Theory of morphological transformation of viral capsid shell during the maturation process in the HK97 bacteriophage and similar viruses

NASA Astrophysics Data System (ADS)

Konevtsova, O. V.; Lorman, V. L.; Rochal, S. B.

2016-05-01

We consider the symmetry and physical origin of collective displacement modes playing a crucial role in the morphological transformation during the maturation of the HK97 bacteriophage and similar viruses. It is shown that the experimentally observed hexamer deformation and pentamer twist in the HK97 procapsid correspond to the simplest irreducible shear strain mode of a spherical shell. We also show that the icosahedral faceting of the bacteriophage capsid shell is driven by the simplest irreducible radial displacement field. The shear field has the rotational icosahedral symmetry group I while the radial field has the full icosahedral symmetry Ih. This difference makes their actions independent. The radial field sign discriminates between the icosahedral and the dodecahedral shapes of the faceted capsid shell, thus making the approach relevant not only for the HK97-like viruses but also for the parvovirus family. In the frame of the Landau-Ginzburg formalism we propose a simple phenomenological model valid for the first reversible step of the HK97 maturation process. The calculated phase diagram illustrates the discontinuous character of the virus shape transformation. The characteristics of the virus shell faceting and expansion obtained in the in vitro and in vivo experiments are related to the decrease in the capsid shell thickness and to the increase of the internal capsid pressure.

Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs

PubMed Central

Baker, T. S.; Olson, N. H.; Fuller, S. D.

1999-01-01

Viruses are cellular parasites. The linkage between viral and host functions makes the study of a viral life cycle an important key to cellular functions. A deeper understanding of many aspects of viral life cycles has emerged from coordinated molecular and structural studies carried out with a wide range of viral pathogens. Structural studies of viruses by means of cryo-electron microscopy and three-dimensional image reconstruction methods have grown explosively in the last decade. Here we review the use of cryo-electron microscopy for the determination of the structures of a number of icosahedral viruses. These studies span more than 20 virus families. Representative examples illustrate the use of moderate- to low-resolution (7- to 35-Å) structural analyses to illuminate functional aspects of viral life cycles including host recognition, viral attachment, entry, genome release, viral transcription, translation, proassembly, maturation, release, and transmission, as well as mechanisms of host defense. The success of cryo-electron microscopy in combination with three-dimensional image reconstruction for icosahedral viruses provides a firm foundation for future explorations of more-complex viral pathogens, including the vast number that are nonspherical or nonsymmetrical. PMID:10585969

The Crystallographic Structure of Panicum Mosaic Virus (PMV)

PubMed Central

Makino, Debora L.; Larson, Steven B.; McPherson, Alexander

2012-01-01

The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9 Å resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P21 with a=411.7 Å, b=403.9 Å and c=412.5 Å, with β=89.7°. The asymmetric unit was two entire T=3 virus particles, or 360 protein subunits. The structure was solved by conventional molecular replacement from two distant homologues, Cocksfoot Mottle Virus (CfMV) and Tobacco Necrosis Virus (TNV), of ~20% sequence identity followed by phase extension. The model was initially refined with exact icosahedral constraints and then with icosahedral restraints. The virus has Ca++ ions octahedrally coordinated by six aspartic acid residues on quasi threefold axes, which is completely different than for either CfMV or TNV. Amino terminal residues 1–53, 1–49 and 1-21 of the A, B and C subunits, respectively, and the four C-terminal residues (239-242) are not visible in electron density maps. The additional ordered residues of the C chain form a prominent “arm” that intertwines with symmetry equivalent “arms” at icosahedral threefold axes, as was seen in both CfMV and TNV. A 17 nucleotide hairpin segment of genomic RNA is icosahedrally ordered and bound at 60 equivalent sites at quasi twofold A–B subunit interfaces at the interior surface of the capsid. This segment of RNA may serve as a conformational switch for coat protein subunits, as has been proposed for similar RNA segments in other viruses. PMID:23123270

Cryo-Electron Microscopy of Viruses Infecting Bacterium

NASA Astrophysics Data System (ADS)

Chiu, Wah

2010-03-01

Single particle cryo-EM can yield structures of infectious bacterial viruses with and without imposed icosahedral symmetry at subnanometer resolution. Reconstructions of infectious and empty phage particles show substantial differences in the portal vertex protein complex at one of the 12 pentameric vertices in the icosahedral virus particle through which the viral genomes are packaged or released. In addition, electron cryo-tomography of viruses during infecting its bacterial host cell displayed multiple conformations of the tail fiber of the virus. Our structural observations by single particle and tomographic reconstructions suggest a mechanism whereby the viral tail fibers, upon binding to the host cell, induce a cascade of structural alterations of the portal vertex protein complex that triggers DNA release.

Virus templated plasmonic nanoclusters with icosahedral symmetry via directed assembly

NASA Astrophysics Data System (ADS)

Ratna, Banahalli; Fontana, Jake; Dressick, Walter; Phelps, Jamie; Johnson, John; Sampson, Travian; Rendell, Ronald; Soto, Carissa

2015-03-01

Controlling the spatial and orientational order of plasmonic nanoparticles may lead to structures with novel electromagnetic properties and applications such as sub-wavelength imaging and ultra-sensitive chemical sensors. Here we report the directed assembly of three-dimensional, icosahedral plasmonic nanoclusters with resonances at visible wavelengths. We show using transmission electron microcopy and in situ dynamic light scattering the nanoclusters consist of twelve gold nanospheres attached to thiol groups at predefined locations on the surface of a genetically engineered cowpea mosaic virus with icosahedral symmetry. We measured the bulk absorbance from aqueous suspensions of nanoclusters and reproduced the major features of the spectrum using finite-element simulations. Furthermore, because the viruses are easily produced in gram quantities the directed assembly approach is capable of high-throughput, providing a strategy to realize large quantities for applications. NRL summer intern under the HBCU/MI Summer Research Program.

Monitoring Physiological Changes in Haloarchaeal Cell during Virus Release

PubMed Central

Svirskaitė, Julija; Oksanen, Hanna M.; Daugelavičius, Rimantas; Bamford, Dennis H.

2016-01-01

The slow rate of adsorption and non-synchronous release of some archaeal viruses have hindered more thorough analyses of the mechanisms of archaeal virus release. To address this deficit, we utilized four viruses that infect Haloarcula hispanica that represent the four virion morphotypes currently known for halophilic euryarchaeal viruses: (1) icosahedral internal membrane-containing SH1; (2) icosahedral tailed HHTV-1; (3) spindle-shaped His1; and (4) pleomorphic His2. To discern the events occurring as the progeny viruses exit, we monitored culture turbidity, as well as viable cell and progeny virus counts of infected and uninfected cultures. In addition to these traditional metrics, we measured three parameters associated with membrane integrity: the binding of the lipophilic anion phenyldicarbaundecaborane, oxygen consumption, and both intra- and extra-cellular ATP levels. PMID:26927156

Archaeal Haloarcula californiae Icosahedral Virus 1 Highlights Conserved Elements in Icosahedral Membrane-Containing DNA Viruses from Extreme Environments.

PubMed

Demina, Tatiana A; Pietilä, Maija K; Svirskaitė, Julija; Ravantti, Janne J; Atanasova, Nina S; Bamford, Dennis H; Oksanen, Hanna M

2016-07-19

Despite their high genomic diversity, all known viruses are structurally constrained to a limited number of virion morphotypes. One morphotype of viruses infecting bacteria, archaea, and eukaryotes is the tailless icosahedral morphotype with an internal membrane. Although it is considered an abundant morphotype in extreme environments, only seven such archaeal viruses are known. Here, we introduce Haloarcula californiae icosahedral virus 1 (HCIV-1), a halophilic euryarchaeal virus originating from salt crystals. HCIV-1 also retains its infectivity under low-salinity conditions, showing that it is able to adapt to environmental changes. The release of progeny virions resulting from cell lysis was evidenced by reduced cellular oxygen consumption, leakage of intracellular ATP, and binding of an indicator ion to ruptured cell membranes. The virion contains at least 12 different protein species, lipids selectively acquired from the host cell membrane, and a 31,314-bp-long linear double-stranded DNA (dsDNA). The overall genome organization and sequence show high similarity to the genomes of archaeal viruses in the Sphaerolipoviridae family. Phylogenetic analysis based on the major conserved components needed for virion assembly-the major capsid proteins and the packaging ATPase-placed HCIV-1 along with the alphasphaerolipoviruses in a distinct, well-supported clade. On the basis of its virion morphology and sequence similarities, most notably, those of its core virion components, we propose that HCIV-1 is a member of the PRD1-adenovirus structure-based lineage together with other sphaerolipoviruses. This addition to the lineage reinforces the notion of the ancient evolutionary links observed between the viruses and further highlights the limits of the choices found in nature for formation of a virion. Under conditions of extreme salinity, the majority of the organisms present are archaea, which encounter substantial selective pressure, being constantly attacked by viruses. Regardless of the enormous viral sequence diversity, all known viruses can be clustered into a few structure-based viral lineages based on their core virion components. Our description of a new halophilic virus-host system adds significant insights into the largely unstudied field of archaeal viruses and, in general, of life under extreme conditions. Comprehensive molecular characterization of HCIV-1 shows that this icosahedral internal membrane-containing virus exhibits conserved elements responsible for virion organization. This places the virus neatly in the PRD1-adenovirus structure-based lineage. HCIV-1 further highlights the limited diversity of virus morphotypes despite the astronomical number of viruses in the biosphere. The observed high conservation in the core virion elements should be considered in addressing such fundamental issues as the origin and evolution of viruses and their interplay with their hosts. Copyright © 2016 Demina et al.

