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Journal of Structural Biology

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https://www.readbyqxmd.com/read/30321594/comparing-cryo-em-structures
#1
EDITORIAL
Catherine L Lawson, Wah Chiu
No abstract text is available yet for this article.
October 12, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30312643/structural-insights-into-the-specificity-and-catalytic-mechanism-of-mycobacterial-nucleotide-pool-sanitizing-enzyme-mutt2
#2
Amandeep Singh, Sheikh Mohammad Arif, Pau Biak Sang, Umesh Varshney, M Vijayan
Mis-incorporation of modified nucleotides, such as 5-methyl-dCTP or 8-oxo-dGTP, in DNA can be detrimental to genomic integrity. MutT proteins are sanitization enzymes which function by hydrolyzing such nucleotides and regulating the pool of free nucleotides in the cytoplasm. Mycobacterial genomes have a set of four MutT homologs, namely, MutT1, MutT2, MutT3 and MutT4. Mycobacterial MutT2 hydrolyzes 5m-dCTP and 8-oxo-dGTP to their respective monophosphate products. Additionally, it can hydrolyze canonical nucleotides dCTP and CTP, with a suggested role in sustaining their optimal levels in the nucleotide pool...
October 9, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30296492/using-scipion-for-stream-image-processing-at-cryo-em-facilities
#3
J Gómez-Blanco, J M de la Rosa-Trevín, R Marabini, L Del Cano, A Jiménez, M Martínez, R Melero, T Majtner, D Maluenda, J Mota, Y Rancel, E Ramírez-Aportela, J L Vilas, M Carroni, S Fleischmann, E Lindahl, A W Ashton, M Basham, D K Clare, K Savage, C A Siebert, G G Sharov, C O S Sorzano, P Conesa, J M Carazo
Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed a modular workflow system called Scipion (de la Rosa-Trevín et al., 2016). We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detailed evaluation of the data quality before the acquisition is finished...
October 5, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30287387/crystal-structure-of-a-biliverdin-bound-phycobiliprotein-interdependence-of-oligomerization-and-chromophorylation
#4
Juan Pablo Fuenzalida-Werner, Robert Janowski, Kanuj Mishra, Ina Weidenfeld, Dierk Niessing, Vasilis Ntziachristos, Andre C Stiel
Small, ultra-red fluorescence protein (smURFP) introduces the non-native biliverdin (BV) chromophore to phycobiliproteins (PBPs), allowing them to be used as transgenic labels for in vivo mammalian imaging. Presently, no structural information exists for PBPs bound to the non-native BV chromophore, which limits the further development of smURFP and related proteins as imaging labels or indicators. Here we describe the first crystal structure of a PBP bound to BV. The structures of smURFP-Y56R with BV and smURFP-Y56F without BV reveal unique oligomerization interfaces different from those in wild-type PBPs bound to native chromophores...
October 1, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30287386/tailored-disorder-in-calcite-organization-in-tergite-cuticle-of-the-supralittoral-isopod-tylos-europaeus-arcangeli-1938
#5
Bastian H M Seidl, Erika Griesshaber, Helge-Otto Fabritius, Christian Reisecker, Sabine Hild, Stefano Taiti, Wolfgang W Schmahl, Andreas Ziegler
The crustacean cuticle forms skeletal elements consisting of chitin-protein fibrils reinforced by amorphous and crystalline calcium carbonate and phosphate minerals. The edges of skeletal elements are of particular interest. They are subject to repeated strain and stress because they form transitions to the arthrodial membranes connecting them. These allow for relative movements of skeletal elements. In this study, we investigate structure, chemical composition, mineral organization and local mechanical properties of the anterior and posterior edges of the tergite cuticle in the conglobating beach isopod Tylos europaeus and compare these with the protective dorsal region of the tergites...
October 1, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30273658/map-challenge-analysis-using-a-pair-comparison-method-based-on-fourier-shell-correlation
#6
R Marabini, M Kazemi, C O S Sorzano, J M Carazo
This document presents the analysis performed over the Map Challenge dataset using a new algorithm which we refer to as Pair Comparison Method. The new algorithm, which is described in detail in the text, is able to sort reconstructions based on a figure of merit and assigns a level of significance to the sorting. That is, it shows how likely the sorting is due to chance or if it reflects real differences.
September 28, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30273657/dnp-nmr-of-biomolecular-assemblies
#7
Kristaps Jaudzems, Tatyana Polenova, Guido Pintacuda, Hartmut Oschkinat, Anne Lesage
Dynamic Nuclear Polarization (DNP) is an effective approach to alleviate the inherently low sensitivity of solid-state NMR (ssNMR) under magic angle spinning (MAS) towards large-sized multi-domain complexes and assemblies. DNP relies on a polarization transfer at cryogenic temperatures from unpaired electrons to adjacent nuclei upon continuous microwave irradiation. This is usually made possible via the addition in the sample of a polarizing agent. The first pioneering experiments on biomolecular assemblies were reported in the early 2000s on bacteriophages and membrane proteins...
