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Cryo electron microscopy

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https://www.readbyqxmd.com/read/29350229/aggregate-evolution-in-aqueous-solutions-of-a-gemini-surfactant-derived-from-dehydroabietic-acid
#1
Lin Feng, Danhua Xie, Binglei Song, Jiayu Zhang, Xiaomei Pei, Zhenggang Cui
Innovations in surfactant structure are a feasible way to probe molecular self-assembly principles. Herein, the solution behaviour of a newly synthesized Gemini surfactant derived from dehydroabietic acid, abbreviated R-(EO)-E-R, was investigated using surface tension, fluorescence, isothermal titration calorimetry (ITC), rheology, freeze-fracture transmission electron microscopy (FF-TEM) and cryogenic transmission electron microscopy (cryo-TEM) methods. R-(EO)-E-R has two large, rigid hydrophobic groups. At low concentrations, R-(EO)-E-R forms micelles with an aggregation number of approximately 10, which is smaller than those of Gemini surfactants containing flexible alkyl tails...
January 19, 2018: Soft Matter
https://www.readbyqxmd.com/read/29348055/high-resolution-structures-of-mitochondrial-ribosomes-and-their-functional-implications
#2
REVIEW
Philipp Bieri, Basil J Greber, Nenad Ban
Mitochondrial ribosomes (mitoribosomes) almost exclusively synthesize essential components of the oxidative phosphorylation machinery. Dysfunction of mitochondrial protein biosynthesis leads to human diseases and plays an important role in the altered metabolism of cancer cells. Recent developments in cryo-electron microscopy enabled the structural characterization of complete yeast and mammalian mitoribosomes at near-atomic resolution. Despite originating from ancestral bacterial ribosomes, mitoribosomes have diverged in their composition and architecture...
January 15, 2018: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29345638/molecular-mechanism-of-promoter-opening-by-rna-polymerase-iii
#3
Matthias K Vorländer, Heena Khatter, Rene Wetzel, Wim J H Hagen, Christoph W Müller
RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs. Here we present structures of Pol III preinitiation complexes, comprising the 17-subunit Pol III and the heterotrimeric transcription factor TFIIIB, bound to a natural promoter in different functional states. Electron cryo-microscopy reconstructions, varying from 3.7 Å to 5.5 Å resolution, include two early intermediates in which the DNA duplex is closed, an open DNA complex, and an initially transcribing complex with RNA in the active site...
January 17, 2018: Nature
https://www.readbyqxmd.com/read/29345620/functional-role-of-the-type-1-pilus-rod-structure-in-mediating-host-pathogen-interactions
#4
Caitlin N Spaulding, Henry Louis Schreiber, Weili Zheng, Karen W Dodson, Jennie E Hazen, Matt S Conover, Fengbin Wang, Pontus Svenmarker, Areli Luna-Rico, Olivera Francetic, Magnus Andersson, Scott Hultgren, Edward H Egelman
Uropathogenic E. coli (UPEC), which cause urinary tract infections (UTI), utilize type 1 pili, a chaperone usher pathway (CUP) pilus, to cause UTI and colonize the gut. The pilus rod, comprised of repeating FimA subunits, provides a structural scaffold for displaying the tip adhesin, FimH. We solved the 4.2 Å resolution structure of the type 1 pilus rod using cryo-electron microscopy. Residues forming the interactive surfaces that determine the mechanical properties of the rod were maintained by selection based on a global alignment of fimA sequences...
January 18, 2018: ELife
https://www.readbyqxmd.com/read/29345600/an-open-source-storage-solution-for-cryo-electron-microscopy-samples
#5
Eveline Ultee, Fred Schenkel, Wen Yang, Susanne Brenzinger, Jamie S Depelteau, Ariane Briegel
Cryo-electron microscopy (cryo-EM) enables the study of biological structures in situ in great detail and to solve protein structures at Ångstrom level resolution. Due to recent advances in instrumentation and data processing, the field of cryo-EM is a rapidly growing. Access to facilities and national centers that house the state-of-the-art microscopes is limited due to the ever-rising demand, resulting in long wait times between sample preparation and data acquisition. To improve sample storage, we have developed a cryo-storage system with an efficient, high storage capacity that enables sample storage in a highly organized manner...
