Journal of Structural Biology

ScienceDirect RSS
  • Investigation of resins suitable for the preparation of biological sample for 3-D electron microscopy
    [Jan 2015]

    Publication date: Available online 26 November 2014
    Source:Journal of Structural Biology

    Author(s): Caroline Kizilyaprak , Giovanni Longo , Jean Daraspe , Bruno M. Humbel

    In the last two decades, the third-dimension has become a focus of attention in electron microscopy to better understand the interactions within subcellular compartments. Initially, transmission electron tomography (TEM tomography) was introduced to image the cell volume in semi-thin sections (∼500nm). With the introduction of the focused ion beam scanning electron microscope, a new tool, FIB–SEM tomography, became available to image much larger volumes. During TEM tomography and FIB–SEM tomography, the resin section is exposed to a high electron/ion dose such that the stability of the resin embedded biological sample becomes an important issue. The shrinkage of a resin section in each dimension, especially in depth, is a well-known phenomenon. To ensure the dimensional integrity of the final volume of the cell, it is important to assess the properties of the different resins and determine the formulation which has the best stability in the electron/ion beam. Here, eight different resin formulations were examined. The effects of radiation damage were evaluated after different times of TEM irradiation. To get additional information on mass-loss and the physical properties of the resins (stiffness and adhesion), the topography of the irradiated areas was analysed with atomic force microscopy (AFM). Further, the behaviour of the resins was analysed after ion milling of the surface of the sample with different ion currents. In conclusion, two resin formulations, Hard Plus and the mixture of Durcupan/Epon, emerged that were considerably less affected and reasonably stable in the electron/ion beam and thus suitable for the 3-D investigation of biological samples.





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

    Publication date: November 2014
    Source:Journal of Structural Biology, Volume 188, Issue 2









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

    Publication date: November 2014
    Source:Journal of Structural Biology, Volume 188, Issue 2









    Categories: Journal Articles
  • Structural insights into enzymatic activity and substrate specificity determination by a single amino acid in nitrilase from Syechocystis sp. PCC6803
    [Jan 2015]

    Publication date: November 2014
    Source:Journal of Structural Biology, Volume 188, Issue 2

    Author(s): Lujia Zhang , Bo Yin , Chao Wang , Shuiqin Jiang , Hualei Wang , Y. Adam Yuan , Dongzhi Wei

    Nitrilases are enzymes widely expressed in prokaryotes and eukaryotes that utilize a Cys–Glu–Lys catalytic triad to hydrolyze non-peptide carbon–nitrogen bonds. Nitrilase from Syechocystis sp. Strain PCC6803 (Nit6803) shows hydrolysis activity towards a broad substrate spectrum, ranging from mononitriles to dinitriles and from aromatic nitriles to aliphatic nitriles. Yet, the structural principle of the substrate specificity of this nitrilase is still unknown. We report the crystal structure of Nit6803 at 3.1Å resolution and propose a structural mechanism of substrate selection. Our mutagenesis data exhibited that the aromaticity of the amino acid at position 146 of Nit6803 is absolutely required for its nitrilase activity towards any substrates tested. Moreover, molecular docking and dynamic simulation analysis indicated that the distance between the sulfhydryl group of the catalytic cysteine residue and the cyano carbon of the substrate plays a crucial role in determining the nitrilase catalytic activity of Nit6803 and its mutants towards different nitrile substrates.





    Categories: Journal Articles
  • Efficient cryoprotection of macromolecular crystals using vapor diffusion of volatile alcohols
    [Jan 2015]

    Publication date: November 2014
    Source:Journal of Structural Biology, Volume 188, Issue 2

    Author(s): Christopher Farley , Douglas H. Juers

    Macromolecular X-ray crystallography, usually done at cryogenic temperature to limit radiation damage, often requires liquid cryoprotective soaking that can be labor intensive and damaging to crystals. Here we describe a method for cryoprotection that uses vapor diffusion of volatile cryoprotective agents into loop-mounted crystals. The crystal is mounted into a vial containing a small volume of an alcohol-based cryosolution. After a short incubation with the looped crystal sitting in the cryosolution vapor, the crystal is transferred directly from the vial into the cooling medium. Effective for several different protein crystals, the approach obviates the need for liquid soaking and opens up a heretofore underutilized class of cryoprotective agents for macromolecular crystallography.





