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https://www.readbyqxmd.com/read/29149348/mechanistic-insight-into-the-assembly-of-the-hera-nura-helicase-nuclease-dna-end-resection-complex
#1
Zainab Ahdash, Andy M Lau, Robert Thomas Byrne, Katja Lammens, Alexandra Stüetzer, Henning Urlaub, Paula J Booth, Eamonn Reading, Karl-Peter Hopfner, Argyris Politis
The HerA-NurA helicase-nuclease complex cooperates with Mre11 and Rad50 to coordinate the repair of double-stranded DNA breaks. Little is known, however, about the assembly mechanism and activation of the HerA-NurA. By combining hybrid mass spectrometry with cryo-EM, computational and biochemical data, we investigate the oligomeric formation of HerA and detail the mechanism of nucleotide binding to the HerA-NurA complex from thermophilic archaea. We reveal that ATP-free HerA and HerA-DNA complexes predominantly exist in solution as a heptamer and act as a DNA loading intermediate...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29149017/the-ms6-mycolyl-arabinogalactan-esterase-lysb-is-essential-for-an-efficient-mycobacteriophage-induced-lysis
#2
Adriano M Gigante, Cheri M Hampton, Rebecca S Dillard, Filipa Gil, Maria João Catalão, José Moniz-Pereira, Elizabeth R Wright, Madalena Pimentel
All dsDNA phages encode two proteins involved in host lysis, an endolysin and a holin that target the peptidoglycan and cytoplasmic membrane, respectively. Bacteriophages that infect Gram-negative bacteria encode additional proteins, the spanins, involved in disruption of the outer membrane. Recently, a gene located in the lytic cassette was identified in the genomes of mycobacteriophages, which encodes a protein (LysB) with mycolyl-arabinogalactan esterase activity. Taking in consideration the complex mycobacterial cell envelope that mycobacteriophages encounter during their life cycle, it is valuable to evaluate the role of these proteins in lysis...
November 17, 2017: Viruses
https://www.readbyqxmd.com/read/29148969/the-structure-of-the-copi-coat-determined-within-the-cell
#3
Yury S Bykov, Miroslava Schaffer, Svetlana O Dodonova, Sahradha Albert, Jürgen M Plitzko, Wolfgang Baumeister, Benjamin D Engel, John Ag Briggs
COPI-coated vesicles mediate trafficking within the Golgi apparatus and from the Golgi to the endoplasmic reticulum. The structures of membrane protein coats, including COPI, have been extensively studied with in vitro reconstitution systems using purified components. In a previous paper (Dodonova et al., 2017), we determined a complete structural model of the in vitro reconstituted COPI coat. Here, we applied cryo-focused ion beam milling, cryo-electron tomography and subtomogram averaging to determine the native structure of the COPI coat within vitrified Chlamydomonas reinhardtii cells...
November 17, 2017: ELife
https://www.readbyqxmd.com/read/29147002/capturing-an-initial-intermediate-during-the-p450nor-enzymatic-reaction-using-time-resolved-xfel-crystallography-and-caged-substrate
#4
Takehiko Tosha, Takashi Nomura, Takuma Nishida, Naoya Saeki, Kouta Okubayashi, Raika Yamagiwa, Michihiro Sugahara, Takanori Nakane, Keitaro Yamashita, Kunio Hirata, Go Ueno, Tetsunari Kimura, Tamao Hisano, Kazumasa Muramoto, Hitomi Sawai, Hanae Takeda, Eiichi Mizohata, Ayumi Yamashita, Yusuke Kanematsu, Yu Takano, Eriko Nango, Rie Tanaka, Osamu Nureki, Osami Shoji, Yuka Ikemoto, Hironori Murakami, Shigeki Owada, Kensuke Tono, Makina Yabashi, Masaki Yamamoto, Hideo Ago, So Iwata, Hiroshi Sugimoto, Yoshitsugu Shiro, Minoru Kubo
Time-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers a crystallographic method to track enzymatic reactions. Here we demonstrate the application of this method using fungal NO reductase, a heme-containing enzyme, at room temperature. Twenty milliseconds after caged-NO photolysis, we identify a NO-bound form of the enzyme, which is an initial intermediate with a slightly bent Fe-N-O coordination geometry at a resolution of 2...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29146944/structure-of-the-transcription-activator-target-tra1-within-the-chromatin-modifying-complex-saga
