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https://www.readbyqxmd.com/read/28635493/the-structure-of-lamin-filaments-in-somatic-cells-as-revealed-by-cryo-electron-tomography
#1
Y Turgay, O Medalia
Metazoan nuclei are equipped with nuclear lamina - a thin layer of intermediate filaments (IFs) mostly built of nuclear lamins facing the inner nuclear membrane (INM). The nuclear lamina serves as an interaction hub for INM-proteins, soluble nuclear factors and DNA. It confers structural and mechanical stability to the nucleus, transduces mechanical forces and biochemical signals across the nuclear envelope (NE) and regulates the organization of chromatin. By utilizing cryo-electron tomography (cryo-ET), we recently provided an unprecedented view into the 3D organization of lamin filaments within the lamina meshwork in mammalian somatic cells...
June 21, 2017: Nucleus
https://www.readbyqxmd.com/read/28632757/molecular-mechanism-of-drp1-assembly-studied-in-vitro-by-cryo-electron-microscopy
#2
Kaustuv Basu, Driss Lajoie, Tristan Aumentado-Armstrong, Jin Chen, Roman I Koning, Blaise Bossy, Mihnea Bostina, Attila Sik, Ella Bossy-Wetzel, Isabelle Rouiller
Mitochondria are dynamic organelles that continually adapt their morphology by fusion and fission events. An imbalance between fusion and fission has been linked to major neurodegenerative diseases, including Huntington's, Alzheimer's, and Parkinson's diseases. A member of the Dynamin superfamily, dynamin-related protein 1 (DRP1), a dynamin-related GTPase, is required for mitochondrial membrane fission. Self-assembly of DRP1 into oligomers in a GTP-dependent manner likely drives the division process. We show here that DRP1 self-assembles in two ways: i) in the presence of the non-hydrolysable GTP analog GMP-PNP into spiral-like structures of ~36 nm diameter; and ii) in the presence of GTP into rings composed of 13-18 monomers...
2017: PloS One
https://www.readbyqxmd.com/read/28630499/spatio-temporal-analysis-of-coding-and-long-noncoding-transcripts-during-maize-endosperm-development
#3
Eun-Deok Kim, Yuqing Xiong, Youngjae Pyo, Dong-Hwan Kim, Byung-Ho Kang, Sibum Sung
The maize endosperm consists of three major compartmentalized cell types: the starchy endosperm (SE), the basal endosperm transfer cell layer (BETL), and the aleurone cell layer (AL). Differential genetic programs are activated in each cell type to construct functionally and structurally distinct cells. To compare gene expression patterns involved in maize endosperm cell differentiation, we isolated transcripts from cryo-dissected endosperm specimens enriched with BETL, AL, or SE at 8, 12, and 16 days after pollination (DAP)...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630159/the-mystery-behind-membrane-insertion-a-review-of-the-complement-membrane-attack-complex
#4
REVIEW
Charles Bayly-Jones, Doryen Bubeck, Michelle A Dunstone
The membrane attack complex (MAC) is an important innate immune effector of the complement terminal pathway that forms cytotoxic pores on the surface of microbes. Despite many years of research, MAC structure and mechanism of action have remained elusive, relying heavily on modelling and inference from biochemical experiments. Recent advances in structural biology, specifically cryo-electron microscopy, have provided new insights into the molecular mechanism of MAC assembly. Its unique 'split-washer' shape, coupled with an irregular giant β-barrel architecture, enable an atypical mechanism of hole punching and represent a novel system for which to study pore formation...
August 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28630150/cryo-electron-tomography-an-ideal-method-to-study-membrane-associated-proteins
#5
REVIEW
Michelle A Dunstone, Alex de Marco
Cryo-electron tomography (cryo-ET) is a three-dimensional imaging technique that makes it possible to analyse the structure of complex and dynamic biological assemblies in their native conditions. The latest technological and image processing developments demonstrate that it is possible to obtain structural information at nanometre resolution. The sample preparation required for the cryo-ET technique does not require the isolation of a protein and other macromolecular complexes from its native environment. Therefore, cryo-ET is emerging as an important tool to study the structure of membrane-associated proteins including pores...
