Journal of Structural Biology

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  • Paper of the Year Award
    [Feb 2015]

    Publication date: Available online 17 January 2015
    Source:Journal of Structural Biology









    Categories: Journal Articles
  • Corrigendum to “A clarification of the terms used in comparing semi-automated particle selection algorithms in cryo-EM” [J. Struct. Biol. 175 (2011) 348–352]
    [Feb 2015]

    Publication date: Available online 16 January 2015
    Source:Journal of Structural Biology

    Author(s): Robert Langlois , Joachim Frank







    Categories: Journal Articles
  • Evidence of compositional and ultrastructural shifts during the development of calcareous tubes in the biofouling tubeworm, Hydroides elegans
    [Feb 2015]

    Publication date: Available online 16 January 2015
    Source:Journal of Structural Biology

    Author(s): Vera Bin San Chan , Olev Vinn , Chaoyi Li , Xingwen Lu , Anatoliy B. Kudryavtsev , J. William Schopf , Kaimin Shih , Tong Zhang , Vengatesen Thiyagarajan

    The serpulid tubeworm, Hydroides elegans, is an ecologically and economically important species whose biology has been fairly well studied, especially in the context of larval development and settlement on man-made objects (biofouling). Nevertheless, ontogenetic changes associated with calcareous tube composition and structures have not yet been studied. Here, the ultrastructure and composition of the calcareous tubes built by H. elegans was examined in the three early calcifying juvenile stages and in the adult using XRD, FTIR, ICP-OES, SEM and Raman spectroscopy. Ontogenetic shifts in carbonate mineralogy were observed, for example, juvenile tubes contained more amorphous calcium carbonate and were predominantly aragonitic whereas adult tubes were bimineralic with considerably more calcite. The mineral composition gradually shifted during the tube development as shown by a decrease in Sr/Ca and an increase of Mg/Ca ratios with the tubeworm’s age. The inner tube layer contained calcite, whereas the outer layer contained aragonite. Similarly, the tube complexity in terms of ultrastructure was associated with development. The sequential appearance of unoriented ultrastructures followed by oriented ultrastructures may reflect the evolutionary history of serpulid tube biominerals. As aragonitic structures are more susceptible to dissolution under ocean acidification (OA) conditions but are more difficult to be removed by anti-fouling treatments, the early developmental stages of the tubeworms may be vulnerable to OA but act as the important target for biofouling control.





    Categories: Journal Articles
  • Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance
    [Feb 2015]

    Publication date: Available online 16 January 2015
    Source:Journal of Structural Biology

    Author(s): M. Bangera , R. Panigrahi , S.R. Sagurthi , H.S. Savithri , M.R.N. Murthy

    In many organisms “Universal Stress Proteins” (USPs) are induced in response to a variety of environmental stresses. Here we report the structures of two USPs, YnaF and YdaA from Salmonella typhimurium determined at 1.8Å and 2.4Å resolutions, respectively. YnaF consists of a single USP domain and forms a tetrameric organization stabilized by interactions mediated through chloride ions. YdaA is a larger protein consisting of two tandem USP domains. Two protomers of YdaA associate to form a structure similar to the YnaF tetramer. YdaA showed ATPase activity and an ATP binding motif G-2X-G-9X-G(S/T/N) was found in its C-terminal domain. The residues corresponding to this motif were not conserved in YnaF although YnaF could bind ATP. However, unlike YdaA, YnaF did not hydrolyse ATP in vitro. Disruption of interactions mediated through chloride ions by selected mutations converted YnaF into an ATPase. Residues that might be important for ATP hydrolysis could be identified by comparing the active sites of native and mutant structures. Only the C-terminal domain of YdaA appears to be involved in ATP hydrolysis. The structurally similar N-terminal domain was found to bind a zinc ion near the segment equivalent to the phosphate binding loop of the C-terminal domain. Mass spectrometric analysis showed that YdaA might bind a ligand of approximate molecular weight 800daltons. Structural comparisons suggest that the ligand, probably related to an intermediate in lipid A biosynthesis, might bind at a site close to the zinc ion. Therefore, the N-terminal domain of YdaA binds zinc and might play a role in lipid metabolism. Thus, USPs appear to perform several distinct functions such as ATP hydrolysis, altering membrane properties and chloride sensing.