January 18, 2018: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/29344776/dawning-of-a-new-era-in-trp-channel-structural-biology-by-cryo-electron-microscopy
#6
REVIEW
M Gregor Madej, Christine M Ziegler
Cryo-electron microscopy (cryo-EM) permits the determination of atomic protein structures by averaging large numbers of individual projection images recorded at cryogenic temperatures-a method termed single-particle analysis. The cryo-preservation traps proteins within a thin glass-like ice layer, making literally a freeze image of proteins in solution. Projections of randomly adopted orientations are merged to reconstruct a 3D density map. While atomic resolution for highly symmetric viruses was achieved already in 2009, the development of new sensitive and fast electron detectors has enabled cryo-EM for smaller and asymmetrical proteins including fragile membrane proteins...
January 17, 2018: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/29342139/structure-and-mutagenesis-reveal-essential-capsid-protein-interactions-for-kshv-replication
#7
Xinghong Dai, Danyang Gong, Hanyoung Lim, Jonathan Jih, Ting-Ting Wu, Ren Sun, Z Hong Zhou
Kaposi's sarcoma-associated herpesvirus (KSHV) causes Kaposi's sarcoma, a cancer that commonly affects patients with AIDS and which is endemic in sub-Saharan Africa. The KSHV capsid is highly pressurized by its double-stranded DNA genome, as are the capsids of the eight other human herpesviruses. Capsid assembly and genome packaging of herpesviruses are prone to interruption and can therefore be targeted for the structure-guided development of antiviral agents. However, herpesvirus capsids-comprising nearly 3,000 proteins and over 1,300 Å in diameter-present a formidable challenge to atomic structure determination and functional mapping of molecular interactions...
January 17, 2018: Nature
https://www.readbyqxmd.com/read/29341918/asymmetric-flow-field-flow-fractionation-for-the-characterization-of-globule-size-distribution-in-complex-formulations-a-cyclosporine-ophthalmic-emulsion-case
#8
Haiou Qu, Jiang Wang, Yong Wu, Jiwen Zheng, Yellela S R Krishnaiah, Mohammad Absar, Stephanie Choi, Muhammad Ashraf, Celia N Cruz, Xiaoming Xu
Commonly used characterization techniques such as cryogenic-transmission electron microscopy (cryo-TEM) and batch-mode dynamic light scattering (DLS) are either time consuming or unable to offer high resolution to discern the poly-dispersity of complex drug products like cyclosporine ophthalmic emulsions. Here, a size-based separation and characterization method for globule size distribution using an asymmetric flow field flow fractionation (AF4) is reported for comparative assessment of cyclosporine ophthalmic emulsion drug products (model formulation) with a wide size span and poly-dispersity...
January 13, 2018: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/29337113/volta-phase-plate-data-collection-facilitates-image-processing-and-cryo-em-structure-determination
#9
Ottilie von Loeffelholz, Gabor Papai, Radostin Danev, Alexander G Myasnikov, S Kundhavai Natchiar, Isabelle Hazemann, Jean-François Ménétret, Bruno P Klaholz
A current bottleneck in structure determination of macromolecular complexes by cryo electron microscopy (cryo-EM) is the large amount of data needed to obtain high-resolution 3D reconstructions, including through sorting into different conformations and compositions with advanced image processing. Additionally, it may be difficult to visualize small ligands that bind in sub-stoichiometric levels. Volta phase plates (VPP) introduce a phase shift in the contrast transfer and drastically increase the contrast of the recorded low-dose cryo-EM images while preserving high frequency information...