August 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28629030/high-degradation-rate-of-fe-20mn-based-bio-alloys-by-accumulative-cryo-rolling-and-annealing
#6
Hanning Li, Yanan Wang, Qiuming Peng
A new strategy of accumulative cryo-rolling (ACR) at liquid nitrogen temperature and annealing was performed to improve degradation rate of Fe-Mn-based implants. Differing from as-cast and ACRed Fe-Mn-based alloys with single-phase austenite, ACRed-annealed sample mainly consists of austenite and non-equilibrium Fe5C2 precipitate. ACR-annealed sample shows a degradation rate of 0.0388mA·cm(-2), which is 4.6 times higher than as-cast alloy. Pitting corrosion plays a dominant role in both as-cast and ACRed samples...
October 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28628789/challenges-and-opportunities-in-the-high-resolution-cryo-em-visualization-of-microtubules-and-their-binding-partners
#7
REVIEW
Eva Nogales, Elizabeth H Kellogg
As non-crystallizable polymers, microtubules have been the target of cryo-electron microscopy (cryo-EM) studies since the technique was first established. Over the years, image processing strategies have been developed that take care of the unique, pseudo-helical symmetry of the microtubule. With recent progress in data quality and data processing, cryo-EM reconstructions are now reaching resolutions that allow the generation of atomic models of microtubules and the factors that bind them. These include cellular partners that contribute to microtubule cellular functions, or small ligands that interfere with those functions in the treatment of cancer...
June 16, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28628788/cryo-em-structures-of-human-%C3%AE-secretase
#8
REVIEW
Guanghui Yang, Rui Zhou, Yigong Shi
γ-secretase, a membrane-embedded aspartate protease, catalyzes peptide bond hydrolysis of a large variety of type I integral membrane proteins exemplified by amyloid precursor protein (APP). Cleavage of APP leads to formation of β-amyloid plaque, which is a hallmark of Alzheimer's disease (AD). Over 200 AD-associated mutations are mapped to presenilin 1 (PS1), the catalytic component of γ-secretase. In the past three years, several cryo-electron microscopy (cryo-EM) structures of human γ-secretase have been determined at near atomic resolutions...
June 16, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28628133/hbv-rna-pre-genome-encodes-specific-motifs-that-mediate-interactions-with-the-viral-core-protein-that-promote-nucleocapsid-assembly
#9
Nikesh Patel, Simon J White, Rebecca F Thompson, Richard Bingham, Eva U Weiß, Daniel P Maskell, Adam Zlotnick, Eric C Dykeman, Roman Tuma, Reidun Twarock, Neil A Ranson, Peter G Stockley
Formation of the hepatitis B virus nucleocapsid is an essential step in the viral lifecycle, but its assembly is not fully understood. We report the discovery of sequence-specific interactions between the viral pre-genome and the hepatitis B core protein that play roles in defining the nucleocapsid assembly pathway. Using RNA SELEX and bioinformatics, we identified multiple regions in the pre-genomic RNA with high affinity for core protein dimers. These RNAs form stem-loops with a conserved loop motif that trigger sequence-specific assembly of virus-like particles (VLPs) at much higher fidelity and yield than in the absence of RNA...
June 19, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28628127/rosettaes-a-sampling-strategy-enabling-automated-interpretation-of-difficult-cryo-em-maps
#10
Brandon Frenz, Alexandra C Walls, Edward H Egelman, David Veesler, Frank DiMaio
Accurate atomic modeling of macromolecular structures into cryo-electron microscopy (cryo-EM) maps is a major challenge, as the moderate resolution makes accurate placement of atoms difficult. We present Rosetta enumerative sampling (RosettaES), an automated tool that uses a fragment-based sampling strategy for de novo model completion of macromolecular structures from cryo-EM density maps at 3-5-Å resolution. On a benchmark set of nine proteins, RosettaES was able to identify near-native conformations in 85% of segments...