Unlocking Internal Prestress from Protein Nanoshells

NASA Astrophysics Data System (ADS)

Klug, W. S.; Roos, W. H.; Wuite, G. J. L.

2012-10-01

The capsids of icosahedral viruses are closed shells assembled from a hexagonal lattice of proteins with fivefold angular defects located at the icosahedral vertices. Elasticity theory predicts that these disclinations are subject to an internal compressive prestress, which provides an explanation for the link between size and shape of capsids. Using a combination of experiment and elasticity theory we investigate the question of whether macromolecular assemblies are subject to residual prestress, due to basic geometric incompatibility of the subunits. Here we report the first direct experimental test of the theory: by controlled removal of protein pentamers from the icosahedral vertices, we measure the mechanical response of so-called “whiffle ball” capsids of herpes simplex virus, and demonstrate the signature of internal prestress locked into wild-type capsids during assembly.

The 3.2 Angstrom Resolution Structure of the Polymorphic Cowpea Chlorotic Mottle Virus Ribonucleoprotein Particle

NASA Astrophysics Data System (ADS)

Speir, Jeffrey Alan

Structural studies of the polymorphic cowpea chlorotic mottle virus have resulted in high resolution structures for two distinct icosahedral ribonucleoprotein particle conformations dependent upon whether acidic or basic pH conditions prevail. CCMV is stable below pH 6.5, however metal-free particles maintain a 10% increase in hydrodynamic volume at pH >=q 7.5. Identification of this swollen' form of CCMV, which can easily be disrupted with 1M NaCl, led to the first reassembly of an icosahedral virus in vitro from purified viral protein and RNA to form infectious particles, and its assembly has been the subject of biochemical and biophysical investigations for over twenty-five years. Under well defined conditions of pH, ionic strength and divalent metal ion concentration, CCMV capsid protein or capsid protein and RNA will reassemble to form icosahedral particles of various sizes, sheets, tubes, rosettes, and a variety of laminar structures which resemble virion structures from non-related virus families. Analysis of native particles at 3.2A resolution and swollen particles at 28A resolution has suggested that the chemical basis for the formation of polymorphic icosahedral and anisometric structures is: (i) hexamers formed of beta-barrel subunits stabilized by an unusual hexameric parallel beta structure made up of their N-termini, (ii) the location of protein-RNA interactions, (iii) divalent metal cation binding sites that regulate quasi-symmetrical subunit associations, (iv) charge repulsion across the same interfaces when lacking divalent metal ions at basic pH, which induces the formation of sixty 20A diameter portals for RNA release, and (v) a novel, C-terminal-based, subunit dimer assembly unit. The use of C- and N-terminal arms in CCMV has not been observed in other icosahedral RNA virus structures determined at near atomic resolution, however, their detailed interactions and roles in stabilizing the quaternary organization of CCMV are related to that found in the atomic structures of the DNA tumor papovaviruses (SV40 and polyoma). The swollen structure is closely similar to the expanded form of tomato bushy stunt virus (TBSV) previously determined at 8A resolution by X-ray crystallography.

Curating viscoelastic properties of icosahedral viruses, virus-based nanomaterials, and protein cages.

PubMed

Kant, Ravi; Rayaprolu, Vamseedhar; McDonald, Kaitlyn; Bothner, Brian

2018-06-01

The beauty, symmetry, and functionality of icosahedral virus capsids has attracted the attention of biologists, physicists, and mathematicians ever since they were first observed. Viruses and protein cages assemble into functional architectures in a range of sizes, shapes, and symmetries. To fulfill their biological roles, these structures must self-assemble, resist stress, and are often dynamic. The increasing use of icosahedral capsids and cages in materials science has driven the need to quantify them in terms of structural properties such as rigidity, stiffness, and viscoelasticity. In this study, we employed Quartz Crystal Microbalance with Dissipation technology (QCM-D) to characterize and compare the mechanical rigidity of different protein cages and viruses. We attempted to unveil the relationships between rigidity, radius, shell thickness, and triangulation number. We show that the rigidity and triangulation numbers are inversely related to each other and the comparison of rigidity and radius also follows the same trend. Our results suggest that subunit orientation, protein-protein interactions, and protein-nucleic acid interactions are important for the resistance to deformation of these complexes, however, the relationships are complex and need to be explored further. The QCM-D based viscoelastic measurements presented here help us elucidate these relationships and show the future prospect of this technique in the field of physical virology and nano-biotechnology.

Archaeal Viruses Multiply: Temporal Screening in a Solar Saltern

PubMed Central

Atanasova, Nina S.; Demina, Tatiana A.; Buivydas, Andrius; Bamford, Dennis H.; Oksanen, Hanna M.

2015-01-01

Hypersaline environments around the world are dominated by archaea and their viruses. To date, very little is known about these viruses and their interaction with the host strains when compared to bacterial and eukaryotic viruses. We performed the first culture-dependent temporal screening of haloarchaeal viruses and their hosts in the saltern of Samut Sakhon, Thailand, during two subsequent years (2009, 2010). Altogether we obtained 36 haloarchaeal virus isolates and 36 archaeal strains, significantly increasing the number of known archaeal virus isolates. Interestingly, the morphological distribution of our temporal isolates (head-tailed, pleomorphic, and icosahedral membrane-containing viruses) was similar to the outcome of our previous spatial survey supporting the observations of a global resemblance of halophilic microorganisms and their viruses. Myoviruses represented the most abundant virus morphotype with strikingly broad host ranges. The other viral morphotypes (siphoviruses, as well as pleomorphic and icosahedral internal membrane-containing viruses) were more host-specific. We also identified a group of Halorubrum strains highly susceptible to numerous different viruses (up to 26). This high virus sensitivity, the abundance of broad host range viruses, and the maintenance of infectivity over a period of one year suggest constant interplay of halophilic microorganisms and their viruses within an extreme environment. PMID:25866903

Archaeal viruses multiply: temporal screening in a solar saltern.

PubMed

Atanasova, Nina S; Demina, Tatiana A; Buivydas, Andrius; Bamford, Dennis H; Oksanen, Hanna M

2015-04-10

Hypersaline environments around the world are dominated by archaea and their viruses. To date, very little is known about these viruses and their interaction with the host strains when compared to bacterial and eukaryotic viruses. We performed the first culture-dependent temporal screening of haloarchaeal viruses and their hosts in the saltern of Samut Sakhon, Thailand, during two subsequent years (2009, 2010). Altogether we obtained 36 haloarchaeal virus isolates and 36 archaeal strains, significantly increasing the number of known archaeal virus isolates. Interestingly, the morphological distribution of our temporal isolates (head-tailed, pleomorphic, and icosahedral membrane-containing viruses) was similar to the outcome of our previous spatial survey supporting the observations of a global resemblance of halophilic microorganisms and their viruses. Myoviruses represented the most abundant virus morphotype with strikingly broad host ranges. The other viral morphotypes (siphoviruses, as well as pleomorphic and icosahedral internal membrane-containing viruses) were more host-specific. We also identified a group of Halorubrum strains highly susceptible to numerous different viruses (up to 26). This high virus sensitivity, the abundance of broad host range viruses, and the maintenance of infectivity over a period of one year suggest constant interplay of halophilic microorganisms and their viruses within an extreme environment.

Characterization of a Nepovirus causing a leaf mottling disease in Petunia hybrida

USDA-ARS?s Scientific Manuscript database

This report describes the complete genome sequence and characterization of a new virus infecting petunia. Icosahedral virus-like particles were isolated from Petunia hybrida cuttings with interveinal chlorotic mottling. The virus was transmitted by mechanical inoculation from infected to healthy P. ...

Fourth class of convex equilateral polyhedron with polyhedral symmetry related to fullerenes and viruses.

PubMed

Schein, Stan; Gayed, James Maurice

2014-02-25

The three known classes of convex polyhedron with equal edge lengths and polyhedral symmetry--tetrahedral, octahedral, and icosahedral--are the 5 Platonic polyhedra, the 13 Archimedean polyhedra--including the truncated icosahedron or soccer ball--and the 2 rhombic polyhedra reported by Johannes Kepler in 1611. (Some carbon fullerenes, inorganic cages, icosahedral viruses, geodesic structures, and protein complexes resemble these fundamental shapes.) Here we add a fourth class, "Goldberg polyhedra," which are also convex and equilateral. We begin by decorating each of the triangular facets of a tetrahedron, an octahedron, or an icosahedron with the T vertices and connecting edges of a "Goldberg triangle." We obtain the unique set of internal angles in each planar face of each polyhedron by solving a system of n equations and n variables, where the equations set the dihedral angle discrepancy about different types of edge to zero, and the variables are a subset of the internal angles in 6gons. Like the faces in Kepler's rhombic polyhedra, the 6gon faces in Goldberg polyhedra are equilateral and planar but not equiangular. We show that there is just a single tetrahedral Goldberg polyhedron, a single octahedral one, and a systematic, countable infinity of icosahedral ones, one for each Goldberg triangle. Unlike carbon fullerenes and faceted viruses, the icosahedral Goldberg polyhedra are nearly spherical. The reasoning and techniques presented here will enable discovery of still more classes of convex equilateral polyhedra with polyhedral symmetry.

Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology

PubMed Central

Legendre, Matthieu; Bartoli, Julia; Shmakova, Lyubov; Jeudy, Sandra; Labadie, Karine; Adrait, Annie; Lescot, Magali; Poirot, Olivier; Bertaux, Lionel; Bruley, Christophe; Couté, Yohann; Rivkina, Elizaveta; Abergel, Chantal; Claverie, Jean-Michel

2014-01-01

The largest known DNA viruses infect Acanthamoeba and belong to two markedly different families. The Megaviridae exhibit pseudo-icosahedral virions up to 0.7 μm in diameter and adenine–thymine (AT)-rich genomes of up to 1.25 Mb encoding a thousand proteins. Like their Mimivirus prototype discovered 10 y ago, they entirely replicate within cytoplasmic virion factories. In contrast, the recently discovered Pandoraviruses exhibit larger amphora-shaped virions 1 μm in length and guanine–cytosine-rich genomes up to 2.8 Mb long encoding up to 2,500 proteins. Their replication involves the host nucleus. Whereas the Megaviridae share some general features with the previously described icosahedral large DNA viruses, the Pandoraviruses appear unrelated to them. Here we report the discovery of a third type of giant virus combining an even larger pandoravirus-like particle 1.5 μm in length with a surprisingly smaller 600 kb AT-rich genome, a gene content more similar to Iridoviruses and Marseillevirus, and a fully cytoplasmic replication reminiscent of the Megaviridae. This suggests that pandoravirus-like particles may be associated with a variety of virus families more diverse than previously envisioned. This giant virus, named Pithovirus sibericum, was isolated from a >30,000-y-old radiocarbon-dated sample when we initiated a survey of the virome of Siberian permafrost. The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health. PMID:24591590

Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology.

PubMed

Legendre, Matthieu; Bartoli, Julia; Shmakova, Lyubov; Jeudy, Sandra; Labadie, Karine; Adrait, Annie; Lescot, Magali; Poirot, Olivier; Bertaux, Lionel; Bruley, Christophe; Couté, Yohann; Rivkina, Elizaveta; Abergel, Chantal; Claverie, Jean-Michel

2014-03-18

The largest known DNA viruses infect Acanthamoeba and belong to two markedly different families. The Megaviridae exhibit pseudo-icosahedral virions up to 0.7 μm in diameter and adenine-thymine (AT)-rich genomes of up to 1.25 Mb encoding a thousand proteins. Like their Mimivirus prototype discovered 10 y ago, they entirely replicate within cytoplasmic virion factories. In contrast, the recently discovered Pandoraviruses exhibit larger amphora-shaped virions 1 μm in length and guanine-cytosine-rich genomes up to 2.8 Mb long encoding up to 2,500 proteins. Their replication involves the host nucleus. Whereas the Megaviridae share some general features with the previously described icosahedral large DNA viruses, the Pandoraviruses appear unrelated to them. Here we report the discovery of a third type of giant virus combining an even larger pandoravirus-like particle 1.5 μm in length with a surprisingly smaller 600 kb AT-rich genome, a gene content more similar to Iridoviruses and Marseillevirus, and a fully cytoplasmic replication reminiscent of the Megaviridae. This suggests that pandoravirus-like particles may be associated with a variety of virus families more diverse than previously envisioned. This giant virus, named Pithovirus sibericum, was isolated from a >30,000-y-old radiocarbon-dated sample when we initiated a survey of the virome of Siberian permafrost. The revival of such an ancestral amoeba-infecting virus used as a safe indicator of the possible presence of pathogenic DNA viruses, suggests that the thawing of permafrost either from global warming or industrial exploitation of circumpolar regions might not be exempt from future threats to human or animal health.

Dynamic and Kinetic Assembly Studies of an Icosahedral Virus Capsid

NASA Astrophysics Data System (ADS)

Lee, Kelly

2011-03-01

Hepatitis B virus has an icosahedrally symmetrical core particle (capsid), composed of either 90 or 120 copies of a dimeric protein building block. We are using time-resolved, solution small-angle X-ray scattering and single-molecule fluorescence microscopy to probe the core particle assembly reaction at the ensemble and individual assembly levels. Our experiments to date reveal the assembly process to be highly cooperative with minimal population of stable intermediate species. Solution conditions, particularly salt concentration, appears to influence the partitioning of assembly products into the two sizes of shells. Funding from NIH R00-GM080352 and University of Washington.

Theoretical and Numerical Modeling of faceted Ionic crystalline vesicles

NASA Astrophysics Data System (ADS)

Olvera de La Cruz, Monica

2007-03-01

Icosahedral shape is found in several natural structures including large viruses, large fullerenes and cationic-anionic vesicles. Faceting into icosahedral shape can occur in large crystalline membranes via elasticity theory. Icosahedral symmetry is found in small systems of particles with short-range interactions on a sphere. Dr G. Vernizzi and I show a novel electrostatic-driven mechanism of ionic crystalline shells faceting into icosahedral shapes even for systems with a small number of particles. Icosahedral shape is possible in cationic and anionic molecules adsorbed onto spherical interfaces, such as emulsions or other immiscible liquid droplets because the large concentration of charges at the interface can lead to ionic crystals on the curved interface. Such self-organized ionic structures favors the formation of flat surfaces. We find that these ionic crystalline shells can have lower energy when faceted into icosahedra along particular directions. Indeed, the ``ionic'' buckling is driven by preferred bending directions of the planar ionic structure, along which is more likely for the icosahedral shape to develop an edge. Since only certain orientations are allowed, rotational symmetry is broken. One can hope to exploit this mechanism to generate functional materials where, for instance, proteins with specific charge groups can orient at specific directions along an icosahedral cationic-anionic vesicle.

Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus

NASA Astrophysics Data System (ADS)

Hespenheide, B. M.; Jacobs, D. J.; Thorpe, M. F.

2004-11-01

The cowpea chlorotic mottle virus (CCMV) has a protein cage, or capsid, which encloses its genetic material. The structure of the capsid consists of 180 copies of a single protein that self-assemble inside a cell to form a complete capsid with icosahedral symmetry. The icosahedral surface can be naturally divided into pentagonal and hexagonal faces, and the formation of either of these faces has been proposed to be the first step in the capsid assembly process. We have used the software FIRST to analyse the rigidity of pentameric and hexameric substructures of the complete capsid to explore the viability of certain capsid assembly pathways. FIRST uses the 3D pebble game to determine structural rigidity, and a brief description of this algorithm, as applied to body-bar networks, is given here. We find that the pentameric substructure, which corresponds to a pentagonal face on the icosahedral surface, provides the best structural properties for nucleating the capsid assembly process, consistent with experimental observations.

Presence of Two Virus-Like Particles in Penicillium citrinum

PubMed Central

Volterra, L.; Cassone, A.; Tonolo, A.; Bruzzone, M. L.

1975-01-01

Two icosahedral virus-like particles (28 and 19 nm in diameter, respectively) have been detected in sporogenic and asporogenic segregants of a strain of Penicillium citrinum. The distribution of the two particles differed among the two segregants. Images PMID:50049

Problems in understanding the structure and assembly of viruses

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, J.

1997-12-01

Though viruses infect the cells of all groups of animals, plants, and microorganisms, their structures follow a limited number of general themes; spherical or cylindrical shells built of hundreds of repeated protein subunits enclosing a nucleic acid - DNA or RNA - genome. Since the 1960s it has been known that the protein shells of spherical viruses in fact conform to icosahedral symmetry or to subtle deviations from icosahedral symmetry. The construction of the shell lattices and the transformations they go through in the different stages of the viral life cycle are not fully understood. The shells contain the nucleicmore » in a highly condensed state, of unknown coiling/organization. Features of the well studied bacterial viruses will be reviewed, with examples from adenoviruses, herpesviruses, poliovirus, and HIV. The emergence of new viral disease has led to increased interest in the development of agents which interfere with virus reproduction at the level of the assembly or function of the organized particle. Recently computational approaches to the problem of virus assembly have made important contributions to clarifying shell assembly processes. 1 ref.« less

Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids

NASA Astrophysics Data System (ADS)

Dykeman, Eric C.; Sankey, Otto F.

2010-02-01

We describe a technique for calculating the low-frequency mechanical modes and frequencies of a large symmetric biological molecule where the eigenvectors of the Hessian matrix are determined with full atomic detail. The method, which follows order N methods used in electronic structure theory, determines the subset of lowest-frequency modes while using group theory to reduce the complexity of the problem. We apply the method to three icosahedral viruses of various T numbers and sizes; the human viruses polio and hepatitis B, and the cowpea chlorotic mottle virus, a plant virus. From the normal-mode eigenvectors, we use a bond polarizability model to predict a low-frequency Raman scattering profile for the viruses. The full atomic detail in the displacement patterns combined with an empirical potential-energy model allows a comparison of the fully atomic normal modes with elastic network models and normal-mode analysis with only dihedral degrees of freedom. We find that coarse-graining normal-mode analysis (particularly the elastic network model) can predict the displacement patterns for the first few (˜10) low-frequency modes that are global and cooperative.

