Segmentation by Classification: A Novel and Reliable Approach for Semi-Automatic Selection of HIV/SIV Envelope Spikes
We describe a semiautomated approach to segment Env spikes from the membrane envelope of Simian Immunodeficiency Virus visualized by cryoelectron tomography of frozen-hydrated specimens. Multivariate data analysis is applied to a large set of overlapping subvolumes extracted semiautomatically from the viral envelope and does not utilize a template of the target structure. The major manual step used in the method involves determination of six points that define an ellipsoid approximating the virion shape. The approach is robust to departures of the actual virion from this starting ellipsoid. A point cage of sufficient densi...
Source: Journal of Structural Biology - November 15, 2019 Category: Biology Source Type: research
Recognition of different base tetrads by RHAU (DHX36): X-ray crystal structure of the G4 recognition motif bound to the 3′-end tetrad of a DNA G-quadruplex
We report a X-ray co-crystal structure at 1.5 Å resolution of an N-terminal fragment of RHAU bound to an exposed tetrad of a parallel-stranded G-quadruplex. The RHAU peptide folds into an L-shaped α-helix, and binds to a G-quadruplex through π-stacking and electrostatic interactions. X-ray crystal structure of our complex identified key amino acid residues important for G-quadruplex-peptide binding interaction at the 3′-end G•G•G•G tetrad. Together with previous solution and crystal structures of RHAU bound to the 5′-end G•G•G•G and G•G•A•T tetrads, our crystal structure highlights the occurrence...
Source: Journal of Structural Biology - November 13, 2019 Category: Biology Source Type: research
Structural and functional investigation of AerF, a NADPH-dependent alkenal double bond reductase participating in the biosynthesis of Choi moiety of aeruginosin
In this study, functional and mechanistic analyses of AerF from Microcystis aeruginosa were performed. Observation of enzymatic assay demonstrates that AerF is a NADPH-dependent alkenal double bond reductase that catalyzes the reduction of dihydro-4-hydroxyphenylpyruvate (H2HPP) to generate tetrahydro-4-hydroxyphenylpyruvate (H4HPP), which is the third step of the biosynthetic pathway from prephenate to Choi. Comparative structural analysis indicates that ligand binding-induced conformational change of AerF is different from that of the other SDR superfamily reductase using H2HPP as a substrate. Analyses of NADPH and subst...
Source: Journal of Structural Biology - November 12, 2019 Category: Biology Source Type: research
Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections
Publication date: Available online 11 November 2019Source: Journal of Structural BiologyAuthor(s): Eric J. Verbeke, Yi Zhou, Andrew P. Horton, Anna L. Mallam, David W. Taylor, Edward M. MarcotteAbstractSingle particle analysis for structure determination in cryo-electron microscopy is traditionally applied to samples purified to near homogeneity as current reconstruction algorithms are not designed to handle heterogeneous mixtures of structures from many distinct macromolecular complexes. We extend on long established methods and demonstrate that relating two-dimensional projection images by their common lines in a graphic...
Source: Journal of Structural Biology - November 12, 2019 Category: Biology Source Type: research
Corrigendum to “Fourier-space TEM reconstructions with symmetry adapted functions for all rotational point groups” [J. Struct. Biol. 182 (2013) 87–92]
Publication date: Available online 8 November 2019Source: Journal of Structural BiologyAuthor(s): Stefano Trapani, Jorge Navaza (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - November 10, 2019 Category: Biology Source Type: research
Conformational properties of L-fucose and the tetrasaccharide building block of the sulfated L-fucan from Lytechinus variegatus
Publication date: Available online 4 November 2019Source: Journal of Structural BiologyAuthor(s): Francisco F. Bezerra, William P. Vignovich, AyoOluwa O. Aderibigbe, Hao Liu, Joshua S. Sharp, Robert J. Doerksen, Vitor H. PominAbstractAlthough the 3D structure of carbohydrates is known to contribute to their biological roles, conformational studies of sugars are challenging because their chains are flexible in solution and consequently the number of 3D structural restraints is limited. Here, we investigate the conformational properties of the tetrasaccharide building block of the Lytechinus variegatus sulfated fucan compose...
Source: Journal of Structural Biology - November 6, 2019 Category: Biology Source Type: research
Tidy up cryo-EM sample grids with 3D printed tools
Publication date: Available online 4 November 2019Source: Journal of Structural BiologyAuthor(s): Tasuku Hamaguchi, Koji YonekuraAbstractCryo-EM technology has developed to the point of high-throughput structure determination of biological macromolecules embedded in vitreous ice. Nonetheless, challenging targets need extensive sample screening, often of many cryo-EM sample grids prepared under various conditions. We have designed and made tools for manipulating sample grids in storage cases. These tools are made of a plastic fiber using a wide-use 3D printer, a fused deposition modeling type, and polished under acetone gas...