#5
Grigory Sharov, Karine Voltz, Alexandre Durand, Olga Kolesnikova, Gabor Papai, Alexander G Myasnikov, Annick Dejaegere, Adam Ben Shem, Patrick Schultz
The transcription co-activator complex SAGA is recruited to gene promoters by sequence-specific transcriptional activators and by chromatin modifications to promote pre-initiation complex formation. The yeast Tra1 subunit is the major target of acidic activators such as Gal4, VP16, or Gcn4 but little is known about its structural organization. The 430 kDa Tra1 subunit and its human homolog the transformation/transcription domain-associated protein TRRAP are members of the phosphatidyl 3-kinase-related kinase (PIKK) family...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29146871/postcatalytic-spliceosome-structure-reveals-mechanism-of-3-splice-site-selection
#6
Max E Wilkinson, Sebastian M Fica, Wojciech P Galej, Christine M Norman, Andrew J Newman, Kiyoshi Nagai
Introns are removed from eukaryotic mRNA precursors by the spliceosome in two transesterification reactions-branching and exon ligation. The mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3.7Å cryo-EM structure of the yeast P complex spliceosome immediately after exon ligation. The 3'-splice site AG dinucleotide is recognized through non-Watson-Crick pairing with the 5'-splice site and the branch point adenosine. After the branching reaction protein factors work together to remodel the spliceosome and stabilize a conformation competent for 3'-splice site docking, thereby promoting exon ligation...
November 16, 2017: Science
https://www.readbyqxmd.com/read/29146813/structural-basis-of-bacterial-transcription-activation
#7
Bin Liu, Chuan Hong, Rick K Huang, Zhiheng Yu, Thomas A Steitz
In bacteria, the activation of gene transcription at many promoters is simple and only involves a single activator. The cyclic adenosine 3',5'-monophosphate receptor protein (CAP), a classic activator, is able to activate transcription independently through two different mechanisms. Understanding the class I mechanism requires an intact transcription activation complex (TAC) structure at a high resolution. Here we report a high-resolution cryo-electron microscopy structure of an intact Escherichia coli class I TAC containing a CAP dimer, a σ(70)-RNA polymerase (RNAP) holoenzyme, a complete class I CAP-dependent promoter DNA, and a de novo synthesized RNA oligonucleotide...
November 17, 2017: Science
https://www.readbyqxmd.com/read/29146805/the-structural-basis-of-flagellin-detection-by-naip5-a-strategy-to-limit-pathogen-immune-evasion
#8
Jeannette L Tenthorey, Nicole Haloupek, José Ramón López-Blanco, Patricia Grob, Elise Adamson, Ella Hartenian, Nicholas A Lind, Natasha M Bourgeois, Pablo Chacón, Eva Nogales, Russell E Vance
Robust innate immune detection of rapidly evolving pathogens is critical for host defense. Nucleotide-binding domain leucine-rich repeat (NLR) proteins function as cytosolic innate immune sensors in plants and animals. However, the structural basis for ligand-induced NLR activation has so far remained unknown. NAIP5 (NLR family, apoptosis inhibitory protein 5) binds the bacterial protein flagellin and assembles with NLRC4 to form a multiprotein complex called an inflammasome. Here we report the cryo-electron microscopy structure of the assembled ~1...
November 17, 2017: Science
https://www.readbyqxmd.com/read/29144446/structure-and-assembly-of-the-ebola-virus-nucleocapsid
#9
William Wan, Larissa Kolesnikova, Mairi Clarke, Alexander Koehler, Takeshi Noda, Stephan Becker, John A G Briggs
Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause haemorrhagic fever. Filoviruses are within the order Mononegavirales, which also includes rabies virus, measles virus, and respiratory syncytial virus. Mononegaviruses have non-segmented, single-stranded negative-sense RNA genomes that are encapsidated by nucleoprotein and other viral proteins to form a helical nucleocapsid. The nucleocapsid acts as a scaffold for virus assembly and as a template for genome transcription and replication...
