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Single particle electron microscopy

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https://www.readbyqxmd.com/read/28323402/single-particle-observation-of-sv40-vp1-polyanion-induced-assembly-shows-that-substrate-size-and-structure-modulate-capsid-geometry
#1
Chenglei Li, Andrew R Kneller, Stephen C Jacobson, Adam Zlotnick
Simian virus 40 capsid protein (VP1) is a unique system for studying substrate-dependent assembly of a nanoparticle. Here, we investigate a simplest case of this system where twelve VP1 pentamers and a single polyanion, e.g. RNA, form a T=1 particle. To test the roles of polyanion substrate length and structure during assembly, we characterized the assembly products with size exclusion chromatography, transmission electron microscopy, and single-particle resistive-pulse sensing. We found that a 500 nt RNA has the optimal length and structure for assembly of uniform T=1 particles...
March 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28318486/structural-basis-of-transcription-arrest-by-coliphage-hk022-nun-in-an-escherichia-coli-rna-polymerase-elongation-complex
#2
Jin Young Kang, Paul Dominic B Olinares, James Chen, Elizabeth A Campbell, Arkady Mustaev, Brian T Chait, Max E Gottesman, Seth A Darst
Coliphage HK022 Nun blocks superinfection by coliphage λ by stalling RNA polymerase (RNAP) translocation specifically on λΔNA.To provide a structural framework to understand how Nun blocks RNAP translocation, we determined structures of Escherichia coli RNAP ternary elongation complexes (TECs) with and without Nun by single-particle cryo-electron microscopy. Nun fits tightly into the TEC by taking advantage of gaps between the RNAP and the nucleic acids. The C-terminal segment of Nun interacts with the RNAP β and β' subunits inside the RNAP active site cleft as well as with nearly every element of the nucleic-acid scaffold, essentially crosslinking the RNAP and the nucleic acids to prevent translocation, a mechanism supported by the effects of Nun amino acid substitutions...
March 20, 2017: ELife
https://www.readbyqxmd.com/read/28314154/streamlined-approach-to-mapping-the-magnetic-induction-of-skyrmionic-materials
#3
Jordan J Chess, Sergio A Montoya, Tyler R Harvey, Colin Ophus, Simon Couture, Vitaliy Lomakin, Eric E Fullerton, Benjamin J McMorran
Recently, Lorentz transmission electron microscopy (LTEM) has helped researchers advance the emerging field of magnetic skyrmions. These magnetic quasi-particles, composed of topologically non-trivial magnetization textures, have a large potential for application as information carriers in low-power memory and logic devices. LTEM is one of a very few techniques for direct, real-space imaging of magnetic features at the nanoscale. For Fresnel-contrast LTEM, the transport of intensity equation (TIE) is the tool of choice for quantitative reconstruction of the local magnetic induction through the sample thickness...
February 28, 2017: Ultramicroscopy
https://www.readbyqxmd.com/read/28302852/structures-of-the-cyanobacterial-circadian-oscillator-frozen-in-a-fully-assembled-state
#4
Joost Snijder, Jan M Schuller, Anika Wiegard, Philip Lössl, Nicolas Schmelling, Ilka M Axmann, Jürgen M Plitzko, Friedrich Förster, Albert J R Heck
Cyanobacteria have a robust circadian oscillator, known as the Kai system. Reconstituted from the purified protein components KaiC, KaiB, and KaiA, it can tick autonomously in the presence of adenosine 5'-triphosphate (ATP). The KaiC hexamers enter a natural 24-hour reaction cycle of autophosphorylation and assembly with KaiB and KaiA in numerous diverse forms. We describe the preparation of stoichiometrically well-defined assemblies of KaiCB and KaiCBA, as monitored by native mass spectrometry, allowing for a structural characterization by single-particle cryo-electron microscopy and mass spectrometry...
March 17, 2017: Science
https://www.readbyqxmd.com/read/28287545/method-to-visualize-and-analyze-membrane-interacting-proteins-by-transmission-electron-microscopy
#5
Ramakrishnan B Kumar, Lin Zhu, Hans Hebert, Caroline Jegerschöld
Monotopic proteins exert their function when attached to a membrane surface, and such interactions depend on the specific lipid composition and on the availability of enough area to perform the function. Nanodiscs are used to provide a membrane surface of controlled size and lipid content. In the absence of bound extrinsic proteins, sodium phosphotungstate-stained nanodiscs appear as stacks of coins when viewed from the side by transmission electron microscopy (TEM). This protocol is therefore designed to intentionally promote stacking; consequently, the prevention of stacking can be interpreted as the binding of the membrane-binding protein to the nanodisc...
