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Journal of Structural Biology

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
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
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
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
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
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
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
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
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
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
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
Friedrich Förster, Abraham J Koster
No abstract text is available yet for this article.
December 1, 2016: Journal of Structural Biology
Ahmad Ali-Ahmad, Marie-Line Garron, Véronique Zamboni, Nicolas Lenfant, Didier Nurizzo, Bernard Henrissat, Jean-Guy Berrin, Yves Bourne, Florence Vincent
Bacteria from the human gut are equipped with an arsenal of carbohydrate-active enzymes that degrade dietary and host-derived glycans. In this study, we present the 2.5Å resolution crystal structure of a member (GH39wh2) from the human gut bacteria Bacteroides cellulosilyticus WH2 representative of a new subgroup within family GH39. Together with 6 other GHs, GH39wh2 belongs to a polysaccharide utilization locus (PUL) that could be involved in detecting, binding and hydrolysing a specific carbohydrate species from the intestinal tract...
November 24, 2016: Journal of Structural Biology
Stefan A Arnold, Stefan Albiez, Andrej Bieri, Anastasia Syntychaki, Ricardo Adaixo, Robb A McLeod, Kenneth N Goldie, Henning Stahlberg, Thomas Braun
We present a sample preparation method for cryo-electron microscopy (cryo-EM) that requires only 3 to 20 nanoliters of sample to prepare a cryo-EM grid, depending on the protocol used. The sample is applied and spread on the grid by a microcapillary. The procedure does not involve any blotting steps, and real-time monitoring allows the water film thickness to be assessed and decreased to an optimum value prior to vitrification. We demonstrate that the method is suitable for high-resolution cryo-EM and will enable alternative electron microscopy approaches, such as single-cell visual proteomics...
November 15, 2016: Journal of Structural Biology
Rui Yan, Kunpeng Li, Wen Jiang
Minimization of the astigmatism of the objective lens is a critical daily instrument alignment task essential for high resolution TEM imaging. Fast and sensitive detection of astigmatism is needed to provide real-time feedback and adjust the stigmators to efficiently reduce astigmatism. Currently the method used by many microscopists isto visually examine the roundness of a diffractogram (Thon rings) and iteratively adjust the stigmators to make the Thon rings circular. This subjective method is limited by poor sensitivity and potentially biased by the astigmatism of human eyes...
November 9, 2016: Journal of Structural Biology
María L Cerutti, Lisandro H Otero, Clara Smal, Leonardo Pellizza, Fernando A Goldbaum, Sebastián Klinke, Martín Aran
The Pfam PF04536 TPM_phosphatase family is a broadly conserved family of domains found across prokaryotes, plants and invertebrates. Despite having a similar protein fold, members of this family have been implicated in diverse cellular processes and found in varied subcellular localizations. Very recently, the biochemical characterization of two evolutionary divergent TPM domains has shown that they are able to hydrolyze phosphate groups from different substrates. However, there are still incorrect functional annotations and uncertain relationships between the structure and function of this family of domains...
November 1, 2016: Journal of Structural Biology
Matthias Rief, Daniel J Müller
No abstract text is available yet for this article.
January 2017: Journal of Structural Biology
Bogdan I Costescu, Sebastian Sturm, Frauke Gräter
Protein unfolding often does not obey a simple two-state behavior. Previous single molecule force spectroscopy studies demonstrated stretched exponential kinetics of protein unfolding under a constant pulling force, the molecular origin of which remains subject to debate. We here set out to extensively sample the mechanical unfolding of ubiquitin and NuG2 by Molecular Dynamics (MD) simulations. Both proteins show kinetics best fit by stretched exponentials, with stretching exponents similar to those found in experiments, even though static disorder is absent in our short MD simulations...
January 2017: Journal of Structural Biology
Franziska Kriegel, Niklas Ermann, Jan Lipfert
Nucleic acids are central to the storage and transmission of genetic information. Mechanical properties, along with their sequence, both enable and fundamentally constrain the biological functions of DNA and RNA. For small deformations from the equilibrium conformations, nucleic acids are well described by an isotropic elastic rod model. However, external forces and torsional strains can induce conformational changes, giving rise to a complex force-torque phase diagram. This review focuses on magnetic tweezers as a powerful tool to precisely determine both the elastic parameters and conformational transitions of nucleic acids under external forces and torques at the single-molecule level...
January 2017: Journal of Structural Biology
Sandra Posch, Camilo Aponte-Santamaría, Richard Schwarzl, Andreas Karner, Matthias Radtke, Frauke Gräter, Tobias Obser, Gesa König, Maria A Brehm, Hermann J Gruber, Roland R Netz, Carsten Baldauf, Reinhard Schneppenheim, Robert Tampé, Peter Hinterdorfer
The von Willebrand factor (VWF) is a glycoprotein in the blood that plays a central role in hemostasis. Among other functions, VWF is responsible for platelet adhesion at sites of injury via its A1 domain. Its adjacent VWF domain A2 exposes a cleavage site under shear to degrade long VWF fibers in order to prevent thrombosis. Recently, it has been shown that VWF A1/A2 interactions inhibit the binding of platelets to VWF domain A1 in a force-dependent manner prior to A2 cleavage. However, whether and how this interaction also takes place in longer VWF fragments as well as the strength of this interaction in the light of typical elongation forces imposed by the shear flow of blood remained elusive...
January 2017: Journal of Structural Biology
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