January 11, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29334398/formation-of-shelf-stable-pickering-high-internal-phase-emulsions-hipe-through-the-inclusion-of-whey-protein-microgels
#10
Somayeh Zamani, Nicholas Malchione, Michael J Selig, Alireza Abbaspourrad
High internal phase emulsions (HIPE) prepared using whey protein microgels (WPMs) as a surfactant were demonstrated to have substantially higher stability than HIPEs prepared using similar loadings of non-gelled whey protein isolate (WPI) or Tween 20. Microgel colloids were prepared from WPI solutions by heat treatment at 85 °C in a narrow pH range (5.8-6.0) to particle sizes of approximately 90, 160 and 350 nm in diameter. ζ-potentials of the WPM increased in negativity with decreasing particle size from -7...
January 15, 2018: Food & Function
https://www.readbyqxmd.com/read/29334109/a-multifunctional-supramolecular-hydrogel-preparation-properties-and-molecular-assembly
#11
Lin Wang, Xuefeng Shi, Yaqian Wu, Jian Zhang, Yuejun Zhu, Jinben Wang
A novel supramolecular hydrogel was designed and constructed by molecular self-assembly of a cationic gemini surfactant, 1,3-bis(N,N-dimethyl-N-cetylammonium)-2-propylacrylate dibromide (AGC16), and an anionic aromatic compound, trisodium 1,3,6-naphthalenetrisulfonate (NTS). Owing to its unique structure, the hydrogel (abbreviated as AGC16/NTS) has the potential to be used as a multifunctional drug delivery system. The structure and properties of AGC16/NTS were characterized by rheological measurements, differential scanning calorimetry, variable-temperature 1H nuclear magnetic resonance, ultraviolet-visible spectroscopy, variable-temperature fluorescence emission spectroscopy, cryogenic scanning electron microscopy, transmission electron microscopy and X-ray diffraction methods...
January 15, 2018: Soft Matter
https://www.readbyqxmd.com/read/29332952/disentangling-orthogonal-matrices
#12
Teng Zhang, Amit Singer
Motivated by a certain molecular reconstruction methodology in cryo-electron microscopy, we consider the problem of solving a linear system with two unknown orthogonal matrices, which is a generalization of the well-known orthogonal Procrustes problem. We propose an algorithm based on a semi-definite programming (SDP) relaxation, and give a theoretical guarantee for its performance. Both theoretically and empirically, the proposed algorithm performs better than the naïve approach of solving the linear system directly without the orthogonal constraints...
July 1, 2017: Linear Algebra and its Applications
https://www.readbyqxmd.com/read/29330128/exploiting-ion-channel-structure-to-assess-rare-variant-pathogenicity
#13
Brett M Kroncke, Tao Yang, Prince Kannankeril, M Benjamin Shoemaker, Dan M Roden
BACKGROUND: A 27-year-old female was seen for long QT syndrome. She was found to be a carrier of two variants, KCNQ1 Val162Met and KCNH2 Ser55Leu, and both were annotated as pathogenic by a diagnostic laboratory in part because of sequence proximity to other known pathogenic variants. OBJECTIVE: To assess the relationship between both the KCNQ1 and KCNH2 variants and clinical significance using protein structure, in vitro functional assays, and familial segregation...
January 9, 2018: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/29325008/mineralized-trichomes-in-boraginales-complex-microscale-heterogeneity-and-simple-phylogenetic-patterns
#14
Adeel Mustafa, Hans-Jürgen Ensikat, Maximilian Weigend
Background and Aims: Boraginales are often characterized by a dense cover of stiff, mineralized trichomes, which may act as a first line of defence against herbivores. Recent studies have demonstrated that the widely reported silica and calcium carbonate in plant trichomes may be replaced by calcium phosphate. The present study investigates mineralization patterns in 42 species from nine families of the order Boraginales to investigate detailed patterns of mineralization and the possible presence of a phylogenetic signal in different mineralization patterns...
January 6, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29324323/multidisciplinary-characterization-of-u-vi-sequestration-by-acidovorax-facilis-for-bioremediation-purposes
#15
E Krawczyk-Bärsch, U Gerber, K Müller, H Moll, A Rossberg, R Steudtner, M L Merroun
The contamination of the environment by U may affect plant life and consequently may have an impact on animal and human health. The present work describes U(VI) sequestration by Acidovorax facilis using a multidisciplinary approach combining wet chemistry, transmission electron microscopy, and spectroscopy methods (e.g. cryo-time resolved laser-induced fluorescence spectroscopy, extended X-ray absorption fine structure spectroscopy, and in-situ attenuated total reflection Fourier transform infrared spectroscopy)...
