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Cryo electron microscopy

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https://www.readbyqxmd.com/read/28106900/vesicle-formation-by-proton-transfer-driven-short-tailed-fatty-acids-of-c4-c8-chain-length-in-water
#1
Li-Chun Chen, Hong-Peng Wang, Yu-Hao Deng, Shao-Ping Deng
Ultrashort single-chain fatty acids self-assemble to form vesicles under certain proton-driven conditions. The protonation provides a larger charge area around the hydrophilic carbonyl headgroups, and proton shift as the key driving parameter was studied. The ultrashort fatty acids (C4-C8) formed stable unilamellar vesicles predominantly through out the whole range of tested pH levels (6.5-9.5). A proton-driven self-assembly process and effects on the phase transition were characterized by dynamic light scattering, transmission electron microscopy and cryo-transmission electron microscopy...
January 20, 2017: Soft Matter
https://www.readbyqxmd.com/read/28106271/mapping-the-intermediate-digestion-phases-of-human-healthy-intestinal-contents-from-distal-ileum-and-caecum-at-fasted-and-fed-state-conditions
#2
Thuy Tran, Dimitrios G Fatouros, Maria Vertzoni, Christos Reppas, Anette Müllertz
OBJECTIVES: To investigate at the ultrastructural level, the colloidal phases formed in the lumen of the distal ileum and caecum of healthy adults. METHODS: Cryogenic transmission electron microscopy (Cryo-TEM) was employed to image the intermediate colloidal phases of human intestinal contents collected from distal ileum and caecum of two healthy volunteers under fasted and fed state conditions. KEY FINDINGS: In samples collected both in the fasted and fed states, Cryo-TEM study revealed the presence of large spherical unilamellar and occasionally bi-lamellar and oligolamellar vesicles with diameters ranging from 50 to 200 nm for both volunteers in distal ileum and caecum...
January 20, 2017: Journal of Pharmacy and Pharmacology
https://www.readbyqxmd.com/read/28102751/extracellular-vesicles-from-activated-platelets-a-semiquantitative-cryo-electron-microscopy-and-immuno-gold-labeling-study
#3
Alain R Brisson, Sisareuth Tan, Romain Linares, Céline Gounou, Nicolas Arraud
Cells release membrane vesicles in their surrounding medium either constitutively or in response to activating signals. Two main types of extracellular vesicles (EVs) are commonly distinguished based on their mechanism of formation, membrane composition and size. According to the current model, EVs shed from the plasma membrane, often called microvesicles, expose phosphatidylserine (PS) and range in size from 100 nm to 1 µm, while EVs originating from endosomal multi-vesicular bodies, called exosomes, contain tetraspanin proteins, including CD63, and range in size from 50 to 100 nm...
January 19, 2017: Platelets
https://www.readbyqxmd.com/read/28102121/inflammasomes-in-myeloid-cells-warriors-within
#4
Sushmita Jha, W June Brickey, Jenny Pan-Yun Ting
The inflammasome is a large multimeric protein complex comprising an effector protein that demonstrates specificity for a variety of activators or ligands; an adaptor molecule; and procaspase-1, which is converted to caspase-1 upon inflammasome activation. Inflammasomes are expressed primarily by myeloid cells and are located within the cell. The macromolecular inflammasome structure can be visualized by cryo-electron microscopy. This complex has been found to play a role in a variety of disease models in mice, and several have been genetically linked to human diseases...
January 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28100648/multi-scale-structural-analysis-of-plant-er-pm-contact-sites
#5
Heather E McFarlane, Eun Kyoung Lee, Laura S van Bezouwen, Bradford Ross, Abel Rosado, A Lacey Samuels
Membrane contact sites (MCS) are recognized across eukaryotic systems as important nanostructures. Endoplasmic reticulum (ER)-plasma membrane (PM) contact sites (EPCS) are involved in excitation-contraction coupling, signalling, and plant responses to stress. In this report, we perform a multi-scale structural analysis of Arabidopsis EPCS that combine live cell imaging, quantitative transmission electron microscopy (TEM), and electron tomography over a developmental gradient. To place EPCS in the context of the entire cortical ER, we examined GFP-HDEL in living cells over a developmental gradient, then SYT1-GFP was used as a specific marker of EPCS...
