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Journal of Structural Biology

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https://www.readbyqxmd.com/read/28625887/time-resolved-cryo-electron-microscopy-recent-progress
#1
Joachim Frank
Time-resolved cryo-electron microscopy (cryo-EM) combines the known advantages of single-particle cryo-EM in visualizing molecular structure with the ability to dissect the time progress of a reaction between molecules in vitro. Here some of the recent progress of this methodology and its first biological applications are outlined.
June 15, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28619651/structure-and-electrochemistry-of-proteins-harboring-iron-sulfur-clusters-of-different-nuclearities-part-i-4fe-4s-2fe-2s-iron-sulfur-proteins
#2
REVIEW
Piero Zanello
In a recent series of review papers we have updated structure/electrochemistry of metalloproteins harboring single types of iron-sulfur clusters, namely {Fe(Cys)4}, {[Fe2S2](Cys)4}, {[Fe2S2](Cys)3(X)} (X = Asp, Arg, His), {[Fe2S2](Cys)2(His)2}, {[Fe3S4](Cys)3}, {[Fe4S4](Cys)4} and {[Fe4S4](S(γ)Cys)3(nonthiolate ligand)} cores, and their synthetic analogs. We now face with iron-sulfur proteins harboring iron-sulfur centres of different nuclearities. In this picture we start with proteins containing [4Fe-4S]+[2Fe-2S] clusters...
June 12, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28602716/tracking-the-amyloidogenic-core-of-iapp-amyloid-fibrils-insights-from-micro-raman-spectroscopy
#3
Nikolaos N Louros, Paraskevi L Tsiolaki, Fotis A Baltoumas, Georgios D Chryssikos, Vassilis Gionis, Stavros J Hamodrakas, Vassiliki A Iconomidou
Human islet amyloid polypeptide (hIAPP) is the major protein component of extracellular amyloid deposits, located in the islets of Langerhans, a hallmark of type II diabetes. The underlying mechanisms of IAPP aggregation have not yet been clearly defined, although the highly amyloidogenic sequence of the protein has been extensively studied. Several segments have been highlighted as aggregation-prone regions (APRs), with much attention focused on the central 8-17 and 20-29 stretches. In this work, we employ micro-Raman spectroscopy to identify specific regions that are contributing to or are excluded from the amyloidogenic core of IAPP amyloid fibrils...
June 5, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28602715/microstructure-dependent-binding-of-pigment-epithelium-derived-factor-pedf-to-type-i-collagen-fibrils
#4
Meagan Cauble, Phillip Yang, Ulrich Baumann, Jan M Gebauer, Bradford G Orr, Le T Duong, Mark M Banaszak Holl
Pigment epithelium-derived factor (PEDF) is a multifunctional extracellular protein. In addition to its known antiangiogenic and neurotrophic roles in collagen rich tissues, PEDF is thought to be involved in collagen fibril assembly due to its sequence specific binding to the collagen fibril and high expression in regions of active bone formation. In order to image the presence of the protein on the fibrils, PEDF was recombinantly made with a strep tag (strep-PEDF) and then gold nanoparticles conjugated to streptavidin (AuNP) were used as a secondary tag...
June 5, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28578008/an-adventure-with-don
#5
Richard Henderson
No abstract text is available yet for this article.
May 31, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28576556/correlative-super-resolution-fluorescence-and-electron-microscopy-using-conventional-fluorescent-proteins-in-vacuo
#6
Christopher J Peddie, Marie-Charlotte Domart, Xenia Snetkov, Peter O'Toole, Banafshe Larijani, Michael Way, Susan Cox, Lucy M Collinson
Super-resolution light microscopy, correlative light and electron microscopy, and volume electron microscopy are revolutionising the way in which biological samples are examined and understood. Here, we combine these approaches to deliver super-accurate correlation of fluorescent proteins to cellular structures. We show that YFP and GFP have enhanced blinking properties when embedded in acrylic resin and imaged under partial vacuum, enabling in vacuo single molecule localisation microscopy. In conventional section-based correlative microscopy experiments, the specimen must be moved between imaging systems and/or further manipulated for optimal viewing...
