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https://www.readbyqxmd.com/read/29213060/structural-characterization-of-site-modified-nanocapsid-with-monodispersed-gold-clusters
#1
Marie C Stark, Mo A Baikoghli, Tanja Lahtinen, Sami Malola, Li Xing, Michelle Nguyen, Marina Nguyen, Aria Sikaroudi, Varpu Marjomäki, Hannu Häkkinen, R Holland Cheng
Hepatitis E Virus-like particles self-assemble in to noninfectious nanocapsids that are resistant to proteolytic/acidic mucosal delivery conditions. Previously, the nanocapsid was engineered to specifically bind and enter breast cancer cells, where successful tumor targeting was demonstrated in animal models. In the present study, the nanocapsid surface was modified with a solvent-exposed cysteine to conjugate monolayer protected gold nanoclusters (AuNC). Unlike commercially available gold nanoparticles, AuNCs monodisperse in water and are composed of a discrete number of gold atoms, forming a crystalline gold core...
December 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146870/structure-of-the-yeast-spliceosomal-postcatalytic-p-complex
#2
Shiheng Liu, Xueni Li, Lingdi Zhang, Jiansen Jiang, Ryan C Hill, Yanxiang Cui, Kirk C Hansen, Z Hong Zhou, Rui Zhao
The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, B(act), C, C*, and ILS complexes revealed mechanisms of 5' splice site (ss) recognition, branching, and intron release, but lacked information on 3' ss recognition, exon ligation and release. Here, we report a cryoEM structure of the postcatalytic P complex at 3.3Å resolution, revealing that 3' ss is mainly recognized through non-Watson-Crick basepairing with the 5' ss and branch point. Furthermore, an unidentified protein becomes stably associated with the P complex, securing the 3' exon and potentially regulating Prp22 activity...
November 16, 2017: Science
https://www.readbyqxmd.com/read/29107896/cryoem-based-hybrid-modeling-approaches-for-structure-determination
#3
REVIEW
C Keith Cassidy, Benjamin A Himes, Zaida Luthey-Schulten, Peijun Zhang
Recent advances in cryo-electron microscopy (cryoEM) have dramatically improved the resolutions at which vitrified biological specimens can be studied, revealing new structural and mechanistic insights over a broad range of spatial scales. Bolstered by these advances, much effort has been directed toward the development of hybrid modeling methodologies for the construction and refinement of high-fidelity atomistic models from cryoEM data. In this brief review, we will survey the key elements of cryoEM-based hybrid modeling, providing an overview of available computational tools and strategies as well as several recent applications...
November 3, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29104918/atoms-out-of-blobs-cryoem-takes-the-nobel-prize-in-chemistry
#4
EDITORIAL
Carolyn Bertozzi
No abstract text is available yet for this article.
October 25, 2017: ACS Central Science
https://www.readbyqxmd.com/read/29100109/big-data-in-cryoem-automated-collection-processing-and-accessibility-of-em-data
#5
REVIEW
Philip R Baldwin, Yong Zi Tan, Edward T Eng, William J Rice, Alex J Noble, Carl J Negro, Michael A Cianfrocco, Clinton S Potter, Bridget Carragher
The scope and complexity of cryogenic electron microscopy (cryoEM) data has greatly increased, and will continue to do so, due to recent and ongoing technical breakthroughs that have led to much improved resolutions for macromolecular structures solved using this method. This big data explosion includes single particle data as well as tomographic tilt series, both generally acquired as direct detector movies of ∼10-100 frames per image or per tilt-series. We provide a brief survey of the developments leading to the current status, and describe existing cryoEM pipelines, with an emphasis on the scope of data acquisition, methods for automation, and use of cloud storage and computing...
October 31, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29073020/tectonic-conformational-changes-of-a-coronavirus-spike-glycoprotein-promote-membrane-fusion
#6
Alexandra C Walls, M Alejandra Tortorici, Joost Snijder, Xiaoli Xiong, Berend-Jan Bosch, Felix A Rey, David Veesler
The tremendous pandemic potential of coronaviruses was demonstrated twice in the past few decades by two global outbreaks of deadly pneumonia. The coronavirus spike (S) glycoprotein initiates infection by promoting fusion of the viral and cellular membranes through conformational changes that remain largely uncharacterized. Here we report the cryoEM structure of a coronavirus S glycoprotein in the postfusion state, showing large-scale secondary, tertiary, and quaternary rearrangements compared with the prefusion trimer and rationalizing the free-energy landscape of this conformational machine...
October 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29067766/molprobity-more-and-better-reference-data-for-improved-all-atom-structure-validation
#7
Christopher J Williams, Jeffrey J Headd, Nigel W Moriarty, Michael G Prisant, Lizbeth L Videau, Lindsay N Deis, Vishal Verma, Daniel A Keedy, Bradley J Hintze, Vincent B Chen, Swati Jain, Steven M Lewis, W Bryan Arendall, Jack Snoeyink, Paul D Adams, Simon C Lovell, Jane S Richardson, David C Richardson
This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix...
October 25, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29051543/cryoem-structure-of-saccharomyces-cerevisiae-u1-snrnp-offers-insight-into-alternative-splicing
#8
Xueni Li, Shiheng Liu, Jiansen Jiang, Lingdi Zhang, Sara Espinosa, Ryan C Hill, Kirk C Hansen, Z Hong Zhou, Rui Zhao
U1 snRNP plays a critical role in 5'-splice site recognition and is a frequent target of alternative splicing factors. These factors transiently associate with human U1 snRNP and are not amenable for structural studies, while their Saccharomyces cerevisiae (yeast) homologs are stable components of U1 snRNP. Here, we report the cryoEM structure of yeast U1 snRNP at 3.6 Å resolution with atomic models for ten core proteins, nearly all essential domains of its RNA, and five stably associated auxiliary proteins...
October 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/29038012/the-structure-of-the-actin-smooth-muscle-myosin-motor-domain-complex-in-the-rigor-state
#9
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 14, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29035172/a-pul25-dimer-interfaces-the-pseudorabies-virus-capsid-and-tegument
#10
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)...
November 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28978703/atomic-structures-of-minor-proteins-vi-and-vii-in-the-human-adenovirus
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
EDITORIAL
Wah Chiu, Kenneth H Downing
No abstract text is available yet for this article.
October 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
#20
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
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