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Journal of Structural Biology

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https://www.readbyqxmd.com/read/28823563/alpha-repeat-proteins-%C3%AE-rep-as-expression-and-crystallization-helpers
#1
Anne Chevrel, Agnes Mesneau, Dyana Sanchez, Louisa Celma, Sophie Quevillon-Cheruel, Andrea Cavagnino, Sylvie Nessler, Ines Li de la Sierra-Gallay, Herman van Tilbeurgh, Philippe Minard, Marie Valerio-Lepiniec, Agathe Urvoas
We have previously described a highly diverse library of artificial repeat proteins based on thermostable HEAT-like repeats, named αRep. αReps binding specifically to proteins difficult to crystallize have been selected and in several examples, they made possible the crystallization of these proteins. To further simplify the production and crystallization experiments we have explored the production of chimeric protein corresponding to covalent association between the targets and their specific binders strengthened by a linker...
August 16, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28813641/aim2-inflammasome-activation-and-regulation-a-structural-perspective
#2
Bing Wang, Qian Yin
Absent in melanoma 2 (AIM2) inflammasome is a multi-protein platform that recognizes aberrant cytoplasmic dsDNA and induces cytokine maturation, release and pyroptosis. It is composed of AIM2, apoptosis-associated speck-like protein containing a CARD (ASC), and caspase-1. Recent X-ray crystallographic and high resolution cryo-electron microscopic (cryo-EM) studies have revealed a series of structures in AIM2 inflammasome activation and regulation. One prominent feature common in multiple steps is the assembly of high-order structures, especially helical filaments nucleated by upstream molecules, rather than stoichiometric complexes...
August 13, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28778734/coalignment-of-osteocyte-canaliculi-and-collagen-fibers-in-human-osteonal-bone
#3
Felix Repp, Philip Kollmannsberger, Andreas Roschger, Andrea Berzlanovich, Gerlinde M Gruber, Paul Roschger, Wolfgang Wagermaier, Richard Weinkamer
During bone formation osteocytes get connected with each other via a dense network of canaliculi within the mineralized bone matrix. Important functions attributed to the osteocyte network include the control of bone remodeling and a contribution to mineral homeostasis. To detect structural clues of the formation and functionality of the network, this study analyzes the structure and orientation of the osteocyte lacuno-canalicular network (OLCN), specifically in relation to the concentric bone lamellae within human osteons...
August 1, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28760695/structural-and-functional-analyses-of-a-timp-and-mmp-in-the-ligament-of-pinctada-fucata
#4
Kazuki Kubota, Yasushi Tsuchihashi, Toshihiro Kogure, Kaoru Maeyama, Fumihiro Hattori, Shigeharu Kinoshita, Shohei Sakuda, Hiromichi Nagasawa, Etsuro Yoshimura, Michio Suzuki
The bivalve hinge ligament is the hard tissue that functions to open and close shells. The ligament contains fibrous structures consisting of aragonite crystals surrounded by a dense organic matrix. This organic matrix may contribute to the formation of fibrous aragonite crystals, but the mechanism underlying this formation remains unclear. In this study, we identified a novel ligament-specific protein, Pinctada fucata tissue inhibitor of metalloproteinase (PfTIMP), from the fibrous organic matrix between aragonite crystals in the ligament using the amino acid sequence and cDNA cloning methods...
July 29, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28760694/effects-of-tissue-fixation-and-dehydration-on-tendon-collagen-nanostructure
#5
Mikael J Turunen, Hanifeh Khayyeri, Manuel Guizar-Sicairos, Hanna Isaksson
Collagen is the most prominent protein in biological tissues. Tissue fixation is often required for preservation or sectioning of the tissue. This may affect collagen nanostructure and potentially provide incorrect information when analyzed after fixation. We aimed to unravel the effect of 1) ethanol and formalin fixation and 2) 24h air-dehydration on the organization and structure of collagen fibers at the nano-scale using small and wide angle X-ray scattering. Samples were divided into 4 groups: ethanol fixed, formalin fixed, and two untreated sample groups...
