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Journal of Structural Biology

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https://www.readbyqxmd.com/read/28705712/hydrolysis-of-diadenosine-polyphosphates-exploration-of-an-additional-role-of-mycobacterium-smegmatis-mutt1
#1
S M Arif, U Varshney, M Vijayan
Diadenosine polyphosphates (ApnA, n=2-6), particularly Ap4A, are involved in several important physiological processes. The substantial sequence identity of the Nudix hydrolase domain (domain 1) of Mycobacterium smegmatis MutT1 (MsMutT1) with a known Ap4A hydrolase suggested that MsMutT1 could also hydrolyse diadenosine polyphosphates. Biochemical experiments yielded results in conformity with this suggestion, with Ap4A as the best among the substrates. ATP is a product in all experiments; small amounts of ADP were also observed in the experiments involving Ap4A and Ap6A...
July 10, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28698109/myelin-structure-in-unfixed-single-nerve-fibers-scanning-x-ray-microdiffraction-with-a-beam-size-of-200-nm
#2
Hideyo Inouye, Fong-Hsu Kuo, Andrew R Denninger, Britta Weinhausen, Manfred Burghammer, Daniel A Kirschner
Previous raster-scanning with a 1 μm x-ray beam of individual, myelinated fibers from glutaraldehyde-fixed rat sciatic nerve revealed a spatially-dependent variation in the diffraction patterns from single fibers. Analysis indicated differences in the myelin periodicity, membrane separations, distribution of proteins, and orientaion of membrane lamellae. As chemical fixation is known to produce structural artifacts, we sought to determine in the current study whether the structural heterogeneity is intrinsic to unfixed myelin...
July 8, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28658599/scipioncloud-an-integrative-and-interactive-gateway-for-large-scale-cryo-electron-microscopy-image-processing-on-commercial-and-academic-clouds
#3
Jesús Cuenca-Alba, Laura Del Cano, Josué Gómez Blanco, José Miguel de la Rosa Trevín, Pablo Conesa Mingo, Roberto Marabini, Carlos Oscar S Sorzano, Jose María Carazo
New instrumentation for cryo electron microscopy (cryoEM) has significantly increased data collection rate as well as data quality, creating bottlenecks at the image processing level. Current image processing model of moving the acquired images from the data source (electron microscope) to desktops or local clusters for processing is encountering many practical limitations. However, computing may also take place in distributed and decentralized environments. In this way, cloud is a new form of accessing computing and storage resources on demand...
June 25, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28655593/collagen-fibril-organization-within-rat-vertebral-bone-modified-with-metastatic-involvement
#4
Mikhail Burke, Ahmad Golaraei, Ayelet Atkins, Margarete Akens, Virginijus Barzda, Cari Whyne
Metastatic involvementdiminishes themechanical integrity of vertebral bone, howeveritsspecificimpact on the structural characteristics of a primary constituent of bone tissue,the collagen-I fibril matrix, has not been adequately characterized. Female athymic rats were inoculated with HeLa or Ace-1 cancer cells lines producing osteolytic or mixed (osteolytic & osteoblastic) metastases respectively. A maximum of 21 days was allowed between inoculation and rat sacrifice for vertebrae extraction. Linear polarization-in, polarization-out (PIPO) second harmonic generation (SHG) and transmission electron microscopy (TEM) imaging was utilized to assess the impact of metastatic involvement on collagen fibril organization...
June 24, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28647540/reversible-swelling-of-sbmv-is-associated-with-reversible-disordering
#5
Jade Li, Carl Fricks, Donald L D Caspar, Ivan Rayment
The structures of the compact and swollen southern bean mosaic virus (SBMV) particles have been compared by X-ray diffraction and proton magnetic resonance (PMR). Small-angle X-ray scattering showed that removal of divalent cations at alkaline pH causes the particle diameter to increase from 289Å in the native SBMV by 12% in solution and by 9% in microcrystals. The swelling is fully reversible upon re-addition of Ca(2+)and Mg(2+) ions, as shown by the X-ray patterns at 6 Å resolution and by the 270 MHz PMR spectra...
June 21, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28647539/chemical-addressability-of-potato-virus-x-for-its-applications-in-bio-nanotechnology
#6
Duc H T Le, He Hu, Ulrich Commandeur, Nicole F Steinmetz
Potato virus X (PVX), a type member of the plant virus potexvirus group, offers a unique nanotechnology platform based on its high aspect ratio and flexible filamentous shape. The PVX platform has already been engineered and studied for its uses in imaging, drug delivery, and immunotherapies. While genetic engineering procedures are well established for PVX, there is limited information about chemical conjugation strategies for functionalizing PVX, partly due to the lack of structural information of PVX at high resolution...
June 21, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28645735/serum-amyloid-a-self-assembles-with-phospholipids-to-form-stable-protein-rich-nanoparticles-with-a-distinct-structure-a-hypothetical-function-of-saa-as-a-molecular-mop-in-immune-response
#7
Nicholas M Frame, Shobini Jayaraman, Donald L Gantz, Olga Gursky
Serum amyloid A (SAA) is an acute-phase protein whose action in innate immunity and lipid homeostasis is unclear. Most circulating SAA binds plasma high-density lipoproteins (HDL) and reroutes lipid transport. In vivo SAA binds existing lipoproteins or generates them de novo upon lipid uptake from cells. We explored the products of SAA-lipid interactions and lipoprotein remodeling in vitro. SAA complexes with palmitoyl-oleoyl phosphocholine (POPC) were analyzed for structure and stability using circular dichroism and fluorescence spectroscopy, electron microscopy, gel electrophoresis and gel filtration...
June 20, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28625887/time-resolved-cryo-electron-microscopy-recent-progress
#8
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 16, 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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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/28527712/insulin-fibrillation-the-influence-and-coordination-of-zn-2
#18
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
#19
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
#20
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
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