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Journal of Structural Biology

Piero Zanello
In the context of the plethora of proteins harboring iron-sulfur clusters we have already reviewed structure/electrochemistry of metalloproteins expressing single types of iron-sulfur clusters (namely: {Fe(Cys)4}, { [Fe2S2](Cys)4}, { [Fe2S2](Cys)3(X)} (X = Asp, Arg, His), { [Fe2S2](Cys)2(His)2}, { [Fe3S4](Cys)3}, { [Fe4S4](Cys)4} and { [Fe4S4](SγCys)3(nonthiolate ligand) } cores) and their synthetic analogs. More recently we are focussing on structure/electrochemistry of metalloproteins harboring iron-sulfur centres of different nuclearities...
February 8, 2018: Journal of Structural Biology
Marco Salomone-Stagni, Joseph D Bartho, Ivan Polsinelli, Dom Bellini, Martin A Walsh, Nicola Demitri, Stefano Benini
The Gram-negative bacterium Erwinia amylovora is the etiological agent of fire blight, a devastating disease which affects Rosaceae such as apple, pear and quince. The siderophore desferrioxamine E plays an important role in bacterial pathogenesis by scavenging iron from the host. DfoJ, DfoA and DfoC are the enzymes responsible for desferrioxamine production starting from lysine. We have determined the crystal structures of each enzyme in the desferrioxamine E pathway and demonstrate that the biosynthesis involves the concerted action of DfoJ, followed by DfoA and lastly DfoC...
February 8, 2018: Journal of Structural Biology
Jose-Jesus Fernandez, Sam Li, Tanmay A M Bharat, David A Agard
Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal tilt-series alignment and thus deterioration of the reconstruction quality. Here we present a novel approach to tilt-series alignment and tomographic reconstruction that considers the beam-induced sample motion through the tilt-series. It extends the standard fiducial-based alignment approach in cryoET by introducing quadratic polynomials to model the sample motion...
February 2, 2018: Journal of Structural Biology
Anna Kluza, Ewa Niedzialkowska, Katarzyna Kurpiewska, Zuzanna Wojdyla, Matthew Quesne, Ewa Kot, Przemyslaw J Porebski, Tomasz Borowski
Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum (opium poppy), which belongs to the non-heme 2-oxoglutarate/Fe(II)-dependent dioxygenases (ODD) family, is a key enzyme in the morphine biosynthesis pathway. Initially, T6ODM was characterized as an enzyme catalyzing O-demethylation of thebaine to neopinone and oripavine to morphinone, however the substrate range of T6ODM was recently expanded to a number of various benzylisoquinoline alkaloids. Here, we present crystal structures of T6ODM in complexes with 2-oxoglutarate (T6ODM:2OG, PDB: 5O9W) and succinate (T6ODM:SIN, PDB: 5O7Y)...
February 2, 2018: Journal of Structural Biology
Ashwani Sharma, Samuel F Gerard, Natacha Olieric, Michel O Steinmetz
Centrioles are microtubule-based structures that play essential roles in cell division and cilia biogenesis. Cep120 is an important protein for correct centriole formation and mutations in the Cep120 gene cause severe human diseases like Joubert syndrome and complex ciliopathies. Here, we show that Cep120 contains three consecutive C2 domains that are followed by a coiled-coil dimerization domain. Surprisingly, unlike the classical C2 domains, all three Cep120 C2 domains lack calcium- and phospholipid-binding activities...
February 1, 2018: Journal of Structural Biology
Alice Ballone, Federica Centorrino, Madita Wolter, Christian Ottmann
The deviant Ras activation machinery is found in approximately 30% of all human cancers. SOS1 is an important protagonist of this pathway that plays a key-role in aberrant cell proliferation and differentiation. Interaction of SOS1 with 14-3-3 proteins modulates SOS1 activity in Ras-MAPK signaling. In the present study, we analyze the 14-3-3/SOS1 protein-protein interaction (PPI) by different biochemical assays and report the high resolution crystal structure of a 13-mer motif of SOS1 bound to 14-3-3ζ. These structural and functional insights are important for the evaluation of this PPI interface for small-molecule stabilization as a new starting point for modulating the Ras-Raf-MAPK pathway...