January 18, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28099415/structure-of-a-eukaryotic-cyclic-nucleotide-gated-channel
#6
Minghui Li, Xiaoyuan Zhou, Shu Wang, Ioannis Michailidis, Ye Gong, Deyuan Su, Huan Li, Xueming Li, Jian Yang
Cyclic-nucleotide-gated channels are essential for vision and olfaction. They belong to the voltage-gated ion channel superfamily but their activities are controlled by intracellular cyclic nucleotides instead of transmembrane voltage. Here we report a 3.5-Å-resolution single-particle electron cryo-microscopy structure of a cyclic-nucleotide-gated channel from Caenorhabditis elegans in the cyclic guanosine monophosphate (cGMP)-bound open state. The channel has an unusual voltage-sensor-like domain, accounting for its deficient voltage dependence...
January 18, 2017: Nature
https://www.readbyqxmd.com/read/28094514/structural-model-of-the-tubular-assembly-of-the-rous-sarcoma-virus-capsid-protein
#7
Jaekyun Jeon, Xin Qiao, Ivan Hung, Alok K Mitra, Ambroise Desfosses, Daniel Huang, Peter L Gor'kov, Rebecca C Craven, Richard L Kingston, Zhehong Gan, Fangqiang Zhu, Bo Chen
The orthoretroviral capsid protein (CA) assembles into polymorphic capsids, whose architecture, assembly and stability are still being investigated. The N-terminal and C-terminal domains of CA (NTD and CTD, respectively) engage in both homotypic and heterotypic interactions to create the capsid. Hexameric turrets formed by the NTD decorate the majority of the capsid surface. We report nearly-complete solid-state NMR (ssNMR) resonance assignments of Rous sarcoma virus (RSV) CA, assembled into hexamer tubes that mimic the authentic capsid...
January 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28089452/co-folding-of-a-flif-flig-split-domain-forms-the-basis-of-the-ms-c-ring-interface-within-the-bacterial-flagellar-motor
#8
Michael J Lynch, Robert Levenson, Eun A Kim, Ria Sircar, David F Blair, Frederick W Dahlquist, Brian R Crane
The interface between the membrane (MS) and cytoplasmic (C) rings of the bacterial flagellar motor couples torque generation to rotation within the membrane. The structure of the C-terminal helices of the integral membrane protein FliF (FliFC) bound to the N terminal domain of the switch complex protein FliG (FliGN) reveals that FliGN folds around FliFC to produce a topology that closely resembles both the middle and C-terminal domains of FliG. The interface is consistent with solution-state nuclear magnetic resonance, small-angle X-ray scattering, in vivo interaction studies, and cellular motility assays...
December 31, 2016: Structure
https://www.readbyqxmd.com/read/28088125/computational-methods-for-analyzing-conformational-variability-of-macromolecular-complexes-from-cryo-electron-microscopy-images
#9
REVIEW
Slavica Jonić
Thanks to latest technical advances in cryo-electron microscopy (cryo-EM), structures of macromolecular complexes (viruses, ribosomes, etc.) are now often obtained at near-atomic resolution. Also, studies of conformational changes of complexes, in connection with their function, are gaining ground. Conformational variability analysis is usually done by classifying images in a number of discrete classes supposedly representing all conformational states present in the specimen. However, discrete classes cannot be meaningfully defined when the conformational change is continuous (the specimen contains a continuum of states instead of a few discrete states)...
January 11, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28086931/the-release-and-trans-synaptic-transmission-of-tau-via-exosomes
#10
Yipeng Wang, Varun Balaji, Senthilvelrajan Kaniyappan, Lars Krüger, Stephan Irsen, Katharina Tepper, RamReddy Chandupatla, Walter Maetzler, Anja Schneider, Eckhard Mandelkow, Eva-Maria Mandelkow
BACKGROUND: Tau pathology in AD spreads in a hierarchical pattern, whereby it first appears in the entorhinal cortex, then spreads to the hippocampus and later to the surrounding areas. Based on this sequential appearance, AD can be classified into six stages ("Braak stages"). The mechanisms and agents underlying the progression of Tau pathology are a matter of debate. Emerging evidence indicates that the propagation of Tau pathology may be due to the transmission of Tau protein, but the underlying pathways and Tau species are not well understood...
