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Journal of Structural Biology

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https://www.readbyqxmd.com/read/28344036/focus-the-interface-between-data-collection-and-data-processing-in-cryo-em
#1
Nikhil Biyani, Ricardo D Righetto, Robert McLeod, Daniel Caujolle-Bert, Daniel Castano-Diez, Kenneth N Goldie, Henning Stahlberg
We present a new software package called Focus that interfaces cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner while new data is being acquired at the microscope. It provides the functionality required to remotely monitor the progress of data collection and data processing, which is essential now that automation in cryo-EM allows a steady flow of images of single particles, two-dimensional crystals, or electron tomography data to be recorded in overnight sessions...
March 23, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28343010/structural-and-dynamics-studies-of-the-tetr-family-protein-cprb-from-streptomyces-coelicolor-in-complex-with-its-biological-operator-sequence
#2
Hussain Bhukya, Asis K Jana, Neelanjana Sengupta, Ruchi Anand
In Streptomycetes, tetracycline repressor family of transcription regulators (TetR-FTRs) controls various biological processes including antibiotic biosynthesis, cellular morphology and innate resistance. Here, we focus on understanding the structural basis of transcription regulation by CprB, a member of TetR-FTRs from S. coelicolor. CprB is implicated as a receptor of γ-butyrolactones, a class of quorum sensing molecules, responsible for initiating secondary metabolic pathways. In order to understand the molecular mechanism of DNA recognition, the X-ray structure of CprB in complex with its biological relevant operator sequence was solved to a resolution of 3...
March 22, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28323140/organic-crystal-lattices-in-the-axial-filament-of-silica-spicules-of-demospongiae
#3
Peter Werner, Horst Blumtritt, Filipe Natalio
The skeletal system of Demospongiae consists of siliceous spicules, which are composed of an axial channel containing an organic axial filament (AF) surrounded by a compact layer of hydrated amorphous silica. Here we report the ultrastructural investigations of the AF of siliceous spicules from two Demospongiae: Suberites domuncula and Tethya aurantium. Electron microscopy, electron diffraction and elemental mapping analyses on both longitudinal and transversal cross-sections yield that spicules's AF consist of a three-dimensional crystal lattice of six-fold symmetry...
March 18, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28286227/ultrastructural-material-and-crystallographic-description-of-endophytic-masses-a-possible-damage-response-in-shark-and-ray-tessellated-calcified-cartilage
#4
Ronald Seidel, Michael Blumer, Paul Zaslansky, David Knötel, Daniel R Huber, James C Weaver, Peter Fratzl, Sidney Omelon, Luca Bertinetti, Mason N Dean
The cartilaginous endoskeletons of Elasmobranchs (sharks and rays) are reinforced superficially by minute, mineralized tiles, called tesserae. Unlike the bony skeletons of other vertebrates, elasmobranch skeletons have limited healing capability and their tissues' mechanisms for avoiding damage or managing it when it does occur are largely unknown. Here we describe an aberrant type of mineralized elasmobranch skeletal tissue called endophytic masses (EPMs), which grow into the uncalcified cartilage of the skeleton, but exhibit a strikingly different morphology compared to tesserae and other elasmobranch calcified tissues...
March 9, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28268178/structural-insights-into-the-architecture-of-the-shigella-flexneri-virulence-factor-icsa-virg-and-motifs-involved-in-polar-distribution-and-secretion
#5
Stefan Leupold, Petra Büsing, Philippe J Mas, Darren J Hart, Andrea Scrima
IcsA/VirG is a key virulence factor of the human pathogen Shigella flexneri, acting as both an adhesin and actin-polymerizing factor during infection. We identified a soluble expression construct of the IcsA/VirG α-domain using the ESPRIT library screening system and determined its structure to 1.9Å resolution. In addition to the previously characterized autochaperone domain, our structure reveals a new domain, which shares a common fold with the autochaperone domains of various autotransporters. We further provide insight into the previously structurally uncharacterized β-helix domain that harbors the polar targeting motif and passenger-associated transport repeat...
March 6, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28263875/molecular-architecture-of-an-n-formyltransferase-from-salmonella-enterica-o60
#6
Colin R Woodford, James B Thoden, Hazel M Holden
N-formylated sugars are found on the lipopolysaccharides of various pathogenic Gram negative bacteria including Campylobacter jejuni 81116, Francisella tularensis, Providencia alcalifaciens O30, and Providencia alcalifaciens O40. The last step in the biosynthetic pathways for these unusual sugars is catalyzed by N-formyltransferases that utilize N(10)-formyltetrahydrofolate as the carbon source. The substrates are dTDP-linked amino sugars with the functional groups installed at either the C-3' or C-4' positions of the pyranosyl rings...