Single-particle cryo-electron microscopy of Rift Valley fever virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sherman, Michael B.; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555; Freiberg, Alexander N.

2009-04-25

Rift Valley fever virus (RVFV; Bunyaviridae; Phlebovirus) is an emerging human and veterinary pathogen causing acute hepatitis in ruminants and has the potential to cause hemorrhagic fever in humans. We report a three-dimensional reconstruction of RVFV vaccine strain MP-12 (RVFV MP-12) by cryo-electron microcopy using icosahedral symmetry of individual virions. Although the genomic core of RVFV MP-12 is apparently poorly ordered, the glycoproteins on the virus surface are highly symmetric and arranged on a T = 12 icosahedral lattice. Our RVFV MP-12 structure allowed clear identification of inter-capsomer contacts and definition of possible glycoprotein arrangements within capsomers. This structure providesmore » a detailed model for phleboviruses, opens new avenues for high-resolution structural studies of the bunyavirus family, and aids the design of antiviral diagnostics and effective subunit vaccines.« less

The diversity of the orthoreoviruses: molecular taxonomy and phylogentic divides.

USDA-ARS?s Scientific Manuscript database

The family Reoviridae is a diverse group of viruses with double-stranded ribonucleic acid (RNA) genomes contained within icosahedral, layered protein capsids. Within the Reoviridae, the Orthoreovirus genus includes viruses that infect reptiles, birds and mammals (including humans). Recent sequencing...

Imaging and Quantitation of a Succession of Transient Intermediates Reveal the Reversible Self-Assembly Pathway of a Simple Icosahedral Virus Capsid.

PubMed

Medrano, María; Fuertes, Miguel Ángel; Valbuena, Alejandro; Carrillo, Pablo J P; Rodríguez-Huete, Alicia; Mateu, Mauricio G

2016-11-30

Understanding the fundamental principles underlying supramolecular self-assembly may facilitate many developments, from novel antivirals to self-organized nanodevices. Icosahedral virus particles constitute paradigms to study self-assembly using a combination of theory and experiment. Unfortunately, assembly pathways of the structurally simplest virus capsids, those more accessible to detailed theoretical studies, have been difficult to study experimentally. We have enabled the in vitro self-assembly under close to physiological conditions of one of the simplest virus particles known, the minute virus of mice (MVM) capsid, and experimentally analyzed its pathways of assembly and disassembly. A combination of electron microscopy and high-resolution atomic force microscopy was used to structurally characterize and quantify a succession of transient assembly and disassembly intermediates. The results provided an experiment-based model for the reversible self-assembly pathway of a most simple (T = 1) icosahedral protein shell. During assembly, trimeric capsid building blocks are sequentially added to the growing capsid, with pentamers of building blocks and incomplete capsids missing one building block as conspicuous intermediates. This study provided experimental verification of many features of self-assembly of a simple T = 1 capsid predicted by molecular dynamics simulations. It also demonstrated atomic force microscopy imaging and automated analysis, in combination with electron microscopy, as a powerful single-particle approach to characterize at high resolution and quantify transient intermediates during supramolecular self-assembly/disassembly reactions. Finally, the efficient in vitro self-assembly achieved for the oncotropic, cell nucleus-targeted MVM capsid may facilitate its development as a drug-encapsidating nanoparticle for anticancer targeted drug delivery.

Reconstruction of viruses from solution x-ray scattering data

NASA Astrophysics Data System (ADS)

Zheng, Yibin; Doerschuk, Peter C.; Johnson, John E.

1995-08-01

A model-based method for reconstructing the 3D structure of icosahedrally-symmetric viruses from solution x-ray scattering is presented. An example of the reconstruction, for data from cowpea mosaic virus, is described. The major opportunity provided by solution x-ray scattering is the ability to study the dynamics of virus particles in solution, information that is not accessible to crystal x-ray diffraction experiments.

Soft materials design via self assembly of functionalized icosahedral particles

NASA Astrophysics Data System (ADS)

Muthukumar, Vidyalakshmi Chockalingam

In this work we simulate self assembly of icosahedral building blocks using a coarse grained model of the icosahedral capsid of virus 1m1c. With significant advancements in site-directed functionalization of these macromolecules [1], we propose possible application of such self-assembled materials for drug delivery. While there have been some reports on organization of viral particles in solution through functionalization, exploiting this behaviour for obtaining well-ordered stoichiometric structures has not yet been explored. Our work is in well agreement with the earlier simulation studies of icosahedral gold nanocrystals, giving chain like patterns [5] and also broadly in agreement with the wet lab works of Finn, M.G. et al., who have shown small predominantly chain-like aggregates with mannose-decorated Cowpea Mosaic Virus (CPMV) [22] and small two dimensional aggregates with oligonucleotide functionalization on the CPMV capsid [1]. To quantify the results of our Coarse Grained Molecular Dynamics Simulations I developed analysis routines in MATLAB using which we found the most preferable nearest neighbour distances (from the radial distribution function (RDF) calculations) for different lengths of the functional groups and under different implicit solvent conditions, and the most frequent coordination number for a virus particle (histogram plots further using the information from RDF). Visual inspection suggests that our results most likely span the low temperature limits explored in the works of Finn, M.G. et al., and show a good degree of agreement with the experimental results in [1] at an annealing temperature of 4°C. Our work also reveals the possibility of novel stoichiometric N-mer type aggregates which could be synthesized using these capsids with appropriate functionalization and solvent conditions.

Single-particle cryo-electron microscopy of Rift Valley fever virus

PubMed Central

Sherman, Michael B.; Freiberg, Alexander N.; Holbrook, Michael R.; Watowich, Stanley J.

2009-01-01

Rift Valley fever virus (RVFV; Bunyaviridae; Phlebovirus) is an emerging human veterinary pathogen causing acute hepatitis in ruminants and has the potential to Single-particle cryo-EM reconstruction of RVFV MP-12 hemorrhagic fever in humans. We report a three-dimensional reconstruction of RVFV vaccine strain MP-12 (RVFV MP-12) by cryo-electron microcopy using icosahedral symmetry of individual virions. Although the genomic core of RVFV MP-12 is apparently poorly ordered, the glycoproteins on the virus surface are highly symmetric and arranged on a T=12 icosahedral lattice. Our RVFV MP-12 structure allowed clear identification of inter-capsomer contacts and definition of possible glycoprotein arrangements within capsomers. This structure provides a detailed model for phleboviruses, opens new avenues for high-resolution structural studies of the bunyavirus family, and aids the design of antiviral diagnostics and effective subunit-vaccines. PMID:19304307

ICTV Virus taxonomy profile: Asfarviridae

USDA-ARS?s Scientific Manuscript database

The family Asfarviridae includes the single species African swine fever virus, isolates of which have linear dsDNA genomes of 170-194 kbp. Virons have an internal core, an internal lipid membrane, an icosahedral capsid and an outer lipid envelope. Infection of domestic pigs and wild boar results i...

Cryo-Electron Tomography of Rubella Virus

PubMed Central

Battisti, Anthony J.; Yoder, Joshua D.; Plevka, Pavel; Winkler, Dennis C.; Mangala Prasad, Vidya; Kuhn, Richard J.; Frey, Teryl K.; Steven, Alasdair C.

2012-01-01

Rubella virus is the only member of the Rubivirus genus within the Togaviridae family and is the causative agent of the childhood disease known as rubella or German measles. Here, we report the use of cryo-electron tomography to examine the three-dimensional structure of rubella virions and compare their structure to that of Ross River virus, a togavirus belonging the genus Alphavirus. The ectodomains of the rubella virus glycoproteins, E1 and E2, are shown to be organized into extended rows of density, separated by 9 nm on the viral surface. We also show that the rubella virus nucleocapsid structure often forms a roughly spherical shell which lacks high density at its center. While many rubella virions are approximately spherical and have dimensions similar to that of the icosahedral Ross River virus, the present results indicate that rubella exhibits a large degree of pleomorphy. In addition, we used rotation function calculations and other analyses to show that approximately spherical rubella virions lack the icosahedral organization which characterizes Ross River and other alphaviruses. The present results indicate that the assembly mechanism of rubella virus, which has previously been shown to differ from that of the alphavirus assembly pathway, leads to an organization of the rubella virus structural proteins that is different from that of alphaviruses. PMID:22855483

Cryo-electron tomography of rubella virus.

