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Journal of Structural Biology

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https://www.readbyqxmd.com/read/28193500/helical-reconstruction-in-relion
#1
Shaoda He, Sjors H W Scheres
We describe a new implementation for the reconstruction of helical assemblies in the empirical Bayesian framework of RELION. Our approach calculates optimal linear filters for the 3D reconstruction by embedding helical symmetry operators in Fourier-space, and deals with deviations from perfect helical symmetry through Gaussian-shaped priors on the orientations of individual segments. By incorporating our approach into the standard pipeline for single-particle analysis in RELION, our implementation aims to be easily accessible for non-experienced users...
February 10, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28192191/the-crystal-structure-of-the-hsp90-co-chaperone-cpr7-from-saccharomyces-cerevisiae
#2
Yu Qiu, Qiangqiang Ge, Mingxing Wang, Hui Lv, Mohammad Ebrahimi, Liwen Niu, Maikun Teng, Xu Li
The versatility of Hsp90 can be attributed to the variety of co-chaperone proteins that modulate the role of Hsp90 in many cellular processes. As a co-chaperone of Hsp90, Cpr7 is essential for accelerating the cell growth in an Hsp90-containing trimeric complex. Here, we report the crystal structure of Cpr7 at a resolution of 1.8 Å. It consists of an N-terminal PPI domain and a C-terminal TPR domain, and exhibits a U-shape conformation. Our studies revealed the aggregation state of Cpr7 in solution and the interaction properties between Cpr7 and the MEEVD sequence from the C-terminus of Hsp90...
February 9, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28189793/structures-of-a-glucose-tolerant-%C3%AE-glucosidase-provide-insights-into-its-mechanism
#3
Panjiao Pang, Li-Chuang Cao, Yu-Huan Liu, Wei Xie, Zhong Wang
Cellulose can be converted to ethanol via the fermentation of glucose, which is considered as a promising green alternative for transportation fuels. The conversion of cellulose to glucose needs three enzymes, in which β-glucosidase (BGL) plays an essential role. However, BGL is inhibited by its own product glucose, greatly limiting its applications in industry. We previously obtained a novel BGL named Bgl6 with a high glucose tolerance. Further engineering through random mutagenesis produced a triple mutant M3 with improved thermostability...
February 9, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28167161/structure-determination-of-contaminant-proteins-using-the-marathonmr-procedure
#4
Kaushik Hatti, Ansuman Biswas, Santosh Chaudhary, Venkatareddy Dadireddy, Kanagaraj Sekar, Narayanaswamy Srinivasan, Mathur R N Murthy
In the recent decades, essential steps of protein structure determination such as phasing by multiple isomorphous replacement and multi wave length anomalous dispersion, molecular replacement, refinement of the structure determined and its validation have been fully automated. Several computer program suites that execute all these steps as a pipeline operation have been made available. In spite of these great advances, determination of a protein structure may turn out to be a challenging task for a variety of reasons...
February 3, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28161413/relaxed-and-active-thin-filament-structures-a-new-structural-basis-for-the-regulatory-mechanism
#5
Danielle M Paul, John M Squire, Edward P Morris
The structures of muscle thin filaments reconstituted using skeletal actin and cardiac troponin and tropomyosin have been determined with and without bound Ca(2+) using electron microscopy and reference-free single particle analysis. The resulting density maps have been fitted with atomic models of actin, tropomyosin and troponin showing that: (i) the polarity of the troponin complex is consistent with our 2009 findings, with large shape changes in troponin between the two states; (ii) without Ca(2+) the tropomyosin pseudo-repeats all lie at almost equivalent positions in the 'blocked' position on actin (over subdomains 1 and 2); (iii) in the active state the tropomyosin pseudo-repeats are all displaced towards subdomains 3 and 4 of actin, but the extent of displacement varies within the regulatory unit depending upon the axial location of the pseudo-repeats with respect to troponin...
February 1, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28115258/cryo-em-analysis-of-a-domain-antibody-bound-rotary-atpase-complex
#6
Roberta B Davies, Callum Smits, Andrew Sw Wong, Daniela Stock, Mary Christie, Sara Sandin, Alastair G Stewart
The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has been extensively studied both structurally and functionally for many years. Here we provide an 8.7 Å resolution cryo-electron microscopy 3D reconstruction of this complex bound to single-domain antibody fragments, small monomeric antibodies containing just the variable heavy domain. Docking of known structures into the density revealed the molecular orientation of the domain antibodies, suggesting that structure determination of co-domain antibody:protein complexes could be a useful avenue for unstable or smaller proteins...
