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https://www.readbyqxmd.com/read/28511991/calculation-of-the-cross-sectional-shape-of-a-fibril-from-equatorial-scattering
#1
Biel Roig-Solvas, Lee Makowski
An alternate formulation of helical diffraction theory is used to generate cross-sectional shapes of fibrous structures from equatorial scattering. We demonstrate this approach with computationally generated scattering intensities and then apply it to scattering data from Tobacco Mosaic Virus (TMV) and in vitro assembled fibrils of Aβ40 peptides. Refining the cross-sectional shape of TMV from SAXS data collected on a 26 mg/ml solution resulted in a circular shape with outer diameter of ∼ 180Å and inner diameter of ∼ 40Å consistent with the known structure of TMV...
May 13, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28506635/cryoem-structure-of-an-influenza-virus-receptor-binding-site-antibody-antigen-interface
#2
Yuhang Liu, Junhua Pan, Simon Jenni, Donald D Raymond, Tim Caradonna, Khoi T Do, Aaron G Schmidt, Stephen C Harrison, Nikolaus Grigorieff
Structure-based vaccine design depends on extensive structural analyses of antigen-antibody complexes. Single-particle electron cryomicroscopy (cryoEM) can circumvent some of the problems of x-ray crystallography as a pipeline for obtaining the required structures. We have examined the potential of single-particle cryoEM for determining the structure of influenza-virus hemagglutinin (HA):single-chain Fv (scFv) complexes, by studying a complex we failed to crystallize in pursuing an extended project of the human immune response to influenza vaccines...
May 12, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28490590/the-c-terminus-of-the-herpes-simplex-virus-pul25-protein-is-required-for-release-of-viral-genomes-from-capsids-bound-to-nuclear-pores
#3
Jamie B Huffman, Gina R Daniel, Erik Falck-Pedersen, Alexis Huet, Greg A Smith, James F Conway, Fred L Homa
The herpes simplex virus (HSV) capsid is released into the cytoplasm after fusion of viral and host membranes, whereupon dynein-dependent trafficking along microtubules targets it to the nuclear envelope. Binding of the capsid to the nuclear pore complex (NPC) is mediated by the capsid protein pUL25 and the capsid-tethered tegument protein pUL36. Temperature-sensitive mutants in both pUL25 and pUL36 dock at the NPC but fail to release DNA. The uncoating reaction has been difficult to study due to the rapid release of the genome once the capsid interacts with the nuclear pore...
May 10, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28433496/a-novel-storage-system-for-cryoem-samples
#4
Giovanna Scapin, Winifred W Prosise, Michael K Wismer, Corey Strickland
We present here a new CryoEM grid boxes storage system designed to simplify sample labeling, tracking and retrieval. The system is based on the crystal pucks widely used by the X-ray crystallographic community for storage and shipping of crystals. This system is suitable for any cryoEM laboratory, but especially for large facilities that will need accurate tracking of large numbers of samples coming from different sources.
April 19, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28396445/cryoem-structure-of-a-prokaryotic-cyclic-nucleotide-gated-ion-channel
#5
Zachary M James, Andrew J Borst, Yoni Haitin, Brandon Frenz, Frank DiMaio, William N Zagotta, David Veesler
Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) ion channels play crucial physiological roles in phototransduction, olfaction, and cardiac pace making. These channels are characterized by the presence of a carboxyl-terminal cyclic nucleotide-binding domain (CNBD) that connects to the channel pore via a C-linker domain. Although cyclic nucleotide binding has been shown to promote CNG and HCN channel opening, the precise mechanism underlying gating remains poorly understood...
