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The Donald L. D. Caspar Structural Biology Symposium at Florida State University
Publication date: December 2017 Source:Journal of Structural Biology, Volume 200, Issue 3 Author(s): Piotr Fajer, Kenneth Taylor, Alexei Soares (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - December 14, 2017 Category: Biology Source Type: research

Structural characterization of ribT from Bacillus subtilis reveals it as a GCN5-related N-acetyltransferase
Publication date: Available online 11 December 2017 Source:Journal of Structural Biology Author(s): Ritika Srivastava, Amanpreet Kaur, Charu Sharma, Subramanian Karthikeyan In bacteria, biosynthesis of riboflavin occurs through a series of enzymatic steps starting with one molecule of GTP and two molecules of ribulose-5-phosphate. In Bacillus subtilis (B. subtilis) the genes (ribD/G, ribE, ribA, ribH and ribT) which are involved in riboflavin biosynthesis are organized in an operon referred as rib operon. All the genes of rib operon are characterized functionally except for ribT. The ribT gene with unknown function is fou...
Source: Journal of Structural Biology - December 12, 2017 Category: Biology Source Type: research

Structural changes of homodimers in the PDB
Publication date: Available online 9 December 2017 Source:Journal of Structural Biology Author(s): Ryotaro Koike, Takayuki Amemiya, Tatsuya Horii, Motonori Ota Protein complexes are involved in various biological phenomena. These complexes are intrinsically flexible, and structural changes are essential to their functions. To perform a large-scale automated analysis of the structural changes of complexes, we combined two original methods. An application, SCPC, compares two structures of protein complexes and decides the match of binding mode. Another application, Motion Tree, identifies rigid-body motions in various sizes...
Source: Journal of Structural Biology - December 10, 2017 Category: Biology Source Type: research

Studying assembly of the BAM complex in native membranes by cellular solid-state NMR spectroscopy
Publication date: Available online 29 November 2017 Source:Journal of Structural Biology Author(s): Cecilia Pinto, Deni Mance, Manon Julien, Mark Daniels, Markus Weingarth, Marc Baldus Significant progress has been made in obtaining structural insight into the assembly of the β-barrel assembly machinery complex (BAM). These crystallography and electron microscopy studies used detergent as a membrane mimetic and revealed structural variations in the central domain, BamA, as well as in the lipoprotein BamC. We have used cellular solid-state NMR spectroscopy to examine the entire BamABCDE complex in native outer membran...
Source: Journal of Structural Biology - December 9, 2017 Category: Biology Source Type: research

Comparative mechanical unfolding studies of spectrin domains R15, R16 and R17
Publication date: Available online 5 December 2017 Source:Journal of Structural Biology Author(s): Anna V. Glyakina, Ilya V. Likhachev, Nikolay K. Balabaev, Oxana V. Galzitskaya Spectrins belong to repetitive three-helix bundle proteins that have vital functions in multicellular organisms and are of potential value in nanotechnology. To reveal the unique physical features of repeat proteins we have studied the structural and mechanical properties of three repeats of chicken brain α-spectrin (R15, R16 and R17) at the atomic level under stretching at constant velocities (0.01, 0.05 and 0.1Å·ps–1) an...
Source: Journal of Structural Biology - December 6, 2017 Category: Biology Source Type: research

Photosome membranes merge and organize tending towards rhombohedral symmetry when light is emitted
Publication date: Available online 5 December 2017 Source:Journal of Structural Biology Author(s): Malika Ouldali, Virginie Maury, Gisèle Nicolas, Jean Lepault Polynoid worm elytra emit light when mechanically or electrically stimulated. Specialized cells, the photocytes, contain light emitting machineries, the photosomes. Successive stimulations induce light intensity variations and show a coupling within and between photosomes. Here, we describe, using electron tomography of cryo-substituted elytra and freeze-fracturing, the structural transition associated to light emission: undulating tubules come closer, organ...
Source: Journal of Structural Biology - December 6, 2017 Category: Biology Source Type: research

Correlative imaging reveals physiochemical heterogeneity of microcalcifications in human breast carcinomas
Publication date: Available online 6 December 2017 Source:Journal of Structural Biology Author(s): Jennie A.M.R. Kunitake, Siyoung Choi, Kayla X. Nguyen, Meredith M. Lee, Frank He, Daniel Sudilovsky, Patrick G. Morris, Maxine S. Jochelson, Clifford A. Hudis, David A. Muller, Peter Fratzl, Claudia Fischbach, Admir Masic, Lara A. Estroff Microcalcifications (MCs) are routinely used to detect breast cancer in mammography. Little is known, however, about their materials properties and associated organic matrix, or their correlation to breast cancer prognosis. We combine histopathology, Raman microscopy, and electron microscop...
Source: Journal of Structural Biology - December 6, 2017 Category: Biology Source Type: research

