keyword
MENU ▼
Read by QxMD icon Read
search

Cryo electron microscopy

keyword
https://www.readbyqxmd.com/read/27906161/structural-basis-for-arfa-rf2-mediated-translation-termination-on-mrnas-lacking-stop-codons
#1
Paul Huter, Claudia Müller, Bertrand Beckert, Stefan Arenz, Otto Berninghausen, Roland Beckmann, Daniel N Wilson
In bacteria, ribosomes stalled on truncated mRNAs lacking a stop codon are rescued by either the transfer-messenger RNA (tmRNA), alternative rescue factor A (ArfA) or ArfB rescue systems(1). While tmRNA- and ArfB-ribosome structures have been elucidated(2-7), structural insight into how ArfA recognizes the presence of truncated mRNAs and recruits the canonical termination release factor RF2 to rescue the stalled ribosomes is lacking. Here we present a cryo-electron microscopy reconstruction of a ribosome stalled on a truncated mRNA in the presence of ArfA and RF2...
December 1, 2016: Nature
https://www.readbyqxmd.com/read/27906160/mechanistic-insights-into-the-alternative-translation-termination-by-arfa-and-rf2
#2
Chengying Ma, Daisuke Kurita, Ningning Li, Yan Chen, Hyouta Himeno, Ning Gao
During cellular translation of mRNAs by ribosomes, various situations that would result in the pausing or stalling of translation apparatus at elongation and termination steps often occur(1-6). Except for programmed stalling, which is usually utilized by the cells to exert regulatory purposes(5,7,8), ribosomes stalled on mRNAs need to be terminated and recycled to maintain adequate cellular translation capacity(9). A large source of ribosome stalling originates in aberrant mRNAs that lack a stop codon. Transcriptional errors and misprocessing of primary transcripts, as well as undesired mRNA cleavage, all contribute to the formation of non-stop mRNAs...
December 1, 2016: Nature
https://www.readbyqxmd.com/read/27905396/atomic-structure-of-the-innexin-6-gap-junction-channel-determined-by-cryo-em
#3
Atsunori Oshima, Kazutoshi Tani, Yoshinori Fujiyoshi
Innexins, a large protein family comprising invertebrate gap junction channels, play an essential role in nervous system development and electrical synapse formation. Here we report the cryo-electron microscopy structures of Caenorhabditis elegans innexin-6 (INX-6) gap junction channels at atomic resolution. We find that the arrangements of the transmembrane helices and extracellular loops of the INX-6 monomeric structure are highly similar to those of connexin-26 (Cx26), despite the lack of significant sequence similarity...
December 1, 2016: Nature Communications
https://www.readbyqxmd.com/read/27902397/vesivirus-2117-capsids-more-closely-resemble-sapovirus-and-lagovirus-particles-than-other-known-vesivirus-structures
#4
Michaela Conley, Edward Emmott, Richard Orton, David Taylor, Daniel Carneiro, Kazuyoshi Murata, Ian Goodfellow, Grant Hansman, David Bhella
Vesivirus 2117 is an adventitious agent that in 2009, was identified as a contaminant of CHO cells propagated in bioreactors at a pharmaceutical manufacturing plant belonging to Genzyme. The consequent interruption in supply of Fabrazyme and Cerezyme (drugs used to treat Fabry and Gaucher disease respectively), caused significant economic losses. Vesivirus 2117 is a member of the Caliciviridae; a family of small icosahedral viruses encoding a positive sense RNA genome. We have used cryo-electron microscopy and three dimensional image reconstruction to calculate a structure of vesivirus 2117 virus like particles as well as feline calicivirus and a chimeric sapovirus...
November 14, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27899666/structures-of-human-srp72-complexes-provide-insights-into-srp-rna-remodeling-and-ribosome-interaction
#5
Matthias M M Becker, Karine Lapouge, Bernd Segnitz, Klemens Wild, Irmgard Sinning
Co-translational protein targeting and membrane protein insertion is a fundamental process and depends on the signal recognition particle (SRP). In mammals, SRP is composed of the SRP RNA crucial for SRP assembly and function and six proteins. The two largest proteins SRP68 and SRP72 form a heterodimer and bind to a regulatory site of the SRP RNA. Despite their essential roles in the SRP pathway, structural information has been available only for the SRP68 RNA-binding domain (RBD). Here we present the crystal structures of the SRP68 protein-binding domain (PBD) in complex with SRP72-PBD and of the SRP72-RBD bound to the SRP S domain (SRP RNA, SRP19 and SRP68) detailing all interactions of SRP72 within SRP...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899638/structure-and-folding-of-the-tetrahymena-telomerase-rna-pseudoknot
#6
Darian D Cash, Juli Feigon
Telomerase maintains telomere length at the ends of linear chromosomes using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). An essential part of TER is the template/pseudoknot domain (t/PK) which includes the template, for adding telomeric repeats, template boundary element (TBE), and pseudoknot, enclosed in a circle by stem 1. The Tetrahymena telomerase holoenzyme catalytic core (p65-TER-TERT) was recently modeled in our 9 Å resolution cryo-electron microscopy map by fitting protein and TER domains, including a solution NMR structure of the Tetrahymena pseudoknot...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27890596/monoacyl-phosphatidylcholine-inhibits-the-formation-of-lipid-multilamellar-structures-during-in-vitro-lipolysis-of-self-emulsifying-drug-delivery-systems
#7
Thuy Tran, Scheyla D V S Siqueira, Heinz Amenitsch, Thomas Rades, Anette Müllertz
The colloidal structures formed during lipolysis of self-emulsifying drug delivery systems (SEDDS) might affect the solubilisation and possibly the absorption of drugs. The aim of the current study is to elucidate the structures formed during the in vitro lipolysis of four SEDDS containing medium-chain glycerides and caprylocaproyl polyoxyl-8 glycerides (Labrasol), with or without monoacyl phosphatidylcholine (MAPC). In situ synchrotron small-angle X-ray scattering (SAXS) was combined with ex situ cryogenic transmission electron microscopy (cryo-TEM) and dynamic light scattering (DLS) to elucidate the generated structures...