March 2, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28263874/biophysical-properties-of-cardiomyocyte-surface-explored-by-multiparametric-afm
#7
Georges Smolyakov, Marie Cauquil, Childerick Severac, Véronique Lachaize, Céline Guilbeau-Frugier, Jean-Michel Sénard, Céline Galés, Etienne Dague
PeakForce Quantitative Nanomechanical Mapping (PeakForce QNM) multiparametric AFM mode was adapted to qualitative and quantitative study of the lateral membrane of cardiomyocytes (CMs), extending this powerful mode to the study of soft cells. On living CM, PeakForce QNM depicted the crests and hollows periodic alternation of cell surface architecture previously described using AFM Force Volume (FV) mode. PeakForce QNM analysis provided better resolution in terms of pixel number compared to FV mode and reduced acquisition time, thus limiting the consequences of spontaneous living adult CM dedifferentiation once isolated from the cardiac tissue...
March 2, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28259651/monolayer-crystal-streptavidin-support-films-provide-an-internal-standard-of-cryo-em-image-quality
#8
Bong-Gyoon Han, Zoe Watson, Jamie H D Cate, Robert M Glaeser
Analysis of images of biotinylated Escherichia coli 70S ribosome particles, bound to streptavidin affinity grids, demonstrates that the image-quality of particles can be predicted by the image-quality of the monolayer crystalline support film. The quality of the Thon rings is also a good predictor of the image-quality of particles, but only when images of the streptavidin crystals extend to relatively high resolution. When the estimated resolution of streptavidin was 5 Å or worse, for example, the ribosomal density map obtained from 22,697 particles went to only 9...
March 1, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28246039/survos-super-region-volume-segmentation-workbench
#9
Imanol Luengo, Michele C Darrow, Matthew C Spink, Ying Sun, Wei Dai, Cynthia Y He, Wah Chiu, Tony Pridmore, Alun W Ashton, Elizabeth M H Duke, Mark Basham, Andrew P French
Segmentation of biological volumes is a crucial step needed to fully analyse their scientific content. Not having access to convenient tools with which to segment or annotate the data means many biological volumes remain under-utilised. Automatic segmentation of biological volumes is still a very challenging research field, and current methods usually require a large amount of manually-produced training data to deliver a high-quality segmentation. However, the complex appearance of cellular features and the high variance from one sample to another, along with the time-consuming work of manually labelling complete volumes, makes the required training data very scarce or non-existent...
February 25, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28254382/a-direct-imaging-cryo-em-study-of-shedding-extracellular-vesicles-from-leukemic-monocytes
#10
Na'ama Koifman, Idan Biran, Anat Aharon, Benjamin Brenner, Yeshayahu Talmon
The human leukemia monocytic cell line (THP-1) is known to shed extracellular vesicles (EVs) under various stimulations. We studied the effects of two types of common stimulation types, lipopolysaccharide (LPS) and starvation conditions by high resolution cryogenic electron microscopy, namely, cryo-SEM and cryo-TEM. Cryo-SEM data of cells undergoing EV blebbing and shedding is presented here for the first time. The high-resolution images show good agreement with models describing the membrane processes of shedding...
February 22, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28254381/vitrification-after-multiple-rounds-of-sample-application-and-blotting-improves-particle-density-on-cryo-electron-microscopy-grids
#11
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...
February 22, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28223045/crystal-structures-reveal-a-new-and-novel-foxo1-binding-site-within-the-human-glucose-6-phosphatase-catalytic-subunit-1-gene-promoter
#12
Puja Singh, Eun Hee Han, James A Endrizzi, Richard M O'Brien, Young-In Chi
Human glucose-6-phosphatase plays a vital role in blood glucose homeostasis and holds promise as a therapeutic target for diabetes. Expression of its catalytic subunit gene 1 (G6PC1) is tightly regulated by metabolic-response transcription factors such as FoxO1 and CREB. Although at least three potential FoxO1 binding sites (insulin response elements, IREs) and one CREB binding site (cAMP response element, CRE) within the proximal region of the G6PC1 promoter have been identified, the interplay between FoxO1 and CREB and between FoxO1 bound at multiple IREs has not been well characterized...
February 20, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28223044/7%C3%A3-7-rmsd-matrix-a-new-method-for-quantitative-comparison-of-the-transmembrane-domain-structures-in-the-g-protein-coupled-receptors
#13
Ting Wang, Yang Wang, Leihan Tang, Yong Duan, Haiguang Liu
The G-protein coupled receptors (GPCRs) share a conserved heptahelical fold in the transmembrane (TM) region, but the exact arrangements of the seven TM helices vary with receptors and their activation states. The differences or the changes have been observed in the experimentally solved structures, but have not been systematically and quantitatively investigated due to lack of suitable methods. In this work, we describe a novel method, called 7×7 RMSD matrix that is proposed specifically for comparing the characteristic 7TM bundle structures of GPCRs...
February 20, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28193500/helical-reconstruction-in-relion
#14
Shaoda He, Sjors H W Scheres
We describe a new implementation for the reconstruction of helical assemblies in the empirical Bayesian framework of RELION. Our approach calculates optimal linear filters for the 3D reconstruction by embedding helical symmetry operators in Fourier-space, and deals with deviations from perfect helical symmetry through Gaussian-shaped priors on the orientations of individual segments. By incorporating our approach into the standard pipeline for single-particle analysis in RELION, our implementation aims to be easily accessible for non-experienced users...
