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Journal of Structural Biology

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 motifs, functions and distribution across the major taxonomic kingdoms of life and within organisms...
October 7, 2017: Journal of Structural Biology
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 scanning electron microscopy and using this methodology, generated a 3D reconstruction of an entire C...
October 1, 2017: Journal of Structural Biology
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 is likely to be complex, involving more than a single structural aspect of striated muscle, the thick filament itself, would be a prime site for regulatory function because it must bear all of the tension produced by both its associated myosin motors and any externally applied force...
September 27, 2017: Journal of Structural Biology
Jie-Jie Lv, Fang Ma, Fu-Chun Li, Chong-Hong Zhang, Jia-Ni Chen
Studies on the formation and stability of vaterite by bacteria in experimental systems are of great importance for understanding the mechanism by which microbes contribute to carbonate mineralization. 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...
September 25, 2017: Journal of Structural Biology
Daniel Sanchez-deAlcazar, Sara H Mejias, Kevin Erazo, Begoña Sot, Aitziber L Cortajarena
In nature, assembled protein structures offer the most complex functional structures. The understanding of the mechanisms ruling protein-protein interactions opens the door to manipulate protein assemblies in a rational way. Proteins are versatile scaffolds with great potential as tools in nanotechnology and biomedicine because of their chemical, structural, and functional versatility. Currently, bottom-up self-assembly based on biomolecular interactions of small and well-defined components, is an attractive approach to biomolecular engineering and biomaterial design...
September 22, 2017: Journal of Structural Biology
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 the proposed algorithm is that it finds the global optimum for the orientations given the common lines...
September 21, 2017: Journal of Structural Biology
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 proteins, as implied by variations in the length of the polyQ tract required to trigger the onset of a given polyQ disease...
September 18, 2017: Journal of Structural Biology
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-standing debate as to whether tesserae are more like bone (Coll 1-based) or calcified cartilage in their matrix composition. We demonstrate that stingray (Urobatis halleri) tesserae are bipartite, having an upper Coll I-based "cap" that merges into a lower Coll II-based "body" zone, although tesserae are surrounded by cartilage...
September 15, 2017: Journal of Structural Biology
Juntaek Oh, Dong-Gi Lee, Yong-Sun Bahn, Sangkee Rhee
The fungal pathogen Cryptococcus neoformans is a causative agent of meningoencephalitis in humans. For its pathogenicity, the inositol polyphosphate biosynthetic pathway plays critical roles. Recently, Ipk1 from C. neoformans (CnIpk1) was identified as an inositol 1,3,4,5,6-pentakisphosphate 2-kinase that catalyzes the phosphorylation of IP5 to form IP6, a substrate for subsequent reaction to produce inositol pyrophosphates, such as PP-IP5/IP7. Furthermore, it was shown that deletion of IPK1 significantly reduces the virulence of C...
September 15, 2017: Journal of Structural Biology
R D Bruce Fraser, David A D Parry
For the past 50years 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 analysis of the fine structure of the 1nm equatorial region of the X-ray diffraction pattern of quill we show that the observed pattern is consistent with the (8+0) model and we are also able to assign values to the various parameters...
September 8, 2017: Journal of Structural Biology
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 building blocks with compatible interfaces, it is possible to rapidly build non-symmetric large structures (> 1000 amino acids) that match three-dimensional geometric descriptions provided by the user...
September 7, 2017: Journal of Structural Biology
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_3758, namely yrInv (for Y. ruckeri invasin) and yrIlm (for Y. ruckeri invasin-like molecule)...
September 6, 2017: Journal of Structural Biology
Simon Hansen, Patrick Ernst, Sebastian L B König, Christian Reichen, Christina Ewald, Daniel Nettels, Peer R E Mittl, Benjamin Schuler, Andreas Plückthun
Designed armadillo repeat proteins (dArmRPs) were developed to create a modular peptide binding technology where each of the structural repeats binds two residues of the target peptide. An essential prerequisite for such a technology is a dArmRP geometry that matches the peptide bond length. To this end, we determined a large set (n=27) of dArmRP X-ray structures, of which 12 were previously unpublished, to calculate curvature parameters that define their geometry. Our analysis shows that consensus dArmRPs exhibit curvatures close to the optimal range for modular peptide recognition...