November 23, 2016: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/27881198/practical-experience-with-hole-free-phase-plates-for-cryo-electron-microscopy
#8
Michael Marko, Chyongere Hsieh, Eric Leith, David Mastronarde, Sohei Motoki
Phase plate (PP) imaging has proven to be valuable in transmission cryo electron microscopy of unstained, native-state biological specimens. Many PP types have been described, however until the recent implementation of the "hole-free" phase plate (HFPP), imaging has been challenging. We found the HFPP to be simple to construct and to set up in the transmission electron microscopy, but care in implementing automated data collection is needed. Performance may be variable, both initially and over time, thus it is important to monitor and evaluate image quality by observing the power spectrum...
November 24, 2016: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/27875256/mechanistic-insight-into-eukaryotic-60s-ribosomal-subunit-biogenesis-by-cryo-electron-microscopy
#9
REVIEW
Basil J Greber
Eukaryotic ribosomes, the protein-producing factories of the cell, are composed of four ribosomal RNA molecules and roughly 80 proteins. Their biogenesis is a complex process that involves more than 200 biogenesis factors that facilitate the production, modification, and assembly of ribosomal components and the structural transitions along the maturation pathways of the pre-ribosomal particles. Here, I review recent structural and mechanistic insights into the biogenesis of the large ribosomal subunit that were furthered by cryo-electron microscopy of natively purified pre-60S particles and in vitro reconstituted ribosome assembly factor complexes...
November 2016: RNA
https://www.readbyqxmd.com/read/27870689/zika-virus-and-diagnostics
#10
Claudia Raja Gabaglia
PURPOSE OF REVIEW: The purpose of this review is to present what is known about the Zika virus (ZIKV) at the time of writing this review. The viral structure and its phylogeny, as well as the limitations of current available techniques used for diagnosis, are discussed. RECENT FINDINGS: Crystallography and cryo-electron microscopy of the whole ZIKV, or a few of its proteins, are confirming its overall antigenic relatedness to other flaviviruses. Sequencing has revealed its dynamic genetic variation and has placed the Western cluster of Zika isolates within the Asian phylogenic tree...
November 18, 2016: Current Opinion in Pediatrics
https://www.readbyqxmd.com/read/27869059/site-specific-preparation-of-intact-solid-liquid-interfaces-by-label-free-in-situ-localization-and-cryo-focused-ion-beam-lift-out
#11
Michael J Zachman, Emily Asenath-Smith, Lara A Estroff, Lena F Kourkoutis
Scanning transmission electron microscopy (STEM) allows atomic scale characterization of solid-solid interfaces, but has seen limited applications to solid-liquid interfaces due to the volatility of liquids in the microscope vacuum. Although cryo-electron microscopy is routinely used to characterize hydrated samples stabilized by rapid freezing, sample thinning is required to access the internal interfaces of thicker specimens. Here, we adapt cryo-focused ion beam (FIB) "lift-out," a technique recently developed for biological specimens, to prepare intact internal solid-liquid interfaces for high-resolution structural and chemical analysis by cryo-STEM...
November 21, 2016: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/27867185/absorption-mechanism-of-dhp107-an-oral-paclitaxel-formulation-that-forms-a-hydrated-lipidic-sponge-phase
#12
Yura Jang, Hye Jin Chung, Jung Wan Hong, Cheol-Won Yun, Hesson Chung
Paclitaxel is a most widely used anticancer drug with low oral bioavailability, thus it is currently administered via intravenous infusion. DHP107 is a lipid-based paclitaxel formulation that can be administered as an oral solution. In this study, we investigated the mechanism of paclitaxel absorption after oral administration of DHP107 in mice and rats by changing the dosing interval, and evaluated the influence of bile excretion. DHP107 was orally administered to mice at various dosing intervals (2, 4, 8, 12, 24 h) to examine how residual DHP107 affected paclitaxel absorption during subsequent administration...
November 21, 2016: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/27865558/ligand-binding-to-ryanodine-receptors-revealed-through-cryo-electron-microscopy
#13
Filip Van Petegem
No abstract text is available yet for this article.
