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Journal of Structural Biology

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https://www.readbyqxmd.com/read/28527712/insulin-fibrillation-the-influence-and-coordination-of-zn-2
#1
Christian Grundahl Frankær, Pernille Sønderby, Maria Blanner Bang, Ramona Valentina Mateiu, Minna Groenning, Jens Bukrinski, Pernille Harris
Protein amyloid fibrillation is obtaining much focus because it is connected with amyloid-related human diseases such as Alzheimer's disease, diabetes mellitus type 2, or Parkinson's disease. The influence of metal ions on the fibrillation process and whether it is implemented in the amyloid fibrils has been debated for some years. We have therefore investigated the influence and binding geometry of zinc in fibrillated insulin using extended X-ray absorption fine-structure and X-ray absorption near-edge structure spectroscopy...
May 17, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28522226/electron-crystallography-reveals-that-substrate-release-from-the-pts-iic-glucose-transporter-is-coupled-to-a-subtle-conformational-change
#2
David Kalbermatter, Po-Lin Chiu, Jean-Marc Jeckelmann, Zöhre Ucurum, Thomas Walz, Dimitrios Fotiadis
The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) is a structurally and functionally complex system that mediates sugar uptake in bacteria. Besides several soluble subunits, the glucose-specific PTS includes the integral membrane protein IICB that couples the transmembrane transport of glucose to its phosphorylation. Here, we used electron crystallography of sugar-embedded tubular crystals of the glucose-specific IIC transport domain from Escherichia coli (ecIIC(glc)) to visualize the structure of the transporter in the presence and absence of its substrate...
May 15, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28511991/calculation-of-the-cross-sectional-shape-of-a-fibril-from-equatorial-scattering
#3
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 26 mg/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/28506935/retrosynthesis-of-caco3-via-amorphous-precursor-particles-using-gastroliths-of-the-red-claw-lobster-cherax-quadricarinatus
#4
Andrónico Neira-Carrillo, María Soledad Fernández, Gonzalo Poblete Hevia, José Luis Arias, Denis Gebauer, Helmut Cölfen
Gastroliths are highly calcified structures formed in the cardiac stomach wall of crustaceans for the temporary storage of amorphous CaCO3 (ACC). The gastrolithic ACC is stabilized by the presence of biomolecules, and represents a novel model for research into biomineralization. For the first time, an in vitro biomimetic retrosynthesis of scaffolds of gastrolithic matrices with CaCO3 is presented. With the help of synthetic polyacrylic (PAA) and phytic (PA) acids, amorphous precursor particles were stabilized in double (DD) and gas (GD) diffusion crystallization assays...
May 12, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28495594/elevated-%C3%AE-s-ms-timescale-backbone-dynamics-in-the-transition-state-analog-form-of-arginine-kinase
#5
Omar Davulcu, Yu Peng, Rafael Brüschweiler, Jack J Skalicky, Michael S Chapman
Arginine kinase catalyzes reversible phosphoryl transfer between arginine and ATP. Crystal structures of arginine kinase in an open, substrate-free form and closed, transition state analog (TSA) complex indicate that the enzyme undergoes substantial domain and loop rearrangements required for substrate binding, catalysis, and product release. Nuclear magnetic resonance (NMR) has shown that substrate-free arginine kinase is rigid on the ps-ns timescale (average S(2)=0.84±0.08) yet quite dynamic on the µs-ms timescale (35 residues with Rex, 12%), and that movements of the N-terminal domain and the loop comprising residues I182-G209 are rate-limiting on catalysis...
May 8, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28483603/van-der-waals-interactions-govern-c-%C3%AE-d-glucopyranosyl-triazoles-nm-inhibitory-potency-in-human-liver-glycogen-phosphorylase
#6
Anastassia L Kantsadi, George A Stravodimos, Efthimios Kyriakis, Demetra S M Chatzileontiadou, Theodora G A Solovou, Sándor Kun, Éva Bokor, László Somsák, Demetres D Leonidas
3-(C-Glucopyranosyl)-5aryl-1,2,4-triazoles with an aryl moiety larger than phenyl have been shown to have strong inhibitory potency (Ki values in the range of upper nM) for human liver glycogen phosphorylase (hlGP), a pharmacologically relevant target for diabetes type 2. In this study we investigate in a comparative manner the inhibitory effect of the above triazoles and their respective imidazoles on hlGPa. Kinetic studies show that the imidazole derivatives are 6-8 times more potent than their corresponding triazoles...