March 5, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28284056/depth-sectioning-combined-with-atom-counting-in-haadf-stem-to-retrieve-the-3d-atomic-structure
#6
M Alania, T Altantzis, A De Backer, I Lobato, S Bals, S Van Aert
Aberration correction in scanning transmission electron microscopy (STEM) has greatly improved the lateral and depth resolution. When using depth sectioning, a technique during which a series of images is recorded at different defocus values, single impurity atoms can be visualised in three dimensions. In this paper, we investigate new possibilities emerging when combining depth sectioning and precise atom-counting in order to reconstruct nanosized particles in three dimensions. Although the depth resolution does not allow one to precisely locate each atom within an atomic column, it will be shown that the depth location of an atomic column as a whole can be measured precisely...
November 9, 2016: Ultramicroscopy
https://www.readbyqxmd.com/read/28283532/molecular-architecture-of-the-n-type-atpase-rotor-ring-from-burkholderia-pseudomallei
#7
Sarah Schulz, Martin Wilkes, Deryck J Mills, Werner Kühlbrandt, Thomas Meier
The genome of the highly infectious bacterium Burkholderia pseudomallei harbors an atp operon that encodes an N-type rotary ATPase, in addition to an operon for a regular F-type rotary ATPase. The molecular architecture of N-type ATPases is unknown and their biochemical properties and cellular functions are largely unexplored. We studied the B. pseudomallei N1No-type ATPase and investigated the structure and ion specificity of its membrane-embedded c-ring rotor by single-particle electron cryo-microscopy. Of several amphiphilic compounds tested for solubilizing the complex, the choice of the low-density, low-CMC detergent LDAO was optimal in terms of map quality and resolution...
March 10, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28283067/transporters-revealed
#8
Jyh-Yeuan Lee, Daniel M Rosenbaum
The subfamily C ATP-binding cassette (ABCC) transporters mediate multidrug resistance and ion conductance regulation. Recent atomic or near-atomic resolution structures of three physiologically significant ABCC transporters (MRP1, SUR1, and CFTR), determined by using single-particle cryo-electron microscopy (cryo-EM), reveal structural details that help explain the wide functional diversity of this ABC transporter subfamily.
March 9, 2017: Cell
https://www.readbyqxmd.com/read/28273348/performance-evaluation-of-18-f-radioluminescence-microscopy-using-computational-simulation
#9
Qian Wang, Debanti Sengupta, Tae Jin Kim, Guillem Pratx
PURPOSE: Radioluminescence microscopy can visualize the distribution of beta-emitting radiotracers in live single cells with high resolution. Here, we perform a computational simulation of (18) F positron imaging using this modality to better understand how radioluminescence signals are formed and to assist in optimizing the experimental setup and image processing. METHODS: First, the transport of charged particles through the cell and scintillator and the resulting scintillation is modeled using the GEANT4 Monte-Carlo simulation...
March 8, 2017: Medical Physics
https://www.readbyqxmd.com/read/28273047/sensing-of-single-electrons-using-micro-and-nano-technologies-a-review
#10
Jubayer Jalil, Yong Zhu, Chandima Ekanayake, Yong Ruan
During the last three decades, the remarkable dynamic features of microelectromechanical systems (MEMS) and nanoelectromechanical systems (NEMS), and advances in solid-state electronics hold much potential for the fabrication of extremely sensitive charge sensors. These sensors have a broad range of applications, such as those involving the measurement of ionization radiation, detection of bio-analyte and aerosol particles, mass spectrometry, scanning tunneling microscopy, and quantum computation. Designing charge sensors (also known as charge electrometers) for electrometry is deemed significant because of the sensitivity and resolution issues in the range of micro- and nano-scales...