September 28, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30266596/structural-characterization-of-the-sporulation-protein-germ-from-bacillus-subtilis
#8
Jennyfer Trouve, Ahmed Mohamed, Francisco Leisico, Carlos Contreras-Martel, Bowen Liu, Caroline Mas, David Z Rudner, Christopher D A Rodrigues, Cecile Morlot
The Gram-positive bacterium Bacillus subtilis responds to starvation by entering a morphological differentiation process leading to the formation of a highly resistant spore. Early in the sporulation process, the cell asymmetrically divides into a large compartment (the mother cell) and a smaller one (the forespore), which will maturate into a resistant spore. Proper development of the forespore requires the assembly of a multiprotein complex called the SpoIIIA-SpoIIQ complex or "A-Q complex". This complex involves the forespore protein SpoIIQ and eight mother cell proteins (SpoIIIAA to SpoIIIAH), many of which share structural similarities with components of specialized secretion systems and flagella found in Gram-negative bacteria...
September 25, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30261282/fast-multiscale-reconstruction-for-cryo-em
#9
Laurène Donati, Masih Nilchian, Carlos Oscar S Sorzano, Michael Unser
We present a multiscale reconstruction framework for single-particle analysis (SPA). The representation of three-dimensional (3D) objects with scaled basis functions permits the reconstruction of volumes at any desired scale in the real-space. This multiscale approach generates interesting opportunities in SPA for the stabilization of the initial volume problem or the 3D iterative refinement procedure. In particular, we show that reconstructions performed at coarse scale are more robust to angular errors and permit gains in computational speed...
September 24, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30248462/direct-evidence-supporting-the-existence-of-a-helical-dislocation-in-protofilament-packing-in-the-intermediate-filaments-of-oxidized-trichocyte-keratin
#10
R D Bruce Fraser, David A D Parry
The X-ray diffraction patterns of quill and hair, as well as other trichocyte keratin appendages, contain meridional reflections that can be indexed on an axial repeat of 470 Å. Unusually, however, many of the expected orders are not observed. A possible explanation, proposed by Fraser and MacRae (1983), was that the intermediate filaments (IF) that constitute the fibrillar component of the filament/matrix texture consist of 4-chain protofilaments arranged on a surface lattice subject to a helical dislocation...
September 21, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30244006/structural-modulation-of-a-periplasmic-sugar-binding-protein-probes-into-its-evolutionary-ancestry
#11
Suman Pandey, Prashant S Phale, Prasenjit Bhaumik
Substrate-binding proteins (SBPs) are periplasmic proteins consisting of two α/β domains joined by a hinge region with specificity towards cognate ligands. Based on three-dimensional fold, sugar-specific SBPs have been classified into cluster B and cluster D-I. The analysis of sequences and structures of sugar-binding pocket of cluster D-I SBPs revealed the presence of extra residues on two loops (L1, L2) and a helix (H1) in few members of this family, that binds specifically to monosaccharides. Presence of conserved histidine in L2 and tryptophan in H1 can be considered as the identity marks for the cluster D-I monosaccharide-binding SBPs...
September 20, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30237066/automation-and-assessment-of-de-novo-modeling-with-pathwalking-in-near-atomic-resolution-cryoem-density-maps
#12
Muyuan Chen, Matthew L Baker
With the rapidly growing number of macromolecular structures solved to near-atomic resolution using electron cryomicroscopy (cryoEM), map interpretation and model building directly from the density without the use of structural templates has become increasingly important. As part of the 2015/2016 Map and Model Challenge, we attempted to assess our latest de novo modeling tool, Pathwalking, in terms of performance and usability, as well as identify areas for future improvements. In total, we applied Pathwalking to six density maps between 3 and 4...
September 17, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30205196/advances-in-instrumentation-and-methodology-for-solid-state-nmr-of-biological-assemblies
#13
Rachel W Martin, John E Kelly, Jessica I Kelz
Many advances in instrumentation and methodology have furthered the use of solid-state NMR as a technique for determining the structures and studying the dynamics of molecules involved in complex biological assemblies. Solid-state NMR does not require large crystals, has no inherent size limit, and with appropriate isotopic labeling schemes, supports solving one component of a complex assembly at a time. It is complementary to cryo-EM, in that it provides local, atomic-level detail that can be modeled into larger-scale structures...
September 8, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30194983/polyserine-repeats-promote-coiled-coil-mediated-fibril-formation-and-length-dependent-protein-aggregation
#14
Elena Lilliu, Veronica Villeri, Ilaria Pelassa, Federico Cesano, Domenica Scarano, Ferdinando Fiumara
Short polyserine (polyS) repeats are frequently found in proteins and longer ones are produced in neurological disorders such as Huntington disease (HD) owing to translational frameshifting or non-ATG-dependent translation, together with polyglutamine (polyQ) and polyalanine (polyA) repeats, forming intracellular aggregates. However, the physiological and pathological structures of polyS repeats are not clearly understood. Early studies highlighted their structural versatility, similar to other homopolymers whose conformation is influenced by the surrounding protein context...
