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Single particle electron microscopy

Lulu Cui, Rui Li, Yunchen Zhang, Ya Meng, Hongbo Fu, Jianmin Chen
Continuous HONO measurement was conducted to study the formation features of HONO during the haze episodes at Shanghai, China. The HONO concentration ranged from 0.26 to 5.84ppb and averaged at 2.31ppb during the measurement period. The HONO concentration during the haze episode (P1), the haze-fog episode (P2) and the clean period (P3) were 2.80, 2.35 and 1.78ppb, respectively. Heterogeneous conversion of NO2 was the dominate pathway for nocturnal HONO formation, and the heterogeneous conversion efficiency of NO2 to HONO was closely associated with the PM2...
March 1, 2018: Science of the Total Environment
C O S Sorzano, E Fernández-Giménez, V Peredo-Robinson, J Vargas, T Majtner, G Caffarena, J Otón, J L Vilas, J M de la Rosa-Trevín, R Melero, J Gómez-Blanco, J Cuenca, L Del Cano, P Conesa, R Marabini, J M Carazo
The introduction of Direct Electron Detector (DED) videos in the Electron Microscope field has boosted Single Particle Analysis to a point in which it is currently considered to be a key technique in Structural Biology. In this article we introduce an approach to estimate the DED camera gain at each pixel from the movies themselves. This gain is needed to have the set of recorded frames into a coherent gray level range, homogeneous over the whole image. The algorithm does not need any other input than the DED movie itself, being capable of providing an estimate of the camera gain image, helping to identify dead pixels and cases of incorrectly calibrated cameras...
March 15, 2018: Journal of Structural Biology
Peng Cao, Xiaodong Su, Xiaowei Pan, Zhenfeng Liu, Wenrui Chang, Mei Li
Around photosystem II (PSII), the peripheral antenna system absorbs sunlight energy and transfers it to the core complex where the water-splitting and oxygen-evolving reaction takes place. The peripheral antennae in plants are composed of various light-harvesting complexes II (LHCII). Recently, the three-dimensional structure of the C2 S2 M2 -type PSII-LHCII supercomplex from Pisum sativum (PsPSII) has been solved at 2.7-Å resolution using the single-particle cryo-electron microscopy method. The large homodimeric supercomplex has a total molecular weight of >1400 kDa...
March 14, 2018: Biochimica et Biophysica Acta
Giorgio Vilardi, Thanasis Mpouras, Dimitris Dermatas, Nicola Verdone, Angeliki Polydera, Luca Di Palma
Carbon Nanotubes (CNTs) and nano Zero-Valent Iron (nZVI) particles, as well as two nanocomposites based on these novel nanomaterials, were employed as nano-adsorbents for the removal of hexavalent chromium, selenium and cobalt, from aqueous solutions. Nanomaterials characterization included the determination of their point of zero charge and particle size distribution. CNTs were further analyzed using scanning electron microscopy, thermogravimetric analysis and Raman spectroscopy to determine their morphology and structural properties...
March 5, 2018: Chemosphere
Jonathan M Grimes, David R Hall, Alun W Ashton, Gwyndaf Evans, Robin L Owen, Armin Wagner, Katherine E McAuley, Frank von Delft, Allen M Orville, Thomas Sorensen, Martin A Walsh, Helen M Ginn, David I Stuart
Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and cryo-crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments...
February 1, 2018: Acta Crystallographica. Section D, Structural Biology
Yohei Ishida, Akihiro Morita, Tomoharu Tokunaga, Tetsu Yonezawa
We herein present the preparation of short, bulky cationic thiolate (thiocholine) protected fluorescent Au nanoclusters via sputter deposition over a liquid polymer matrix. The obtained Au nanoclusters showed near-infrared fluorescence and had an average core diameter of 1.7 ± 0.6 nm, which is too large compared with that of the reported fluorescent Au nanoclusters prepared via chemical means. We revealed the mechanism of formation of this unique material using single-particle electron microscopy, optical measurements, X-ray photoelectron spectroscopy (XPS), and high-performance liquid chromatography fractionations...
March 12, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
David E Timm, Valorie Bowman, Russell Madsen, Charles Rauch
Protein arginine methyl transferase 5 (PRMT5) is a signaling protein and histone modifying enzyme that is important in many cellular processes, including regulation of eukaryotic gene transcription. Reported here is a 3.7 Å structure of PRMT5, solved in complex with regulatory binding subunit MEP50 (methylosome associated protein 50, WDR77, p44), by single particle (SP) cryo-Electron Microscopy (cryo-EM) using micrographs of particles that are visibly crowded and aggregated. Despite suboptimal micrograph appearance, this cryo-EM structure is in good agreement with previously reported crystal structures of the complex, which revealed a 450 kDa hetero-octameric assembly having internal D2 symmetry...