April 7, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28267165/unravelling-charge-separation-via-surface-built-in-electric-fields-within-single-particulate-photocatalysts
#11
Ruotian Chen, Jian Zhu, Hongyu An, Fengtao Fan, Can Li
Kelvin Probe Force Microscopy (KPFM) and spatially resolved surface photovoltage (SRSPV) techniques were employed to reveal built-in electric fields and surface photogenerated charge distribution on single particulate photocatalysts. The photogenerated holes and electrons spread over the whole surface of the particulate photocatalyst are imaged on n-type BiVO4 and p-type Cu2O single particles, respectively. It is demonstrated that the built-in electric field in the surface Space Charge Region (SCR) dictates the charge separation/transfer processes and allows the drift of one kind of the photogenerated carriers to the surface, while holding another kind of the carriers in the bulk...
March 7, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28263324/cryo-em-structure-of-a-metazoan-separase-securin-complex-at-near-atomic-resolution
#12
Andreas Boland, Thomas G Martin, Ziguo Zhang, Jing Yang, Xiao-Chen Bai, Leifu Chang, Sjors H W Scheres, David Barford
Separase is a caspase-family protease that initiates chromatid segregation by cleaving the kleisin subunits (Scc1 and Rec8) of cohesin, and regulates centrosome duplication and mitotic spindle function through cleavage of kendrin and Slk19. To understand the mechanisms of securin regulation of separase, we used single-particle cryo-electron microscopy (cryo-EM) to determine a near-atomic-resolution structure of the Caenorhabditis elegans separase-securin complex. Separase adopts a triangular-shaped bilobal architecture comprising an N-terminal tetratricopeptide repeat (TPR)-like α-solenoid domain docked onto the conserved C-terminal protease domain...
March 6, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28260612/monitoring-a-simple-hydrolysis-process-in-an-organic-solid-by-observing-methyl-group-rotation
#13
Peter A Beckmann, Joseph M Bohen, Jamie Ford, William P Malachowski, Clelia W Mallory, Frank B Mallory, Andrew R McGhie, Arnold L Rheingold, Gilbert J Sloan, Steven T Szewczyk, Xianlong Wang, Kraig A Wheeler
We report a variety of experiments and calculations and their interpretations regarding methyl group (CH3) rotation in samples of pure 3-methylglutaric anhydride (1), pure 3-methylglutaric acid (2), and samples where the anhydride is slowly absorbing water from the air and converting to the acid [C6H8O3(1) + H2O → C6H10O4(2)]. The techniques are solid state (1)H nuclear magnetic resonance (NMR) spin-lattice relaxation, single-crystal X-ray diffraction, electronic structure calculations in both isolated molecules and in clusters of molecules that mimic the crystal structure, field emission scanning electron microscopy, differential scanning calorimetry, and high resolution (1)H NMR spectroscopy...
January 29, 2017: Solid State Nuclear Magnetic Resonance
https://www.readbyqxmd.com/read/28257993/release-of-monomers-from-composite-dust
#14
S M Cokic, R C Duca, L Godderis, P H Hoet, J W Seo, B Van Meerbeek, K L Van Landuyt
OBJECTIVES: Dental personnel are more at risk to develop asthmatic disease, but the exact reason is so far unknown. During abrasive procedures, dental personnel are exposed to nano-sized dust particles released from dental composite. The aim of this study was to investigate whether respirable composite dust may also release monomers. METHODS: Respirable (<5μm) composite dust was collected and the release of methacrylate monomers and Bisphenol A (BPA) in water and ethanol was evaluated by liquid chromatography/mass spectroscopy (LC-MS/MS)...
March 1, 2017: Journal of Dentistry
https://www.readbyqxmd.com/read/28257778/interaction-between-the-photoprotective-protein-lhcsr3-and-c2s2-photosystem-ii-supercomplex-in-chlamydomonas-reinhardtii
#15
Dmitriy A Semchonok, K N Sathish Yadav, Pengqi Xu, Bartlomiej Drop, Roberta Croce, Egbert J Boekema
Photosynthetic organisms can thermally dissipate excess of absorbed energy in high-light conditions in a process known as non-photochemical quenching (NPQ). In the green alga Chlamydomonas reinhardtii this process depends on the presence of the light-harvesting protein LHCSR3, which is only expressed in high light. LHCSR3 has been shown to act as a quencher when associated with the Photosystem II supercomplex and to respond to pH changes, but the mechanism of quenching has not been elucidated yet. In this work we have studied the interaction between LHCSR3 and Photosystem II C2S2 supercomplexes by single particle electron microscopy...