Automated tracing of helical assemblies from electron cryo-micrographs
Publication date: Available online 1 December 2017 Source:Journal of Structural Biology Author(s): Stefan T. Huber, Tanja Kuhm, Carsten Sachse Structure determination of helical specimens commonly requires datasets from thousands of micrographs often obtained by automated cryo-EM data acquisition. Interactive tracing of helical assemblies from such a number of micrographs is labor-intense and time-consuming. Here, we introduce an automated tracing tool MicHelixTrace that precisely locates helix traces from micrographs of rigid as well as very flexible helical assemblies with small numbers of false positives. The computer ...
Source: Journal of Structural Biology - December 2, 2017 Category: Biology Source Type: research

Studying the assembly of the BAM complex in native membranes by cellular solid-state NMR spectroscopy
Publication date: Available online 29 November 2017 Source:Journal of Structural Biology Author(s): Cecilia Pinto, Deni Mance, Manon Julien, Mark Daniels, Markus Weingarth, Marc Baldus Significant progress has been made in obtaining a structural insight into the assembly of the β-barrel assembly machinery complex (BAM). These crystallography and electron microscopy studies used detergent as a membrane mimetic and revealed structural variations in the central domain, BamA, as well as the lipoprotein BamC. We have used cellular solid-state NMR spectroscopy to examine the entire BamABCDE complex in native outer membrane...
Source: Journal of Structural Biology - November 30, 2017 Category: Biology Source Type: research

Direct Regulation of p190RhoGEF by Activated Rho and Rac GTPases.
Publication date: Available online 28 November 2017 Source:Journal of Structural Biology Author(s): Olugbenga Dada, Stephen Gutowski, Chad A. Brautigam, Zhe Chen, Paul C. Sternweis Rho family GTPases regulate a wide range of cellular processes. This includes cellular dynamics where three subfamilies, Rho, Rac, and Cdc42, are known to regulate cell shape and migration though coordinate action. Activation of Rho proteins largely depends on Rho Guanine nucleotide Exchange Factors (RhoGEFs) through a catalytic Dbl homology (DH) domain linked to a pleckstrin homology (PH) domain that subserves various functions. The PH domains...
Source: Journal of Structural Biology - November 29, 2017 Category: Biology Source Type: research

MRCZ – A file format for cryo-TEM data with fast compression
Publication date: Available online 23 November 2017 Source:Journal of Structural Biology Author(s): Robert A. McLeod, Ricardo Diogo Righetto, Andy Stewart, Henning Stahlberg The introduction of fast CMOS detectors is moving the field of transmission electron microscopy into the computer science field of big data. Automated data pipelines control the instrument and initial processing steps which imposes more onerous data transfer and archiving requirements. Here we conduct a technical demonstration whereby storage and read/write times are improved 10× at a dose rate of 1 e−/pix/frame for data from a Gatan K2 di...
Source: Journal of Structural Biology - November 28, 2017 Category: Biology Source Type: research

MRCZ - A file format for cryo-TEM data with fast compression
Publication date: Available online 23 November 2017 Source:Journal of Structural Biology Author(s): Robert A. McLeod, Ricardo Diogo Righetto, Andy Stewart, Henning Stahlberg The introduction of fast CMOS detectors is moving the field of transmission electron microscopy into the computer science field of big data. Automated data pipelines control the instrument and initial processing steps which imposes more onerous data transfer and archiving requirements. Here we conduct a technical demonstration whereby storage and read/write times are improved 10x at a dose rate of 1 e-/pix/frame for data from a Gatan K2 direct-detecti...
Source: Journal of Structural Biology - November 24, 2017 Category: Biology Source Type: research

Mapping of recent brachiopod microstructure: a tool for environmental studies
Publication date: Available online 23 November 2017 Source:Journal of Structural Biology Author(s): Facheng Ye, Gaia Crippa, Lucia Angiolini, Uwe Brand, GianCarlo Capitani, Maggie Cusack, Claudio Garbelli, Erika Griesshaber, Elizabeth Harper, Wolfgang Schmahl Shells of brachiopods are excellent archives for environmental reconstructions in the recent and distant past as their microstructure and geochemistry respond to climate and environmental forcings. We studied the morphology and size of the basic structural unit, the secondary layer fibre, of the shells of several extant brachiopod taxa to derive a model correlating m...
Source: Journal of Structural Biology - November 24, 2017 Category: Biology Source Type: research

