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https://www.readbyqxmd.com/read/29038012/the-structure-of-the-actin-smooth-muscle-myosin-motor-domain-complex-in-the-rigor-state
#1
Chaity Banerjee, Zhongjun Hu, Zhong Huang, J Anthony Warrington, Dianne W Taylor, Kathleen M Trybus, Susan Lowey, Kenneth A Taylor
Myosin-based motility utilizes catalysis of ATP to drive the relative sliding of F-actin and myosin. The earliest detailed model based on cryo-electron microscopy (cryoEM) and X-ray crystallography postulated that higher actin affinity and lever arm movement were coupled to closure of a feature of the myosin head dubbed the actin-binding cleft. Several studies since then using crystallography of myosin-V and cryoEM structures of F-actin bound myosin-I, -II and -V have provided details of this model. The smooth muscle myosin II interaction with F-actin may differ from those for striated and non-muscle myosin II due in part to different lengths of important surface loops...
October 13, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29035172/a-pul25-dimer-interfaces-the-pseudorabies-virus-capsid-and-tegument
#2
Yun-Tao Liu, Jiansen Jiang, Kevin Patrick Bohannon, Xinghong Dai, G W Gant Luxton, Wong Hoi Hui, Guo-Qiang Bi, Gregory Allan Smith, Z Hong Zhou
Inside the virions of α-herpesviruses, tegument protein pUL25 anchors the tegument to capsid vertices through direct interactions with tegument proteins pUL17 and pUL36. In addition to promoting virion assembly, both pUL25 and pUL36 are critical for intracellular microtubule-dependent capsid transport. Despite these essential roles during infection, the stoichiometry and precise organization of pUL25 and pUL36 on the capsid surface remain controversial due to the insufficient resolution of existing reconstructions from cryo-electron microscopy (cryoEM)...
October 16, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28978703/atomic-structures-of-minor-proteins-vi-and-vii-in-the-human-adenovirus
#3
Xinghong Dai, Lily Wu, Ren Sun, Z Hong Zhou
Human adenoviruses (Ad) are dsDNA viruses associated with infectious diseases, yet better known as tools for gene delivery and oncolytic anti-cancer therapy. Atomic structures of Ad provide the basis for the development of antivirals and for engineering efforts towards more effective applications. Since 2010, atomic models of human Ad5 have been independently derived from photographic film cryoEM and X-ray crystallography, but discrepancies exist concerning the assignment of cement proteins IIIa, VIII and IX...
October 4, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28948231/potyvirus-virion-structure-shows-conserved-protein-fold-and-rna-binding-site-in-ssrna-viruses
#4
Miguel Zamora, Eduardo Méndez-López, Xabier Agirrezabala, Rebeca Cuesta, José L Lavín, M Amelia Sánchez-Pina, Miguel A Aranda, Mikel Valle
Potyviruses constitute the second largest genus of plant viruses and cause important economic losses in a large variety of crops; however, the atomic structure of their particles remains unknown. Infective potyvirus virions are long flexuous filaments where coat protein (CP) subunits assemble in helical mode bound to a monopartite positive-sense single-stranded RNA [(+)ssRNA] genome. We present the cryo-electron microscopy (cryoEM) structure of the potyvirus watermelon mosaic virus at a resolution of 4.0 Å...
September 2017: Science Advances
https://www.readbyqxmd.com/read/28929138/cryoem-structure-of-mxb-reveals-a-novel-oligomerization-interface-critical-for-hiv-restriction
#5
Frances J D Alvarez, Shaoda He, Juan R Perilla, Sooin Jang, Klaus Schulten, Alan N Engelman, Sjors H W Scheres, Peijun Zhang
Human dynamin-like, interferon-induced myxovirus resistance 2 (Mx2 or MxB) is a potent HIV-1 inhibitor. Antiviral activity requires both the amino-terminal region of MxB and protein oligomerization, each of which has eluded structural determination due to difficulties in protein preparation. We report that maltose binding protein-fused, full-length wild-type MxB purifies as oligomers and further self-assembles into helical arrays in physiological salt. Guanosine triphosphate (GTP), but not guanosine diphosphate, binding results in array disassembly, whereas subsequent GTP hydrolysis allows its reformation...