January 13, 2017: Molecular Neurodegeneration
https://www.readbyqxmd.com/read/28077875/structural-basis-of-co-translational-quality-control-by-arfa-and-rf2-bound-to-ribosome
#11
Fuxing Zeng, Yanbo Chen, Jonathan Remis, Mrinal Shekhar, James C Phillips, Emad Tajkhorshid, Hong Jin
Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown...
January 11, 2017: Nature
https://www.readbyqxmd.com/read/28076346/cryo-em-structure-of-a-human-spliceosome-activated-for-step-2-of-splicing
#12
Karl Bertram, Dmitry E Agafonov, Wen-Ti Liu, Olexandr Dybkov, Cindy L Will, Klaus Hartmuth, Henning Urlaub, Berthold Kastner, Holger Stark, Reinhard Lu Hrmann
Spliceosome rearrangements facilitated by RNA helicase Prp16 before catalytic step 2 of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after Prp16 action (C*). The architecture of the catalytic U2-U6 RNP core of the human C* spliceosome is highly similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated (by ~20 Å) from the catalytic centre, and its position close to the U6 snRNA ACAGA box is stabilised by interactions with the Prp8 RNase H-like and Prp17 WD40 domains...
January 11, 2017: Nature
https://www.readbyqxmd.com/read/28076345/structure-of-a-spliceosome-remodelled-for-exon-ligation
#13
Sebastian M Fica, Chris Oubridge, Wojciech P Galej, Max E Wilkinson, Xiao-Chen Bai, Andrew J Newman, Kiyoshi Nagai
The spliceosome excises introns from pre-mRNAs in two sequential trans-esterifications - branching and exon ligation(1) - catalysed at a single catalytic metal site in U6 snRNA(2,3). The recent structures of the spliceosomal C complex(4,5) with the cleaved 5'-exon and lariat-3'-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5'-splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site(4)...
January 11, 2017: Nature
https://www.readbyqxmd.com/read/28067914/structure-of-the-immature-zika-virus-at-9-%C3%A3-resolution
#14
Vidya Mangala Prasad, Andrew S Miller, Thomas Klose, Devika Sirohi, Geeta Buda, Wen Jiang, Richard J Kuhn, Michael G Rossmann
The current Zika virus (ZIKV) epidemic is characterized by severe pathogenicity in both children and adults. Sequence changes in ZIKV since its first isolation are apparent when pre-epidemic strains are compared with those causing the current epidemic. However, the residues that are responsible for ZIKV pathogenicity are largely unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of the immature ZIKV at 9-Å resolution. The cryo-EM map was fitted with the crystal structures of the precursor membrane and envelope glycoproteins and was shown to be similar to the structures of other known immature flaviviruses...
January 9, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28059770/a-supramolecular-assembly-mediates-lentiviral-dna-integration
#15
Allison Ballandras-Colas, Daniel P Maskell, Erik Serrao, Julia Locke, Paolo Swuec, Stefán R Jónsson, Abhay Kotecha, Nicola J Cook, Valerie E Pye, Ian A Taylor, Valgerdur Andrésdóttir, Alan N Engelman, Alessandro Costa, Peter Cherepanov
Retroviral integrase (IN) functions within the intasome nucleoprotein complex to catalyze insertion of viral DNA into cellular chromatin. Using cryo-electron microscopy, we now visualize the functional maedi-visna lentivirus intasome at 4.9 angstrom resolution. The intasome comprises a homo-hexadecamer of IN with a tetramer-of-tetramers architecture featuring eight structurally distinct types of IN protomers supporting two catalytically competent subunits. The conserved intasomal core, previously observed in simpler retroviral systems, is formed between two IN tetramers, with a pair of C-terminal domains from flanking tetramers completing the synaptic interface...