January 20, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28115257/higher-order-structures-in-purine-and-pyrimidine-metabolism
#7
REVIEW
Iva Chitrakar, Deborah M Kim-Holzapfel, Weijie Zhou, Jarrod B French
The recent discovery of several forms of higher order protein structures in cells has shifted the paradigm of how we think about protein organization and metabolic regulation in cells. These dynamic and controllable protein assemblies, which are composed of dozens or hundreds of copies of an enzyme or related enzymes, have emerged as important players in myriad cellular processes. We are only beginning to appreciate the breadth of function of these types of macromolecular assemblies. These higher order structures, which can be assembled in response to varied cellular stimuli including changing metabolite concentrations or signaling cascades, give the cell the capacity to modulate levels of biomolecules both temporally and spatially...
January 20, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28111328/on-the-geometry-of-regular-icosahedral-capsids-containing-disymmetrons
#8
Kai-Siang Ang, Laura P Schaposnik
Large icosahedral virus capsids are composed of symmetrons, organized arrangements of capsomers. There are three types of symmetrons: disymmetrons, trisymmetrons, and pentasymmetrons, which have different shapes and are centered on the icosahedral 2-fold, 3-fold and 5-fold axes of symmetry, respectively. Sinkovits and Baker (2010) gave a classification of all possible ways of building an icosahedral structure solely from trisymmetrons and pentasymmetrons, which requires the triangulation number T to be odd...
January 19, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28057518/structural-and-molecular-determinants-affecting-the-interaction-of-retinol-with-human-crbp1
#9
Ilaria Menozzi, Francesca Vallese, Eugenia Polverini, Claudia Folli, Rodolfo Berni, Giuseppe Zanotti
Four cellular retinol-binding protein (CRBP) types (CRBP1,2,3,4) are encoded in the human genome. Here, we report on X-ray analyses of human apo- and holo-CRBP1, showing nearly identical structures, at variance with the results of a recent study on the same proteins containing a His-Tag, which appears to be responsible for a destabilizing effect on the apoprotein. The analysis of crystallographic B-factors for our structures indicates that the putative portal region, in particular α-helix-II, along with Arg58 and the E-F loop, is the most flexible part of both apo- and holoprotein, consistent with its role in ligand uptake and release...
January 2, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28038834/robust-image-alignment-for-cryogenic-transmission-electron-microscopy
#10
Robert A McLeod, Julia Kowal, Philippe Ringler, Henning Stahlberg
Cryo-electron microscopy recently experienced great improvements in structure resolution due to direct electron detectors with improved contrast and fast read-out leading to single electron counting. High frames rates enabled dose fractionation, where a long exposure is broken into a movie, permitting specimen drift to be registered and corrected. The typical approach for image registration, with high shot noise and low contrast, is multi-reference (MR) cross-correlation. Here we present the software package Zorro, which provides robust drift correction for dose fractionation by use of an intensity-normalized cross-correlation and logistic noise model to weight each cross-correlation in the MR model and filter each cross-correlation optimally...
December 27, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/28025153/direct-observation-of-the-crystallographic-relationship-between-interlamellar-membranes-and-aragonite-tablets
#11
Jun Xu, Gangsheng Zhang
Nacre is one of the most attractive models for understanding the fundamental principles of biomineralization and for designing bio-inspired materials due to its simple structure but with unusual mechanical properties. It is made up of lamellae of aragonite tablets bonded together by the organic interlamellar membranes (ILMs), of which the latter occupy less than 5 wt% of nacre. For a long time, previous authors failed to directly observe the crystallographic relationship between the ILM and aragonite tablet...
December 23, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/28017791/conditions-to-minimize-soft-single-biomolecule-deformation-when-imaging-with-atomic-force-microscopy
#12
Christian Godon, Jean-Marie Teulon, Michael Odorico, Christian Basset, Matthieu Meillan, Luc Vellutini, Shu-Wen W Chen, Jean-Luc Pellequer
A recurrent interrogation when imaging soft biomolecules using atomic force microscopy (AFM) is the putative deformation of molecules leading to a bias in recording true topographical surfaces. Deformation of biomolecules comes from three sources: sample instability, adsorption to the imaging substrate, and crushing under tip pressure. To disentangle these causes, we measured the maximum height of a well-known biomolecule, the tobacco mosaic virus (TMV), under eight different experimental conditions positing that the maximum height value is a specific indicator of sample deformations...
December 22, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/28013022/nano-scale-actin-network-characterization-of-fibroblast-cells-lacking-functional-arp2-3-complex
#13
Karen L Anderson, Christopher Page, Mark F Swift, Praveen Suraneni, Mandy E W Janssen, Thomas D Pollard, Rong Li, Niels Volkmann, Dorit Hanein
Arp2/3 complex is thought to be the primary protrusive force generator in cell migration by controlling the assembly and turnover of the branched filament network that pushes the leading edge of moving cells forward. However, mouse fibroblasts without functional Arp2/3 complex migrate at rates similar to wild-type cells, contradicting this paradigm. We show by correlative fluorescence and large-scale cryo-tomography studies combined with automated actin-network analysis that the absence of functional Arp2/3 complex has profound effects on the nano-scale architecture of actin networks...