Open Questions on the 3D Structures of Collagen Containing Vertebrate Mineralized Tissues: A Perspective
Publication date: Available online 22 November 2017 Source:Journal of Structural Biology Author(s): Ron Shahar, Steve Weiner Our current understanding of the structures of vertebrate mineralized tissues is largely based on light microscopy/histology and projections of 3D structures onto 2D planes using electron microscopy. We know little about the fine details of these structures in 3D at the length scales of their basic building blocks, the inherent variations of structure within a tissue and the cell-extracellular tissue interfaces. This limits progress in understanding tissue formation, relating structure to mechanical...
Source: Journal of Structural Biology - November 23, 2017 Category: Biology Source Type: research

Bone morphogenetic protein signaling through ACVR1 and BMPR1A negatively regulates bone mass along with alterations in bone composition
This study examined the effects of disrupting bone morphogenetic protein (BMP) signaling through BMP receptors on bone quantity and bone quality. More specifically, we disrupted two BMP receptors, Acvr1 and Bmpr1a, respectively, in Osterix-expressing osteogenic progenitor cells in mice. We examined the structural changes to the femora from 3-month old male and female conditional knockout (cKO) mice using micro-computed tomography (micro-CT) and histology, as well as compositional changes to both cortical and trabecular compartments of bone using Raman spectroscopy. We found that the deletion of Acvr1 and Bmpr1a, respective...
Source: Journal of Structural Biology - November 23, 2017 Category: Biology Source Type: research

New crystal forms of the integral membrane Escherichia coli quinol:fumarate reductase suggest that ligands control domain movement
Publication date: Available online 20 November 2017 Source:Journal of Structural Biology Author(s): C.A. Starbird, Thomas M. Tomasiak, Prashant K. Singh, Victoria Yankovskaya, Elena Maklashina, Michael Eisenbach, Gary Cecchini, T.M. Iverson Quinol:fumarate reductase (QFR) is an integral membrane protein and a member of the respiratory Complex II superfamily. Although the structure of Escherichia coli QFR was first reported almost twenty years ago, many open questions of catalysis remain. Here we report two new crystal forms of QFR, one grown from the lipidic cubic phase and one grown from dodecyl maltoside micelles. QFR c...
Source: Journal of Structural Biology - November 22, 2017 Category: Biology Source Type: research

Assessment of the Transmembrane Domain Structures in GPCR Dock 2013 Models
Publication date: Available online 21 November 2017 Source:Journal of Structural Biology Author(s): Ting Wang, Haiguang Liu, Yong Duan The community-wide blind prediction of G-protein coupled receptor (GPCR) structures and ligand docking has been conducted three times and the quality of the models was primarily assessed by the accuracy of ligand binding modes. The seven transmembrane (TM) helices of the receptors were taken as a whole; thus the model quality within the 7TM domains has not been evaluated. Here we evaluate the 7TM domain structures in the models submitted for the last round of prediction - GPCR Dock 2013. A...
Source: Journal of Structural Biology - November 22, 2017 Category: Biology Source Type: research

Development of a new protein labeling system to map subunits and domains of macromolecular complexes for electron microscopy
Publication date: Available online 21 November 2017 Source:Journal of Structural Biology Author(s): Zuben P. Brown, Takao Arimori, Kenji Iwasaki, Junichi Takagi Several gene fusion technologies have been successfully applied to label particular subunits or domains within macromolecular complexes to enable positional mapping of electron microscopy (EM) density maps, but exogenous fusion of a protein domain into the target polypeptide can cause unwanted structural and functional outcomes. Fab fragments from antibodies can be used as labeling reagents during EM visualization without gene manipulation of the target protein, b...
Source: Journal of Structural Biology - November 22, 2017 Category: Biology Source Type: research

Identification of interfaces involved in weak interactions with application to F-actin-aldolase rafts
Publication date: Available online 13 November 2017 Source:Journal of Structural Biology Author(s): Guiqing Hu, Dianne W. Taylor, Jun Liu, Kenneth A. Taylor Macromolecular interactions occur with widely varying affinities. Strong interactions form well defined interfaces but weak interactions are more dynamic and variable. Weak interactions can collectively lead to large structures such as microvilli via cooperativity and are often the precursors of much stronger interactions, e.g. the initial actin-myosin interaction during muscle contraction. Electron tomography combined with subvolume alignment and classification is an...
Source: Journal of Structural Biology - November 14, 2017 Category: Biology Source Type: research