September 2017: Science Advances
https://www.readbyqxmd.com/read/28891250/guidelines-for-using-bsoft-for-high-resolution-reconstruction-and-validation-of-biomolecular-structures-from-electron-micrographs
#6
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
https://www.readbyqxmd.com/read/28888105/cryoem-structures-of-spliceosomal-complexes-reveal-the-molecular-mechanism-of-pre-mrna-splicing
#7
REVIEW
Sjors Hw Scheres, Kiyoshi Nagai
The spliceosome is an intricate molecular machine which catalyses the removal of introns from eukaryotic mRNA precursors by two trans-esterification reactions (branching and exon ligation) to produce mature mRNA with uninterrupted protein coding sequences. The structures of the spliceosome in several key states determined by electron cryo-microscopy have greatly advanced our understanding of its molecular mechanism. The catalytic RNA core is formed during the activation of the fully assembled B to Bact complex and remains largely unchanged throughout the splicing cycle...
September 6, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28885980/domain-topology-of-human-rasal
#8
Jorge Cuellar, José María Valpuesta, Alfred Wittinghofer, Begoña Sot
Rasal is a modular multi-domain protein of the GAP1 (GTPase-activating protein 1) family; its four known members, GAP1m, Rasal, GAP1IP4BP and Capri, have a Ras GTPase-activating domain (RasGAP). This domain supports the intrinsically slow GTPase activity of Ras by actively participating in the catalytic reaction. In the case of Rasal, GAP1IP4BP and Capri, their remaining domains are responsible for converting the RasGAP domains into dual Ras- and Rap-GAPs, via an incompletely understood mechanism. Although Rap proteins are small GTPase homologues of Ras, their catalytic residues are distinct, which reinforces the importance of determining the structure of full-length GAP1 family proteins...
September 26, 2017: Biological Chemistry
https://www.readbyqxmd.com/read/28827185/best-practices-for-managing-large-cryoem-facilities
#9
REVIEW
Bart Alewijnse, Alun W Ashton, Melissa G Chambers, Songye Chen, Anchi Cheng, Mark Ebrahim, Edward T Eng, Wim J H Hagen, Abraham J Koster, Claudia S López, Natalya Lukoyanova, Joaquin Ortega, Ludovic Renault, Steve Reyntjens, William J Rice, Giovanna Scapin, Raymond Schrijver, Alistair Siebert, Scott M Stagg, Valerie Grum-Tokars, Elizabeth R Wright, Shenping Wu, Zhiheng Yu, Z Hong Zhou, Bridget Carragher, Clinton S Potter
This paper provides an overview of the discussion and presentations from the Workshop on the Management of Large CryoEM Facilities held at the New York Structural Biology Center, New York, NY on February 6-7, 2017. A major objective of the workshop was to discuss best practices for managing cryoEM facilities. The discussions were largely focused on supporting single-particle methods for cryoEM and topics included: user access, assessing projects, workflow, sample handling, microscopy, data management and processing, and user training...
September 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28815591/engineering-defined-membrane-embedded-elements-of-ampa-receptor-induces-opposing-gating-modulation-by-cornichon-3-and-stargazin
#10
Natalie M Hawken, Elena I Zaika, Terunaga Nakagawa
KEY POINTS: The AMPA-type ionotropic glutamate receptors (AMPARs) mediate the majority of excitatory synaptic transmission and their function impacts learning, cognition and behaviour. The gating of AMPARs occurs in milliseconds, precisely controlled by a variety of auxiliary subunits that are expressed differentially in the brain, but the difference in mechanisms underlying AMPAR gating modulation by auxiliary subunits remains elusive and is investigated. The elements of the AMPAR that are functionally recruited by auxiliary subunits, stargazin and cornichon 3, are located not only in the extracellular domains but also in the lipid-accessible surface of the AMPAR...
October 15, 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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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