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Cryo electron microscopy

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https://www.readbyqxmd.com/read/28648726/taking-the-measure-of-microed
#1
REVIEW
Jose A Rodriguez, David S Eisenberg, Tamir Gonen
It is now possible to routinely determine atomic resolution structures by electron cryo-microscopy (cryoEM), facilitated in part by the method known as micro electron-diffraction (MicroED). Since its initial demonstration in 2013, MicroED has helped determine a variety of protein structures ranging in molecular weight from a few hundred Daltons to several hundred thousand Daltons. Some of these structures were novel while others were previously known. The resolutions of structures obtained thus far by MicroED range from 3...
June 22, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28648606/the-structure-of-the-r2tp-complex-defines-a-platform-for-recruiting-diverse-client-proteins-to-the-hsp90-molecular-chaperone-system
#2
Angel Rivera-Calzada, Mohinder Pal, Hugo Muñoz-Hernández, Juan R Luque-Ortega, David Gil-Carton, Gianluca Degliesposti, J Mark Skehel, Chrisostomos Prodromou, Laurence H Pearl, Oscar Llorca
The R2TP complex, comprising the Rvb1p-Rvb2p AAA-ATPases, Tah1p, and Pih1p in yeast, is a specialized Hsp90 co-chaperone required for the assembly and maturation of multi-subunit complexes. These include the small nucleolar ribonucleoproteins, RNA polymerase II, and complexes containing phosphatidylinositol-3-kinase-like kinases. The structure and stoichiometry of yeast R2TP and how it couples to Hsp90 are currently unknown. Here, we determine the 3D organization of yeast R2TP using sedimentation velocity analysis and cryo-electron microscopy...
June 6, 2017: Structure
https://www.readbyqxmd.com/read/28645943/the-structure-of-the-tetanus-toxin-reveals-ph-mediated-domain-dynamics
#3
Geoffrey Masuyer, Julian Conrad, Pål Stenmark
The tetanus neurotoxin (TeNT) is a highly potent toxin produced by Clostridium tetani that inhibits neurotransmission of inhibitory interneurons, causing spastic paralysis in the tetanus disease. TeNT differs from the other clostridial neurotoxins by its unique ability to target the central nervous system by retrograde axonal transport. The crystal structure of the tetanus toxin reveals a "closed" domain arrangement stabilised by two disulphide bridges, and the molecular details of the toxin's interaction with its polysaccharide receptor...
June 23, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28645916/structures-and-dynamics-of-hibernating-ribosomes-from-staphylococcus-aureus-mediated-by-intermolecular-interactions-of-hpf
#4
Iskander Khusainov, Quentin Vicens, Rustam Ayupov, Konstantin Usachev, Alexander Myasnikov, Angelita Simonetti, Shamil Validov, Bruno Kieffer, Gulnara Yusupova, Marat Yusupov, Yaser Hashem
In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen Staphylococcus aureus containing a long variant of the hibernation-promoting factor (SaHPF) that we solved using cryo-electron microscopy. Our reconstructions reveal that the N-terminal domain (NTD) of SaHPF binds to the 30S subunit as observed for shorter variants of HPF in other species...