PubMed

Battisti, Anthony J; Yoder, Joshua D; Plevka, Pavel; Winkler, Dennis C; Prasad, Vidya Mangala; Kuhn, Richard J; Frey, Teryl K; Steven, Alasdair C; Rossmann, Michael G

2012-10-01

Rubella virus is the only member of the Rubivirus genus within the Togaviridae family and is the causative agent of the childhood disease known as rubella or German measles. Here, we report the use of cryo-electron tomography to examine the three-dimensional structure of rubella virions and compare their structure to that of Ross River virus, a togavirus belonging the genus Alphavirus. The ectodomains of the rubella virus glycoproteins, E1 and E2, are shown to be organized into extended rows of density, separated by 9 nm on the viral surface. We also show that the rubella virus nucleocapsid structure often forms a roughly spherical shell which lacks high density at its center. While many rubella virions are approximately spherical and have dimensions similar to that of the icosahedral Ross River virus, the present results indicate that rubella exhibits a large degree of pleomorphy. In addition, we used rotation function calculations and other analyses to show that approximately spherical rubella virions lack the icosahedral organization which characterizes Ross River and other alphaviruses. The present results indicate that the assembly mechanism of rubella virus, which has previously been shown to differ from that of the alphavirus assembly pathway, leads to an organization of the rubella virus structural proteins that is different from that of alphaviruses.

Shape transformation of viral capsids and HIV

NASA Astrophysics Data System (ADS)

Nguyen, Toan

2005-03-01

We present a continuum description of the shape transformation of viral capsids. The cone-like HIV virus is shown to be an thermodynamic stable shape, intermediate between icosahedral and sphero-cylinder capsid shapes. A generalized Caspar-Klug classification is introduced to describe spherical, conical and cylinderical shapes of virus.

Development and evaluation of a loop-mediated isothermal amplification assay for rapid detection of lymphocystis disease virus.

PubMed

Li, Qiong; Yue, Zhiqin; Liu, Hong; Liang, Chengzhu; Zheng, Xiaolong; Zhao, Yuran; Chen, Xiao; Xiao, Xizhi; Chen, Changfu

2010-02-01

A loop-mediated isothermal amplification (LAMP) assay was developed for the detection of lymphocystis disease virus (LCDV). A set of five specific primers, two inner and two outer primers and a loop primer, were designed on the basis of the major capsid protein gene of LCDV. The reaction time and temperatures were optimized for 60 min at 63 degrees C, respectively. LAMP amplification products were detected by a ladder-like appearance on agarose gel electrophoresis or a naked-eye inspection of a color change in the reaction tube by addition of SYBR Green I. The assay was specific for LCDV, and there was no cross-reactivity with white spot syndrome virus (WSSV) or six other Iridoviridae viruses (epizootic hematopoietic necrosis virus, EHNV; tiger frog virus, TFV; Bohle iridovirus, BIV; soft-shelled turtle iridovirus, STIV; infectious spleen and kidney necrosis virus, ISKNV; red sea bream iridovirus, RSIV). The detection limit of the LAMP assay was 15 fg, which was similar to that of real-time quantitative polymerase chain reaction (PCR) and 10-fold higher than the conventional PCR. The LAMP assay was evaluated using 109 clinical samples, and the results indicated the suitability and simplicity of the test as a rapid, field diagnostic tool for detection of LCDV. The LCDV LAMP assay has potential for early diagnosis of LCDV infection. 2009 Elsevier B.V. All rights reserved.

Structure of large dsDNA viruses

PubMed Central

Klose, Thomas; Rossmann, Michael G.

2015-01-01

Nucleocytoplasmic large dsDNA viruses (NCLDVs) encompass an ever-increasing group of large eukaryotic viruses, infecting a wide variety of organisms. The set of core genes shared by all these viruses includes a major capsid protein with a double jelly-roll fold forming an icosahedral capsid, which surrounds a double layer membrane that contains the viral genome. Furthermore, some of these viruses, such as the members of the Mimiviridae and Phycodnaviridae have a unique vertex that is used during infection to transport DNA into the host. PMID:25003382

Structure of Sputnik, a virophage, at 3.5-Å resolution

PubMed Central

Zhang, Xinzheng; Sun, Siyang; Xiang, Ye; Wong, Jimson; Klose, Thomas; Raoult, Didier; Rossmann, Michael G.

2012-01-01

“Sputnik” is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-Å resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double “jelly-roll” major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible. PMID:23091035

Structure of Sputnik, a virophage, at 3.5-Å resolution.

PubMed

Zhang, Xinzheng; Sun, Siyang; Xiang, Ye; Wong, Jimson; Klose, Thomas; Raoult, Didier; Rossmann, Michael G

2012-11-06

"Sputnik" is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-Å resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double "jelly-roll" major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible.

The microviridae: Diversity, assembly, and experimental evolution.

PubMed

Doore, Sarah M; Fane, Bentley A

2016-04-01

The Microviridae, comprised of ssDNA, icosahedral bacteriophages, are a model system for studying morphogenesis and the evolution of assembly. Historically limited to the φX174-like viruses, recent results demonstrate that this richly diverse family is broadly divided into two groups. The defining feature appears to be whether one or two scaffolding proteins are required for assembly. The single-scaffolding systems contain an internal scaffolding protein, similar to many dsDNA viruses, and have a more complex coat protein fold. The two-scaffolding protein systems (φX174-like) encode an internal and external species, as well as an additional structural protein: a spike on the icosahedral vertices. Here, we discuss recent in silico and in vivo evolutionary analyses conducted with chimeric viruses and/or chimeric proteins. The results suggest 1) how double scaffolding systems can evolve into single and triple scaffolding systems; and 2) how assembly is the critical factor governing adaptation and the maintenance of species boundaries. Copyright © 2016 Elsevier Inc. All rights reserved.

Fourth class of convex equilateral polyhedron with polyhedral symmetry related to fullerenes and viruses

PubMed Central

Schein, Stan; Gayed, James Maurice

2014-01-01

The three known classes of convex polyhedron with equal edge lengths and polyhedral symmetry––tetrahedral, octahedral, and icosahedral––are the 5 Platonic polyhedra, the 13 Archimedean polyhedra––including the truncated icosahedron or soccer ball––and the 2 rhombic polyhedra reported by Johannes Kepler in 1611. (Some carbon fullerenes, inorganic cages, icosahedral viruses, geodesic structures, and protein complexes resemble these fundamental shapes.) Here we add a fourth class, “Goldberg polyhedra,” which are also convex and equilateral. We begin by decorating each of the triangular facets of a tetrahedron, an octahedron, or an icosahedron with the T vertices and connecting edges of a “Goldberg triangle.” We obtain the unique set of internal angles in each planar face of each polyhedron by solving a system of n equations and n variables, where the equations set the dihedral angle discrepancy about different types of edge to zero, and the variables are a subset of the internal angles in 6gons. Like the faces in Kepler’s rhombic polyhedra, the 6gon faces in Goldberg polyhedra are equilateral and planar but not equiangular. We show that there is just a single tetrahedral Goldberg polyhedron, a single octahedral one, and a systematic, countable infinity of icosahedral ones, one for each Goldberg triangle. Unlike carbon fullerenes and faceted viruses, the icosahedral Goldberg polyhedra are nearly spherical. The reasoning and techniques presented here will enable discovery of still more classes of convex equilateral polyhedra with polyhedral symmetry. PMID:24516137

Membrane Remodeling by the Double-Barrel Scaffolding Protein of Poxvirus

PubMed Central

Hijnen, Marcel; Schult, Philipp; Pettikiriarachchi, Anne; Mitra, Alok K.; Coulibaly, Fasséli

2011-01-01

In contrast to most enveloped viruses, poxviruses produce infectious particles that do not acquire their internal lipid membrane by budding through cellular compartments. Instead, poxvirus immature particles are generated from atypical crescent-shaped precursors whose architecture and composition remain contentious. Here we describe the 2.6 Å crystal structure of vaccinia virus D13, a key structural component of the outer scaffold of viral crescents. D13 folds into two jellyrolls decorated by a head domain of novel fold. It assembles into trimers that are homologous to the double-barrel capsid proteins of adenovirus and lipid-containing icosahedral viruses. We show that, when tethered onto artificial membranes, D13 forms a honeycomb lattice and assembly products structurally similar to the viral crescents and immature particles. The architecture of the D13 honeycomb lattice and the lipid-remodeling abilities of D13 support a model of assembly that exhibits similarities with the giant mimivirus. Overall, these findings establish that the first committed step of poxvirus morphogenesis utilizes an ancestral lipid-remodeling strategy common to icosahedral DNA viruses infecting all kingdoms of life. Furthermore, D13 is the target of rifampicin and its structure will aid the development of poxvirus assembly inhibitors. PMID:21931553

Mechanisms of Size Control and Polymorphism in Viral Capsid Assembly

PubMed Central

Elrad, Oren M.; Hagan, Michael F.

2009-01-01

We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one morphology, but adaptively assemble into different icosahedral morphologies around nanoparticle cargoes with varying sizes, as seen in recent experiments with brome mosaic virus (BMV) capsid proteins. Adaptive cargo encapsidation requires moderate cargo-subunit interaction strengths; stronger interactions frustrate assembly by stabilizing intermediates with incommensurate curvature. We compare simulation results to experiments with cowpea chlorotic mottle virus empty capsids and BMV capsids assembled on functionalized nanoparticles, and suggest new cargo encapsidation experiments. Finally, we find that both empty and templated capsids maintain the precise spatial ordering of subunit conformations seen in the crystal structure even if interactions that preserve this arrangement are favored by as little as the thermal energy, consistent with experimental observations that different subunit conformations are highly similar. PMID:18950240

Sequence and structural characterization of great salt lake bacteriophage CW02, a member of the T7-like supergroup.