November 4, 2016: Cell Calcium
https://www.readbyqxmd.com/read/27864160/blotting-free-and-lossless-cryo-electron-microscopy-grid-preparation-from-nanoliter-sized-protein-samples-and-single-cell-extracts
#14
Stefan A Arnold, Stefan Albiez, Andrej Bieri, Anastasia Syntychaki, Ricardo Adaixo, Robb A McLeod, Kenneth N Goldie, Henning Stahlberg, Thomas Braun
We present a sample preparation method for cryo-electron microscopy (cryo-EM) that requires only 3 to 20 nanoliters of sample to prepare a cryo-EM grid, depending on the protocol used. The sample is applied and spread on the grid by a microcapillary. The procedure does not involve any blotting steps, and real-time monitoring allows the water film thickness to be assessed and decreased to an optimum value prior to vitrification. We demonstrate that the method is suitable for high-resolution cryo-EM and will enable alternative electron microscopy approaches, such as single-cell visual proteomics...
November 15, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27862777/deriving-structural-information-from-experimentally-measured-data-on-biomolecules
#15
REVIEW
Wilfred F van Gunsteren, Jane R Allison, Xavier Daura, Jožica Dolenc, Niels Hansen, Alan E Mark, Chris Oostenbrink, Victor H Rusu, Lorna J Smith
During the past half century, the number and accuracy of experimental techniques that can deliver values of observables for biomolecular systems have been steadily increasing. The conversion of a measured value Q(exp) of an observable quantity Q into structural information is, however, a task beset with theoretical and practical problems: 1) insufficient or inaccurate values of Q(exp) , 2) inaccuracies in the function Q(r→) used to relate the quantity Q to structure r→ , 3) how to account for the averaging inherent in the measurement of Q(exp) , 4) how to handle the possible multiple-valuedness of the inverse r→(Q) of the function Q(r→) , to mention a few...
November 8, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27860084/cryo-em-as-a-tool-for-structure-based-drug-development
#16
Felipe Merino, Stefan Raunser
For decades, X-ray crystallography and NMR have been the major techniques to study the atomic structure of macromolecules. However, because of size, instability, low yield, and other factors, many macromolecules are recalcitrant to crystallization or NMR studies. Electron cryo microscopy (cryo-EM) does not depend on crystals and has therefore been the method of choice for many macromolecular complexes that could not be crystallized, but atomic resolution was mostly beyond its reach. Capable of sensing directly the incident electrons, a new generation of detectors has recently revolutionized the field, with structures of macromolecules being now solved routinely to near-atomic resolution...
November 10, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27859904/espc-forms-a-filamentous-structure-in-the-cell-envelope-of-mycobacterium-tuberculosis-and-impacts-esx-1-secretion
#17
Ye Lou, Jan Rybniker, Claudia Sala, Stewart T Cole
Pathogenicity of Mycobacterium tuberculosis (M. tb) is mediated by the ESX-1 secretion system, which exports EsxA and EsxB, the major virulence factors that are co-secreted with EspA and EspC. Functional information about ESX-1 components is scarce. Here, we show that EspC associates with EspA in the cytoplasm and membrane, then polymerizes during secretion from M. tb. EspC was localized by immuno-gold electron microscopy in whole cells or cryo-sections as a surface-exposed filamentous structure that seems to span the cell envelope...
November 10, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27852434/crenactin-forms-actin-like-double-helical-filaments-regulated-by-arcadin-2
#18
Thierry Izoré, Danguole Kureisaite-Ciziene, Stephen H McLaughlin, Jan Löwe
The similarity of eukaryotic actin to crenactin, a filament-forming protein from the crenarchaeon Pyrobaculum calidifontis supports the theory of a common origin of Crenarchaea and Eukaryotes. Monomeric structures of crenactin and actin are similar, although their filament architectures were suggested to be different. Here we report that crenactin forms bona fide double helical filaments that show exceptional similarity to eukaryotic F-actin. With cryo-electron microscopy and helical reconstruction we solved the structure of the crenactin filament to 3...
November 17, 2016: ELife
https://www.readbyqxmd.com/read/27849042/the-fluctuating-ribosome-thermal-molecular-dynamics-characterized-by-neutron-scattering
#19
Giuseppe Zaccai, Francesca Natali, Judith Peters, Martina Řihová, Ella Zimmerman, J Ollivier, J Combet, Marie-Christine Maurel, Anat Bashan, Ada Yonath
Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the 'lubricant' for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions...
November 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27837536/environmental-scanning-electron-microscope-imaging-of-vesicle-systems
#20
Yvonne Perrie, Habib Ali, Daniel J Kirby, Afzal U R Mohammed, Sarah E McNeil, Anil Vangala
The structural characteristics of liposomes have been widely investigated and there is certainly a strong understanding of their morphological characteristics. Imaging of these systems, using techniques such as freeze-fracturing methods, transmission electron microscopy, and cryo-electron imaging, has allowed us to appreciate their bilayer structures and factors which can influence this. However, there are few methods which all us to study these systems in their natural hydrated state; commonly the liposomes are visualized after drying, staining, and/or fixation of the vesicles...
2017: Methods in Molecular Biology
keyword
keyword
45910
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"