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https://www.readbyqxmd.com/read/28815591/engineering-defined-membrane-embedded-elements-of-ampa-receptor-induces-opposing-gating-modulation-by-cnih3-and-stargazin
#1
Natalie Hawken, Elena Zaika, Terunaga Nakagawa
During excitatory synaptic transmission, various structurally unrelated transmembrane auxiliary subunits control the function of AMPA receptors (AMPARs), but the underlying mechanisms remain unclear. We identified lipid-exposed residues in the transmembrane domain (TMD) of GluA2 subunit of AMPARs that are critical for the function of AMPAR auxiliary subunits, stargazin (Stg) and cornichon 3 (CNIH3). These residues are essential for stabilizing the AMPAR-CNIH3 complex in detergents and overlap with the contacts made between GluA2 TMD and Stg in the cryoEM structures...
August 17, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28801059/editorial-overview-cryo-electron-microscopy-exciting-advances-in-cryoem-herald-a-new-era-in-structural-biology
#2
EDITORIAL
Wah Chiu, Kenneth H Downing
No abstract text is available yet for this article.
August 8, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28781998/the-advent-of-structural-biology-in-situ-by-single-particle-cryo-electron-tomography
#3
Jesús G Galaz-Montoya, Steven J Ludtke
Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ...
2017: Biophysics Reports
https://www.readbyqxmd.com/read/28743795/capturing-protein-communities-by-structural-proteomics-in-a-thermophilic-eukaryote
#4
Panagiotis L Kastritis, Francis J O'Reilly, Thomas Bock, Yuanyue Li, Matt Z Rogon, Katarzyna Buczak, Natalie Romanov, Matthew J Betts, Khanh Huy Bui, Wim J Hagen, Marco L Hennrich, Marie-Therese Mackmull, Juri Rappsilber, Robert B Russell, Peer Bork, Martin Beck, Anne-Claude Gavin
The arrangement of proteins into complexes is a key organizational principle for many cellular functions. Although the topology of many complexes has been systematically analyzed in isolation, their molecular sociology in situ remains elusive. Here, we show that crude cellular extracts of a eukaryotic thermophile, Chaetomium thermophilum, retain basic principles of cellular organization. Using a structural proteomics approach, we simultaneously characterized the abundance, interactions, and structure of a third of the C...
July 25, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28728814/a-tour-de-force-the-discovery-properties-and-function-of-piezo-channels
#5
P A Gottlieb
Mechanical transducers appear throughout cell biology and are used to convert mechanical stress into chemical or electrical signals that allow the cell to respond to environmental changes. In the past six years, a eukaryotic mechanical channel family with two members, Piezo1 and Piezo2, has been identified. Piezo1 was shown to be a cation-selective channel that does not require ancillary proteins for activity. Mouse Piezo1 is large, with over 2500 amino acids, and is not homologous to other ion channels. Both piezo channels have rapid voltage-dependent inactivation with a reversal potential near 0mV...
2017: Current Topics in Membranes
https://www.readbyqxmd.com/read/28658599/scipioncloud-an-integrative-and-interactive-gateway-for-large-scale-cryo-electron-microscopy-image-processing-on-commercial-and-academic-clouds
#6
Jesús Cuenca-Alba, Laura Del Cano, Josué Gómez Blanco, José Miguel de la Rosa Trevín, Pablo Conesa Mingo, Roberto Marabini, Carlos Oscar S Sorzano, Jose María Carazo
New instrumentation for cryo electron microscopy (cryoEM) has significantly increased data collection rate as well as data quality, creating bottlenecks at the image processing level. Current image processing model of moving the acquired images from the data source (electron microscope) to desktops or local clusters for processing is encountering many practical limitations. However, computing may also take place in distributed and decentralized environments. In this way, cloud is a new form of accessing computing and storage resources on demand...
June 25, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28653905/structure-and-in-situ-organisation-of-the-pyrococcus-furiosus-archaellum-machinery
#7
Bertram Daum, Janet Vonck, Annett Bellack, Paushali Chaudhury, Robert Reichelt, Sonja-Verena Albers, Reinhard Rachel, Werner Kühlbrandt
The archaellum is the macromolecular machinery that Archaea use for propulsion or surface adhesion, enabling them to proliferate and invade new territories. The molecular composition of the archaellum and of the motor that drives it appears to be entirely distinct from that of the functionally equivalent bacterial flagellum and flagellar motor. Yet, the structure of the archaellum machinery is scarcely known. Using combined modes of electron cryo-microscopy (cryoEM), we have solved the structure of the Pyrococcus furiosus archaellum filament at 4...
June 27, 2017: ELife
https://www.readbyqxmd.com/read/28648726/taking-the-measure-of-microed
#8
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/28572576/embuilder-a-template-matching-based-automatic-model-building-program-for-high-resolution-cryo-electron-microscopy-maps
#9
Niyun Zhou, Hongwei Wang, Jiawei Wang
The resolution of electron-potential maps in single-particle cryo-electron microscopy (cryoEM) is approaching atomic or near- atomic resolution. However, no program currently exists for de novo cryoEM model building at resolutions exceeding beyond 3.5 Å. Here, we present a program, EMBuilder, based on template matching, to generate cryoEM models at high resolution. The program identifies features in both secondary-structure and Cα stages. In the secondary structure stage, helices and strands are identified with pre-computed templates, and the voxel size of the entire map is then refined to account for microscopic magnification errors...
June 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28511991/calculation-of-the-cross-sectional-shape-of-a-fibril-from-equatorial-scattering
#10
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 26mg/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
#11
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 variable-domain fragment complexes, by studying a complex we failed to crystallize in pursuing an extended project on the human immune response to influenza vaccines...
June 16, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28490590/the-c-terminus-of-the-herpes-simplex-virus-ul25-protein-is-required-for-release-of-viral-genomes-from-capsids-bound-to-nuclear-pores
#12
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...
August 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28433496/a-novel-storage-system-for-cryoem-samples
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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