    Categories: Journal Articles
  • Super-sampling SART with ordered subsets
    [Jan 2015]

    Publication date: November 2014
    Source:Journal of Structural Biology, Volume 188, Issue 2

    Author(s): Michael Kunz , Achilleas S. Frangakis

    In tomography, the quality of the reconstruction is essential because the complete cascade of the subsequent analysis is based on it. To date, weighted back-projection (WBP) has been the most commonly used technique due to its versatility and performance in sub-tomogram averaging. Here we present super-sampling SART that is based on the simultaneous algebraic reconstruction technique. While algebraic reconstruction techniques typically produce better contrast and lately showed a significant improvement in terms of processing speed, sub-tomogram averages derived from those reconstructions were inferior in resolution compared to those derived from WBP data. Super-sampling SART, however, outperforms both in term of contrast and the resolution achieved in sub-tomogram averaging several other tested methods and in particular WBP. The main feature of super-sampling SART, as the name implies, is the super-sampling option – by which parameter-based up-sampling and down-sampling are used to reduce artifacts. In particular, the aliasing that is omnipresent in the reconstruction can be practically eliminated without a significant increase in the computational time. Furthermore, super-sampling SART reaches convergence within a single iteration, making the processing time comparable to WBP, and eliminating the ambiguity of parameter-controlled convergence times. We find that grouping of projections increases the contrast, while when projections are used individually the resolution can be maximized. Using sub-tomogram averaging of ribosomes as a test case, we show that super-sampling SART achieves equal or better sub-tomogram averaging results than WBP, which is of particular importance in cryo-electron tomography.





    Categories: Journal Articles
  • Changes in tissue directionality reflect differences in myelin content after demyelination in mice spinal cords
    [Jan 2015]

    Publication date: November 2014
    Source:Journal of Structural Biology, Volume 188, Issue 2

    Author(s): Mohammad K. Ansari , Heather Y.F. Yong , Luanne Metz , V. Wee Yong , Yunyan Zhang

    Changes in myelin integrity are key manifestations of many neurological diseases including multiple sclerosis but precise measurement of myelin in vivo is challenging. The goal of this study was to evaluate myelin content in histological images obtained from a lysolecithin mouse model of demyelination, using a new quantitative method named structure tensor analysis. Injury was targeted at the dorsal column of mice spinal cords. We obtained 16 histological images stained with luxol fast blue for myelin from 9 mice: 9 images from lesion epicenter and 7 from a distant area 500-μm away from the epicenter. In each image, we categorized 3 tissue types: healthy, completely demyelinated, and partially demyelinated. Structure tensor analysis was applied to quantify the coherency (anisotropy), energy (trace of dominant directions), and angular entropy (degree of disorder) of each tissue. We found that completely demyelinated lesions had significantly lower coherency and energy but higher angular entropy than partially demyelinated and healthy tissues at both the epicenter and distant areas of the injury. In addition, the coherency of healthy tissue was greater than partially demyelinated tissue at each site. Within tissue category, we did not find differences in any measure between spinal cord locations. Our findings suggest that greater myelin integrity is associated with better tissue anisotropy, independent of injury location. Structure tensor analysis may serve as a new tool for quantitative measurement of myelin content in white matter, and this may help understand disease mechanisms and development in MS and other demyelinating disorders.





    Categories: Journal Articles
  • Designability landscape reveals sequence features that define axial helix rotation in four-helical homo-oligomeric antiparallel coiled-coil structures
    [Jan 2015]

    Publication date: November 2014
    Source:Journal of Structural Biology, Volume 188, Issue 2

    Author(s): Krzysztof Szczepaniak , Grzegorz Lach , Janusz M. Bujnicki , Stanislaw Dunin-Horkawicz

    Coiled coils are widespread protein domains comprising α-helices wound around each other in a regular fashion. Owing to their regularity, coiled-coil structures can be fully described by parametric equations. This in turn makes them an excellent model for studying sequence–structure relationships in proteins. Here, we used computational design to identify sequence features that determine the degree of helix axial rotation in four-helical homo-oligomeric antiparallel coiled coils. We designed 135,000 artificial sequences for a repertoire of backbone models representing all theoretically possible axial rotation states. Analysis of the designed sequences revealed features that precisely define the rotation of the helices. Based on these features we implemented a bioinformatic tool, which given a coiled-coil sequence, predicts the rotation of the helices in its structure. Moreover, we showed that another structural parameter, helix axial shift, is coupled to helix axial rotation and that dependence between these two parameters narrows the number of possible axial rotation states.