February 11, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28189793/structures-of-a-glucose-tolerant-%C3%AE-glucosidase-provide-insights-into-its-mechanism
#15
Panjiao Pang, Li-Chuang Cao, Yu-Huan Liu, Wei Xie, Zhong Wang
Cellulose can be converted to ethanol via the fermentation of glucose, which is considered as a promising green alternative for transportation fuels. The conversion of cellulose to glucose needs three enzymes, in which β-glucosidase (BGL) plays an essential role. However, BGL is inhibited by its own product glucose, greatly limiting its applications in industry. We previously obtained a novel BGL named Bgl6 with a high glucose tolerance. Further engineering through random mutagenesis produced a triple mutant M3 with improved thermostability...
February 9, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28161413/relaxed-and-active-thin-filament-structures-a-new-structural-basis-for-the-regulatory-mechanism
#16
Danielle M Paul, John M Squire, Edward P Morris
The structures of muscle thin filaments reconstituted using skeletal actin and cardiac troponin and tropomyosin have been determined with and without bound Ca(2+) using electron microscopy and reference-free single particle analysis. The resulting density maps have been fitted with atomic models of actin, tropomyosin and troponin showing that: (i) the polarity of the troponin complex is consistent with our 2009 findings, with large shape changes in troponin between the two states; (ii) without Ca(2+) the tropomyosin pseudo-repeats all lie at almost equivalent positions in the 'blocked' position on actin (over subdomains 1 and 2); (iii) in the active state the tropomyosin pseudo-repeats are all displaced towards subdomains 3 and 4 of actin, but the extent of displacement varies within the regulatory unit depending upon the axial location of the pseudo-repeats with respect to troponin...
February 1, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28192191/the-crystal-structure-of-the-hsp90-co-chaperone-cpr7-from-saccharomyces-cerevisiae
#17
Yu Qiu, Qiangqiang Ge, Mingxing Wang, Hui Lv, Mohammad Ebrahimi, Liwen Niu, Maikun Teng, Xu Li
The versatility of Hsp90 can be attributed to the variety of co-chaperone proteins that modulate the role of Hsp90 in many cellular processes. As a co-chaperone of Hsp90, Cpr7 is essential for accelerating the cell growth in an Hsp90-containing trimeric complex. Here, we report the crystal structure of Cpr7 at a resolution of 1.8Å. It consists of an N-terminal PPI domain and a C-terminal TPR domain, and exhibits a U-shape conformation. Our studies revealed the aggregation state of Cpr7 in solution and the interaction properties between Cpr7 and the MEEVD sequence from the C-terminus of Hsp90...
March 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28167161/structure-determination-of-contaminant-proteins-using-the-marathonmr-procedure
#18
Kaushik Hatti, Ansuman Biswas, Santosh Chaudhary, Venkatareddy Dadireddy, Kanagaraj Sekar, Narayanaswamy Srinivasan, Mathur R N Murthy
In the recent decades, essential steps of protein structure determination such as phasing by multiple isomorphous replacement and multi wave length anomalous dispersion, molecular replacement, refinement of the structure determined and its validation have been fully automated. Several computer program suites that execute all these steps as a pipeline operation have been made available. In spite of these great advances, determination of a protein structure may turn out to be a challenging task for a variety of reasons...
March 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28115258/cryo-em-analysis-of-a-domain-antibody-bound-rotary-atpase-complex
#19
Roberta B Davies, Callum Smits, Andrew S W Wong, Daniela Stock, Mary Christie, Sara Sandin, Alastair G Stewart
The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has been extensively studied both structurally and functionally for many years. Here we provide an 8.7Å resolution cryo-electron microscopy 3D reconstruction of this complex bound to single-domain antibody fragments, small monomeric antibodies containing just the variable heavy domain. Docking of known structures into the density revealed the molecular orientation of the domain antibodies, suggesting that structure determination of co-domain antibody:protein complexes could be a useful avenue for unstable or smaller proteins...
March 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28115257/higher-order-structures-in-purine-and-pyrimidine-metabolism
#20
REVIEW
Iva Chitrakar, Deborah M Kim-Holzapfel, Weijie Zhou, Jarrod B French
The recent discovery of several forms of higher order protein structures in cells has shifted the paradigm of how we think about protein organization and metabolic regulation. These dynamic and controllable protein assemblies, which are composed of dozens or hundreds of copies of an enzyme or related enzymes, have emerged as important players in myriad cellular processes. We are only beginning to appreciate the breadth of function of these types of macromolecular assemblies. These higher order structures, which can be assembled in response to varied cellular stimuli including changing metabolite concentrations or signaling cascades, give the cell the capacity to modulate levels of biomolecules both temporally and spatially...
March 2017: Journal of Structural Biology
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