June 23, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28638320/membrane-fusion-involved-in-neurotransmission-glimpse-from-electron-microscope-and-molecular-simulation
#5
REVIEW
Zhiwei Yang, Lu Gou, Shuyu Chen, Na Li, Shengli Zhang, Lei Zhang
Membrane fusion is one of the most fundamental physiological processes in eukaryotes for triggering the fusion of lipid and content, as well as the neurotransmission. However, the architecture features of neurotransmitter release machinery and interdependent mechanism of synaptic membrane fusion have not been extensively studied. This review article expounds the neuronal membrane fusion processes, discusses the fundamental steps in all fusion reactions (membrane aggregation, membrane association, lipid rearrangement and lipid and content mixing) and the probable mechanism coupling to the delivery of neurotransmitters...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28636915/probing-the-structural-dynamics-of-the-nmda-receptor-activation-by-coarse-grained-modeling
#6
Wenjun Zheng, Han Wen, Gary J Iacobucci, Gabriela K Popescu
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. High-resolution structures have been solved for an allosterically inhibited and agonist-bound form of a functional NMDA receptor; however, other key functional states (particularly the active open-channel state) were only resolved at moderate resolutions by cryo-electron microscopy (cryo-EM). To decrypt the mechanism of the NMDA receptor activation, structural modeling is essential to provide presently missing information about structural dynamics...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636906/flexible-fitting-of-atomic-models-into-cryo-em-density-maps-guided-by-helix-correspondences
#7
Hang Dou, Derek W Burrows, Matthew L Baker, Tao Ju
Although electron cryo-microscopy (cryo-EM) has recently achieved resolutions of better than 3 Å, at which point molecular modeling can be done directly from the density map, analysis and annotation of a cryo-EM density map still primarily rely on fitting atomic or homology models to the density map. In this article, we present, to our knowledge, a new method for flexible fitting of known or modeled protein structures into cryo-EM density maps. Unlike existing methods that are guided by local density gradients, our method is guided by correspondences between the α-helices in the density map and model, and does not require an initial rigid-body fitting step...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28632757/molecular-mechanism-of-drp1-assembly-studied-in-vitro-by-cryo-electron-microscopy
#8
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/28630159/the-mystery-behind-membrane-insertion-a-review-of-the-complement-membrane-attack-complex
#9
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/28628789/challenges-and-opportunities-in-the-high-resolution-cryo-em-visualization-of-microtubules-and-their-binding-partners
#10
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
#11
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
#12
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
#13
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/28625887/time-resolved-cryo-electron-microscopy-recent-progress
#14
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 16, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28624735/advances-in-high-resolution-cryo-em-of-oligomeric-enzymes
#15
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/28623663/structural-mechanism-of-atp-independent-transcription-initiation-by-rna-polymerase-i
#16
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
#17
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/28615198/polymorphic-nature-of-htlv-1-particle-cores-as-revealed-through-characterization-of-a-chronically-infected-cell-line
#18
Morgan E Meissner, Luiza Mendonça, Wei Zhang, Louis M Mansky
Human T-cell leukemia virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia (ATL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HTLV-1 cell-to-cell transmission is dependent on the release of infectious virus particles into the virological synapse. HTLV-1 particle structure is still poorly understood, and previous studies have analyzed viruses produced by transformed lymphocytic cell lines chronically infected with HTLV-1, particularly the MT-2 cell line, which harbors truncated proviruses and expresses aberrant forms of the Gag protein...
June 14, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28611252/the-primary-enveloped-virion-of-herpes-simplex-virus-1-its-role-in-nuclear-egress
#19
William W Newcomb, Juan Fontana, Dennis C Winkler, Naiqian Cheng, J Bernard Heymann, Alasdair C Steven
Many viruses migrate between different cellular compartments for successive stages of assembly. The HSV-1 capsid assembles in the nucleus and then transfers into the cytoplasm. First, the capsid buds through the inner nuclear membrane, becoming coated with nuclear egress complex (NEC) protein. This yields a primary enveloped virion (PEV) whose envelope fuses with the outer nuclear membrane, releasing the capsid into the cytoplasm. We investigated the associated molecular mechanisms by isolating PEVs from US3-null-infected cells and imaging them by cryo-electron microscopy and tomography...
June 13, 2017: MBio
https://www.readbyqxmd.com/read/28609682/cryo-em-of-bacterial-pili-and-archaeal-flagellar-filaments
#20
REVIEW
Edward H Egelman
Recent advances in cryo-electron microscopy (cryo-EM) have opened up the possibility that a large class of biological structures, helical polymers, may now be readily reconstructed at near-atomic resolution. This will have a huge impact, since most of these structures are unlikely to be crystallized. This review focuses on new cryo-EM studies involving three classes of bacterial pili (chaperone-usher, mating, and Type IV) as well as on archaeal flagellar filaments. While it has long been known that one domain within archaeal flagellar filaments is homologous to a domain within bacterial Type IV pilins, the new studies shed light on how homologous and even highly conserved subunits can pack together in different ways with only small changes in sequence...
June 10, 2017: Current Opinion in Structural Biology
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