September 6, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30179659/structural-flexibility-in-the-helicobacter-pylori-peptidyl-prolyl-cis-trans-isomerase-hp0175-is-achieved-through-an-extension-of-the-chaperone-helices
#15
Ayat Yaseen, Gerald F Audette
Helicobacter pylori infects the gastric epithelium of half the global population, where infections can persist into adenocarcinomas and peptic ulcers. H. pylori secretes several proteins that lend to its pathogenesis and survival including VacA, CagA, γ-glutamyltransferase and HP0175. HP0175, also known as HpCBF2, classified as a peptidyl-prolyl cis,trans-isomerase, has been shown to induce apoptosis through a cascade of mechanisms initiated though its interaction with toll like receptor 4 (TLR4). Here, we report the structure of apo-HP0175 at 2...
September 1, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30145327/a-new-algorithm-for-high-resolution-reconstruction-of-single-particles-by-electron-microscopy
#16
C O S Sorzano, J Vargas, J M de la Rosa-Trevín, A Jiménez, D Maluenda, R Melero, M Martínez, E Ramírez-Aportela, P Conesa, J L Vilas, R Marabini, J M Carazo
The Map Challenge organized by the Electron Microscopy Data Bank has prompted the development of an Xmipp high resolution reconstruction protocol (which we will refer to as highres) that is integrated in the software platform Scipion. In this work we describe the details of the image angular alignment and map reconstruction steps in our new method. This algorithm is similar to the standard projection matching approach with some important modifications, especially in the area of detecting significant features in the reconstructed volume...
August 24, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30144506/assessment-of-structural-features-in-cryo-em-density-maps-using-sse-and-side-chain-z-scores
#17
Grigore Pintilie, Wah Chiu
We introduce a new method for assessing resolvability of structural features in density maps from Cryo-Electron Microscopy (Cryo-EM) using fitted or derived models. It calculates Z-scores for secondary structure elements (SSEs) and side chains. Z-scores capture how much larger the cross-correlation score (CCS) is for atoms in such features at their placed locations compared to the CCS at displaced positions. Z-scores are larger when the structural features are well-resolved, as confirmed by visual analysis...
August 23, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30125694/structural-behavior-of-keratin-associated-protein-8-1-in-human-hair-as-revealed-by-a-monoclonal-antibody
#18
Hiroki Akiba, Emina Ikeuchi, Javkhlan Ganbat, Hiroki Fujikawa, Osamu Arai-Kusano, Hiroko Iwanari, Makoto Nakakido, Takao Hamakubo, Yutaka Shimomura, Kouhei Tsumoto
Keratin-associated protein 8.1 (KAP8.1) is a hair protein whose structure, biochemical roles, and protein distribution patterns have not been well characterized. In this study, we generated a monoclonal antibody against human KAP8.1 to analyze the protein's roles and distribution in the human hair shaft. Using this antibody, we revealed that KAP8.1 was predominantly expressed in discrete regions of the keratinizing zone of the hair shaft cortex. The protein expression patterns paralleled the distribution of KAP8...
August 18, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30125693/structural-and-functional-analyses-of-calcium-ion-response-factors-in-the-mantle-of-pinctada-fucata
#19
Akihiro Matsuura, Ko Yoshimura, Hiroyuki Kintsu, Takashi Atsumi, Yasushi Tsuchihashi, Takeshi Takeuchi, Noriyuki Satoh, Lumi Negishi, Shohei Sakuda, Tomiko Asakura, Yuki Imura, Etsuro Yoshimura, Michio Suzuki
The pearl oyster, Pinctada fucata, is cultured for pearl production in Japan. The shell of the pearl oyster consists of calcium carbonate and a small amount of organic matrix. Despite many studies of the shell matrix proteins, the mechanism by which calcium elements are transported from the mantle to the shell remains unclear. Investigating the molecular mechanism of calcium transportation, we prepared artificial seawater with a high concentration of calcium ions (10ASW) to induce calcification in the pearl oyster...
August 17, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/30125692/the-analysis-of-subtle-internal-communications-through-mutation-studies-in-periplasmic-metal-uptake-protein-clas-znua2
#20
Gunjan Saini, Nidhi Sharma, Vikram Dalal, Ashish Warghane, Dilip Kumar Ghosh, Pravindra Kumar, Ashwani Kumar Sharma
The subtle internal communications through an intricate network of interactions play a key role in metal-binding and release in periplasmic metal uptake proteins of cluster A-I family, a component of ABC transport system. These proteins have evolved different mechanisms of metal-binding and release through sequence and thereby structure-function divergence. The CLas-ZnuA2 from Candidatus Liberibacter asiaticus (CLA), in previous studies, showed a lower metal-binding affinity. The subtle communications within and between domains from crystal structure analysis revealed that protein seems to prefer a metal-free state...
August 17, 2018: Journal of Structural Biology
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