April 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28389949/structural-study-of-the-bacterial-flagellar-basal-body-by-electron-cryomicroscopy-and-image-analysis
#6
Akihiro Kawamoto, Keiichi Namba
The bacterial flagellum is a large assembly of about 30 different proteins and is divided into three parts: filament, hook, and basal body. The machineries for its crucial functions, such as torque generation, rotational switch regulation, protein export, and assembly initiation, are all located around the basal body. Although high-resolution structures of the filament and hook have already been revealed, the structure of the basal body remains elusive. Recently, the purification protocol for the MS ring, which is the core ring of the basal body, has been improved for the structural study of the MS ring by electron cryomicroscopy (cryoEM) and single particle image analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28355133/an-allosteric-transport-mechanism-for-the-acrab-tolc-multidrug-efflux-pump
#7
Zhao Wang, Guizhen Fan, Corey F Hryc, James N Blaza, Irina I Serysheva, Michael F Schmid, Wah Chiu, Ben F Luisi, Dijun Du
Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell envelope. Here, we report the near-atomic resolution cryoEM structures of the Escherichia coli AcrAB-TolC multidrug efflux pump in resting and drug transport states, revealing a quaternary structural switch that allosterically couples and synchronizes initial ligand binding with channel opening. Within the transport-activated state, the channel remains open even though the pump cycles through three distinct conformations...
March 29, 2017: ELife
https://www.readbyqxmd.com/read/28346143/action-of-cmg-with-strand-specific-dna-blocks-supports-an-internal-unwinding-mode-for-the-eukaryotic-replicative-helicase
#8
Lance Langston, Mike O'Donnell
Replicative helicases are ring-shaped hexamers that encircle DNA for duplex unwinding. The currently accepted view of hexameric helicase function is by steric exclusion, where the helicase encircles one DNA strand and excludes the other, acting as a wedge with an external DNA unwinding point during translocation. Accordingly, strand-specific blocks only affect these helicases when placed on the tracking strand, not the excluded strand. We examined the effect of blocks on the eukaryotic CMG and, contrary to expectations, blocks on either strand inhibit CMG unwinding...
March 27, 2017: ELife
https://www.readbyqxmd.com/read/28323617/cryoem-structures-of-membrane-pore-and-prepore-complex-reveal-cytolytic-mechanism-of-pneumolysin
#9
Katharina van Pee, Alexander Neuhaus, Edoardo D'Imprima, Deryck J Mills, Werner Kühlbrandt, Özkan Yildiz
Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of Streptococcus pneumoniae, by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain 3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel...
March 21, 2017: ELife
https://www.readbyqxmd.com/read/28300075/a-human-antibody-against-zika-virus-crosslinks-the-e-protein-to-prevent-infection
#10
S Saif Hasan, Andrew Miller, Gopal Sapparapu, Estefania Fernandez, Thomas Klose, Feng Long, Andrei Fokine, Jason C Porta, Wen Jiang, Michael S Diamond, James E Crowe, Richard J Kuhn, Michael G Rossmann
The recent Zika virus (ZIKV) epidemic has been linked to unusual and severe clinical manifestations including microcephaly in fetuses of infected pregnant women and Guillian-Barré syndrome in adults. Neutralizing antibodies present a possible therapeutic approach to prevent and control ZIKV infection. Here we present a 6.2 Å resolution three-dimensional cryo-electron microscopy (cryoEM) structure of an infectious ZIKV (strain H/PF/2013, French Polynesia) in complex with the Fab fragment of a highly therapeutic and neutralizing human monoclonal antibody, ZIKV-117...
March 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28287545/method-to-visualize-and-analyze-membrane-interacting-proteins-by-transmission-electron-microscopy
#11
Ramakrishnan B Kumar, Lin Zhu, Hans Hebert, Caroline Jegerschöld
Monotopic proteins exert their function when attached to a membrane surface, and such interactions depend on the specific lipid composition and on the availability of enough area to perform the function. Nanodiscs are used to provide a membrane surface of controlled size and lipid content. In the absence of bound extrinsic proteins, sodium phosphotungstate-stained nanodiscs appear as stacks of coins when viewed from the side by transmission electron microscopy (TEM). This protocol is therefore designed to intentionally promote stacking; consequently, the prevention of stacking can be interpreted as the binding of the membrane-binding protein to the nanodisc...