    Categories: Journal Articles
  • Crystal structures for short-chain pentraxin from zebrafish demonstrate a cyclic trimer with new recognition and effector faces
    [Feb 2015]

    Publication date: Available online 13 January 2015
    Source:Journal of Structural Biology

    Author(s): Rong Chen , Jianxun Qi , Hongyu Yuan , Yanan Wu , Wei Hu , Chun Xia

    Short-chain pentraxins (PTXs), including CRP and SAP, are innate pattern recognition receptors that play vital roles in the recognition and elimination of various pathogenic bacteria by triggering the classical complement pathway through C1q. Similar to antibodies, pentraxins can also activate opsonisation and phagocytosis by interacting with Fc receptors (FcRs). Various structural studies on human PTXs have been performed, but there are no reports about the crystal structure of bony fish pentraxins. Here, the crystal structures of zebrafish PTX (Dare-PTX-Ca and Dare-PTX) are presented. Both Dare-PTX-Ca and Dare-PTX are cyclic trimers, which are new forms of crystallised pentraxins. The structures reveal that the ligand-binding pocket (LBP) in the recognition face of Dare-PTX is deep and narrow. Homology modelling shows that LBPs from different Dare-PTX loci differ in shape, reflecting their specific recognition abilities. Furthermore, in comparison with the structure of hCPR, a new C1q binding mode was identified in Dare-PTX. In addition, the FcR-binding sites of hSAP are partially conserved in Dare-PTX. These results will shed light on the understanding of a primitive PTX in bony fish, which evolved approximately 450 million years ago.





    Categories: Journal Articles
  • Cover 2 - Editorial Board
    [Feb 2015]

    Publication date: January 2015
    Source:Journal of Structural Biology, Volume 189, Issue 1









    Categories: Journal Articles
  • Table of Contents / barcode
    [Feb 2015]

    Publication date: January 2015
    Source:Journal of Structural Biology, Volume 189, Issue 1









    Categories: Journal Articles
  • The scrunchworm hypothesis: Transitions between A-DNA and B-DNA provide the driving force for genome packaging in double-stranded DNA bacteriophages
    [Feb 2015]

    Publication date: January 2015
    Source:Journal of Structural Biology, Volume 189, Issue 1

    Author(s): Stephen C. Harvey

    Double-stranded DNA bacteriophages have motors that drive the genome into preformed capsids, using the energy released by hydrolysis of ATP to overcome the forces opposing DNA packaging. Viral packaging motors are the strongest of all biological motors, but it is not known how they generate these forces. Several models for the process of mechanochemical force generation have been put forward, but there is no consensus on which, if any, of these is correct. All the existing models assume that protein-generated forces drive the DNA forward. The scrunchworm hypothesis proposes that the DNA molecule is the active force-generating core of the motor, not simply a substrate on which the motor operates. The protein components of the motor dehydrate a section of the DNA, converting it from the B form to the A form and shortening it by about 23%. The proteins then rehydrate the DNA, which converts back to the B form. Other regions of the motor grip and release the DNA to capture the shortening–lengthening motions of the B→A→B cycle (“scrunching”), so that DNA is pulled into the motor and pushed forward into the capsid. This DNA-centric mechanism provides a quantitative physical explanation for the magnitude of the forces generated by viral packaging motors. It also provides a simple explanation for the fact that each of the steps in the burst cycle advances the DNA by 2.5 base pairs. The scrunchworm hypothesis is consistent with a large body of published data, and it makes four experimentally testable predictions.