June 19, 2017: Nature Methods
https://www.readbyqxmd.com/read/28625929/verification-of-a-novel-atrial-fibrillation-cryoablation-dosing-algorithm-guided-by-time-to-pulmonary-vein-isolation-results-from-the-cryo-dosing-study-cryoballoon-ablation-dosing-based-on-the-assessment-of-time-to-effect-and-pulmonary-vein-isolation-guidance
#11
Arash Aryana, David N Kenigsberg, Marcin Kowalski, Charles H Koo, Hae W Lim, Padraig Gearoid O'Neill, Mark R Bowers, Robert B Hokanson, Kenneth A Ellenbogen
BACKGROUND: There are no recommendations on the optimal dosing for cryoablation of atrial fibrillation (Cryo-AF). OBJECTIVE: We developed and prospectively tested a Cryo-AF dosing protocol guided exclusively by time-to-pulmonary vein (PV) isolation (TT-PVI) in patients undergoing a first-time Cryo-AF. METHODS: In this multicenter study, we examined the acute/long-term safety/efficacy of Cryo-AF using the proposed dosing algorithm (Cryo-AFDosing, n=355) against a conventional, non-standardized approach (Cryo-AFConventional, n=400) in a non-randomized fashion...
June 15, 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/28625887/time-resolved-cryo-electron-microscopy-recent-progress
#12
Joachim Frank
Time-resolved cryo-electron microscopy (cryo-EM) combines the known advantages of single-particle cryo-EM in visualizing molecular structure with the ability to dissect the time progress of a reaction between molecules in vitro. Here some of the recent progress of this methodology and its first biological applications are outlined.
June 15, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28624735/advances-in-high-resolution-cryo-em-of-oligomeric-enzymes
#13
REVIEW
Janet Vonck, Deryck J Mills
Recent advances in cryo-electron microscopy instrumentation and software have made it possible to obtain atomic resolution structures of macromolecular complexes with a small amount of material at low concentration and without the need for crystallisation. Oligomeric enzymes are particularly well suited for this technique because of their symmetry and often large size or rigid structure and can be used to explore the limits of the technique. Conformational changes can reach their full extent in solution, not hampered by crystal contacts, and multiple conformations in a sample can be separated computationally...
June 15, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28624568/towards-a-mechanistic-understanding-of-core-promoter-recognition-from-cryo-em-studies-of-human-tfiid
#14
REVIEW
Eva Nogales, Avinash B Patel, Robert K Louder
TFIID is a critical component of the eukaryotic transcription pre-initiation complex (PIC) required for the recruitment of RNA Pol II to the start site of protein-coding genes. Within the PIC, TFIID's role is to recognize and bind core promoter sequences and recruit the rest of the PIC components. Due to its size and its conformational complexity, TFIID poses a serious challenge for structural characterization. The small amounts of purified TFIID that can be obtained by present methods of purification from endogenous sources has limited structural studies to cryo-EM visualization, which requires very small amounts of sample...
June 15, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28623663/structural-mechanism-of-atp-independent-transcription-initiation-by-rna-polymerase-i
#15
Yan Han, Chunli Yan, Thi Hoang Duong Nguyen, Ashleigh J Jackobel, Ivaylo Ivanov, Bruce A Knutson, Yuan He
Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location...
June 17, 2017: ELife
https://www.readbyqxmd.com/read/28622565/a-shear-induced-network-of-aligned-wormlike-micelles-in-a-sugar-based-molecular-gel-from-gelation-to-biocompatibility-assays
#16
Juliette Fitremann, Barbara Lonetti, Emiliano Fratini, Isabelle Fabing, Bruno Payré, Christelle Boulé, Isabelle Loubinoux, Laurence Vaysse, Luis Oriol
A new low molecular weight hydrogelator with a saccharide (lactobionic) polar head linked by azide-alkyne click chemistry was prepared in three steps. It was obtained in high purity without chromatography, by phase separation and ultrafiltration of the aqueous gel. Gelation was not obtained reproducibly by conventional heating-cooling cycles and instead was obtained by shearing the aqueous solutions, from 2 wt% to 0.25 wt%. This method of preparation favored the formation of a quite unusual network of interconnected large but thin 2D-sheets (7nm-thick) formed by the association side-by-side of long and aligned 7nm diameter wormlike micelles...