January 31, 2018: Journal of Structural Biology
E L McBride, A Rao, G Zhang, J D Hoyne, G N Calco, B C Kuo, Q He, A A Prince, I D Pokrovskaya, B Storrie, A A Sousa, M A Aronova, R D Leapman
Microscopies based on focused electron probes allow the cell biologist to image the 3D ultrastructure of eukaryotic cells and tissues extending over large volumes, thus providing new insight into the relationship between cellular architecture and function of organelles. Here we compare two such techniques: electron tomography in conjunction with axial bright-field scanning transmission electron microscopy (BF-STEM), and serial block face scanning electron microscopy (SBF-SEM). The advantages and limitations of each technique are illustrated by their application to determining the 3D ultrastructure of human blood platelets, by considering specimen geometry, specimen preparation, beam damage and image processing methods...
January 31, 2018: Journal of Structural Biology
Andrei N Lupas, Alasdair C Steven
No abstract text is available yet for this article.
January 30, 2018: Journal of Structural Biology
Venkata P Dandey, Hui Wei, Zhening Zhang, Yong Zi Tan, Priyamvada Acharya, Edward T Eng, William J Rice, Peter A Kahn, Clinton S Potter, Bridget Carragher
We present an update describing new features and applications of Spotiton, a novel instrument for vitrifying samples for cryoEM. We have used Spotiton to prepare several test specimens that can be reconstructed using routine single particle analysis to ∼3 Å resolution, indicating that the process has no apparent deleterious effect on the sample integrity. The system is now in routine and continuous use in our lab and has been used to successfully vitrify a wide variety of samples.
January 20, 2018: Journal of Structural Biology
Ottilie von Loeffelholz, Gabor Papai, Radostin Danev, Alexander G Myasnikov, S Kundhavai Natchiar, Isabelle Hazemann, Jean-François Ménétret, Bruno P Klaholz
A current bottleneck in structure determination of macromolecular complexes by cryo electron microscopy (cryo-EM) is the large amount of data needed to obtain high-resolution 3D reconstructions, including through sorting into different conformations and compositions with advanced image processing. Additionally, it may be difficult to visualize small ligands that bind in sub-stoichiometric levels. Volta phase plates (VPP) introduce a phase shift in the contrast transfer and drastically increase the contrast of the recorded low-dose cryo-EM images while preserving high frequency information...
January 11, 2018: Journal of Structural Biology
Trevor Gokey, Andrei S Halavaty, George Minasov, Wayne F Anderson, Misty L Kuhn
Many bacteria require L-rhamnose as a key cell wall component. This sugar is transferred to the cell wall using an activated donor dTDP-L-rhamnose, which is produced by the dTDP-L-rhamnose biosynthetic pathway. We determined the crystal structure of the second enzyme of this pathway dTDP-α-D-glucose 4,6-dehydratase (RfbB) from Bacillus anthracis. Interestingly, RfbB only crystallized in the presence of the third enzyme of the pathway RfbC; however, RfbC was not present in the crystal. Our work represents the first complete structural characterization of the four proteins of this pathway in a single Gram-positive bacterium...
January 10, 2018: Journal of Structural Biology
Nan Xu, David Veesler, Peter C Doerschuk, John E Johnson
The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways...
January 10, 2018: Journal of Structural Biology
Michael R Jones, Joshua Yue, Angela K Wilson
Improper signaling of the nuclear factor-κB (NF-κB) pathway plays a critical role in many inflammatory disease states including cancer, stroke, and viral infections. Although the signaling pathways are known, how these molecular mechanisms respond to changes in the intracellular microenvironment such as pH, ionic strength, and temperature, remains elusive. Molecular dynamics simulations were employed to differentiate the structural dynamics of the NF-kB Inducing Kinase (NIK), a protein kinase responsible for invoking the non-canonical NF-κB pathway, in its native and mutant form, and in the absence and presence of salt concentration in efforts to probe whether changes in the ionic environment stabilize or destabilize the NIK dimer...