Source: Journal of Structural Biology - November 6, 2019 Category: Biology Source Type: research
Lepidosaur ß-Keratin Chains With Four 34-Residue Repeats: Modelling Reveals A Potential Filament-Crosslinking Role
Publication date: Available online 5 November 2019Source: Journal of Structural BiologyAuthor(s): R.D. Bruce Fraser, David A.D. ParryAbstractß-keratin chains contain a characteristic and homologous 34-residue sequence, which is believed to adopt a twisted ß-sheet conformation that assembles in an antiparallel manner with a similar sheet in a second chain to form a ß-sandwich. These sandwiches are, in turn, related to one another by a left-handed four-fold screw axis to generate a helical structure that forms the core of the 3.4 nm diameter filaments observed by electron microscopy and deduced from X-ray fibre diffractio...
Source: Journal of Structural Biology - November 6, 2019 Category: Biology Source Type: research
Identification of a pH Sensor in Influenza Hemagglutinin using X-ray Crystallography
Publication date: Available online 2 November 2019Source: Journal of Structural BiologyAuthor(s): Aleksandar Antanasijevic, Matthew A. Durst, Arnon Lavie, Michael CaffreyAbstractHemagglutnin (HA) mediates entry of influenza virus through a series of conformational changes triggered by the low pH of the endosome. The residue or combination of residues acting as pH sensors has not yet been fully elucidated. In this work, we assay pH effects on the structure of H5 HA by soaking HA crystallized at pH 6.5 in a series of buffers with lower pH, mimicking the conditions of the endosome. We find that HA1-H38, which is conserved in ...
Source: Journal of Structural Biology - November 3, 2019 Category: Biology Source Type: research
How the central domain of dystrophin acts to bridge F-actin to sarcolemmal lipids
Publication date: Available online 2 November 2019Source: Journal of Structural BiologyAuthor(s): Dominique Mias-Lucquin, Raphael Dos Santos Morais, Angélique Chéron, Mélanie Lagarrigue, Steve J Winder, Thomas Chenuel, Javier Pérez, Marie-Sousai Appavou, Anne Martel, Guillaume Alviset, Elisabeth Le Rumeur, Sophie Combet, Jean-François Hubert, Olivier DelalandeAbstractDystrophin is a large intracellular protein that prevents sarcolemmal ruptures by providing a mechanical link between the intracellular actin cytoskeleton and the transmembrane dystroglycan complex. Dystrophin deficiency leads to the severe muscle wasting...
Source: Journal of Structural Biology - November 3, 2019 Category: Biology Source Type: research
Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase
Publication date: Available online 31 October 2019Source: Journal of Structural BiologyAuthor(s): Mohadeseh Majdi Yazdi, Sagar Saran, Tyler Mrozowich, Cheyanne Lehnert, Trushar R. Patel, David A.R. Sanders, David R.J. PalmerAbstractDihydrodipicolinate synthase (DHDPS) from Campylobacter jejuni is a natively homotetrameric enzyme that catalyzes the first unique reaction of (S)-lysine biosynthesis and is feedback-regulated by lysine through binding to an allosteric site. High-resolution structures of the DHDPS-lysine complex have revealed significant insights into the binding events. One key asparagine residue, N84, makes hy...
Source: Journal of Structural Biology - October 31, 2019 Category: Biology Source Type: research
Dimerization of long Hibernation Promoting Factor from Staphylococcus aureus: structural analysis and biochemical characterization
In this study, we solved the crystal structure of CTDSaHPF at 1.6 Å resolution and obtained a precise arrangement of the dimer interface. Residues Phe160, Val162, Thr171, Ile173, Tyr175, Ile185 andThr187 in the dimer interface of SaHPF protein were mutated and the effects were analyzed for the formation of 100S disomes of ribosomes isolated from S. aureus. It was shown that substitution of any of single residues Phe160, Val162, Ile173, Tyr175 and Ile185 in the SaHPF homodimer interface abolished the ribosome dimerization in vitro.Graphical abstract (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - October 26, 2019 Category: Biology Source Type: research
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Publication date: 1 November 2019Source: Journal of Structural Biology, Volume 208, Issue 2Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - October 23, 2019 Category: Biology Source Type: research
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Publication date: 1 November 2019Source: Journal of Structural Biology, Volume 208, Issue 2Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - October 23, 2019 Category: Biology Source Type: research
Disease related single point mutations alter the global dynamics of a tetratricopeptide (TPR) α-solenoid domain
Publication date: Available online 16 October 2019Source: Journal of Structural BiologyAuthor(s): Salomé Llabrés, Maxim I Tsenkov, Stuart A MacGowan, Geoffrey J Barton, Ulrich ZachariaeAbstractTetratricopeptide repeat (TPR) proteins belong to the class of α-solenoid proteins, in which repetitive units of α-helical hairpin motifs stack to form superhelical, often highly flexible structures. TPR domains occur in a wide variety of proteins, and perform key functional roles including protein folding, protein trafficking, cell cycle control and post-translational modification. Here, we look at the TPR domain of the enzyme O...
Source: Journal of Structural Biology - October 19, 2019 Category: Biology Source Type: research