    Categories: Journal Articles
  • Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol
    [Jan 2015]

    Publication date: November 2014
    Source:Journal of Structural Biology, Volume 188, Issue 2

    Author(s): Carlos Oscar S. Sorzano , José Miguel de la Rosa-Trevín , Florence Tama , Slavica Jonić

    This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction.





    Categories: Journal Articles
  • Comparative structure of vertebrate sperm chromatin
    [Jan 2015]

    Publication date: November 2014
    Source:Journal of Structural Biology, Volume 188, Issue 2

    Author(s): Juan Ausió , Rodrigo González-Romero , Christopher L. Woodcock

    A consistent feature of sperm nuclei is its exceptionally compact state in comparison with somatic nuclei. Here, we have examined the structural organization of sperm chromatin from representatives of three vertebrate lineages, bony fish (Danio rerio), birds (Gallus gallus domesticus) and mammals (Mus musculus) using light and transmission electron microscopy (TEM). Although the three sperm nuclei are all highly compact, they differ in morphology and in the complement of compaction-inducing proteins. Whereas zebrafish sperm retain somatic histones and a nucleosomal organization, in the rooster and mouse, histones are largely replaced by small, arginine-rich protamines. In contrast to the mouse, the rooster protamine contains no cysteine residues and lacks the potential stabilizing effects of S–S bonds. Protamine driven chromatin compaction results in a stable, highly condensed chromatin, markedly different from the somatic nucleosome-based beads-on-a-string architecture, but its structure remains poorly understood. When prepared gently for whole mount TEM, the rooster and mouse sperm chromatin reveal striking rod-like units 40–50nm in width. Also present in the mouse, which has very flattened sperm nuclei, but not rooster, where nuclei take the form of elongated cylinders, are toroidal shaped structures, with an external diameter of about 90nm. In contrast, similarly prepared zebrafish sperm exhibit nucleosomal chromatin. We also examined the early stages in the binding of salmine (the salmon protamine) to defined sequence DNA. These images suggest an initial side-by-side binding of linear DNA–protamine complexes leading to the nucleation of thin, flexible rods with the potential to bend, allowing the ends to come into contact and fuse to form toroidal structures. We discuss the relationship between these in vitro observations and the rods and toroids seen in nuclei, and suggest an explanation for the apparent absence of these structures in TEM images of fully condensed sperm nuclei.





    Categories: Journal Articles
  • Crystal structures for short-chain pentraxin from zebrafish demonstrate a cyclic trimer with new recognition and effector faces
    [Jan 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
  • Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site
    [Jan 2015]

    Publication date: Available online 7 January 2015
    Source:Journal of Structural Biology

    Author(s): Chathurada S. Gajadeera , Xinyi Zhang , Yinan Wei , Oleg V. Tsodikov

    Cytoplasmic inorganic pyrophosphatase (PPiase) is an enzyme essential for survival of organisms, from bacteria to human. PPiases are divided into two structurally distinct families: family I PPiases are Mg2+-dependent and present in most archaea, eukaryotes and prokaryotes, whereas the relatively less understood family II PPiases are Mn2+-dependent and present only in some archaea, bacteria and primitive eukaryotes. Staphylococcus aureus (SA), a dangerous pathogen and a frequent cause of hospital infections, contains a family II PPiase (PpaC), which is an attractive potential target for development of novel antibacterial agents. We determined a crystal structure of SA PpaC in complex with catalytic Mn2+ at 2.1Å resolution. The active site contains two catalytic Mn2+ binding sites, each half-occupied, reconciling the previously observed 1:1 Mn2+:enzyme stoichiometry with the presence of two divalent metal ion sites in the apo-enzyme. Unexpectedly, despite the absence of the substrate or products in the active site, the two domains of SA PpaC form a closed active site, a conformation observed in structures of other family II PPiases only in complex with substrate or product mimics. A region spanning residues 295–298, which contains a conserved substrate binding RKK motif, is flipped out of the active site, an unprecedented conformation for a PPiase. Because the mutant of Arg295 to an alanine is devoid of activity, this loop likely undergoes an induced-fit conformational change upon substrate binding and product dissociation. This closed conformation of SA PPiase may serve as an attractive target for rational design of inhibitors of this enzyme.





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

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









    Categories: Journal Articles
  • Table of Contents / barcode
    [Jan 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
    [Jan 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
    [Jan 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
    [Jan 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
    [Jan 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
    [Jan 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
    [Jan 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