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https://www.readbyqxmd.com/read/28925789/motile-cilia-defects-in-diseases-other-than-primary-ciliary-dyskinesia-the-contemporary-diagnostic-and-research-role-for-transmission-electron-microscopy
#1
Hannah M Mitchison, Amelia Shoemark
Ultrastructural studies have underpinned the cell biological and clinical investigations of the varied roles of motile cilia in health and disease, with a long history since the 1950s. Recent developments from transmission electron microscopy (TEM; cryo-electron microscopy, electron tomography) have yielded higher resolution and fresh insights into the structure and function of these complex organelles. Microscopy in ciliated organisms, disease models, and in patients with ciliopathy diseases has dramatically expanded our understanding of the ubiquity, multisystem involvement, and importance of cilia in normal human development...
September 19, 2017: Ultrastructural Pathology
https://www.readbyqxmd.com/read/28925388/structural-step-forward-for-nhej
#2
Go Watanabe, Michael R Lieber, Dewight Williams
In a recent paper published in Cell Research, a cryo-EM structure reveals the interface between DNA-PKcs and the Ku70/80:DNA complex, together forming the DNA-dependent protein kinase holoenzyme in non-homologous DNA end joining. Insight from this structure suggests how an allosteric rearrangement of DNA-PKcs driven by Ku70/80:DNA binding regulates kinase activity in this largest member of a family of structurally homologous phosphoinositide 3-kinase-related protein kinases that includes mTOR, ATR, and ATM.
September 19, 2017: Cell Research
https://www.readbyqxmd.com/read/28925040/thermal-melt-circular-dichroism-spectroscopic-studies-for-identifying-stabilising-amphipathic-molecules-for-the-voltage-gated-sodium-channel-navms
#3
Sam M Ireland, Altin Sula, B A Wallace
Purified integral membrane proteins require amphipathic molecules to maintain their solubility in aqueous solutions. These complexes, in turn, are used in studies to characterise the protein structures by a variety of biophysical and structural techniques, including spectroscopy, crystallography, and cryo-electron microscopy. Typically the amphilphiles used have been detergent molecules, but more recently they have included amphipols, which are polymers of different sizes and compositions designed to create smaller, more well-defined solubilised forms of the membrane proteins...
September 19, 2017: Biopolymers
https://www.readbyqxmd.com/read/28922324/biological-properties-and-therapeutic-value-of-cryopreserved-fat-tissue
#4
Takanobu Mashiko, Szu-Hsien Wu, Koji Kanayama, Rintaro Asahi, Takako Shirado, Masanori Mori, Ataru Sunaga, Shunji Sarukawa, Hirokazu Uda, Kotaro Yoshimura
BACKGROUND: Fat grafting frequently requires multiple treatments and thus repeated liposuction to achieve treatment goals. The purpose of this study is to evaluate whether cryopreservation of adipose tissue may facilitate future fat grafting. METHODS: Lipoaspirates were harvested from six adult females and preserved using two cryopreservation methods: 1) simple cooling to -80˚C (cryo-1); or 2) programmed cooling to -190˚C (cryo-2). Fresh fat, cryo-1 fat, and cryo-2 fat were analyzed both in vitro and in vivo...
September 14, 2017: Plastic and Reconstructive Surgery
https://www.readbyqxmd.com/read/28922082/combinatorial-peptide-based-epitope-mapping-from-ebola-virus-dna-vaccines-and-infections-reveals-residue-level-determinants-of-antibody-binding
#5
Daniel R Ripoll, Daniel A J Mitchell, Lesley C Dupuy, Anders Wallqvist, Connie Schmaljohn, Sidhartha Chaudhury
Ebola virus (EBOV) infection is highly lethal and results in severe febrile bleeding disorders that affect humans and non-human primates. One of the therapeutic approaches for treating EBOV infection focus largely on cocktails of monoclonal antibodies (mAbs) that bind to specific regions of the EBOV glycoprotein (GP) and neutralize the virus. Recent structural studies using cryo-electron microscopy have identified key epitopes for several EBOV mAbs. While such information has yielded deep insights into antibody binding, limitations on resolution of these structures often preclude a residue-level analysis of EBOV epitopes...