January 6, 2017: Science
https://www.readbyqxmd.com/read/28059769/cryo-em-structures-and-atomic-model-of-the-hiv-1-strand-transfer-complex-intasome
#16
Dario Oliveira Passos, Min Li, Renbin Yang, Stephanie V Rebensburg, Rodolfo Ghirlando, Youngmin Jeon, Nikoloz Shkriabai, Mamuka Kvaratskhelia, Robert Craigie, Dmitry Lyumkis
Like all retroviruses, HIV-1 irreversibly inserts a viral DNA (vDNA) copy of its RNA genome into host target DNA (tDNA). The intasome, a higher-order nucleoprotein complex composed of viral integrase (IN) and the ends of linear vDNA, mediates integration. Productive integration into host chromatin results in the formation of the strand transfer complex (STC) containing catalytically joined vDNA and tDNA. HIV-1 intasomes have been refractory to high-resolution structural studies. We used a soluble IN fusion protein to facilitate structural studies, through which we present a high-resolution cryo-electron microscopy (cryo-EM) structure of the core tetrameric HIV-1 STC and a higher-order form that adopts carboxyl-terminal domain rearrangements...
January 6, 2017: Science
https://www.readbyqxmd.com/read/28055037/advances-in-the-field-of-single-particle-cryo-electron-microscopy-over-the-last-decade
#17
Joachim Frank
In single-particle cryo-electron microscopy (cryo-EM), molecules suspended in a thin aqueous layer are rapidly frozen and imaged at cryogenic temperature in the transmission electron microscope. From the random projection views, a three-dimensional image is reconstructed, enabling the structure of the molecule to be obtained. In this article I discuss technological progress over the past decade, which has, in my own field of study, culminated in the determination of ribosome structure at 2.5-Å resolution. I also discuss likely future improvements in methodology...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28052246/synucleins-have-multiple-effects-on-presynaptic-architecture
#18
Karina J Vargas, Nikolas Schrod, Taylor Davis, Ruben Fernandez-Busnadiego, Yumiko V Taguchi, Ulrike Laugks, Vladan Lucic, Sreeganga S Chandra
Synucleins (α, β, γ-synuclein) are a family of abundant presynaptic proteins. α-Synuclein is causally linked to the pathogenesis of Parkinson's disease (PD). In an effort to define their physiological and pathological function or functions, we investigated the effects of deleting synucleins and overexpressing α-synuclein PD mutations, in mice, on synapse architecture using electron microscopy (EM) and cryoelectron tomography (cryo-ET). We show that synucleins are regulators of presynapse size and synaptic vesicle (SV) pool organization...
January 3, 2017: Cell Reports
https://www.readbyqxmd.com/read/28050645/cryo-electron-microscopy-of-an-extremely-halophilic-microbe-technical-aspects
#19
Daniel Bollschweiler, Miroslava Schaffer, C Martin Lawrence, Harald Engelhardt
Most halophilic Archaea of the class Halobacteriaceae depend on the presence of several molar sodium chloride for growth and cell integrity. This poses problems for structural studies, particularly for electron microscopy, where the high salt concentration results in diminished contrast. Since cryo-electron microscopy of intact cells provides new insights into the cellular and molecular organization under close-to-live conditions, we evaluated strategies and conditions to make halophilic microbes available for investigations in situ...
January 3, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28049779/cryoelectron-microscopy-of-fission-yeast
#20
Mary K Morphew, Thomas H Giddings, J Richard McIntosh
Fission yeast cells can be prepared for electron microscopy (EM) in the frozen-hydrated state. This eliminates the requirement for dehydration and heavy metal staining when preparing samples for EM. As with room temperature imaging, however, the yeast must be sectioned to make them thin enough for transmission of the electron beam. Cutting sections of vitreous ice with a microtome is challenging. An alternative method that uses a focused ion beam to make a thin sample by milling away much of the sample at liquid nitrogen temperatures is under development but is not yet available for routine use...
January 3, 2017: Cold Spring Harbor Protocols
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