AdV protein IVa2 is presumed to function as a DNA packaging ATPase. However, a protein that functions as a portal is not yet identified in AdVs. To identify the AdV portal, we performed secondary structure analysis on a set of AdV proteins and compared them with the clip region of the portal proteins of bacteriophages phi29, SPP1 and T4...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28783192/differentiating-between-long-and-short-range-disorder-in-infra-red-spectra-on-the-meaning-of-crystallinity-in-silica
#17
Yotam Asscher, Gregorio Dal Sasso, Luca Nodari, Ivana Angelini, Tiziana Boffa Ballaran, Gilberto Artioli
Local atomic disorder and crystallinity are structural properties that influence greatly the resulting chemical and mechanical properties of inorganic solids, and are used as indicators for different pathways of material formation. Here, these structural properties are assessed in the crystals of quartz based on particle-size-related scattering processes in transmission infra-red spectroscopy. Independent determinations of particle size distributions in the range 2-100 μm of a single crystal of quartz and defective quartz with highly anisotropic micro-crystallites show that particle sizes below the employed wavelength (approx 10 μm) exhibit asymmetric narrowing of absorption peak widths, due to scattering processes that depend on the intra-particle structural defects and long range crystallinity...
August 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28781998/the-advent-of-structural-biology-in-situ-by-single-particle-cryo-electron-tomography
#18
Jesús G Galaz-Montoya, Steven J Ludtke
Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ...
2017: Biophysics Reports
https://www.readbyqxmd.com/read/28777911/multiple-method-analysis-of-tio2-nanoparticle-uptake-in-rice-oryza-sativa-l-plants
#19
Yingqing Deng, Elijah J Petersen, Katie Challis, Savelas A Rabb, Richard David Holbrook, James F Ranville, Bryant C Nelson, Baoshan Xing
Understanding the translocation of nanoparticles (NPs) into plants is challenging because qualitative and quantitative methods are still being developed and the comparability of results among different methods is unclear. In this study, uptake of titanium dioxide NPs and larger bulk particles (BPs) at 5 mg/L and 50 mg/L concentrations in rice plant (Oryza sativa L.) tissues was evaluated using three orthogonal techniques: electron microscopy, single-particle inductively coupled plasma mass spectroscopy (spICP-MS) with two different plant digestion approaches, and total elemental analysis using ICP optical emission spectroscopy...
August 4, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28767662/dust-concentration-measurement-based-on-mie-scattering-of-a-laser-beam
#20
Xiaoyu Yu, Yunbo Shi, Tian Wang, Xu Sun
To realize automatic measurement of the concentration of dust particles in the air, a theory for dust concentration measurement was developed, and a system was designed to implement the dust concentration measurement method based on laser scattering. In the study, the principle of dust concentration detection using laser scattering is studied, and the detection basis of Mie scattering theory is determined. Through simulation, the influence of the incident laser wavelength, dust particle diameter, and refractive index of dust particles on the scattered light intensity distribution are obtained for determining the scattered light intensity curves of single suspended dust particles under different characteristic parameters...
2017: PloS One
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