Phylogenetic Analysis Predicts Structural Divergence for Proteobacterial ClpC Proteins
Publication date: Available online 10 November 2017 Source:Journal of Structural Biology Author(s): Justin M. Miller, Hamza Chaudhary, Justin D. Marsee Regulated proteolysis is required in all organisms for the removal of misfolded or degradation-tagged protein substrates in cellular quality control pathways. The molecular machines that catalyze this process are known as ATP-dependent proteases with examples that include ClpAP and ClpCP. Clp/Hsp100 subunits form ring-structures that couple the energy of ATP binding and hydrolysis to protein unfolding and subsequent translocation of denatured protein into the compartmental...
Source: Journal of Structural Biology - November 10, 2017 Category: Biology Source Type: research

Building the atomic model of a boreal lake virus of unknown fold in a 3.9  Å cryo-EM map
We report here the protocol adopted to build the atomic model of the newly discovered virus FLiP ( Flavobacterium infecting, lipid-containing phage) into 3.9 Å cryo-electron microscopy (cryo-EM) maps. In particular, this report discusses the combination of density modification procedures, automatic model building and bioinformatics tools applied to guide the tracing of the major capsid protein (MCP) of this virus. The protocol outlined here may serve as a reference for future structural determination by cryo-EM of viruses lacking detectable structural homologues. (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - November 8, 2017 Category: Biology Source Type: research

High-vacuum Optical Platform for cryo-CLEM (HOPE): a New Solution for Non-integrated Multiscale Correlative Light and Electron Microscopy
Publication date: Available online 4 November 2017 Source:Journal of Structural Biology Author(s): Shuoguo Li, Gang Ji, Yang Shi, Lasse Hyldgaard Klausen, Tongxin Niu, Shengliu Wang, Xiaojun Huang, Wei Ding, Xiang Zhang, Mingdong Dong, Wei Xu, Fei Sun Cryo-correlative light and electron microscopy (cryo-CLEM) offers a unique way to analyze the high-resolution structural information of cryo-vitrified specimen by cryo-electron microscopy (cryo-EM) with the guide of the search for unique events by cryo-fluorescence microscopy (cryo-FM). To achieve cryo-FM, a trade-off must be made between the temperature and performance of o...
Source: Journal of Structural Biology - November 5, 2017 Category: Biology Source Type: research

Marker-free method for accurate alignment between correlated light, cryo-light, and electron cryo-microscopy data using sample support features
Publication date: Available online 4 November 2017 Source:Journal of Structural Biology Author(s): Karen L. Anderson, Christopher Page, Mark F. Swift, Dorit Hanein, Niels Volkmann Combining fluorescence microscopy with electron cryo-tomography allows, in principle, spatial localization of tagged macromolecular assemblies and structural features within the cellular environment. To allow precise localization and scale integration between the two disparate imaging modalities, accurate alignment procedures are needed. Here, we describe a marker-free method for aligning images from light or cryo-light fluorescence microscopy a...
Source: Journal of Structural Biology - November 5, 2017 Category: Biology Source Type: research

Influence of Physical Activity on Tibial Bone Material Properties in Laying Hens
In this study, a comparison of bone material properties was made for lines of hens created by divergent selection to have high and low bone strength and housed in either individual cages, with restricted mobility, or in an aviary system, with opportunity for increased mobility. Improvement of bone biomechanics in the high line hens and in aviary housing was mainly due to increased bone mass, thicker cortical bone and more medullary bone. However, bone material properties such as cortical and medullary bone mineral composition and crystallinity as well as collagen maturity did not differ between lines. However, bone materia...
Source: Journal of Structural Biology - November 4, 2017 Category: Biology Source Type: research

Rational design of new materials using recombinant structural proteins: current state and future challenges
Publication date: Available online 31 October 2017 Source:Journal of Structural Biology Author(s): Tara D. Sutherland, Mickey G. Huson, Trevor D. Rapson Sequence-definable polymers are seen as a prerequisite for design of future materials, with many polymer scientists regarding such polymers as the holy grail of polymer science. Recombinant proteins are sequence-defined polymers. Proteins are dictated by DNA templates and therefore the sequence of amino acids in a protein is defined, and molecular biology provides tools that allow redesign of the DNA as required. Despite this advantage, proteins are underrepresented in ma...
Source: Journal of Structural Biology - November 1, 2017 Category: Biology Source Type: research