November 16, 2017: Nature
https://www.readbyqxmd.com/read/29143694/cryo-scanning-electron-microscopy-sem-and-scanning-transmission-electron-microscopy-stem-in-sem-for-bio-and-organo-mineral-interface-characterization-in-the-environment
#10
Guillaume Wille, Jennifer Hellal, Patrick Ollivier, Annie Richard, Agnes Burel, Louis Jolly, Marc Crampon, Caroline Michel
Understanding biofilm interactions with surrounding substratum and pollutants/particles can benefit from the application of existing microscopy tools. Using the example of biofilm interactions with zero-valent iron nanoparticles (nZVI), this study aims to apply various approaches in biofilm preparation and labeling for fluorescent or electron microscopy and energy dispersive X-ray spectrometry (EDS) microanalysis for accurate observations. According to the targeted microscopy method, biofilms were sampled as flocs or attached biofilm, submitted to labeling using 4',6-diamidino-2-phenylindol, lectins PNA and ConA coupled to fluorescent dye or gold nanoparticles, and prepared for observation (fixation, cross-section, freezing, ultramicrotomy)...
November 16, 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/29141432/probing-cluster-surface-morphology-by-cryo-spectroscopy-of-n2-on-cationic-nickel-clusters
#11
Sebastian Dillinger, Jennifer Mohrbach, Gereon Niedner-Schatteburg
We present the cryogenic (26 K) IR spectra of selected [Nin(N2)m](+) (n = 5-20, m = 1 - mmax), which strongly reveal n- and m-dependent features in the N2 stretching region, in conjunction with density functional theory modeling of some of these findings. The observed spectral features allow us to refine the kinetic classification [cf. J. Mohrbach, S. Dillinger, and G. Niedner-Schatteburg, J. Chem. Phys. 147, 184304 (2017)] and to define four classes of structure related surface adsorption behavior: Class (1) of Ni6(+), Ni13(+), and Ni19(+) are highly symmetrical clusters with all smooth surfaces of equally coordinated Ni atoms that entertain stepwise N2 adsorption up to stoichiometric N2:Nisurface saturation...
November 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29141423/probing-cluster-surface-morphology-by-cryo-kinetics-of-n2-on-cationic-nickel-clusters
#12
Jennifer Mohrbach, Sebastian Dillinger, Gereon Niedner-Schatteburg
We present the stepwise N2 adsorption kinetics of size selected Nin(+) (n = 5-20) clusters at 26 K as obtained by a hybrid tandem ion trap instrument. Pseudo-first-order kinetic fits confirm consecutive adsorption steps without evidence of cluster isomers and up to adsorption limits, which scale with the cluster size. The reaction rates for the initial N2 adsorption increase smoothly with the cluster size and similar to hard sphere cluster modeling. The isothermal kinetics allow for the tentative elucidation of cluster surface morphologies and for their classification into highly symmetrical clusters with all smooth surfaces, small clusters with rough surfaces, and large clusters with partially rough and smooth surface areas...
November 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29140718/pem-fitter-a-coarse-grained-method-to-validate-protein-candidate-models
#13
Kamal Al Nasr, Christopher Jones, Feras Yousef, Ruba Jebril
The volumetric images produced by Cryo-Electron Microscopy (cryo-EM) technique are used to model macromolecular assemblies and machines. De novo protein modeling uses these images to computationally model the structure of the molecules. Many candidate conformations are usually generated during the intermediate step. Conventionally, each of these candidates is evaluated by time-consuming approaches such as potential energy. We introduce an initial version of a geometrical screening method that uses the skeleton of the cryo-EM images to evaluate candidate structures...
November 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29138585/a-comparative-analysis-of-clinical-outcomes-and-disposable-costs-of-different-catheter-ablation-methods-for-the-treatment-of-atrioventricular-nodal-reentrant-tachycardia
#14
Adam E Berman, Harold Rivner, Robin Chalkley, Vahé Heboyan
Background: Catheter ablation of atrioventricular nodal reentrant tachycardia (AVNRT) is a commonly performed electrophysiology (EP) procedure. Few data exist comparing conventional (CONV) versus novel ablation strategies from both clinical and direct cost perspectives. We sought to investigate the disposable costs and clinical outcomes associated with three different ablation methodologies used in the ablation of AVNRT. Methods: We performed a retrospective review of AVNRT ablations performed at Augusta University Medical Center from 2006 to 2014...