September 18, 2017: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/28921397/a-binding-block-ion-selective-mechanism-revealed-by-a-na-k-selective-channel
#6
Jie Yu, Bing Zhang, Yixiao Zhang, Cong-Qiao Xu, Wei Zhuo, Jingpeng Ge, Jun Li, Ning Gao, Yang Li, Maojun Yang
Mechanosensitive (MS) channels are extensively studied membrane protein for maintaining intracellular homeostasis through translocating solutes and ions across the membrane, but its mechanisms of channel gating and ion selectivity are largely unknown. Here, we identified the YnaI channel as the Na(+)/K(+) cation-selective MS channel and solved its structure at 3.8 Å by cryo-EM single-particle method. YnaI exhibits low conductance among the family of MS channels in E. coli, and shares a similar overall heptamer structure fold with previously studied MscS channels...
September 18, 2017: Protein & Cell
https://www.readbyqxmd.com/read/28919131/optogenetic-targeting-of-cardiac-myocytes-and-non-myocytes-tools-challenges-and-utility
#7
Callum M Johnston, Eva A Rog-Zielinska, Eike M Wülfers, Torsten Houwaart, Urszula Siedlecka, Thomas Knöpfel, Peter Kohl, Franziska Schneider-Warme
In optogenetics, light-activated proteins are used to monitor and modulate cellular behaviour with light. Combining genetic targeting of distinct cellular populations with defined patterns of optical stimulation enables one to study specific cell classes in complex biological tissues. In the current study we attempted to investigate the functional relevance of heterocellular electrotonic coupling in cardiac tissue in situ. In order to do that, we used a Cre-Lox approach to express the light-gated cation channel Channelrhodopsin-2 (ChR2) specifically in either cardiac myocytes or non-myocytes...
September 15, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28916391/zika-virus-structural-biology-and-progress-in-vaccine-development
#8
REVIEW
Hsiao-Han Lin, Bak-Sau Yip, Li-Min Huang, Suh-Chin Wu
The growing number of zika virus (ZIKV) infections plus a 20-fold increase in neonatal microcephaly in newborns in Brazil have raised alarms in many countries regarding the threat to pregnant women. Instances of microcephaly and central nervous system malformations continue to increase in ZIKV outbreak regions. ZIKV is a small enveloped positive-strand RNA virus belonging to the Flavivirus genus of the Flaviviridae family. High-resolution ZIKV structures recently identified by cryo-electron microscopy indicate that the overall ZIKV structure is similar to those of other flaviviruses...
September 12, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28915442/electron-cryo-tomography-captures-macromolecular-complexes-in-native-environments
#9
REVIEW
Lindsay A Baker, Michael Grange, Kay Grünewald
Transmission electron microscopy has a long history in cellular biology. Fixed and stained samples have been used for cellular imaging for over 50 years, but suffer from sample preparation induced artifacts. Electron cryo-tomography (cryoET) instead uses frozen-hydrated samples, without chemical modification, to determine the structure of macromolecular complexes in their native environment. Recent developments in electron microscopes and associated technologies have greatly expanded our ability to visualize cellular features and determine the structures of macromolecular complexes in situ...
September 12, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28912485/serial-millisecond-crystallography-for-routine-room-temperature-structure-determination-at-synchrotrons
#10
Tobias Weinert, Natacha Olieric, Robert Cheng, Steffen Brünle, Daniel James, Dmitry Ozerov, Dardan Gashi, Laura Vera, May Marsh, Kathrin Jaeger, Florian Dworkowski, Ezequiel Panepucci, Shibom Basu, Petr Skopintsev, Andrew S Doré, Tian Geng, Robert M Cooke, Mengning Liang, Andrea E Prota, Valerie Panneels, Przemyslaw Nogly, Ulrich Ermler, Gebhard Schertler, Michael Hennig, Michel O Steinmetz, Meitian Wang, Jörg Standfuss
Historically, room-temperature structure determination was succeeded by cryo-crystallography to mitigate radiation damage. Here, we demonstrate that serial millisecond crystallography at a synchrotron beamline equipped with high-viscosity injector and high frame-rate detector allows typical crystallographic experiments to be performed at room-temperature. Using a crystal scanning approach, we determine the high-resolution structure of the radiation sensitive molybdenum storage protein, demonstrate soaking of the drug colchicine into tubulin and native sulfur phasing of the human G protein-coupled adenosine receptor...