    Categories: Journal Articles
  • Improvement of protein binding sites prediction by selecting amino acid residues’ features
    [Feb 2015]

    Publication date: January 2015
    Source:Journal of Structural Biology, Volume 189, Issue 1

    Author(s): Georgina Mirceva , Andrea Kulakov

    One of the main focuses of bioinformatics community is the study of the relationship between the structure of the protein molecules and their functions. In the literature, there are various methods that consider different protein-derived information for predicting protein functions. In our research, we focus on predicting the protein binding sites, which could be used to functionally annotate the protein structures. In this paper we consider a set of sixteen amino acid residues’ features, and by applying various feature selection techniques we estimate their significance. Although the number of features in our case is not high, we perform feature selection in order to improve the prediction power and time complexity of the prediction models. The results show that by applying proper feature selection technique, the predictive performance of the classification algorithms is improved, i.e., by considering the most relevant features we induce more accurate models than if we consider the entire set of features. Furthermore, the model complexity, as well as the training and testing times are decreased by performing feature selection. We also compare our approach with several existing methods for protein binding sites prediction. The results demonstrate that the existing methods considered in this research are specific and applicable to the group of proteins for which the model was developed, while our approach is more generic and can be applied to a wider class of proteins.





    Categories: Journal Articles
  • Stability of the βB2B3 crystallin heterodimer to increased oxidation by radical probe and ion mobility mass spectrometry
    [Feb 2015]

    Publication date: January 2015
    Source:Journal of Structural Biology, Volume 189, Issue 1

    Author(s): Satoko Akashi , Simin D. Maleknia , Kazumi Saikusa , Kevin M. Downard

    Ion mobility mass spectrometry was employed to study the structure of the βB2B3-crystallin heterodimer following oxidation through its increased exposure to hydroxyl radicals. The results demonstrate that the heterodimer can withstand limited oxidation through the incorporation of up to some 10 oxygen atoms per subunit protein without any appreciable change to its average collision cross section and thus conformation. These results are in accord with the oxidation levels and timescales applicable to radical probe mass spectrometry (RP-MS) based protein footprinting experiments. Following prolonged exposure, the heterodimer is increasingly degraded through cleavage of the backbone of the subunit crystallins rather than denaturation such that heterodimeric structures with altered conformations and ion mobilities were not detected. However, evidence from measurements of oxidation levels within peptide segments, suggest the presence of some aggregated structure involving C-terminal domain segments of βB3 crystallin across residues 115–126 and 152–166. The results demonstrate, for the first time, the ability of ion mobility in conjunction with RP-MS to investigate the stability of protein complexes to, and the onset of, free radical based oxidative damage that has important implications in cataractogenesis.





    Categories: Journal Articles
  • Layered growth of crayfish gastrolith: About the stability of amorphous calcium carbonate and role of additives
    [Feb 2015]

    Publication date: January 2015
    Source:Journal of Structural Biology, Volume 189, Issue 1

    Author(s): Wouter J.E.M. Habraken , Admir Masic , Luca Bertinetti , Ali Al-Sawalmih , Lilah Glazer , Shmuel Bentov , Peter Fratzl , Amir Sagi , Barbara Aichmayer , Amir Berman

    Previous studies on pre-molt gastroliths have shown a typical onion-like morphology of layers of amorphous mineral (mostly calcium carbonate) and chitin, resulting from the continuous deposition and densification of amorphous mineral spheres on a chitin-matrix during time. To investigate the consequences of this layered growth on the local structure and composition of the gastrolith, we performed spatially-resolved Raman, X-ray and SEM–EDS analysis on complete pre-molt gastrolith cross-sections. Results show that especially the abundance of inorganic phosphate, phosphoenolpyruvate (PEP)/citrate and proteins is not uniform throughout the organ but changes from layer to layer. Based on these results we can conclude that ACC stabilization in the gastrolith takes place by more than one compound and not by only one of these additives.