July 28, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28756247/autom-a-novel-automatic-platform-for-electron-tomography-reconstruction
#6
Renmin Han, Xiaohua Wan, Zihao Wang, Yu Hao, Jingrong Zhang, Yu Chen, Xin Gao, Zhiyong Liu, Fei Ren, Fei Sun, Fa Zhang
We have developed a software package towards automatic electron tomography (ET): Automatic Tomography (AuTom). The presented package has the following characteristics: accurate alignment modules for marker-free datasets containing substantial biological structures; fully automatic alignment modules for datasets with fiducial markers; wide coverage of reconstruction methods including a new iterative method based on the compressed-sensing theory that suppresses the "missing wedge" effect; and multi-platform acceleration solutions that support faster iterative algebraic reconstruction...
July 26, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28743638/efficient-3d-ctf-correction-for-cryo-electron-tomography-using-novactf-improves-subtomogram-averaging-resolution-to-3-4-%C3%A3
#7
Beata Turoňová, Florian K M Schur, William Wan, John A G Briggs
Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular complexes to be imaged in three-dimensions in their native environments. Cryo-electron tomograms are reconstructed from projection images taken at defined tilt-angles. In order to recover high-resolution information from cryo-electron tomograms, it is necessary to measure and correct for the contrast transfer function (CTF) of the microscope. Most commonly, this is performed using protocols that approximate the sample as a two-dimensional (2D) plane...
July 22, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28743637/design-considerations-in-coiled-coil-fusion-constructs-for-the-structural-determination-of-a-problematic-region-of-the-human-cardiac-myosin-rod
#8
Michael P Andreas, Gautam Ajay, Jaclyn A Gellings, Ivan Rayment
X-ray structural determination of segments of the myosin rod has proved difficult because of the strong salt-dependent aggregation properties and repeating pattern of charges on the surface of the coiled-coil that lead to the formation of paracrystals. This problem has been resolved in part through the use of globular assembly domains that improve protein folding and prevent aggregation. The primary consideration now in designing coiled-coil fusion constructs for myosin is deciding where to truncate the coiled-coil and which amino acid residues to include from the folding domain...
July 22, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28739483/structural-modeling-for-the-open-state-of-an-nmda-receptor
#9
Xiaodong Pang, Huan-Xiang Zhou
NMDA receptors are tetrameric ligand-gated ion channels that are crucial for neurodevelopment and higher order processes such as learning and memory, and have been implicated in numerous neurological disorders. The lack of a structure for the channel open state has greatly hampered the understanding of the normal gating process and mechanisms of disease-associated mutations. Here we report the structural modeling for the open state of an NMDA receptor. Staring from the crystal structure of the closed state, we repacked the pore-lining helices to generate an initial open model...
July 22, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28734842/hydration-forces-between-aligned-dna-helices-undergoing-b-to-a-conformational-change-in-situ-x-ray-fiber-diffraction-studies-in-a-humidity-and-temperature-controlled-environment
#10
Ryan Case, Hauke Schollmeyer, Phillip Kohl, Eric B Sirota, Roger Pynn, Kai E Ewert, Cyrus R Safinya, Youli Li
Hydration forces between DNA molecules in the A- and B-Form were studied using a newly developed technique enabling simultaneous in situ control of temperature and relative humidity. X-ray diffraction data were collected from oriented calf-thymus DNA fibers in the relative humidity range of 98%-70%, during which DNA undergoes the B- to A-form transition. Coexistence of both forms was observed over a finite humidity range at the transition. The change in DNA separation in response to variation in humidity, i...
July 19, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28705712/hydrolysis-of-diadenosine-polyphosphates-exploration-of-an-additional-role-of-mycobacterium-smegmatis-mutt1
#11
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
#12
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
#13
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
#14
Mikhail Burke, Ahmad Golaraei, Ayelet Atkins, Margarete Akens, Virginijus Barzda, Cari Whyne
Metastatic involvement diminishes the mechanical integrity of vertebral bone, however its specific impact 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 21days 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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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 12, 2017: Journal of Structural Biology
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