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Journal of Structural Biology

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https://www.readbyqxmd.com/read/28433497/clostridium-difficile-toxin-glucosyltransferase-domains-in-complex-with-a-non-hydrolyzable-udp-glucose-analogue
#1
Joseph W Alvin, D Borden Lacy
Clostridium difficile is the leading cause of hospital-acquired diarrhea and pseudomembranous colitis worldwide. The organism produces two homologous toxins, TcdA and TcdB, which enter and disrupt host cell function by glucosylating and thereby inactivating key signalling molecules within the host. As a toxin-mediated disease, there has been a significant interest in identifying small molecule inhibitors of the toxins' glucosyltransferase activities. This study was initiated as part of an effort to identify the mode of inhibition for a small molecule inhibitor of glucosyltransferase activity called apigenin...
April 19, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28433496/a-novel-storage-system-for-cryoem-samples
#2
Giovanna Scapin, Winifred 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/28400129/the-ph-dependent-assembly-of-chaplin-e-from-streptomyces-coelicolor
#3
Mina Dokouhaki, Andrew Hung, Li Day, Sally L Gras
Chaplin E, is one of five self-assembling peptides secreted by Streptomyces coelicolor that assist aerial growth by lowering the surface tension of water. Although the surface activity of a mixture of chaplin peptides has observed to depend on pH, it is unclear how the solvent environment (i.e. pH) influences the structure, assembly and subsequent functionality of these individual peptides. In this study, the conformation and fibril forming propensity of the Chaplin E peptide was assessed as a function of pH using a combination of experimental measurements and molecular dynamics simulations...
April 8, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28392452/mars-a-protein-family-involved-in-the-formation-of-vertical-skeletal-elements
#4
Shai Abehsera, Shani Peles, Jenny Tynyakov, Shmuel Bentov, Eliahu D Aflalo, Shihao Li, Fuhua Li, Jianhai Xiang, Amir Sagi
Vertical organizations of skeletal elements are found in various vertebrate teeth and invertebrate exoskeletons. The molecular mechanism behind the development of such structural organizations is poorly known, although it is generally held that organic matrix proteins play an essential role. While most crustacean cuticular organizations exhibit horizontal chitinous layering, a typical vertical organization is found towards the surface of the teeth in the mandibles of the crayfish Cheraxquadricarinatus. Candidate genes encoding for mandible-forming structural proteins were mined in C...
April 6, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28392451/electron-tomography-simulator-with-realistic-3d-phantom-for-evaluation-of-acquisition-alignment-and-reconstruction-methods
#5
Xiaohua Wan, Tsvi Katchalski, Christopher Churas, Sreya Ghosh, Sebastien Phan, Albert Lawrence, Yu Hao, Ziying Zhou, Ruijuan Chen, Yu Chen, Fa Zhang, Mark H Ellisman
Because of the significance of electron microscope tomography in the investigation of biological structure at nanometer scales, ongoing improvement efforts have been continuous over recent years. This is particularly true in the case of software developments. Nevertheless,verification of improvements delivered by new algorithms and software remains difficult. Current analysis tools do not provide adaptable and consistent methods for quality assessment.This is particularly true with images of biological samples, due to image complexity, variability, low contrast and noise...
April 6, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28390956/the-structure-of-the-amorphous-matrix-of-keratins
#6
Murat Kadir, Xinwei Wang, Bowen Zhu, Jing Liu, Duane Harland, Crisan Popescu
Various keratin fibers, particularly human hairs, were investigated by transmission electron microscopy, TEM, solid-state 1HNMR and Transient Electro-Thermal Technique, TET. The results converge to suggest that the matrix of keratin fiber cortex, far from being amorphous, has a well-defined nano-scale grainy structure, the size of these grains being around 2 - 4 nm. The size of the grains appears to strongly depend on the chemical treatment of the fiber, on the temperature and on the relative humidity of the environment, as well as on the physiological factors at the level of fiber production in follicle...
April 5, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28347808/optimizing-clem-protocols-for-plants-cells-gma-embedding-and-cryosections-as-alternatives-for-preservation-of-gfp-fluorescence-in-arabidopsis-roots
#7
Jessica Marion, Romain Le Bars, Béatrice Satiat-Jeunemaitre, Claire Boulogne
Recently, a number of diverse correlative light and electron microscopy (CLEM) protocols have been developed for several model organisms. However, these CLEM methods have largely bypassed plant cell research, with most protocols having little application to plants. Using autophagosome identification as a biological background, we propose and compare two CLEM protocols that can be performed in most plant research laboratories, providing a good compromise that preserves fluorescent signals as well as ultrastructural features...
March 24, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28344036/focus-the-interface-between-data-collection-and-data-processing-in-cryo-em
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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 5Å 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
#16
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 27, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28254382/a-direct-imaging-cryo-em-study-of-shedding-extracellular-vesicles-from-leukemic-monocytes
#17
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/28223045/crystal-structures-reveal-a-new-and-novel-foxo1-binding-site-within-the-human-glucose-6-phosphatase-catalytic-subunit-1-gene-promoter
#18
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
#19
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
#20
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
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