    Categories: Journal Articles
  • Internal skeletal analysis of the colonial azooxanthellate scleractinian Dendrophyllia cribrosa using microfocus X-ray CT images: Underlying basis for its rigid and highly adaptive colony structure
    [Feb 2015]

    Publication date: January 2015
    Source:Journal of Structural Biology, Volume 189, Issue 1

    Author(s): Asuka Sentoku , Hitomi Morisaki , Shinji Masumoto , Rie Ohno , Takayuki Tomiyama , Yoichi Ezaki

    Dendrophyllid Scleractinia exhibit a variety of colonial morphologies, formed under the strict constraints on (1) budding sites, (2) orientations of the directive septa of offsets, (3) inclination of budding direction, and (4) those constraints in every generation. Dendrophyllia cribrosa exhibits a sympodial dendroid form, characteristically large coralla, and occasional fusions of adjacent branches within the same colony. Adjacent corallites are bound and supported by coenosteum skeleton. This study examined the inner skeletal structures at the junctions of fused branches using a non-destructive microfocus X-ray computed tomography (CT) imaging approach, and considered the reasons for the large colonial sizes and their adaptive significance. Three-dimensional reconstructions of two-dimensional X-ray CT images reveal that individual corallites are not directly connected in fused parts. Additionally, no completely buried individuals were found within fused skeleton. When adjacent branches approach one another, constituent corallites change their growth directions to avoid collisions between the branches. The adjacent branches fuse without a reduction in the number of constituent corallites, leading to the establishment of reticular and rigid colonial structures. In addition, a nearly even distribution of individuals on the colony surface facilitates efficient intake of nutrients. Thus, the growth of large D. cribrosa colonies involves avoidance of collision between constituent individuals, the reinforcement of colonial structure, and efficient uptake of nutrients. These observations provide insights on the dynamics of interrelationships between colony-making mechanisms and the adaptive strategies required under habitat conditions such as specific current activities.





    Categories: Journal Articles
  • Quantitative analysis of mouse pancreatic islet architecture by serial block-face SEM
    [Feb 2015]

    Publication date: January 2015
    Source:Journal of Structural Biology, Volume 189, Issue 1

    Author(s): C.R. Pfeifer , A. Shomorony , M.A. Aronova , G. Zhang , T. Cai , H. Xu , A.L. Notkins , R.D. Leapman

    We have applied serial block-face scanning electron microscopy (SBF-SEM) to measure parameters that describe the architecture of pancreatic islets of Langerhans, microscopic endocrine organs that secrete insulin and glucagon for control of blood glucose. By analyzing entire mouse islets, we show that it is possible to determine (1) the distributions of alpha and beta cells, (2) the organization of blood vessels and pericapillary spaces, and (3) the ultrastructure of the individual secretory cells. Our results show that the average volume of a beta cell is nearly twice that of an alpha cell, and the total mitochondrial volume is about four times larger. In contrast, nuclear volumes in the two cell types are found to be approximately equal. Although the cores of alpha and beta secretory granules have similar diameters, the beta granules have prominent halos resulting in overall diameters that are twice those of alpha granules. Visualization of the blood vessels revealed that every secretory cell in the islet is in contact with the pericapillary space, with an average contact area of 9±5% of the cell surface area. Our data show that consistent results can be obtained by analyzing small numbers of islets. Due to the complicated architecture of pancreatic islets, such precision cannot easily be achieved by using TEM of thin sections.