2018: PloS One
Nate Yoder, Craig Yoshioka, Eric Gouaux
Acid-sensing ion channels (ASICs) are trimeric, proton-gated and sodium-selective members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels and are expressed throughout vertebrate central and peripheral nervous systems. Gating of ASICs occurs on a millisecond time scale and the mechanism involves three conformational states: high pH resting, low pH open and low pH desensitized. Existing X-ray structures of ASIC1a describe the conformations of the open and desensitized states, but the structure of the high pH resting state and detailed mechanisms of the activation and desensitization of the channel have remained elusive...
March 7, 2018: Nature
Timothy Grant, Alexis Rohou, Nikolaus Grigorieff
We have developed new open-source software called cis TEM (computational imaging system for transmission electron microscopy) for the processing of data for high-resolution electron cryo-microscopy and single-particle averaging. cis TEM features a graphical user interface that is used to submit jobs, monitor their progress, and display results. It implements a full processing pipeline including movie processing, image defocus determination, automatic particle picking, 2D classification, ab-initio 3D map generation from random parameters, 3D classification, and high-resolution refinement and reconstruction...
March 7, 2018: ELife
Austin P Spencer, William O Hutson, Shawn Irgen-Gioro, Elad Harel
We demonstrate that high-dimensionality coherent spectroscopy yields "super-resolved" spectra whereby peaks may be localized far below their homogeneous line width by resolving them across multiple, coherently coupled dimensions. We implement this technique using a fifth-order photon-echo spectroscopy called Gradient-Assisted Multidimensional Electronic-Raman Spectroscopy (GAMERS) that combines resonant and non-resonant excitation to disperse the optical response across three spectral dimensions: two involving excitonic transitions and one that encodes phonon energies...
March 7, 2018: Journal of Physical Chemistry Letters
Yuxi Liu, Shane Gonen, Tamir Gonen, Todd O Yeates
Current single-particle cryo-electron microscopy (cryo-EM) techniques can produce images of large protein assemblies and macromolecular complexes at atomic level detail without the need for crystal growth. However, proteins of smaller size, typical of those found throughout the cell, are not presently amenable to detailed structural elucidation by cryo-EM. Here we use protein design to create a modular, symmetrical scaffolding system to make protein molecules of typical size suitable for cryo-EM. Using a rigid continuous alpha helical linker, we connect a small 17-kDa protein (DARPin) to a protein subunit that was designed to self-assemble into a cage with cubic symmetry...
March 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
Xieyang Guo, Alexander G Myasnikov, James Chen, Corinne Crucifix, Gabor Papai, Maria Takacs, Patrick Schultz, Albert Weixlbaumer
Transcriptional pausing by RNA polymerases (RNAPs) is a key mechanism to regulate gene expression in all kingdoms of life and is a prerequisite for transcription termination. The essential bacterial transcription factor NusA stimulates both pausing and termination of transcription, thus playing a central role. Here, we report single-particle electron cryo-microscopy reconstructions of NusA bound to paused E. coli RNAP elongation complexes with and without a pause-enhancing hairpin in the RNA exit channel...
March 1, 2018: Molecular Cell
Pranesh Kumar, Ashok K Singh, Vinit Raj, Amit Rai, Amit K Keshari, Dinesh Kumar, Biswanath Maity, Anand Prakash, Sabyasachi Maiti, Sudipta Saha
Purpose: The application of betulinic acid (B), a potent antineoplastic agent, is limited due to poor bioavailability, short plasma half-life and inappropriate tissue distribution. Thus, we aimed to prepare novel 50:50 poly(lactic- co -glycolic acid) (PLGA)-loaded B nanoparticles (BNP) and to compare its anti-hepatocellular carcinoma (HCC) activity with parent B. Methods: BNP were synthesized and characterized using different methods such as scanning electron microscopy (SEM), fourier-transform infrared (FTIR) spectrometry and particle size analyses...
2018: International Journal of Nanomedicine
Jacob Bruggemann, Gabriel C Lander, Andrew I Su
Extraction of particles from cryo-electron microscopy (cryo-EM) micrographs is a crucial step in processing single-particle datasets. Although algorithms have been developed for automatic particle picking, these algorithms generally rely on two-dimensional templates for particle identification, which may exhibit biases that can propagate artifacts through the reconstruction pipeline. Manual picking is viewed as a gold-standard solution for particle selection, but it is too time-consuming to perform on data sets of thousands of images...