March 5, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28283532/molecular-architecture-of-the-n-type-atpase-rotor-ring-from-burkholderia-pseudomallei
#12
Sarah Schulz, Martin Wilkes, Deryck J Mills, Werner Kühlbrandt, Thomas Meier
The genome of the highly infectious bacterium Burkholderia pseudomallei harbors an atp operon that encodes an N-type rotary ATPase, in addition to an operon for a regular F-type rotary ATPase. The molecular architecture of N-type ATPases is unknown and their biochemical properties and cellular functions are largely unexplored. We studied the B. pseudomallei N1No-type ATPase and investigated the structure and ion specificity of its membrane-embedded c-ring rotor by single-particle electron cryo-microscopy. Of several amphiphilic compounds tested for solubilizing the complex, the choice of the low-density, low-CMC detergent LDAO was optimal in terms of map quality and resolution...
April 2017: EMBO Reports
https://www.readbyqxmd.com/read/28254381/vitrification-after-multiple-rounds-of-sample-application-and-blotting-improves-particle-density-on-cryo-electron-microscopy-grids
#13
Joost Snijder, Andrew J Borst, Annie Dosey, Alexandra C Walls, Anika Burrell, Vijay S Reddy, Justin M Kollman, David Veesler
Single particle cryo-electron microscopy (cryoEM) is becoming widely adopted as a tool for structural characterization of biomolecules at near-atomic resolution. Vitrification of the sample to obtain a dense distribution of particles within a single field of view remains a major bottleneck for the success of such experiments. Here, we describe a simple and cost-effective method to increase the density of frozen-hydrated particles on grids with holey carbon support films. It relies on performing multiple rounds of sample application and blotting prior to plunge freezing in liquid ethane...
April 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28250125/conformational-states-of-a-soluble-uncleaved-hiv-1-envelope-trimer
#14
Yuhang Liu, Junhua Pan, Yongfei Cai, Nikolaus Grigorieff, Stephen C Harrison, Bing Chen
The HIV-1 envelope spike [Env; trimeric (gp160)3 cleaved to (gp120/gp41)3] induces membrane fusion, leading to viral entry. It is also the viral component targeted by neutralizing antibodies. Vaccine development requires production, in quantities suitable for clinical studies, of a recombinant form that resembles functional Env. HIV-1 gp140 trimers-the uncleaved ectodomains of (gp160)3-from a few selected viral isolates adopt a compact conformation with many antigenic properties of native Env spikes. One is currently being evaluated in a clinical trial...
May 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28192420/atomic-resolution-structures-from-fragmented-protein-crystals-with-the-cryoem-method-microed
#15
M Jason de la Cruz, Johan Hattne, Dan Shi, Paul Seidler, Jose Rodriguez, Francis E Reyes, Michael R Sawaya, Duilio Cascio, Simon C Weiss, Sun Kyung Kim, Cynthia S Hinck, Andrew P Hinck, Guillermo Calero, David Eisenberg, Tamir Gonen
Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography...