June 9, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28622523/intracellular-ca-2-sensing-its-role-in-calcium-homeostasis-and-signaling
#17
REVIEW
Rafaela Bagur, György Hajnóczky
Ca(2+) is a ubiquitous intracellular messenger that controls diverse cellular functions but can become toxic and cause cell death. Selective control of specific targets depends on spatiotemporal patterning of the calcium signal and decoding it by multiple, tunable, and often strategically positioned Ca(2+)-sensing elements. Ca(2+) is detected by specialized motifs on proteins that have been biochemically characterized decades ago. However, the field of Ca(2+) sensing has been reenergized by recent progress in fluorescent technology, genetics, and cryo-EM...
June 15, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28621666/9%C3%A3-structure-of-the-copi-coat-reveals-that-the-arf1-gtpase-occupies-two-contrasting-molecular-environments
#18
Svetlana O Dodonova, Patrick Aderhold, Juergen Kopp, Iva Ganeva, Simone Röhling, Wim J Hagen, Irmgard Sinning, Felix Wieland, John Ag Briggs
COPI coated vesicles mediate trafficking within the Golgi apparatus and between the Golgi and the endoplasmic reticulum. Assembly of a COPI coated vesicle is initiated by the small GTPase Arf1 that recruits the coatomer complex to the membrane, triggering polymerization and budding. The vesicle uncoats before fusion with a target membrane. Coat components are structurally conserved between COPI and clathrin/adaptor proteins. Using cryo-electron tomography and subtomogram averaging, we determined the structure of the COPI coat assembled on membranes in vitro at 9 Å resolution...
June 16, 2017: ELife
https://www.readbyqxmd.com/read/28619772/cost-effectiveness-of-hpv-based-cervical-cancer-screening-in-the-public-health-system-in-nicaragua
#19
Nicole G Campos, Mercy Mvundura, Jose Jeronimo, Francesca Holme, Elisabeth Vodicka, Jane J Kim
OBJECTIVES: To evaluate the cost-effectiveness of human papillomavirus (HPV) DNA testing (versus Papanicolaou (Pap)-based screening) for cervical cancer screening in Nicaragua. DESIGN: A previously developed Monte Carlo simulation model of the natural history of HPV infection and cervical cancer was calibrated to epidemiological data from Nicaragua. Cost data inputs were derived using a micro-costing approach in Carazo, Chontales and Chinandega departments; test performance data were from a demonstration project in Masaya department...
June 15, 2017: BMJ Open
https://www.readbyqxmd.com/read/28619716/ratchet-like-polypeptide-translocation-mechanism-of-the-aaa-disaggregase-hsp104
#20
Stephanie N Gates, Adam L Yokom, JiaBei Lin, Meredith E Jackrel, Alexandrea N Rizo, Nathan M Kendsersky, Courtney E Buell, Elizabeth A Sweeny, Korrie L Mack, Edward Chuang, Mariana P Torrente, Min Su, James Shorter, Daniel R Southworth
Hsp100 polypeptide translocases are conserved AAA+ machines that maintain proteostasis by unfolding aberrant and toxic proteins for refolding or proteolytic degradation. The Hsp104 disaggregase from S. cerevisiae solubilizes stress-induced amorphous aggregates and amyloid. The structural basis for substrate recognition and translocation is unknown. Using a model substrate (casein), we report cryo-EM structures at near-atomic resolution of Hsp104 in different translocation states. Substrate interactions are mediated by conserved, pore-loop tyrosines that contact an 80 Å-long unfolded polypeptide along the axial channel...
June 15, 2017: Science
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