Building the atomic model of a boreal lake virus of unknown fold in a 3.9 Å cryo-EM map.
We report here the protocol adopted to build the atomic model of the newly discovered virus FLiP ( Flavobacterium infecting, lipid-containing phage) into 3.9 Å cryo-electron microscopy (cryo-EM) maps. In particular, this report discusses the combination of density modification procedures, automatic model building and bioinformatics tools applied to guide the tracing of the major capsid protein (MCP) of this newly discovered virus. The protocol outlined here may serve as a reference for future structural determination by cryo-EM of viruses lacking detectable structural homologues. Graphical abstract (Source: Journal o...
Source: Journal of Structural Biology - October 28, 2017 Category: Biology Source Type: research

Rapid increase of near atomic resolution virus capsid structures determined by cryo-electron microscopy
Publication date: Available online 27 October 2017 Source:Journal of Structural Biology Author(s): Phuong T. Ho, Vijay S. Reddy The recent technological advances in electron microscopes, detectors, as well as image processing and reconstruction software have brought single particle cryo-electron microscopy (cryo-EM) into prominence for determining structures of bio-molecules at near atomic resolution. This has been particularly true for virus capsids, ribosomes, and other large assemblies, which have been the ideal specimens for structural studies by cryo-EM approaches. An analysis of time series metadata of virus structu...
Source: Journal of Structural Biology - October 27, 2017 Category: Biology Source Type: research

Sup35NMp Morphology Evaluation on Au, Si, Formvar and Mica Surfaces Using AFM, SEM and TEM
Publication date: Available online 25 October 2017 Source:Journal of Structural Biology Author(s): P.A. Sokolov, S.A. Bondarev, M.V. Belousov, G.A. Zhouravleva, N.A. Kasyanenko Prion and some other incurable human neurodegenerative diseases are associated with misfolding of specific proteins, followed by the formation of amyloids. Despite the widespread usage of the transmission electron and of the atomic force microscopy for studing such amyloids, many related methodological issues still have not been studied until now. Here, we consider one of the first amyloids found in Saccharomyces cerevisiae yeast, i.e. Sup35NMp, to...
Source: Journal of Structural Biology - October 25, 2017 Category: Biology Source Type: research

Distinguishing signal from autofluorescence in cryogenic correlated light and electron microscopy of mammalian cells
Publication date: Available online 25 October 2017 Source:Journal of Structural Biology Author(s): Stephen D. Carter, Shrawan K. Mageswaran, Zachary J. Farino, João I. Mamede, Catherine M. Oikonomou, Thomas J. Hope, Zachary Freyberg, Grant J. Jensen In cryogenic correlated light and electron microscopy (cryo-CLEM), frozen targets of interest are identified and located on EM grids by fluorescence microscopy and then imaged at higher resolution by cryo-EM. Whilst working with these methods, we discovered that a variety of mammalian cells exhibit strong punctate autofluorescence when imaged under cryogenic conditions ...
Source: Journal of Structural Biology - October 25, 2017 Category: Biology Source Type: research

Crystallographic and enzymatic insights into the mechanisms of Mg-ADP inhibition in the A1 complex of the A1AO ATP synthase
Publication date: Available online 23 October 2017 Source:Journal of Structural Biology Author(s): Dhirendra Singh, Gerhard Grüber F-ATP synthases are described to have mechanisms which regulate the unnecessary depletion of ATP pool during an energy limited state of the cell. Mg-ADP inhibition is one of the regulatory features where Mg-ADP gets entrapped in the catalytic site, preventing the binding of ATP and further inhibiting ATP hydrolysis. Knowledge about the existence and regulation of the related archaeal-type A1AO ATP synthases (A3B3CDE2FG2 ac) is limited. We demonstrate MgADP inhibition of the enzymatically ...
Source: Journal of Structural Biology - October 24, 2017 Category: Biology Source Type: research

Top surface blade residues and the central channel water molecules are conserved in every repeat of the integrin-like β-propeller structures
Publication date: Available online 17 October 2017 Source:Journal of Structural Biology Author(s): Alexander Denesyuk, Konstantin Denessiouk, Mark S. Johnson An integrin-like β-propeller domain contains seven repeats of a four-stranded antiparallel β-sheet motif (blades). Previously we described a 3D structural motif within each blade of the integrin-type β-propeller. Here, we show unique structural links that join different blades of the β-propeller structure, which together with the structural motif for a single blade are repeated in a β-propeller to provide the functional top face of the barrel...
Source: Journal of Structural Biology - October 18, 2017 Category: Biology Source Type: research