PubMed

Shen, Peter S; Domek, Matthew J; Sanz-García, Eduardo; Makaju, Aman; Taylor, Ryan M; Hoggan, Ryan; Culumber, Michele D; Oberg, Craig J; Breakwell, Donald P; Prince, John T; Belnap, David M

2012-08-01

Halophage CW02 infects a Salinivibrio costicola-like bacterium, SA50, isolated from the Great Salt Lake. Following isolation, cultivation, and purification, CW02 was characterized by DNA sequencing, mass spectrometry, and electron microscopy. A conserved module of structural genes places CW02 in the T7 supergroup, members of which are found in diverse aquatic environments, including marine and freshwater ecosystems. CW02 has morphological similarities to viruses of the Podoviridae family. The structure of CW02, solved by cryogenic electron microscopy and three-dimensional reconstruction, enabled the fitting of a portion of the bacteriophage HK97 capsid protein into CW02 capsid density, thereby providing additional evidence that capsid proteins of tailed double-stranded DNA phages have a conserved fold. The CW02 capsid consists of bacteriophage lambda gpD-like densities that likely contribute to particle stability. Turret-like densities were found on icosahedral vertices and may represent a unique adaptation similar to what has been seen in other extremophilic viruses that infect archaea, such as Sulfolobus turreted icosahedral virus and halophage SH1.

Hepatitis Virus Capsid Polymorphs Respond Differently to Changes in Encapsulated Cargo Size

PubMed Central

He, Li; Porterfield, J. Zachary; van der Schoot, Paul; Zlotnick, Adam; Dragnea, Bogdan

2017-01-01

A templated assembly approach for Hepatitis B virus-like particles was employed to determine how the T = 3 and T = 4 polymorphs of the Hepatitis B virus (HBV) icosahedral cores respond to a systematic, gradual change in the encapsulated cargo size. It was found that assembly into complete virus-like particles occurs cooperatively around a variety of core diameters, albeit the degree of cooperativity varies. Among these virus-like particles, it was found that those of an outer diameter similar to T = 4 are able to accommodate the widest range of cargo sizes. PMID:24010404

Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202.

PubMed

Nissimov, Jozef I; Worthy, Charlotte A; Rooks, Paul; Napier, Johnathan A; Kimmance, Susan A; Henn, Matthew R; Ogata, Hiroyuki; Allen, Michael J

2012-02-01

Emiliania huxleyi virus 202 (EhV-202) is a member of the Coccolithoviridae, a group of viruses that infect the marine coccolithophorid Emiliania huxleyi. EhV-202 has a 160- to 180-nm-diameter icosahedral structure and a genome of approximately 407 kbp, consisting of 485 coding sequences (CDSs). Here we describe the genomic features of EhV-202, together with a draft genome sequence and its annotation, highlighting the homology and heterogeneity of this genome in comparison with the EhV-86 reference genome.

Draft genome sequence of the Coccolithovirus Emiliania huxleyi virus 203.

PubMed

Nissimov, Jozef I; Worthy, Charlotte A; Rooks, Paul; Napier, Johnathan A; Kimmance, Susan A; Henn, Matthew R; Ogata, Hiroyuki; Allen, Michael J

2011-12-01

The Coccolithoviridae are a recently discovered group of viruses that infect the marine coccolithophorid Emiliania huxleyi. Emiliania huxleyi virus 203 (EhV-203) has a 160- to 180-nm-diameter icosahedral structure and a genome of approximately 400 kbp, consisting of 464 coding sequences (CDSs). Here we describe the genomic features of EhV-203 together with a draft genome sequence and its annotation, highlighting the homology and heterogeneity of this genome in comparison with the EhV-86 reference genome.

The icosahedral RNA virus as a grotto: organizing the genome into stalagmites and stalactites.

PubMed

Harvey, Stephen C; Zeng, Yingying; Heitsch, Christine E

2013-03-01

There are two important problems in the assembly of small, icosahedral RNA viruses. First, how does the capsid protein select the viral RNA for packaging, when there are so many other candidate RNA molecules available? Second, what is the mechanism of assembly? With regard to the first question, there are a number of cases where a particular RNA sequence or structure--often one or more stem-loops--either promotes assembly or is required for assembly, but there are others where specific packaging signals are apparently not required. With regard to the assembly pathway, in those cases where stem-loops are involved, the first step is generally believed to be binding of the capsid proteins to these "fingers" of the RNA secondary structure. In the mature virus, the core of the RNA would then occupy the center of the viral particle, and the stem-loops would reach outward, towards the capsid, like stalagmites reaching up from the floor of a grotto towards the ceiling. Those viruses whose assembly does not depend on protein binding to stem-loops could have a different structure, with the core of the RNA lying just under the capsid, and the fingers reaching down into the interior of the virus, like stalactites. We review the literature on these alternative structures, focusing on RNA selectivity and the assembly mechanism, and we propose experiments aimed at determining, in a given virus, which of the two structures actually occurs.

Serial femtosecond X-ray diffraction of enveloped virus microcrystals

DOE PAGES

Lawrence, Robert M.; Conrad, Chelsie E.; Zatsepin, Nadia A.; ...

2015-08-20

Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ~700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ~40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is a pertinent step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.

African Swine Fever Virus Undergoes Outer Envelope Disruption, Capsid Disassembly and Inner Envelope Fusion before Core Release from Multivesicular Endosomes

PubMed Central

Hernáez, Bruno; Guerra, Milagros; Salas, María L.

2016-01-01

African swine fever virus (ASFV) is a nucleocytoplasmic large DNA virus (NCLDV) that causes a highly lethal disease in domestic pigs. As other NCLDVs, the extracellular form of ASFV possesses a multilayered structure consisting of a genome-containing nucleoid successively wrapped by a thick protein core shell, an inner lipid membrane, an icosahedral protein capsid and an outer lipid envelope. This structural complexity suggests an intricate mechanism of internalization in order to deliver the virus genome into the cytoplasm. By using flow cytometry in combination with pharmacological entry inhibitors, as well as fluorescence and electron microscopy approaches, we have dissected the entry and uncoating pathway used by ASFV to infect the macrophage, its natural host cell. We found that purified extracellular ASFV is internalized by both constitutive macropinocytosis and clathrin-mediated endocytosis. Once inside the cell, ASFV particles move from early endosomes or macropinosomes to late, multivesicular endosomes where they become uncoated. Virus uncoating requires acidic pH and involves the disruption of the outer membrane as well as of the protein capsid. As a consequence, the inner viral membrane becomes exposed and fuses with the limiting endosomal membrane to release the viral core into the cytosol. Interestingly, virus fusion is dependent on virus protein pE248R, a transmembrane polypeptide of the inner envelope that shares sequence similarity with some members of the poxviral entry/fusion complex. Collective evidence supports an entry model for ASFV that might also explain the uncoating of other multienveloped icosahedral NCLDVs. PMID:27110717

All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits

PubMed Central

Perilla, Juan R; Schlicksup, Christopher John; Venkatakrishnan, Balasubramanian; Zlotnick, Adam; Schulten, Klaus

2018-01-01

The hepatitis B virus capsid represents a promising therapeutic target. Experiments suggest the capsid must be flexible to function; however, capsid structure and dynamics have not been thoroughly characterized in the absence of icosahedral symmetry constraints. Here, all-atom molecular dynamics simulations are leveraged to investigate the capsid without symmetry bias, enabling study of capsid flexibility and its implications for biological function and cryo-EM resolution limits. Simulation results confirm flexibility and reveal a propensity for asymmetric distortion. The capsid’s influence on ionic species suggests a mechanism for modulating the display of cellular signals and implicates the capsid’s triangular pores as the location of signal exposure. A theoretical image reconstruction performed using simulated conformations indicates how capsid flexibility may limit the resolution of cryo-EM. Overall, the present work provides functional insight beyond what is accessible to experimental methods and raises important considerations regarding asymmetry in structural studies of icosahedral virus capsids. PMID:29708495

Atomic Force Microscopy in Imaging of Viruses and Virus-Infected Cells

PubMed Central

Kuznetsov, Yurii G.; McPherson, Alexander

2011-01-01

Summary: Atomic force microscopy (AFM) can visualize almost everything pertinent to structural virology and at resolutions that approach those for electron microscopy (EM). Membranes have been identified, RNA and DNA have been visualized, and large protein assemblies have been resolved into component substructures. Capsids of icosahedral viruses and the icosahedral capsids of enveloped viruses have been seen at high resolution, in some cases sufficiently high to deduce the arrangement of proteins in the capsomeres as well as the triangulation number (T). Viruses have been recorded budding from infected cells and suffering the consequences of a variety of stresses. Mutant viruses have been examined and phenotypes described. Unusual structural features have appeared, and the unexpectedly great amount of structural nonconformity within populations of particles has been documented. Samples may be imaged in air or in fluids (including culture medium or buffer), in situ on cell surfaces, or after histological procedures. AFM is nonintrusive and nondestructive, and it can be applied to soft biological samples, particularly when the tapping mode is employed. In principle, only a single cell or virion need be imaged to learn of its structure, though normally images of as many as is practical are collected. While lateral resolution, limited by the width of the cantilever tip, is a few nanometers, height resolution is exceptional, at approximately 0.5 nm. AFM produces three-dimensional, topological images that accurately depict the surface features of the virus or cell under study. The images resemble common light photographic images and require little interpretation. The structures of viruses observed by AFM are consistent with models derived by X-ray crystallography and cryo-EM. PMID:21646429

Virus Assembly and Maturation

NASA Astrophysics Data System (ADS)

Johnson, John E.

