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https://www.readbyqxmd.com/read/29351860/microtubule-dynamics-moving-toward-a-multi-scale-approach
#1
REVIEW
Mahya Hemmat, Brian T Castle, David J Odde
Microtubule self-assembly dynamics serve to facilitate many vital cellular functions, such as chromosome segregation during mitosis and synaptic plasticity. However, the detailed atomistic basis of assembly dynamics has remained an unresolved puzzle. A key challenge is connecting together the vast range of relevant length-time scales, events happening at time scales ranging from nanoseconds, such as tubulin molecular interactions (Å-nm), to minutes-hours, such as the cellular response to microtubule dynamics during mitotic progression (μm)...
January 16, 2018: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/29350229/aggregate-evolution-in-aqueous-solutions-of-a-gemini-surfactant-derived-from-dehydroabietic-acid
#2
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/29348366/structures-of-human-prc2-with-its-cofactors-aebp2-and-jarid2
#3
Vignesh Kasinath, Marco Faini, Simon Poepsel, Dvir Reif, Xinyu Ashlee Feng, Goran Stjepanovic, Ruedi Aebersold, Eva Nogales
Transcriptionally repressive histone H3K27 methylation by PRC2 (Polycomb repressive complex 2) is essential for cellular differentiation and development. Here we report cryo-EM structures of human PRC2 in two distinct, active states, while in complex with its cofactors JARID2 and AEBP2. Both cofactors mimic the binding of histone H3 tails. JARID2, methylated by PRC2, mimics a methylated H3 tail to stimulate PRC2 activity, while AEBP2 interacts with the RBAP48 subunit mimicking an unmodified H3 tail. SUZ12 interacts with all other subunits within the assembly and thus contributes to the stability of the complex...
January 18, 2018: Science
https://www.readbyqxmd.com/read/29348055/high-resolution-structures-of-mitochondrial-ribosomes-and-their-functional-implications
#4
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/29347887/cryo-assisted-resection-en-bloc-and-cryoablation-in-situ-of-primary-breast-cancer-coupled-with-intraoperative-ultrasound-guided-tracer-injection-a-preliminary-clinical-study
#5
Nikolai N Korpan, Kecheng Xu, Philipp Schwarzinger, Masashi Watanabe, Gerhard Breitenecker, Le Pivert Patrick
The aim of the study was to perform cryosurgery on a primary breast tumor, coupled with simultaneous peritumoral and intratumoral tracer injection of a blue dye, to evaluate lymphatic mapping. We explored the ability of our strategy to prevent tumor cells, but not that of injected tracers, to migrate to the lymphovascular drainage during conventional resection of frozen breast malignancies. Seventeen patients aged 51 (14) years (mean [standard deviation]), presenting primary breast cancer with stage I to IV, were randomly selected and treated in The Rudolfinerhaus Private Clinic in Vienna, Austria, and included in this preliminary clinical study...
January 1, 2018: Technology in Cancer Research & Treatment
https://www.readbyqxmd.com/read/29345989/assembly-of-copi-and-copii-vesicular-coat-proteins-on-membranes
#6
Julien Béthune, Felix T Wieland
In eukaryotes, distinct transport vesicles functionally connect various intracellular compartments. These carriers mediate transport of membranes for the biogenesis and maintenance of organelles, secretion of cargo proteins and peptides, and uptake of cargo into the cell. Transport vesicles have distinct protein coats that assemble on a donor membrane where they can select cargo and curve the membrane to form a bud. A multitude of structural elements of coat proteins have been solved by X-ray crystallography...
January 18, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29345638/molecular-mechanism-of-promoter-opening-by-rna-polymerase-iii
#7
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
#8
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
#9
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
#10
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/29342982/detection-of-zro%C3%A2-nanoparticles-in-lung-tissue-sections-by-time-of-flight-secondary-ion-mass-spectrometry-and-ion-beam-microscopy
#11
Lothar Veith, Julia Böttner, Antje Vennemann, Daniel Breitenstein, Carsten Engelhard, Jan Meijer, Irina Estrela-Lopis, Martin Wiemann, Birgit Hagenhoff
The increasing use of nanoparticles (NP) in commercial products requires elaborated techniques to detect NP in the tissue of exposed organisms. However, due to the low amount of material, the detection and exact localization of NP within tissue sections is demanding. In this respect, Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) and Ion Beam Microscopy (IBM) are promising techniques, because they both offer sub-micron lateral resolutions along with high sensitivities. Here, we compare the performance of the non-material-consumptive IBM and material-consumptive ToF-SIMS for the detection of ZrO₂ NP (primary size 9-10 nm) in rat lung tissue...
January 15, 2018: Nanomaterials
https://www.readbyqxmd.com/read/29342139/structure-and-mutagenesis-reveal-essential-capsid-protein-interactions-for-kshv-replication
#12
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
#13
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/29339972/evaluation-of-green-tea-extract-as-a-safe-personal-hygiene-against-viral-infections
#14
Yun Ha Lee, Yo Han Jang, Young-Seok Kim, Jinku Kim, Baik Lin Seong
Background: Viral infections often pose tremendous public health concerns as well as economic burdens. Despite the availability of vaccines or antiviral drugs, personal hygiene is considered as effective means as the first-hand measure against viral infections. The green tea catechins, in particular, epigallocatechin-3-gallate (EGCG), are known to exert potent antiviral activity. In this study, we evaluated the green tea extract as a safe personal hygiene against viral infections. Results: Using the influenza virus A/Puerto Rico/8/34 (H1N1) as a model, we examined the duration of the viral inactivating activity of green tea extract (GTE) under prolonged storage at various temperature conditions...
2018: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29337113/volta-phase-plate-data-collection-facilitates-image-processing-and-cryo-em-structure-determination
#15
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/29335562/cryo-em-structure-of-the-exocyst-complex
#16
Kunrong Mei, Yan Li, Shaoxiao Wang, Guangcan Shao, Jia Wang, Yuehe Ding, Guangzuo Luo, Peng Yue, Jun-Jie Liu, Xinquan Wang, Meng-Qiu Dong, Hong-Wei Wang, Wei Guo
The exocyst is an evolutionarily conserved octameric protein complex that mediates the tethering of post-Golgi secretory vesicles to the plasma membrane during exocytosis and is implicated in many cellular processes such as cell polarization, cytokinesis, ciliogenesis and tumor invasion. Using cryo-EM and chemical cross-linking MS (CXMS), we solved the structure of the Saccharomyces cerevisiae exocyst complex at an average resolution of 4.4 Å. Our model revealed the architecture of the exocyst and led to the identification of the helical bundles that mediate the assembly of the complex at its core...
January 15, 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29335561/sub-%C3%A3-ngstr%C3%A3-m-cryo-em-structure-of-a-prion-protofibril-reveals-a-polar-clasp
#17
Marcus Gallagher-Jones, Calina Glynn, David R Boyer, Michael W Martynowycz, Evelyn Hernandez, Jennifer Miao, Chih-Te Zee, Irina V Novikova, Lukasz Goldschmidt, Heather T McFarlane, Gustavo F Helguera, James E Evans, Michael R Sawaya, Duilio Cascio, David S Eisenberg, Tamir Gonen, Jose A Rodriguez
The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-ångström-resolution structure of a protofibril formed by a wild-type segment from the β2-α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named 'polar clasps'.
January 15, 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29334398/formation-of-shelf-stable-pickering-high-internal-phase-emulsions-hipe-through-the-inclusion-of-whey-protein-microgels
#18
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
#19
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
#20
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
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