Online Raman spectroscopy for Structural Biology on beamline ID29 of the ESRF
Publication date: Available online 16 October 2017 Source:Journal of Structural Biology Author(s): David von Stetten, Thierry Giraud, Soi Bui, Roberto A. Steiner, François Fihman, Daniele de Sanctis, Antoine Royant Raman spectroscopy can probe the structure and conformations of specific chemical groups within proteins and may thus be used as a technique complementary to X-ray crystallography. This combined approach can be decisive in resolving ambiguities in the interpretation of enzymatic or X-ray induced processes. Here, we present an online Raman setup developed at the European Synchrotron that allows for interl...
Source: Journal of Structural Biology - October 16, 2017 Category: Biology Source Type: research

RAZA: A Rapid 3D z-crossings Algorithm to segment electron tomograms and extract organelles and macromolecules
Publication date: Available online 13 October 2017 Source:Journal of Structural Biology Author(s): Rubbiya A. Ali, Ahmed M. Mehdi, Rosalba Rothnagel, Nicholas A. Hamilton, Christoph Gerle, Michael J. Landsberg, Ben Hankamer Resolving the 3D architecture of cells to atomic resolution is one of the most ambitious challenges of cellular and structural biology. Central to this process is the ability to automate tomogram segmentation to identify sub-cellular components, facilitate molecular docking and annotate detected objects with associated metadata. Here we demonstrate that RAZA (Rapid 3D z-crossings algorithm) provides a ...
Source: Journal of Structural Biology - October 14, 2017 Category: Biology Source Type: research

The Structure of the Actin-Smooth Muscle Myosin Motor Domain Complex in the Rigor State
Publication date: Available online 14 October 2017 Source:Journal of Structural Biology Author(s): Chaity Banerjee, Zhongjun Hu, Zhong Huang, J. Anthony Warrington, Dianne W. Taylor, Kathleen M. Trybus, Susan Lowey, Kenneth A. Taylor Myosin-based motility utilizes catalysis of ATP to drive the relative sliding of F-actin and myosin. The earliest detailed model based on cryo-electron microscopy (cryoEM) and X-ray crystallography postulated that higher actin affinity and lever arm movement were coupled to closure of a feature of the myosin head dubbed the actin-binding cleft. Several studies since then using crystallography...
Source: Journal of Structural Biology - October 14, 2017 Category: Biology Source Type: research

Classification of β-hairpin repeat proteins
Publication date: Available online 7 October 2017 Source:Journal of Structural Biology Author(s): Daniel B. Roche, Phuong Do Viet, Anastasia Bakulina, Layla Hirsh, Silvio C.E. Tosatto, Andrey V. Kajava In recent years, a number of new protein structures that possess tandem repeats have emerged. Many of these proteins are comprised of tandem arrays of β-hairpins. Today, the amount and variety of the data on these β-hairpin repeat (BHR) structures have reached a level that requires detailed analysis and further classification. In this paper, we classified the BHR proteins, compared structures, sequences of repeat ...
Source: Journal of Structural Biology - October 11, 2017 Category: Biology Source Type: research

Large scale three-dimensional reconstruction of an entire Caenorhabditis elegans larva using AutoCUTS-SEM
Publication date: Available online 1 October 2017 Source:Journal of Structural Biology Author(s): Xixia Li, Gang Ji, Xi Chen, Wei Ding, Lei Sun, Wei Xu, Hua Han, Fei Sun Large scale, high resolution three dimensional (3D) ultrastructural reconstruction of cells and tissues has become increasingly important to our understanding of complex biological systems. There have been a few partial 3D ultra-structures of Caenorhabditis elegans (C. elegans) reported, however 3D reconstruction of a whole nematode has never been achieved. Here, we independently developed a technique called automatic collector of ultrathin sections scann...
Source: Journal of Structural Biology - October 1, 2017 Category: Biology Source Type: research

Vaterite induced by Lysinibacillus sp. GW-2 strain and its stability
In this study, mineralization experiments using Lysinibacillus sp. strain GW-2 were carried out for 72h under shaking conditions and aging experiments using biotic and chemically synthesized vaterite were performed for 60days in distilled water and air. Our results indicate that Lysinibacillus sp. strain GW-2 can induce the formation of vaterite with spherical morphology from an amorphous calcium carbonate precursor. Biogenic vaterite was more stable than chemically synthesized vaterite in distilled water, perhaps due to organic matter secreted by bacteria that enwrapped the vaterite and prevented it from transforming into...
Source: Journal of Structural Biology - September 29, 2017 Category: Biology Source Type: research