March 1, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28254381/vitrification-after-multiple-rounds-of-sample-application-and-blotting-improves-particle-density-on-cryo-electron-microscopy-grids
#16
Joost Snijder, Andrew J Borst, Annie Dosey, Alexandra C Walls, Anika Burrell, Vijay S Reddy, Justin M Kollman, David Veesler
Single particle cryo-electron microscopy (cryoEM) is becoming widely adopted as a tool for structural characterization of biomolecules at near-atomic resolution. Vitrification of the sample to obtain a dense distribution of particles within a single field of view remains a major bottleneck for the success of such experiments. Here, we describe a simple and cost-effective method to increase the density of frozen-hydrated particles on grids with holey carbon support films. It relies on performing multiple rounds of sample application and blotting prior to plunge freezing in liquid ethane...
February 22, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28248494/nanocomposites-of-highly-monodisperse-encapsulated-superparamagnetic-iron-oxide-nanocrystals-homogeneously-dispersed-in-a-poly-ethylene-oxide-melt
#17
Artur Feld, Rieke Koll, Lisa Sarah Fruhner, Margarita Krutyeva, Wim Pyckhout-Hintzen, Christine Weiss, Hauke Heller, Agnes Weimer, Christian Schmidtke, Marie-Sousai Appavou, Emmanuel Kentzinger, Jürgen Allgaier, Horst Weller
Nanocomposite materials based on highly stable encapsulated superparamagnetic iron oxide nanocrystals (SPIONs) were synthesized and characterized by scattering methods and transmission electron microscopy (TEM). The combination of advanced synthesis and encapsulation techniques using different diblock copolymers and the thiol-ene click reaction for crosslinking the polymeric shell results in uniform hybrid SPIONs homogeneously dispersed in a poly(ethylene oxide) matrix. Small angle X-ray scattering (SAXS) and TEM investigations demonstrate the presence of mostly single particles and a negligible amount of dyads...
March 1, 2017: ACS Nano
https://www.readbyqxmd.com/read/28244370/molecular-architecture-of-the-90s-small-subunit-pre-ribosome
#18
Qi Sun, Xing Zhu, Jia Qi, Weidong An, Pengfei Lan, Dan Tan, Rongchang Chen, Bing Wang, Sanduo Zheng, Cheng Zhang, Xining Chen, Wei Zhang, Jing Chen, Meng-Qiu Dong, Keqiong Ye
Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors...
February 28, 2017: ELife
https://www.readbyqxmd.com/read/28243978/evaluation-of-in-vitro-and-in-vivo-anti-urolithiatic-activity-of-silver-nanoparticles-containing-aqueous-leaf-extract-of-tragia-involucrata
#19
Vinodhini Velu, Moonjit Das, Arunai Nambi Raj N, Kamal Dua, Himaja Malipeddi
The present investigation is focused on exploring the anti-urolithiatic potential of aqueous leaf extract of Tragia involucrata (TIA) and its silver nanoparticles (AgNPs) and to quantify the total phenol, flavonoid, terpenoid and sterol contents present in TIA. Quantification results suggested TIA to be a rich source of phenol, flavonoid and terpenoid and less of sterol content. The AgNPs were synthesized by a simple green method using aqueous extract of T. involucrata. The formation of AgNPs was confirmed through UV spectroscopy, particle size analysis, zeta potential, X-ray diffraction and transmission electron microscopy...
February 27, 2017: Drug Delivery and Translational Research
https://www.readbyqxmd.com/read/28239431/tuning-localized-surface-plasmon-resonance-wavelengths-of-silver-nanoparticles-by-mechanical-deformation
#20
Fathima S Ameer, Shilpa Varahagiri, Donald W Benza, Daniel R Willett, Yimei Wen, Fenglin Wang, George Chumanov, Jeffrey N Anker
We describe a simple technique to alter the shape of silver nanoparticles (AgNPs) by rolling a glass tube over them to mechanically compress them. The resulting shape change in turn induces a red-shift in the localized surface plasmon resonance (LSPR) scattering spectrum and exposes new surface area. The flattened particles were characterized by optical and electron microscopy, single nanoparticle scattering spectroscopy, and surface enhanced Raman spectroscopy (SERS). AFM and SEM images show that the AgNPs deform into discs; increasing the applied load from 0 to 100 N increases the AgNP diameter and decreases the height...
September 22, 2016: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
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