2004-03-01

We use two techniques to look at three-dimensional virus structure: electron cryomicroscopy (cryoEM) and X-ray crystallography. Figure 1 is a gallery of virus particles whose structures Timothy Baker, one of my former colleagues at Purdue University, used cryoEM to determine. It illustrates the variety of sizes of icosahedral virus particles. The largest virus particle on this slide is the Herpes simplex virus, around 1200Å in diameter; the smallest we examined was around 250Å in diameter. Viruses bear their genomic information either as positive-sense DNA and RNA, double-strand DNA, double-strand RNA, or negative-strand RNA. Viruses utilize the various structure and function "tactics" seen throughout cell biology to replicate at high levels. Many of the biological principles that we consider general were in fact discovered in the context of viruses ...

Iterative projection algorithms for ab initio phasing in virus crystallography.

PubMed

Lo, Victor L; Kingston, Richard L; Millane, Rick P

2016-12-01

Iterative projection algorithms are proposed as a tool for ab initio phasing in virus crystallography. The good global convergence properties of these algorithms, coupled with the spherical shape and high structural redundancy of icosahedral viruses, allows high resolution phases to be determined with no initial phase information. This approach is demonstrated by determining the electron density of a virus crystal with 5-fold non-crystallographic symmetry, starting with only a spherical shell envelope. The electron density obtained is sufficiently accurate for model building. The results indicate that iterative projection algorithms should be routinely applicable in virus crystallography, without the need for ancillary phase information. Copyright © 2016 Elsevier Inc. All rights reserved.

Ultrastructural morphogenesis of a virus associated with lymphocystis-like lesions in parore Girella tricuspidata (Kyphosidae: Perciformes).

PubMed

Hine, P M; Wakefield, St J; Mackereth, G; Morrison, R

2016-09-26

The morphogenesis of large icosahedral viruses associated with lymphocystis-like lesions in the skin of parore Girella tricuspidata is described. The electron-lucent perinuclear viromatrix comprised putative DNA with open capsids at the periphery, very large arrays of smooth endoplasmic reticulum (sER), much of it with a reticulated appearance (rsER) or occurring as rows of vesicles. Lysosomes, degenerating mitochondria and virions in various stages of assembly, and paracrystalline arrays were also present. Long electron-dense inclusions (EDIs) with 15 nm repeating units split terminally and curled to form tubular structures internalising the 15 nm repeating structures. These tubular structures appeared to form the virion capsids. Large parallel arrays of sER sometimes alternated with aligned arrays of crinkled cisternae along which passed a uniformly wide (20 nm) thread-like structure. Strings of small vesicles near open capsids may also have been involved in formation of an inner lipid layer. Granules with a fine fibrillar appearance also occurred in the viromatrix, and from the presence of a halo around mature virions it appeared that the fibrils may form a layer around the capsid. The general features of virogenesis of large icosahedral dsDNA viruses, the large amount of ER, particularly rsER and the EDIs, are features of nucleo-cytoplasmic large DNA viruses, rather than features of 1 genus or family.

Crystallization and preliminary X-ray diffraction analysis of red clover necrotic mosaic virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, Stanton L.; Guenther, Richard H.; Sit, Tim L.

2010-11-12

Red clover necrotic mosaic virus (RCNMV) is a species that belongs to the Tombusviridae family of plant viruses with a T = 3 icosahedral capsid. RCNMV virions were purified and were crystallized for X-ray analysis using the hanging-drop vapor-diffusion method. Self-rotation functions and systematic absences identified the space group as I23, with two virions in the unit cell. The crystals diffracted to better than 4 {angstrom} resolution but were very radiation-sensitive, causing rapid decay of the high-resolution reflections. The data were processed to 6 {angstrom} in the analysis presented here.

African Swine Fever Virus Gets Undressed: New Insights on the Entry Pathway.

PubMed

Andrés, Germán

2017-02-15

African swine fever virus (ASFV) is a large, multienveloped DNA virus composed of a genome-containing core successively wrapped by an inner lipid envelope, an icosahedral protein capsid, and an outer lipid envelope. In keeping with this structural complexity, recent studies have revealed an intricate entry program. This Gem highlights how ASFV uses two alternative pathways, macropinocytosis and clathrin-mediated endocytosis, to enter into the host macrophage and how the endocytosed particles undergo a stepwise, low pH-driven disassembly leading to inner envelope fusion and core delivery in the cytoplasm. Copyright © 2017 American Society for Microbiology.

Analysis of phases in the structure determination of an icosahedral virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plevka, Pavel; Kaufmann, Bärbel; Rossmann, Michael G.

2012-03-15

The constraints imposed on structure-factor phases by noncrystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to themore » correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These incorrect solutions can be seeded from structure factors belonging to reciprocal-space volumes that lie close to icosahedral NCS axes where the structure amplitudes tend to be large and the phases tend to be 0 or {pi}. Furthermore, the false solutions can spread more easily if there are large errors in defining the envelope designating the region in which NCS averaging is performed.« less

Analysis of phases in the structure determination of an icosahedral virus.

PubMed

Plevka, Pavel; Kaufmann, Bärbel; Rossmann, Michael G

2011-06-01

The constraints imposed on structure-factor phases by noncrystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to the correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These incorrect solutions can be seeded from structure factors belonging to reciprocal-space volumes that lie close to icosahedral NCS axes where the structure amplitudes tend to be large and the phases tend to be 0 or π. Furthermore, the false solutions can spread more easily if there are large errors in defining the envelope designating the region in which NCS averaging is performed. © 2011 International Union of Crystallography

Analysis of phases in the structure determination of an icosahedral virus

PubMed Central

Plevka, Pavel; Kaufmann, Bärbel; Rossmann, Michael G.

2011-01-01

The constraints imposed on structure-factor phases by non­crystallographic symmetry (NCS) allow phase improvement, phase extension to higher resolution and hence ab initio phase determination. The more numerous the NCS redundancy and the greater the volume used for solvent flattening, the greater the power for phase determination. In a case analyzed here the icosahedral NCS phasing appeared to have broken down, although later successful phase extension was possible when the envelope around the NCS region was tightened. The phases from the failed phase-determination attempt fell into four classes, all of which satisfied the NCS constraints. These four classes corresponded to the correct solution, opposite enantiomorph, Babinet inversion and opposite enantiomorph with Babinet inversion. These incorrect solutions can be seeded from structure factors belonging to reciprocal-space volumes that lie close to icosahedral NCS axes where the structure amplitudes tend to be large and the phases tend to be 0 or π. Furthermore, the false solutions can spread more easily if there are large errors in defining the envelope designating the region in which NCS averaging is performed. PMID:21636897

Computing methods for icosahedral and symmetry-mismatch reconstruction of viruses by cryo-electron microscopy

NASA Astrophysics Data System (ADS)

Zhu, Bin; Cheng, Lingpeng; Liu, Hongrong

2018-05-01

Not Available Project supported by the National Key R&D Program of China (Grant No. 2016YFA0501100), the National Natural Science Foundation of China (Grant Nos. 91530321, 31570742, and 31570727), and Science and Technology Planning Project of Hunan Province, China (Grant No. 2017RS3033).

Recovery of Infectious Pariacoto Virus from cDNA Clones and Identification of Susceptible Cell Lines

PubMed Central

Johnson, Karyn N.; Ball, L. Andrew

2001-01-01

Pariacoto virus (PaV) is a nodavirus that was recently isolated in Peru from the Southern armyworm, Spodoptera eridania. Virus particles are non enveloped and about 30 nm in diameter and have T=3 icosahedral symmetry. The 3.0-Å crystal structure shows that about 35% of the genomic RNA is icosahedrally ordered, with the RNA forming a dodecahedral cage of 25-nucleotide (nt) duplexes that underlie the inner surface of the capsid. The PaV genome comprises two single-stranded, positive-sense RNAs: RNA1 (3,011 nt), which encodes the 108-kDa catalytic subunit of the RNA-dependent RNA polymerase, and RNA2 (1,311 nt), which encodes the 43-kDa capsid protein precursor α. In order to apply molecular genetics to the structure and assembly of PaV, we identified susceptible cell lines and developed a reverse genetic system for this virus. Cell lines that were susceptible to infection by PaV included those from Spodoptera exigua, Helicoverpa zea and Aedes albopictus, whereas cells from Drosophila melanogaster and Spodoptera frugiperda were refractory to infection. To recover virus from molecular clones, full-length cDNAs of PaV RNAs 1 and 2 were cotranscribed by T7 RNA polymerase in baby hamster kidney cells that expressed T7 RNA polymerase. Lysates of these cells were infectious both for cultured cells from Helicoverpa zea (corn earworm) and for larvae of Galleria mellonella (greater wax moth). The combination of infectious cDNA clones, cell culture infectivity, and the ability to produce milligram amounts of virus allows the application of DNA-based genetic methods to the study of PaV structure and assembly. PMID:11711613

Recovery of infectious pariacoto virus from cDNA clones and identification of susceptible cell lines.