    Categories: Journal Articles
  • Analysis of acute brain slices by electron microscopy: A correlative light–electron microscopy workflow based on Tokuyasu cryo-sectioning
    [Feb 2015]

    Publication date: January 2015
    Source:Journal of Structural Biology, Volume 189, Issue 1

    Author(s): Celine Loussert Fonta , Andrew Leis , Cliff Mathisen , David S. Bouvier , Willy Blanchard , Andrea Volterra , Ben Lich , Bruno M. Humbel

    Acute brain slices are slices of brain tissue that are kept vital in vitro for further recordings and analyses. This tool is of major importance in neurobiology and allows the study of brain cells such as microglia, astrocytes, neurons and their inter/intracellular communications via ion channels or transporters. In combination with light/fluorescence microscopies, acute brain slices enable the ex vivo analysis of specific cells or groups of cells inside the slice, e.g. astrocytes. To bridge ex vivo knowledge of a cell with its ultrastructure, we developed a correlative microscopy approach for acute brain slices. The workflow begins with sampling of the tissue and precise trimming of a region of interest, which contains GFP-tagged astrocytes that can be visualised by fluorescence microscopy of ultrathin sections. The astrocytes and their surroundings are then analysed by high resolution scanning transmission electron microscopy (STEM). An important aspect of this workflow is the modification of a commercial cryo-ultramicrotome to observe the fluorescent GFP signal during the trimming process. It ensured that sections contained at least one GFP astrocyte. After cryo-sectioning, a map of the GFP-expressing astrocytes is established and transferred to correlation software installed on a focused ion beam scanning electron microscope equipped with a STEM detector. Next, the areas displaying fluorescence are selected for high resolution STEM imaging. An overview area (e.g. a whole mesh of the grid) is imaged with an automated tiling and stitching process. In the final stitched image, the local organisation of the brain tissue can be surveyed or areas of interest can be magnified to observe fine details, e.g. vesicles or gold labels on specific proteins. The robustness of this workflow is contingent on the quality of sample preparation, based on Tokuyasu’s protocol. This method results in a reasonable compromise between preservation of morphology and maintenance of antigenicity. Finally, an important feature of this approach is that the fluorescence of the GFP signal is preserved throughout the entire preparation process until the last step before electron microscopy.





    Categories: Journal Articles
  • The structure of ibuprofen bound to cyclooxygenase-2
    [Feb 2015]

    Publication date: January 2015
    Source:Journal of Structural Biology, Volume 189, Issue 1

    Author(s): Benjamin J. Orlando , Michael J. Lucido , Michael G. Malkowski

    The cyclooxygenases (COX-1 and COX-2) catalyze the rate-limiting step in the biosynthesis of prostaglandins, and are the pharmacological targets of non-steroidal anti-inflammatory drugs (NSAIDs) and COX-2 selective inhibitors (coxibs). Ibuprofen (IBP) is one of the most commonly available over-the-counter pharmaceuticals in the world. The anti-inflammatory and analgesic properties of IBP are thought to arise from inhibition of COX-2 rather than COX-1. While an X-ray crystal structure of IBP bound to COX-1 has been solved, no such structure exists for the cognate isoform COX-2. We have determined the crystal structure of muCOX-2 with a racemic mixture of (R/S)-IBP. Our structure reveals that only the S-isomer of IBP was bound, indicating that the S-isomer possesses higher affinity for COX-2 than the R-isomer. Mutational analysis of Arg-120 and Tyr-355 at the entrance of the cyclooxygenase channel confirmed their role in binding and inhibition of COX-2 by IBP. Our results provide the first atomic level detail of the interaction between IBP and COX-2.





    Categories: Journal Articles
  • Structure of the c-Src-SH3 domain in complex with a proline-rich motif of NS5A protein from the hepatitis C virus
    [Feb 2015]

    Publication date: January 2015
    Source:Journal of Structural Biology, Volume 189, Issue 1