February 13, 2017: Nature Methods
https://www.readbyqxmd.com/read/28181439/cryoem-structure-refinement-by-integrating-nmr-chemical-shifts-with-molecular-dynamics-simulations
#16
Juan R Perilla, Gongpu Zhao, Manman Lu, Jiying Ning, Guangjin Hou, In-Ja L Byeon, Angela M Gronenborn, Tatyana Polenova, Peijun Zhang
Single particle cryoEM has emerged as a powerful method for structure determination of proteins and complexes, complementing X-ray crystallography and NMR spectroscopy. Yet, for many systems, the resolution of cryoEM density map has been limited to 4-6 Å, which only allows for resolving bulky amino acids side chains, thus hindering accurate model building from the density map. On the other hand, experimental chemical shifts (CS) from solution and solid state MAS NMR spectra provide atomic level data for each amino acid within a molecule or a complex; however, structure determination of large complexes and assemblies based on NMR data alone remains challenging...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28165000/high-affinity-anchoring-of-the-decoration-protein-pb10-onto-the-bacteriophage-t5-capsid
#17
Emeline Vernhes, Madalena Renouard, Bernard Gilquin, Philippe Cuniasse, Dominique Durand, Patrick England, Sylviane Hoos, Alexis Huet, James F Conway, Anatoly Glukhov, Vladimir Ksenzenko, Eric Jacquet, Naïma Nhiri, Sophie Zinn-Justin, Pascale Boulanger
Bacteriophage capsids constitute icosahedral shells of exceptional stability that protect the viral genome. Many capsids display on their surface decoration proteins whose structure and function remain largely unknown. The decoration protein pb10 of phage T5 binds at the centre of the 120 hexamers formed by the major capsid protein. Here we determined the 3D structure of pb10 and investigated its capsid-binding properties using NMR, SAXS, cryoEM and SPR. Pb10 consists of an α-helical capsid-binding domain and an Ig-like domain exposed to the solvent...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28148799/computational-prediction-of-the-heterodimeric-and-higher-order-structure-of-gpe1-gpe2-envelope-glycoproteins-encoded-by-hepatitis-c-virus
#18
Holly Freedman, Michael R Logan, Darren Hockman, Julia Koehler Leman, John Lok Man Law, Michael Houghton
Despite the recent success of newly developed direct-acting antivirals against hepatitis C, the disease continues to be a global health threat due to the lack of diagnosis of most carriers and the high cost of treatment. The heterodimer formed by glycoproteins E1 and E2 within the hepatitis C virus (HCV) lipid envelope is a potential vaccine candidate and antiviral target. While the structure of E1/E2 has not yet been resolved, partial crystal structures of the E1 and E2 ectodomains have been determined. The unresolved parts of the structure are within the realm of what can be modeled with current computational modeling tools...
April 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28056362/structures-of-biomolecular-complexes-by-combination-of-nmr-and-cryoem-methods
#19
REVIEW
Philippe Cuniasse, Paulo Tavares, Elena V Orlova, Sophie Zinn-Justin
CryoEM is presently providing structures of biocomplexes considered intractable to analysis by other structural techniques. NMR is playing an important role in delivering structural information on dynamics events and conformational heterogeneity. Impressive results were obtained by combining cryoEM and either liquid- or solid-state NMR, revealing the structures of cellular machines, filaments and amyloid fibrils. NMR solution structures of proteins and nucleic acids were fitted, together with crystallographic structures, into cryoEM maps of large complexes, to decipher their assembly mechanisms and describe their functional dynamics...
April 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28045370/atomic-structures-of-fibrillar-segments-of-hiapp-suggest-tightly-mated-%C3%AE-sheets-are-important-for-cytotoxicity
#20
Pascal Krotee, Jose A Rodriguez, Michael R Sawaya, Duilio Cascio, Francis E Reyes, Dan Shi, Johan Hattne, Brent L Nannenga, Marie E Oskarsson, Stephan Philipp, Sarah Griner, Lin Jiang, Charles G Glabe, Gunilla T Westermark, Tamir Gonen, David S Eisenberg
hIAPP fibrils are associated with Type-II Diabetes, but the link of hIAPP structure to islet cell death remains elusive. Here we observe that hIAPP fibrils are cytotoxic to cultured pancreatic β-cells, leading us to determine the structure and cytotoxicity of protein segments composing the amyloid spine of hIAPP. Using the cryoEM method MicroED, we discover that one segment, 19-29 S20G, forms pairs of β-sheets mated by a dry interface that share structural features with and are similarly cytotoxic to full-length hIAPP fibrils...
January 3, 2017: ELife
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