December 28, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/29323876/revolutionizing-our-understanding-of-amyloidogenic-proteins-by-cryo-electron-microscopy
#16
Paul M Levine, Matthew R Pratt
No abstract text is available yet for this article.
January 11, 2018: Biochemistry
https://www.readbyqxmd.com/read/29322690/microbially-mediated-aluminosilicate-formation-in-acidic-anaerobic-environments-a-cell-scale-chemical-perspective
#17
J Sánchez-España, K Wang, C Falagán, I Yusta, W D Burgos
Through the use of scanning transmission electron microscopy (STEM) combined with other complementary techniques (SEM, cryo-TEM, HRTEM, and EELS), we have studied the interaction of microorganisms inhabiting deep anoxic waters of acidic pit lakes with dissolved aluminum, silica, sulfate, and ferrous iron. These elements were close to saturation (Al, SiO2 ) or present at very high concentrations (0.12 m Fe(II), 0.12-0.22 m SO42- ) in the studied systems. The anaerobic conditions of these environments allowed investigation of geomicrobial interactions that are difficult to see in oxidized, Fe(III)-rich environments...
January 2018: Geobiology
https://www.readbyqxmd.com/read/29320695/decrypting-the-heat-activation-mechanism-of-trpv1-channel-by-molecular-dynamics-simulation
#18
Han Wen, Wenjun Zheng
As a prototype cellular sensor, the TRPV1 cation channel undergoes a closed-to-open gating transition in response to various physical and chemical stimuli including noxious heat. Despite recent progress, the molecular mechanism of heat activation of TRPV1 gating remains enigmatic. Toward decrypting the structural basis of TRPV1 heat activation, we performed extensive molecular dynamics simulations (with cumulative simulation time of ∼11 μs) for the wild-type channel and a constitutively active double mutant at different temperatures (30, 60, and 72°C), starting from a high-resolution closed-channel structure of TRPV1 solved by cryo-electron microscopy...
January 9, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29317278/optimizing-self-wicking-nanowire-grids
#19
Hui Wei, Venkata P Dandey, Zhening Zhang, Ashleigh Raczkowski, Willam J Rice, Bridget Carragher, Clinton S Potter
We have developed a self-blotting TEM grid for use with a novel instrument for vitrifying samples for cryo-electron microscopy (cryoEM). Nanowires are grown on the copper surface of the grid using a simple chemical reaction and the opposite smooth side is used to adhere to a holey sample substrate support, for example carbon or gold. When small volumes of sample are applied to the nanowire grids the wires effectively act as blotting paper to rapidly wick away the liquid, leaving behind a thin film. In this technical note, we present a detailed description of how we make these grids using a variety of substrates fenestrated with either lacey or regularly spaced holes...
January 6, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29313658/lipidic-mesophases-as-novel-nanoreactor-scaffolds-for-organocatalysts-heterogeneously-catalyzed-asymmetric-aldol-reactions-in-confined-water
#20
Michael Duss, Livia Salvati Manni, Laurent Moser, Stephan Handschin, Raffaele Mezzenga, Henning J Jessen, Ehud M Landau
The unique molecular architecture of lipidic cubic phases (LCPs) and their cubosome dispersions comprise a well-defined, curved bilayer that spans the entire 3-D material space, encompassing a network of two periodic, curved and non-intersecting three-dimensional aqueous channels. The ensuing large lipid/water interfacial area renders these biomaterials an interesting matrix for the lateral immobilization of organocatalysts to catalyze organic reactions in confined water. Herein, we report for the first time the design, synthesis, assembly and characterization of catalytically active LCPs and cubosomes, and demonstrate their applicability as self-assembled, biomimetic and recyclable nanoreactor scaffolds...
January 9, 2018: ACS Applied Materials & Interfaces
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