December 21, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/28007449/structural-studies-of-influenza-virus-rnps-by-electron-microscopy-indicate-molecular-contortions-within-np-supra-structures
#14
John R Gallagher, Udana Torian, Dustin M McCraw, Audray K Harris
Ribonucleoprotein (RNP) complexes of influenza viruses are composed of multiple copies of the viral nucleoprotein (NP) that can form filamentous supra-structures. RNPs package distinct viral genomic RNA segments of different lengths into pleomorphic influenza virions. RNPs also function in viral RNA transcription and replication. Different RNP segments have varying lengths, but all must be incorporated into virions during assembly and then released during viral entry for productive infection cycles. RNP structures serve varied functions in the viral replication cycle, therefore understanding their molecular organization and flexibility is essential to understanding these functions...
December 19, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27998708/conformations-of-jnk3%C3%AE-splice-variants-analyzed-by-hydrogen-deuterium-exchange-mass-spectrometry
#15
Ji Young Park, Youngjoo Yun, Ka Young Chung
c-Jun N-terminal kinases (JNKs) are members of the mitogen-activated protein kinase (MAPK) family that regulate apoptosis, inflammation, cytokine production, and metabolism. MAPKs undergo various splicing within their kinase domains. Unlike other MAPKs, JNKs have alternative splicing at the C-terminus, resulting in long and short variants. Functional or conformational effects due to the elongated C-terminal tail in the long splice variants have not been investigated nor has the conformation of the C-terminal tail been analyzed...
December 18, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27989794/synchronous-disruption-of-anisotropic-arrangement-of-the-osteocyte-network-and-collagen-apatite-in-melanoma-bone-metastasis
#16
Aiko Sekita, Aira Matsugaki, Takuya Ishimoto, Takayoshi Nakano
Cancer metastasis to bones increases the risk of fragility fracture by altering bone metabolism and disrupting bone structure. Osteocytes, which organize a dense network that is closely linked with the circumambient matrix, play a key role in regulation of bone microstructure and material properties. The aim of this study was to elucidate the influence of cancer metastasis on the organization of the osteocyte network and collagen/biological apatite (BAp) microstructure in the context of osteocyte/matrix coupling...
December 16, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27956128/the-hhoa-protease-from-synechocystis-sp-pcc-6803-novel-insights-into-structure-and-activity-regulation
#17
Michael Hall, Raik Wagner, Xuan Tam Lam, Christiane Funk, Karina Persson
Proteases play a vital role in the removal of proteins, which become damaged due to temperature or oxidative stress. Important to this process in the cyanobacterium Synechocystis sp. PCC6803 is the family of Deg/HtrA proteases; HhoA (sll1679), HhoB (sll1427) and HtrA (slr1204). While previous studies have elucidated the structures of Deg/HtrA proteases from Escherichia coli and from the chloroplast of the higher plant Arabidopsis thaliana, no structural data have been available for any Deg/HtrA protease from cyanobacteria, the evolutionary ancestor of the chloroplast...
December 9, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27940093/valve-microstructure-and-phylomineralogy-of-new-zealand-chitons
#18
B A Peebles, A M Smith, H G Spencer
The microstructure and mineralogy of chiton valves has been largely ignored in the literature and only described in 29 species to date. Eight species: Acanthochitona zelandica, Notoplax violacea (Family Acanthochitonidae, Suborder Acanthochitonina, Order Chitonida), Chiton glaucus, Onithochiton neglectus, Sypharochiton spelliserpentis, Sypharochiton sinclairi (Family Chitonidae, Suborder, Chitonina, Order Chitonida), Ischnochiton maorianus (Family Ischnochitonidae, Suborder Chitonina, Order Chitonida), and Leptochiton inquinatus (Family Leptochitonidae, Suborder Lepidopleurina, Order Lepidopleurida) were collected from the Otago Peninsula, South Island, New Zealand...
December 9, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27940092/crystal-structures-of-an-archaeal-thymidylate-kinase-from-sulfolobus-tokodaii-provide-insights-into-the-role-of-a-conserved-active-site-arginine-residue
#19
Ansuman Biswas, Arpit Shukla, R S K Vijayan, Jeyaraman Jeyakanthan, Kanagaraj Sekar
Thymidylate kinase (TMK) is a key enzyme that plays an important role in DNA synthesis. Therefore, it serves as an attractive therapeutic target for the development of antibacterial, antiparasitic and anticancer drugs. Herein, we report the biochemical characterization and crystal structure determination of thymidylate kinase from a hyperthermophilic organism Sulfolobus tokodaii (StTMK) in its apo and ADP-bound forms. Our study describes the first three-dimensional structure of an archaeal TMK. StTMK is a thermostable enzyme with optimum activity at 80°C...
December 9, 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27916726/recent-advances-in-electron-tomography
#20
EDITORIAL
Friedrich Förster, Abraham J Koster
No abstract text is available yet for this article.
February 2017: Journal of Structural Biology
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