February 24, 2018: Journal of Structural Biology
Lihui Tian, Ming Fu, Wei Xiong
High-entropy alloys (HEAs) are promising structural materials due to their excellent comprehensive performances. The use of mechanically alloyed powders to deposit HEA coatings through atmospheric plasma spraying (APS) is an effective approach that can broaden the application areas of the HEAs. In this paper, a ductility-brittleness AlCoCrFeNiSi system was chosen as an object of study, and the detailed evolution of the surface morphology, particle size distribution, and microstructure of the powder during mechanical alloying was investigated...
February 23, 2018: Materials
Dorit Hanein, Niels Volkmann
Integrins are bidirectional transmembrane receptors that play central roles in hemostasis and arterial thrombosis. They have been subject to structural studies for many years, in particular using X-ray crystallography, nuclear magnetic resonance spectroscopy, and two-dimensional negative stain electron microscopy. Despite considerable progress, a full consensus on the molecular mechanism of integrin activation is still lacking. Three-dimensional reconstructions of full-length human platelet integrin αIIb β3 in lipid-bilayer nanodiscs obtained by electron cryo-microscopy and single-particle reconstruction have shed new light on the activation process...
2018: Sub-cellular Biochemistry
Gaetano Santulli, Daniel Lewis, Amedee des Georges, Andrew R Marks, Joachim Frank
Ryanodine receptors (RyRs) are ubiquitous intracellular calcium (Ca2+ ) release channels required for the function of many organs including heart and skeletal muscle, synaptic transmission in the brain, pancreatic beta cell function, and vascular tone. In disease, defective function of RyRs due either to stress (hyperadrenergic and/or oxidative overload) or genetic mutations can render the channels leaky to Ca2+ and promote defective disease-causing signals as observed in heat failure, muscular dystrophy, diabetes mellitus, and neurodegerative disease...
2018: Sub-cellular Biochemistry
Dheva Setiaputra, Salar Ahmad, Udit Dalwadi, Anne-Lise Steunou, Shan Lu, James D Ross, Meng-Qiu Dong, Jacques Côté, Calvin K Yip
Conserved from yeast to humans, the NuA4 histone acetyltransferase is a large multisubunit complex essential for cell viability through regulation of gene expression, genome maintenance, metabolism, and cell fate during development and stress. How the different NuA4 subunits work in concert with one another to perform these diverse functions remains unclear, and addressing this central question requires a comprehensive understanding of NuA4's molecular architecture and subunit organization. We have determined the structure of fully assembled native yeast NuA4 by single-particle electron microscopy...
February 20, 2018: Molecular and Cellular Biology
Theresia Gutmann, Kelly H Kim, Michal Grzybek, Thomas Walz, Ünal Coskun
Insulin receptor (IR) signaling plays a critical role in the regulation of metabolism and growth in multicellular organisms. IRs are unique among receptor tyrosine kinases in that they exist exclusively as covalent (αβ) 2 homodimers at the cell surface. Transmembrane signaling by the IR can therefore not be based on ligand-induced dimerization as such but must involve structural changes within the existing receptor dimer. In this study, using glycosylated full-length human IR reconstituted into lipid nanodiscs, we show by single-particle electron microscopy that insulin binding to the dimeric receptor converts its ectodomain from an inverted U-shaped conformation to a T-shaped conformation...
February 16, 2018: Journal of Cell Biology
Ivelin S Georgiev, Michael Gordon Joyce, Rita E Chen, Kwanyee Leung, Krisha McKee, Aliaksandr Druz, Joseph G Van Galen, Masaru Kanekiyo, Yaroslav Tsybovsky, Eun Sung Yang, Yongping Yang, Priyamvada Acharya, Marie Pancera, Paul V Thomas, Timothy Wanninger, Hadi Yassine, Ulrich Baxa, Nicole Doria-Rose, Cheng Cheng, Barney S Graham, John R Mascola, Peter D Kwong
Antigen multimerization on a nanoparticle can result in improved neutralizing antibody responses. A platform that has been successfully used for displaying antigens from a number of different viruses is ferritin, a self-assembling protein nanoparticle that allows the attachment of multiple copies (twenty-four monomers or eight trimers) of a single antigen. Here we design two-component ferritin variants that allow the attachment of two diverse antigens on a single particle in a defined ratio and geometric pattern...
February 16, 2018: ACS Infectious Diseases
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