August 31, 2017: Journal of Structural Biology
Phani R Potluri, Jean Chamoun, James A Cooke, Myriam Badr, Joanna A Guse, Roni Rayes, Nicole M Cordina, Dane McCamey, Piotr G Fajer, Louise J Brown
The absence of a crystal structure of the calcium free state of the cardiac isoform of the troponin complex has hindered our understanding of how the simple binding of Ca(2+) triggers conformational changes in troponin which are then propagated to enable muscle contraction. Here we have used continuous wave (CW) and Double Electron-Electron Resonance (DEER) pulsed EPR spectroscopy to measure distances between TnI and TnC to track the movement of the functionally important regulatory 'switch' region of the cardiac Tn...
August 29, 2017: Journal of Structural Biology
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 PI4P-rich membranes that serve as viral replication organelles. Given the importance of this enzyme in cells, it has to be regulated...
August 29, 2017: Journal of Structural Biology
Matthew C Johnson, Marta Sena-Velez, Brian K Washburn, Georgia N Platt, Stephen Lu, Tess E Brewer, Jason S Lynn, M Elizabeth Stroupe, Kathryn M Jones
Bacteriophages of nitrogen-fixing rhizobial bacteria are revealing a wealth of novel structures, diverse enzyme combinations and genomic features. Here we report the cryo-EM structure of the phage capsid at 4.9-5.7 Å-resolution, the phage particle proteome, and the genome of the Sinorhizobium meliloti-infecting Podovirus ΦM5. This is the first structure of a phage with a capsid and capsid-associated structural proteins related to those of the LUZ24-like viruses that infect Pseudomonas aeruginosa. Like many other Podoviruses, ΦM5 is a T=7 icosahedron with a smooth capsid and short, relatively featureless tail...
August 22, 2017: Journal of Structural Biology
Alexei S Soares, Donald L D Caspar
X-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electrons inside the envelope of the calculated protein density map to equal the number deduced from the atomic model...
August 21, 2017: Journal of Structural Biology
Ali C Akyildiz, Chen-Ket Chai, Cees W J Oomens, Aad van der Lugt, Frank P T Baaijens, Gustav J Strijkers, Frank J H Gijsen
Atherosclerotic plaque rupture is the primary trigger of fatal cardiovascular events. Fibrillar collagen in atherosclerotic plaques and their directionality are anticipated to play a crucial role in plaque rupture. This study aimed assessing 3D fiber orientations and architecture in atherosclerotic plaques for the first time. Seven carotid plaques were imaged ex-vivo with a state-of-the-art Diffusion Tensor Imaging (DTI) technique, using a high magnetic field (9.4 Tesla) MRI scanner. A 3D spin-echo sequence with uni-polar diffusion sensitizing pulsed field gradients was utilized for DTI and fiber directions were assessed from diffusion tensor measurements...
August 21, 2017: Journal of Structural Biology
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 proteins. To further simplify the production and crystallization experiments we have explored the production of chimeric proteins corresponding to covalent association between the targets and their specific binders strengthened by a linker...
August 16, 2017: Journal of Structural Biology
Bing Wang, Qian Yin
Absent in melanoma 2 (AIM2) inflammasome is a multi-protein platform that recognizes aberrant cytoplasmic dsDNA and induces cytokine maturation, release and pyroptosis. It is composed of AIM2, apoptosis-associated speck-like protein containing a CARD (ASC), and caspase-1. Recent X-ray crystallographic and high resolution cryo-electron microscopic (cryo-EM) studies have revealed a series of structures in AIM2 inflammasome activation and regulation. One prominent feature common in multiple steps is the assembly of high-order structures, especially helical filaments nucleated by upstream molecules, rather than stoichiometric complexes...
August 13, 2017: Journal of Structural Biology
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