January 8, 2018: Journal of Structural Biology
Hui Wei, Venkata P Dandey, Zhening Zhang, Ashleigh Raczkowski, Willam J Rice, Bridget Carragher, Clinton S Potter
We have developed a self-blotting TEM grid for use with a novel instrument for vitrifying samples for cryo-electron microscopy (cryoEM). Nanowires are grown on the copper surface of the grid using a simple chemical reaction and the opposite smooth side is used to adhere to a holey sample substrate support, for example carbon or gold. When small volumes of sample are applied to the nanowire grids the wires effectively act as blotting paper to rapidly wick away the liquid, leaving behind a thin film. In this technical note, we present a detailed description of how we make these grids using a variety of substrates fenestrated with either lacey or regularly spaced holes...
January 6, 2018: Journal of Structural Biology
D Geeta, B Shveta, H S Savithri, M R N Murthy
Cellular metabolism of amino acids is controlled by a large number of pyridoxal 5'-phosphate (PLP) dependent enzymes. Diaminopropionate ammonia lyase (DAPAL), a fold type II PLP-dependent enzyme, degrades both the D and L forms of diaminopropionic acid (DAP) to pyruvate and ammonia. Earlier studies on the Escherichia coli DAPAL (EcDAPAL) had suggested that a disulfide bond located close to the active site may be crucial for maintaining the geometry of the substrate entry channel and the active site. In order to obtain further insights into the catalytic properties of DAPAL, structural and functional studies on Salmonella typhimurium DAPAL (StDAPAL) were initiated...
December 30, 2017: Journal of Structural Biology
Andrey V Kajava, Silvio C E Tosatto
No abstract text is available yet for this article.
December 30, 2017: Journal of Structural Biology
Shanshan Guan, Yan Xu, Yongbo Qiao, Ziyu Kuai, Mengdan Qian, Xiaoyu Jiang, Song Wang, Hao Zhang, Wei Kong, Yaming Shan
Neuraminidase (NA) inhibitors can suppress NA activity to block the release of progeny virions and are effective against influenza viruses. As potential anti-flu drugs with unique functions, NA inhibitors are greatly concerned by the worldwide scientists. It has been reported recently that one of the novel quindoline derivatives named 7a, could inhibit both A/Puerto Rico/8/34 (H1N1) NA (NAPR) and A/California/04/09 (H1N1) NA (NACA). However, potential structure differences in the active site could be easily detected between the NAPR and NACA according to the flexibilities of their 150-loops located catalytic site...
December 28, 2017: Journal of Structural Biology
Xiangrui Zeng, Miguel Ricardo Leung, Tzviya Zeev-Ben-Mordehai, Min Xu
Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to automatically isolate different in situ cellular components. In this paper, we propose a convolutional autoencoder-based unsupervised approach to provide a coarse grouping of 3D small subvolumes extracted from tomograms. We demonstrate that the autoencoder can be used for efficient and coarse characterization of features of macromolecular complexes and surfaces, such as membranes...
December 28, 2017: Journal of Structural Biology
N Zeytuni, K A Flanagan, L J Worrall, S C Massoni, A H Camp, N C J Strynadka
Endospore formation in the Gram-positive bacterium Bacillus subtilis initiates in response to nutrient depletion and involves a series of morphological changes that result in the creation of a dormant spore. Early in this developmental process, the cell undergoes an asymmetric cell division that produces the larger mother cell and smaller forespore, the latter destined to become the mature spore. The mother cell septal membrane then engulfs the forespore, at which time an essential channel, the so-called feeding-tube apparatus, is thought to cross both membranes to create a direct conduit between the cells...
December 26, 2017: Journal of Structural Biology
Jonathan Davies, Jay Rees, Sai Man Liu, K Ravi Acharya
Clostridium botulinum neurotoxins (BoNTs) cause the life-threatening condition, botulism. However, while they have the potential to cause serious harm, they are increasingly being utilised for therapeutic applications. BoNTs comprise of seven distinct serotypes termed BoNT/A through BoNT/G, with the most widely characterised being sub-serotype BoNT/A1. Each BoNT consists of three structurally distinct domains, a binding domain (HC), a translocation domain (HN), and a proteolytic domain (LC). The HC domain is responsible for the highly specific targeting of the neurotoxin to neuronal cell membranes...
December 26, 2017: Journal of Structural Biology
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