Coupling between myosin head conformation and the thick filament backbone structure
Publication date: Available online 28 September 2017 Source:Journal of Structural Biology Author(s): Zhongjun Hu, Dianne W. Taylor, Robert J. Edwards, Kenneth A. Taylor The recent high-resolution structure of the thick filament from Lethocerus asynchronous flight muscle shows aspects of thick filament structure never before revealed that may shed some light on how striated muscles function. The phenomenon of stretch activation underlies the function of asynchronous flight muscle. It is most highly developed in flight muscle, but is also observed in other striated muscles such as cardiac muscle. Although stretch activation...
Source: Journal of Structural Biology - September 28, 2017 Category: Biology Source Type: research

Vaterite induced by Lysinibacillus sp. GW –2 strain and its stability
In this study, mineralization experiments using Lysinibacillus sp. strain GW-2 were carried out for 72 h under shaking conditions and aging experiments using biotic and chemically synthesized vaterite were performed for 60 days in distilled water and air. Our results indicate that Lysinibacillus sp. strain GW-2 can induce the formation of vaterite with spherical morphology from an amorphous calcium carbonate precursor. Biogenic vaterite was more stable than chemically synthesized vaterite in distilled water, perhaps due to organic matter secreted by bacteria that enwrapped the vaterite and prevented it from transforming in...
Source: Journal of Structural Biology - September 25, 2017 Category: Biology Source Type: research

Self-assembly of repeat proteins: Concepts and design of new interfaces
We describe an experimental approach to form higher order architectures by a bottom-up assembly of repeated building blocks. For this purpose, we use designed consensus tetratricopeptide repeat proteins (CTPRs). CTPR arrays contain multiple identical repeats that interact through a single inter-repeat interface to form elongated superhelices. Introducing a novel interface along the CTPR superhelix allows two CTPR molecules to assemble into protein nanotubes. We apply three approaches to form protein nanotubes: electrostatic interactions, hydrophobic interactions, and π-π interactions. We isolate and characterize the ...
Source: Journal of Structural Biology - September 23, 2017 Category: Biology Source Type: research

Common Lines Modeling for Reference Free Ab-Initio Reconstruction in Cryo-EM
Publication date: Available online 21 September 2017 Source:Journal of Structural Biology Author(s): Ido Greenberg, Yoel Shkolnisky We consider the problem of estimating an unbiased and reference-free ab-inito model for non-symmetric molecules from images generated by single-particle cryo-electron microscopy. The proposed algorithm finds the globally optimal assignment of orientations that simultaneously respects all common lines between all images. The contribution of each common line to the estimated orientations is weighted according to a statistical model for common lines’ detection errors. The key property of t...
Source: Journal of Structural Biology - September 22, 2017 Category: Biology Source Type: research

Polyglutamine expansion diseases: More than simple repeats
Publication date: Available online 18 September 2017 Source:Journal of Structural Biology Author(s): Alexandra Silva, Ana Viana de Almeida, Sandra Macedo-Ribeiro Polyglutamine (polyQ) repeat-containing proteins are widespread in the human proteome but only nine of them are associated with highly incapacitating neurodegenerative disorders. The genetic expansion of the polyQ tract in disease-related proteins triggers a series of events resulting in neurodegeneration. The polyQ tract plays the leading role in the aggregation mechanism, but other elements modulate the aggregation propensity in the context of the full-length p...
Source: Journal of Structural Biology - September 20, 2017 Category: Biology Source Type: research

Calcified cartilage or bone? Collagens in the tessellated endoskeletons of cartilaginous fish (sharks and rays)
Publication date: Available online 18 September 2017 Source:Journal of Structural Biology Author(s): Ronald Seidel, Michael Blumer, Elisabeth-Judith Pechriggl, Kady Lyons, Brian K. Hall, Peter Fratzl, James C. Weaver, Mason N. Dean The primary skeletal tissue in elasmobranchs –sharks, rays and relatives– is cartilage, forming both embryonic and adult endoskeletons. Only the skeletal surface calcifies, exhibiting mineralized tiles (tesserae) sandwiched between a cartilage core and overlying fibrous perichondrium. These two tissues are based on different collagens (Coll II and I, respectively), fueling a long-st...
Source: Journal of Structural Biology - September 20, 2017 Category: Biology Source Type: research

Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase from Cryptococcus neoformans
In this study, we determined a crystal structure of the apo-form of CnIpk1 at 2.35 Å resolution, the first structure for a fungal Ipk1, using a single-wavelength anomalous dispersion method. Even with a low sequence similarity of 26-28%, its overall structure resembles two other Ipk1 orthologs from Arabidopsis thaliana (AtIpk1) and Mus musculus (MmIpk1), and the most crucial residues in the active site are conserved. Unlike AtIpk1 and MmIpk1, however, metal-binding sites for structural stabilization and conformational variations are absent in CnIpk1. The binding environments for substrate IP5 could be inferred by the...
Source: Journal of Structural Biology - September 16, 2017 Category: Biology Source Type: research