May 30, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28559167/the-stoichiometry-of-the-tmem16a-ion-channel-determined-in-intact-plasma-membranes-of-cos-7-cells-using-liquid-phase-electron-microscopy
#7
Diana B Peckys, Christof Stoerger, Lorenz Latta, Ulrich Wissenbach, Veit Flockerzi, Niels de Jonge
TMEM16A is a membrane protein forming a calcium-activated chloride channel. A homodimeric stoichiometry of the TMEM16 family of proteins has been reported but an important question is whether the protein resides always in a dimeric configuration in the plasma membrane or whether monomers of the protein are also present in its native state within in the intact plasma membrane. We have determined the stoichiometry of the human (h)TMEM16A within whole COS-7 cells in liquid. For the purpose of detecting TMEM16A subunits, single proteins were tagged by the streptavidin-binding peptide within extracellular loops accessible by streptavidin coated quantum dot (QD) nanoparticles...
May 27, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28559166/cryo-fib-specimen-preparation-for-use-in-a-cartridge-type-cryo-tem
#8
Jie He, Chyongere Hsieh, Yongping Wu, Thomas Schmelzer, Pan Wang, Ying Lin, Michael Marko, Haixin Sui
Cryo-electron tomography (cryo-ET) is a well-established technique for studying 3D structural details of subcellular macromolecular complexes and organelles in their nearly native context in the cell. A primary limitation of the application of cryo-ET is the accessible specimen thickness, which is less than the diameters of almost all eukaryotic cells. It has been shown that focused ion beam (FIB) milling can be used to prepare thin, distortion-free lamellae of frozen biological material for high-resolution cryo-ET...
May 27, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28559165/protein-tentacles
#9
Stephen C Harrison
Virus structures were among the earliest illustrations of how regulated protein assembly can proceed by folding of polypeptide-chain segments into complementary sites on partner proteins. I draw on Caspar's image of protein "tentacles" and his metaphor of SV40 pentamers as five-legged, aquatic organisms ("pentopuses") to suggest a helpful vocabulary. "Tentacular interactions" among component subunits organize most subcellular molecular machines. Their selective advantages include facile regulation of both assembly and disassembly by modifying enzymes and by folding chaperones...
May 27, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28552722/a-novel-immuno-gold-labeling-protocol-for-nanobody-based-detection-of-her2-in-breast-cancer-cells-using-immuno-electron-microscopy
#10
M Kijanka, E G van Donselaar, W H Müller, B Dorresteijn, D Popov-Čeleketić, M El Khattabi, C T Verrips, P M P van Bergen En Henegouwen, J A Post
Immuno-electron microscopy is commonly performed with the use of antibodies. In the last decade the antibody fragment indicated as nanobody (VHH or single domain antibody) has found its way to different applications previously done with conventional antibodies. Nanobodies can be selected to bind with high affinity and specificity to different antigens. They are small (molecular weight ca. 15kDa) and are usually easy to produce in microorganisms. Here we have evaluated the feasibility of a nanobody binding to HER2 for application in immuno-electron microscopy...
May 25, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28552721/improved-metrics-for-comparing-structures-of-macromolecular-assemblies-determined-by-3d-electron-microscopy
#11
Agnel Praveen Joseph, Ingvar Lagerstedt, Ardan Patwardhan, Maya Topf, Martyn Winn
Recent developments in 3-dimensional electron microcopy (3D-EM) techniques and a concomitant drive to look at complex molecular structures, have led to a rapid increase in the amount of volume data available for biomolecules. This creates a demand for better methods to analyse the data, including improved scores for comparison, classification and integration of data at different resolutions. To this end, we developed and evaluated a set of scoring functions that compare 3D-EM volumes. To test our scores we used a benchmark set of volume alignments derived from the Electron Microscopy Data Bank...
May 25, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28527712/insulin-fibrillation-the-influence-and-coordination-of-zn-2
#12
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 18, 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
#13
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
#14
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 26mg/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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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