September 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28905417/investigating-the-structural-dynamics-of-the-piezo1-channel-activation-and-inactivation-by-coarse-grained-modeling
#11
Wenjun Zheng, Frederick Sachs
The PIEZO channels, a family of mechanosensitive channels in vertebrates, feature a fast activation by mechanical stimuli (e.g., membrane tension) followed by a slower inactivation. Although a medium-resolution structure of the trimeric form of PIEZO1 was solved by cryo-electron microscopy (cryo-EM), key structural changes responsible for the channel activation and inactivation are still unknown. Toward decrypting the structural mechanism of the PIEZO1 activation and inactivation, we performed systematic coarse-grained modeling using an elastic network model and related modeling/analysis tools (i...
September 14, 2017: Proteins
https://www.readbyqxmd.com/read/28902838/the-cryo-electron-microscopy-structure-of-human-transcription-factor-iih
#12
Basil J Greber, Thi Hoang Duong Nguyen, Jie Fang, Pavel V Afonine, Paul D Adams, Eva Nogales
Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits that add up to a molecular mass of about 500 kDa, TFIIH is also essential for nucleotide excision repair. The seven-subunit TFIIH core complex formed by XPB, XPD, p62, p52, p44, p34, and p8 is competent for DNA repair, while the CDK-activating kinase subcomplex, which includes the kinase activity of CDK7 as well as the cyclin H and MAT1 subunits, is additionally required for transcription initiation...
September 13, 2017: Nature
https://www.readbyqxmd.com/read/28901669/automating-tasks-in-protein-structure-determination-with-the-clipper-python-module
#13
Stuart McNicholas, Tristan Croll, Tom Burnley, Colin M Palmer, Soon Wen Hoh, Huw T Jenkins, Eleanor Dodson, Kevin Cowtan, Jon Agirre
Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine-independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalised for use in both crystallographic and electron cryo-microscopy applications, scripted with the Python language...
September 13, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28898733/manipulation-of-pickering-emulsion-rheology-using-hydrophilically-modified-silica-nanoparticles-in-brine
#14
Christopher Griffith, Hugh Daigle
HYPOTHESIS: Previous work on Pickering emulsions has shown that bromohexadecane-in-water emulsions (50% oil) stabilized with fumed and spherical particles modified with hexadecyl groups develop a noticeable zero shear elastic storage modulus (G'0) of 200Pa and 9Pa, respectively, while in just 50mM NaCl. This high G'0 can be problematic for subsurface applications where brine salinities are higher and on the order of 600mM NaCl. High reservoir salinity coupled with low formation pressure drops could prevent an emulsion with a high G'0 from propagating deep into formation...
September 1, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28894095/atomic-structures-of-coxsackievirus-a6-and-its-complex-with-a-neutralizing-antibody
#15
Longfa Xu, Qingbing Zheng, Shaowei Li, Maozhou He, Yangtao Wu, Yongchao Li, Rui Zhu, Hai Yu, Qiyang Hong, Jie Jiang, Zizhen Li, Shuxuan Li, Huan Zhao, Lisheng Yang, Wangheng Hou, Wei Wang, Xiangzhong Ye, Jun Zhang, Timothy S Baker, Tong Cheng, Z Hong Zhou, Xiaodong Yan, Ningshao Xia
Coxsackievirus A6 (CVA6) has recently emerged as a major cause of hand, foot and mouth disease in children worldwide but no vaccine is available against CVA6 infections. Here, we demonstrate the isolation of two forms of stable CVA6 particles-procapsid and A-particle-with excellent biochemical stability and natural antigenicity to serve as vaccine candidates. Despite the presence (in A-particle) or absence (in procapsid) of capsid-RNA interactions, the two CVA6 particles have essentially identical atomic capsid structures resembling the uncoating intermediates of other enteroviruses...