Alpha repeat proteins ( αRep) as expression and crystallization helpers
Publication date: Available online 16 August 2017 Source:Journal of Structural Biology Author(s): 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 pr...
Source: Journal of Structural Biology - September 8, 2017 Category: Biology Source Type: research

Elfin: an algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks
Publication date: Available online 7 September 2017 Source:Journal of Structural Biology Author(s): Chun-Ting Yeh, T.J. Brunette, David Baker, Simon McIntosh-Smith, Fabio Parmeggiani Computational protein design methods have enabled the design of novel protein structures, but they are often still limited to small proteins and symmetric systems. To expand the size of designable proteins while controlling the overall structure, we developed Elfin, a genetic algorithm for the design of novel proteins with custom shapes using structural building blocks derived from experimentally verified repeat proteins. By combining buildin...
Source: Journal of Structural Biology - September 8, 2017 Category: Biology Source Type: research

Intermediate Filament Structure in Fully Differentiated (Oxidised) Trichocyte Keratin
Publication date: Available online 8 September 2017 Source:Journal of Structural Biology Author(s): R.D. Bruce Fraser, David A.D. Parry For the past 50 years there has been considerable debate over the sub-structure of the fully differentiated (oxidised) trichocyte keratin intermediate filament. Depending on the staining and preparative procedures employed, IF observed in transverse section in the transmission electron microscope have varied in appearance between that of a “ring” and a “ring-core” structure, corresponding to the so-called (8+0) and (7+1) protofilament arrangements. In a new analysi...
Source: Journal of Structural Biology - September 8, 2017 Category: Biology Source Type: research

The repeat structure of two paralogous genes, Yersinia ruckeri Invasin (yrInv) and a “Y. ruckeri Invasin-like molecule”, (yrIlm) sheds light on the evolution of adhesive capacities of a fish pathogen
Publication date: Available online 6 September 2017 Source:Journal of Structural Biology Author(s): Agnieszka Wrobel, Claudio Ottoni, Jack C. Leo, Snorre Gulla, Dirk Linke Inverse autotransporters comprise the recently identified type Ve secretion system and are exemplified by intimin from enterohaemorrhagic Escherichia coli and invasin from enteropathogenic Yersiniae. These proteins share a common domain architecture and promote bacterial adhesion to host cells. Here, we identified and characterized two putative inverse autotransporter genes in the fish pathogen Yersinia ruckeri NVH_1, namely yrInv (for Y. ruckeri invasi...
Source: Journal of Structural Biology - September 7, 2017 Category: Biology Source Type: research

Structural analysis of phosphatidylinositol 4-kinase III β (PI4KB) – 14-3-3 protein complex reveals internal flexibility and explains 14-3-3 mediated protection from degradation in vitro
Publication date: Available online 31 August 2017 Source:Journal of Structural Biology Author(s): Dominika Chalupska, Andrea Eisenreichova, Bartosz Różycki, Lenka Rezabkova, Jana Humpolickova, Martin Klima, Evzen Boura Phosphatidylinositol 4-kinase IIIβ (PI4KB) is responsible for the synthesis of the Golgi and trans-Golgi network (TGN) pool of phosphatidylinositol 4-phospahte (PI4P). PI4P is the defining lipid hallmark of Golgi and TGN and also serves as a signaling lipid and as a precursor for higher phosphoinositides. In addition, PI4KB is hijacked by many single stranded plus RNA (+RNA) viruses to generate...
Source: Journal of Structural Biology - September 2, 2017 Category: Biology Source Type: research

Structural analysis of phosphatidylinositol 4-kinase III β (PI4KB) - 14-3-3 protein complex reveals internal flexibility and explains 14-3-3 mediated protection from degradation in vitro
Publication date: Available online 31 August 2017 Source:Journal of Structural Biology Author(s): Dominika Chalupska, Andrea Eisenreichova, Bartosz Różycki, Lenka Rezabkova, Jana Humpolickova, Martin Klima, Evzen Boura Phosphatidylinositol 4-kinase IIIβ (PI4KB) is responsible for the synthesis of the Golgi and trans-Golgi network (TGN) pool of phosphatidylinositol 4-phospahte (PI4P). PI4P is the defining lipid hallmark of Golgi and TGN and also serves as a signaling lipid and as a precursor for higher phosphoinositides. In addition, PI4KB is hijacked by many single stranded plus RNA (+RNA) viruses to generate...
Source: Journal of Structural Biology - September 1, 2017 Category: Biology Source Type: research