2017: ClinicoEconomics and Outcomes Research: CEOR
https://www.readbyqxmd.com/read/29137237/cryoablation-combined-with-allogenic-natural-killer-cell-immunotherapy-improves-the-curative-effect-in-patients-with-advanced-hepatocellular-cancer
#15
Mao Lin, Shuzhen Liang, Xiaohua Wang, Yinqing Liang, Mingjie Zhang, Jibing Chen, Lizhi Niu, Kecheng Xu
In this study, the clinical efficacy of cryosurgery combined with allogenic natural killer cell immunotherapy for advanced hepatocellular cancer was evaluated. From October 2015 to March 2017, we enrolled 61 patients who met the enrollment criteria and divided them into two groups: 1) the simple cryoablation group (Cryo group, n = 26); and 2) the cryoablation combined with allogenic natural killer cells group (Cryo-NK group, n = 35), the safety and short-term effects were evaluated firstly, then the median progression-free survival, response rate and disease control rate were assessed...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29135688/membrane-microdomains-and-the-regulation-of-hdl-biogenesis
#16
Jacques Genest, Adel Schwertani, Hong Y Choi
PURPOSE OF REVIEW: The major cardio-protective function of HDL is to remove excess cellular cholesterol in the process of HDL particle formation and maturation. The HDL biogenic procedure requiring protein-lipid interactions has been incompletely understood, and here we discuss recent progress and insights into the mechanism of HDL biogenesis. RECENT FINDINGS: The initial and rate-limiting step of HDL biogenesis is the interaction between apoA-I and plasma membrane microdomains created by ATP-binding cassette transporter A1 (ABCA1) transporter...
November 11, 2017: Current Opinion in Lipidology
https://www.readbyqxmd.com/read/29132829/the-lipolytic-degradation-of-highly-structured-cubic-micellar-nanoparticles-of-soy-phosphatidylcholine-and-glycerol-dioleate-by-phospholipase-a2-and-triacylglycerol-lipase
#17
Maria Wadsäter, Justas Barauskas, Fredrik Tiberg, Tommy Nylander
The effects of different lipolytic enzymes on the structure of lipid liquid crystalline nano-particles (LCNP) have been investigated by cryogenic transmission electron microscopy (cryo-TEM) and synchrotron small angle X-ray diffraction (SAXD). Here we used highly structured cubic micellar (Fd3m) nanoparticles of 50/50 (wt%/wt%) soy phosphatidyl choline (SPC)/glycerol dioleate (GDO) as substrate. Two types of lipolytic enzymes were used, phospholipase A2 (PLA2) that catalysis degradation of the phospholipid component, SPC, and porcine pancreatic triacylglycerol lipase (TGL) that facilitate the hydrolysis of the diglyceride, GDO...
November 10, 2017: Chemistry and Physics of Lipids
https://www.readbyqxmd.com/read/29132296/a-fragment-based-method-for-modeling-of-protein-segments-into-cryo-em-density-maps
#18
Jochen Ismer, Alexander S Rose, Johanna K S Tiemann, Peter W Hildebrand
BACKGROUND: Single-particle analysis of electron cryo-microscopy (cryo-EM) is a key technology for elucidation of macromolecular structures. Recent technical advances in hardware and software developments significantly enhanced the resolution of cryo-EM density maps and broadened the applicability and the circle of users. To facilitate modeling of macromolecules into cryo-EM density maps, fast and easy to use methods for modeling are now demanded. RESULTS: Here we investigated and benchmarked the suitability of a classical and well established fragment-based approach for modeling of segments into cryo-EM density maps (termed FragFit)...
November 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29131938/a-crash-course-in-calcium-channels
#19
Gerald W Zamponi
Much progress has been made in understanding the molecular physiology and pharmacology of calcium channels. Recently, there have been tremendous advances in learning about calcium channel structure and function through crystallography and cryo-electron microscopy studies. Here, I will give an overview of our knowledge about calcium channels, and highlight two recent studies that give important insights into calcium channel structure.
November 13, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/29130302/a-cell-mimicking-structure-converting-analog-volume-changes-to-digital-colorimetric-output-with-molecular-selectivity
#20
Zijie Zhang, Yibo Liu, Xiaohan Zhang, Juewen Liu
We herein report a three-component cell-mimicking structure with a peroxidase-like iron oxide nanozyme as the nucleus, a molecularly imprinted hydrogel shell as cytoplasm, and a lipid bilayer membrane. The structure was characterized by cryo and negative stain TEM and also by a calcein leakage test. By introducing charged monomers, the gel shell can swell or shrink in response to salt concentration. By lowering the salt concentration, the gradual 'analog' gel volume change was reflected in a switch-like 'digital' colorimetric output by the burst of membrane and oxidation of substrates such as 3,3',5,5'-tetramethylbenzidine (TMB)...
November 13, 2017: Nano Letters
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