May 5, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28476632/the-fuzzy-image
#7
James Clarage
This article celebrates the variety of Don Caspar's research interests, with particular focus on those scientific investigations beyond the structural biology of viruses for which he is often associated. These lesser known, seemingly backwater projects, allow us to build up a portrait, in both word and image, of this prolific and creative scientist. Exploration of his ideas will reveal a close connection to other structural thinkers and artists throughout history, most notably the 17th century astronomer Johannes Kepler...
May 2, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28465180/application-of-isotope-exchange-based-mass-spectrometry-to-understand-the-mechanism-of-inhibition-of-sickle-hemoglobin-polymerization-upon-oxygenation
#8
Rajdeep Das, Amrita Mitra, Vijay Bhat, Amit Kumar Mandal
Sickle hemoglobin (HbS) polymerization initiates in the deoxy state with the binding of hydrophobic patch formed by the isopropyl group of βVal6 residue of a hemoglobin tetramer with the hydrophobic pocket of another tetramer, whose hydrophobic patch binds to the hydrophobic groove of a third molecule. Subsequent elongation of a single stranded polymer followed by the formation of a double strand and finally combination of seven such pairs of double strands results in a fourteen stranded fibrous polymer. Precipitation of this fiber inside the erythrocytes results in sickling of red blood cells...
April 29, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28461152/substrate-analog-binding-and-electrostatic-surfaces-of-human-manganese-superoxide-dismutase
#9
Jahaun Azadmanesh, Scott R Trickel, Gloria E O Borgstahl
Superoxide dismutases (SODs) are enzymes that play a key role in protecting cells from toxic oxygen metabolites by disproportionation of two molecules of superoxide into molecular oxygen and hydrogen peroxide via cyclic reduction and oxidation at the active site metal. The azide anion is a potent competitive inhibitor that binds directly to the metal and is used as a substrate analog to superoxide in studies of SOD. The crystal structure of human MnSOD-azide complex was solved and shows the putative binding position of superoxide, providing a model for binding to the active site...
April 29, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28456664/identification-of-the-key-interactions-in-structural-transition-pathway-of-ftsz-from-staphylococcus-aureus
#10
Junso Fujita, Ryuhei Harada, Yoko Maeda, Yuki Saito, Eiichi Mizohata, Tsuyoshi Inoue, Yasuteru Shigeta, Hiroyoshi Matsumura
The tubulin-homolog protein FtsZ is essential for bacterial cell division. FtsZ polymerizes to form protofilaments that assemble into a contractile ring-shaped structure in the presence of GTP. Recent studies showed that FtsZ treadmilling coupled with the GTPase activity drives cell wall synthesis and bacterial cell division. The treadmilling caused by assembly and disassembly of FtsZ links to a conformational change of the monomer from a tense (T) to a relaxed (R) state, but considerable controversy still remains concerning the mechanism...
April 27, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28454764/ribosomal-proteins-as-documents-of-the-transition-from-unstructured-poly-peptides-to-folded-proteins
#11
REVIEW
Andrei N Lupas, Vikram Alva
For the most part, contemporary proteins can be traced back to a basic set of a few thousand domain prototypes, many of which were already established in the Last Universal Common Ancestor of life on Earth, around 3.5 billion years ago. The origin of these domain prototypes, however, remains poorly understood. One hypothesis posits that they arose from an ancestral set of peptides, which acted as cofactors of RNA-mediated catalysis and replication. Initially, these peptides were entirely dependent on the RNA scaffold for their structure, but as their complexity increased, they became able to form structures by excluding water through hydrophobic contacts, making them independent of the RNA scaffold...
April 26, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28433497/clostridium-difficile-toxin-glucosyltransferase-domains-in-complex-with-a-non-hydrolyzable-udp-glucose-analogue
#12
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
#13
Giovanna Scapin, Winifred W 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
#14
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
#15
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 Cherax quadricarinatus. Candidate genes encoding for mandible-forming structural proteins were mined in C...
April 7, 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
#16
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
#17
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 (1)H NMR 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 2-4nm. 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
#18
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
#19
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
#20
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
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