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Journal of Structural Biology

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) and constant forces (700 and900pN) using molecular dynamics (MD) simulations at T = 300K...
December 5, 2017: Journal of Structural Biology
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 microscopy to image MCs within snap-frozen human breast tissue and generate micron-scale resolution correlative maps of crystalline phase, trace metals, particle morphology, and organic matrix chemical signatures within high grade ductal carcinoma in situ (DCIS) and invasive cancer...
December 5, 2017: Journal of Structural Biology
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, organize and their number forming photosomes increases...
December 4, 2017: Journal of Structural Biology
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 membranes and obtained data on the BamCDE subcomplex in outer membranes, in addition to synthetic bilayers...
November 29, 2017: Journal of Structural Biology
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 from Lbc RhoGEFs, which specifically activate RhoA, have been shown to bind to activated RhoA...
November 28, 2017: Journal of Structural Biology
Stefan 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 program is fast and has low computational requirements...
November 27, 2017: Journal of Structural Biology
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 microstructural patterns to environmental conditions. Twenty-one adult specimens of six recent brachiopod species adapted to different environmental conditions, from Antarctica, to New Zealand, to the Mediterranean Sea, were chosen for microstructural analysis using SEM, TEM and EBSD...
November 23, 2017: Journal of Structural Biology
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-detection device by combination of integer decimation and lossless compression...
November 23, 2017: Journal of Structural Biology
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 and metabolic functions, and obtaining deeper insights into pathologies and the evolution of these tissues...
November 22, 2017: Journal of Structural Biology
Ce Shi, Gurjit S Mandair, Honghao Zhang, Gloria G Vanrenterghem, Ryan Ridella, Akira Takahashi, Yanshuai Zhang, David H Kohn, Michael D Morris, Yuji Mishina, Hongchen Sun
Bone quantity and bone quality are important factors in determining the properties and the mechanical functions of bone. 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...
November 22, 2017: Journal of Structural Biology
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. Applying the 7 × 7 RMSD matrix analysis described in our prior work, we show that the models vary widely in prediction accuracy of the 7TM structures, exhibiting diverse structural differences from the targets...
November 21, 2017: Journal of Structural Biology
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, but this method requires a panel of high-affinity antibodies that recognize a wide variety of epitopes...
November 20, 2017: Journal of Structural Biology
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 crystals grown from the lipid cubic phase processed as P1, merged to 7.5 Å resolution, and exhibited crystal packing similar to previous crystal forms...
November 17, 2017: Journal of Structural Biology
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 ideal method for the study of weak interactions because a 3-D image is obtained for the individual interactions, which subsequently are characterized collectively...
November 13, 2017: Journal of Structural Biology
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 compartmentalized ClpP protease for degradation...
November 9, 2017: Journal of Structural Biology
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 and from electron cryo-microscopy that takes advantage of sample support features, namely the holes in the carbon film...
November 4, 2017: Journal of Structural Biology
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 objective lens. The temperature of specimen should be kept below devitrification while the distance between the objective lens and specimen should be short enough for high resolution imaging...
November 4, 2017: Journal of Structural Biology
A B Rodriguez-Navarro, H M McCormack, R H Fleming, P Alvarez-Lloret, J Romero-Pastor, N Dominguez-Gasca, Tanya Prozorov, I C Dunn
Laying hens develop a type of osteoporosis that arises from a loss of structural bone, resulting in high incidence of fractures. 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...
November 3, 2017: Journal of Structural Biology
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 materials science. In this publication we investigate the advantages and limitations of using proteins as templates for rational design of new materials...
October 30, 2017: Journal of Structural Biology
Luigi De Colibus, David I Stuart
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...
October 27, 2017: Journal of Structural Biology
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