    Author(s): Julio Bacarizo , Sergio Martínez-Rodríguez , Ana Cámara-Artigas

    The non-structural hepatitis C virus proteins NS5A and NS5B form a complex through interaction with the SH2 and SH3 domains of the non-receptor Src tyrosine kinase, which seems essential for viral replication. We have crystallized the complex between the SH3 domain of the c-Src tyrosine kinase and the C-terminal proline rich motif of the NS5A protein (A349PPIPPPRRKR359). Crystals obtained at neutral pH belong to the space group I41, with a single molecule of the SH3/NS5A complex at the asymmetric unit. The NS5A peptide is bound in a reverse orientation (class II) and the comparison of this structure with those of the high affinity synthetic peptides APP12 and VSL12 shows some important differences at the salt bridge that drives the peptide orientation. Further conformational changes in residues placed apart from the binding site also seem to play an important role in the binding orientation of this peptide. Our results show the interaction of the SH3 domain of the c-Src tyrosine kinase with a proline rich motif in the NS5A protein and point to their potential interaction in vivo.





    Categories: Journal Articles
  • Large area sub-micron chemical imaging of magnesium in sea urchin teeth
    [Feb 2015]

    Publication date: Available online 31 December 2014
    Source:Journal of Structural Biology

    Author(s): Admir Masic , James C. Weaver

    The heterogeneous and site-specific incorporation of inorganic ions can profoundly influence the local mechanical properties of damage tolerant biological composites. Using the sea urchin tooth as a research model, we describe a multi-technique approach to spatially map the distribution of magnesium in this complex multiphase system. Through the combined use of 16-bit backscattered scanning electron microscopy, multi-channel energy dispersive spectroscopy elemental mapping, and diffraction-limited confocal Raman spectroscopy, we demonstrate a new set of high throughput, multi-spectral, high resolution methods for the large scale characterization of mineralized biological materials. In addition, instrument hardware and data collection protocols can be modified such that several of these measurements can be performed on irregularly shaped samples with complex surface geometries and without the need for extensive sample preparation. Using these approaches, in conjunction with whole animal micro-computed tomography studies, we have been able to spatially resolve micron and sub-micron structural features across macroscopic length scales on entire urchin tooth cross-sections and correlate these complex morphological features with local variability in elemental composition.





    Categories: Journal Articles
  • Cover 2 - Editorial Board
    [Feb 2015]

    Publication date: December 2014
    Source:Journal of Structural Biology, Volume 188, Issue 3









    Categories: Journal Articles
  • Table of Contents / barcode
    [Feb 2015]

    Publication date: December 2014
    Source:Journal of Structural Biology, Volume 188, Issue 3









    Categories: Journal Articles
  • Distinct structural features of Rex-family repressors to sense redox levels in anaerobes and aerobes
    [Feb 2015]

    Publication date: December 2014
    Source:Journal of Structural Biology, Volume 188, Issue 3

    Author(s): Yingying Zheng , Tzu-Ping Ko , Hong Sun , Chun-Hsiang Huang , Jianjun Pei , Riyong Qiu , Andrew H.-J. Wang , Juergen Wiegel , Weilan Shao , Rey-Ting Guo

    The Rex-family repressors sense redox levels by alternative binding to NADH or NAD+. Unlike other Rex proteins that regulate aerobic respiration, RSP controls ethanol fermentation in the obligate anaerobe Thermoanaerobacter ethanolicus JW200T. It is also found in other anaerobic microorganisms. Here we present the crystal structures of apo-RSP, RSP/NADH and RSP/NAD+/DNA, which are the first structures of Rex-family members from an obligate anaerobe. RSP functions as a homodimer. It assumes an open conformation when bound to the operator DNA and a closed conformation when not DNA-bound. The DNA binds to the N-terminal winged-helix domain and the dinucleotide, either reduced or oxidized, binds to the C-terminal Rossmann-fold domain. The two distinct orientations of nicotinamide ring, anti in NADH and syn in NAD+, give rise to two sets of protein–ligand interactions. Consequently, NADH binding makes RSP into a closed conformation, which does not bind to DNA. Both the conserved residues and the DNA specificity of RSP show a number of variations from those of the aerobic Rex, reflecting different structural bases for redox-sensing by the anaerobic and aerobic Rex-family members.





    Categories: Journal Articles