September 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/28893988/cryo-em-structure-of-the-bacteriophage-t4-isometric-head-at-3-3-%C3%A3-resolution-and-its-relevance-to-the-assembly-of-icosahedral-viruses
#16
Zhenguo Chen, Lei Sun, Zhihong Zhang, Andrei Fokine, Victor Padilla-Sanchez, Dorit Hanein, Wen Jiang, Michael G Rossmann, Venigalla B Rao
The 3.3-Å cryo-EM structure of the 860-Å-diameter isometric mutant bacteriophage T4 capsid has been determined. WT T4 has a prolate capsid characterized by triangulation numbers (T numbers) Tend = 13 for end caps and Tmid = 20 for midsection. A mutation in the major capsid protein, gp23, produced T=13 icosahedral capsids. The capsid is stabilized by 660 copies of the outer capsid protein, Soc, which clamp adjacent gp23 hexamers. The occupancies of Soc molecules are proportional to the size of the angle between the planes of adjacent hexameric capsomers...
September 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28892495/chlamydomonas-dyx1c1-pf23-is-essential-for-axonemal-assembly-and-proper-morphology-of-inner-dynein-arms
#17
Ryosuke Yamamoto, Jagan M Obbineni, Lea M Alford, Takahiro Ide, Mikito Owa, Juyeon Hwang, Takahide Kon, Kazuo Inaba, Noliyanda James, Stephen M King, Takashi Ishikawa, Winfield S Sale, Susan K Dutcher
Cytoplasmic assembly of ciliary dyneins, a process known as preassembly, requires numerous non-dynein proteins, but the identities and functions of these proteins are not fully elucidated. Here, we show that the classical Chlamydomonas motility mutant pf23 is defective in the Chlamydomonas homolog of DYX1C1. The pf23 mutant has a 494 bp deletion in the DYX1C1 gene and expresses a shorter DYX1C1 protein in the cytoplasm. Structural analyses, using cryo-ET, reveal that pf23 axonemes lack most of the inner dynein arms...
September 11, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28892042/structures-of-the-human-mitochondrial-ribosome-in-native-states-of-assembly
#18
Alan Brown, Sorbhi Rathore, Dari Kimanius, Shintaro Aibara, Xiao-Chen Bai, Joanna Rorbach, Alexey Amunts, V Ramakrishnan
Mammalian mitochondrial ribosomes (mitoribosomes) have less rRNA content and 36 additional proteins compared with the evolutionarily related bacterial ribosome. These differences make the assembly of mitoribosomes more complex than the assembly of bacterial ribosomes, but the molecular details of mitoribosomal biogenesis remain elusive. Here, we report the structures of two late-stage assembly intermediates of the human mitoribosomal large subunit (mt-LSU) isolated from a native pool within a human cell line and solved by cryo-EM to ∼3-Å resolution...
September 11, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28892040/structure-of-a-transcribing-rna-polymerase-ii-dsif-complex-reveals-a-multidentate-dna-rna-clamp
#19
Carrie Bernecky, Jürgen M Plitzko, Patrick Cramer
During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4 Å. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel...
September 11, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28891250/guidelines-for-using-bsoft-for-high-resolution-reconstruction-and-validation-of-biomolecular-structures-from-electron-micrographs
#20
J Bernard Heymann
Cryo-electron microscopy (cryoEM) is becoming popular as a tool to solve biomolecular structures with the recent availability of direct electron detectors allowing automated acquisition of high resolution data. The Bsoft software package, developed over 20 years for analyzing electron micrographs, offers a full workflow for validated single particle analysis with extensive functionality, enabling customization for specific cases. With the increasing use of cryoEM and its automation, proper validation of the results is a bigger concern...
September 10, 2017: Protein Science: a Publication of the Protein Society
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