PubMed

Johnson, K N; Ball, L A

2001-12-01

Pariacoto virus (PaV) is a nodavirus that was recently isolated in Peru from the Southern armyworm, Spodoptera eridania. Virus particles are non enveloped and about 30 nm in diameter and have T=3 icosahedral symmetry. The 3.0-A crystal structure shows that about 35% of the genomic RNA is icosahedrally ordered, with the RNA forming a dodecahedral cage of 25-nucleotide (nt) duplexes that underlie the inner surface of the capsid. The PaV genome comprises two single-stranded, positive-sense RNAs: RNA1 (3,011 nt), which encodes the 108-kDa catalytic subunit of the RNA-dependent RNA polymerase, and RNA2 (1,311 nt), which encodes the 43-kDa capsid protein precursor alpha. In order to apply molecular genetics to the structure and assembly of PaV, we identified susceptible cell lines and developed a reverse genetic system for this virus. Cell lines that were susceptible to infection by PaV included those from Spodoptera exigua, Helicoverpa zea and Aedes albopictus, whereas cells from Drosophila melanogaster and Spodoptera frugiperda were refractory to infection. To recover virus from molecular clones, full-length cDNAs of PaV RNAs 1 and 2 were cotranscribed by T7 RNA polymerase in baby hamster kidney cells that expressed T7 RNA polymerase. Lysates of these cells were infectious both for cultured cells from Helicoverpa zea (corn earworm) and for larvae of Galleria mellonella (greater wax moth). The combination of infectious cDNA clones, cell culture infectivity, and the ability to produce milligram amounts of virus allows the application of DNA-based genetic methods to the study of PaV structure and assembly.

Turnip yellow mosaic virus as a chemoaddressable bionanoparticle.

PubMed

Barnhill, Hannah N; Reuther, Rachel; Ferguson, P Lee; Dreher, Theo; Wang, Qian

2007-01-01

Viruses and virus-like particles (VLPs) have been demonstrated to be robust scaffolds for the construction of nanomaterials. In order to develop new nanoprobes for time-resolved fluoroimmuno assays as well as to investigate the two-dimensional self-assembly of viruses and VLPs, the icosahedral turnip yellow mosaic virus (TYMV) was investigated as a potential building block in our study. TYMV is an icosahedral plant virus with an average diameter of 28 nm that can be isolated inexpensively in gram quantities from turnips or Chinese cabbage. There are 180 coat protein subunits per TYMV capsid. The conventional N-hydroxysuccinimide-mediated amidation reaction was employed for the chemical modification of the viral capsid. Tryptic digestion with sequential MALDI-TOF MS analysis identified that the amino groups of K32 of the flexible N-terminus made the major contribution for the reactivity of TYMV toward N-hydroxysuccinimide ester (NHS) reagents. The reactivity was also monitored with UV-vis absorbance and fluorescence, which revealed that approximately 60 lysines per particle could be addressed. We hypothesized that the flexible A chain contains the reactive lysine because the crystal structure of TYMV has shown that chain A is much more flexible compared to B and C, especially at the N-terminal region where the Lys-32 located. In addition, about 90 to 120 carboxyl groups, located in the most exposed sequence, could be modified with amines catalyzed with 1-(3-dimethylaminopropyl-3-ethylcarbodiimide) hydrochloride (EDC) and sulfo-NHS. TYMV was stable to a wide range of reaction conditions and maintained its integrity after the chemical conjugations. Therefore, it can potentially be employed as a reactive scaffold for the display of a variety of materials for applications in many areas of nanoscience.

Prevalence of virus-like particles within a staghorn scleractinian coral ( Acropora muricata) from the Great Barrier Reef

NASA Astrophysics Data System (ADS)

Patten, N. L.; Harrison, P. L.; Mitchell, J. G.

2008-09-01

Transmission electron microscopy (TEM) was used to determine whether Acropora muricata coral colonies from the Great Barrier Reef (GBR), Australia, harboured virus-like particles (VLPs). VLPs were present in all coral colonies sampled at Heron Island (southern GBR) and in tagged coral colonies sampled in at least two of the three sampling periods at Lizard Island (northern GBR). VLPs were observed within gastrodermal and epidermal tissues, and on rarer occasions, within the mesoglea. These VLPs had similar morphologies to known prokaryotic and eukaryotic viruses in other systems. Icosahedral VLPs were observed most frequently, however, filamentous VLPs (FVLPs) and phage were also noted. There were no clear differences in VLP size, morphology or location within the tissues with respect to sample date, coral health status or site. The most common VLP morphotype exhibited icosahedral symmetry, 120-150 nm in diameter, with an electron-dense core and an electronlucent membrane. Larger VLPs of similar morphology were also common. VLPs occurred as single entities, in groups, or in dense clusters, either as free particles within coral tissues, or within membrane-bound vacuoles. VLPs were commonly observed within the perinuclear region, with mitochondria, golgi apparatus and crescent-shaped particles frequently observed within close proximity. The host(s) of these observed VLPs was not clear; however, the different sizes and morphologies of VLPs observed within A. muricata tissues suggest that viruses are infecting either the coral animal, zooxanthellae, intracellular bacteria and/or other coral-associated microbiota, or that the one host is susceptible to infection from more than one type of virus. These results add to the limited but emerging body of evidence that viruses represent another potentially important component of the coral holobiont.

Recent advances in molecular biology of parasitic viruses.

PubMed

Banik, Gouri Rani; Stark, Damien; Rashid, Harunor; Ellis, John T

2014-01-01

The numerous protozoa that can inhabit the human gastro-intestinal tract are known, yet little is understood of the viruses which infect these protozoa. The discovery, morphologic details, purification methods of virus-like particles, genome and proteome of the parasitic viruses, Entamoeba histolytica, Giardia lamblia, Trichomonas vaginalis, and the Eimeria sp. are described in this review. The protozoan viruses share many common features: most of them are RNA or double-stranded RNA viruses, ranging between 5 and 8 kilobases, and are spherical or icosahedral in shape with an average diameter of 30-40 nm. These viruses may influence the function and pathogenicity of the protozoa which they infect, and may be important to investigate from a clinical perspective. The viruses may be used as specific genetic transfection vectors for the parasites and may represent a research tool. This review provides an overview on recent advances in the field of protozoan viruses.

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification.

PubMed

Sinclair, Robert M; Ravantti, Janne J; Bamford, Dennis H

2017-04-15

Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds. IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly, we detected similarity at the nucleotide level between capsid protein-coding regions from viruses infecting cells belonging to all three domains of life, reproducing a previously established structure-based classification of icosahedral viral capsids. Copyright © 2017 Sinclair et al.

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification

PubMed Central

Sinclair, Robert M.; Ravantti, Janne J.

2017-01-01

ABSTRACT Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds. IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly, we detected similarity at the nucleotide level between capsid protein-coding regions from viruses infecting cells belonging to all three domains of life, reproducing a previously established structure-based classification of icosahedral viral capsids. PMID:28122979

Structure-based engineering of an icosahedral virus for nanomedicine and nanotechnology.

PubMed

Steinmetz, N F; Lin, T; Lomonossoff, G P; Johnson, J E

2009-01-01

A quintessential tenet of nanotechnology is the self-assembly of nanometer-sized components into devices. Biological macromolecular systems such as viral particles were found to be suitable building blocks for nanotechnology for several reasons: viral capsids are extremely robust and can be produced in large quantities with ease, the particles self-assemble into monodisperse particles with a high degree of symmetry and polyvalency, they have the propensity to form arrays, and they offer programmability through genetic and chemical engineering. Here, we review the recent advances in engineering the icosahedral plant virus Cowpea mosaic virus (CPMV) for applications in nano-medicine and -technology. In the first part, we will discuss how the combined knowledge of the structure of CPMV at atomic resolution and the use of chimeric virus technology led to the generation of CPMV particles with short antigenic peptides for potential use as vaccine candidates. The second part focuses on the chemical addressability of CPMV. Strategies to chemically attach functional molecules at designed positions on the exterior surface of the viral particle are described. Biochemical conjugation methods led to the fabrication of electronically conducting CPMV particles and networks. In addition, functional proteins for targeted delivery to mammalian cells were successfully attached to CPMV. In the third part, we focus on the utilization of CPMV as a building block for the generation of 2D and 3D arrays. Overall, the potential applications of viral nanobuilding blocks are manifold and range from nanoelectronics to biomedical applications.

Lipids of Archaeal Viruses

PubMed Central

Roine, Elina; Bamford, Dennis H.

2012-01-01

Archaeal viruses represent one of the least known territory of the viral universe and even less is known about their lipids. Based on the current knowledge, however, it seems that, as in other viruses, archaeal viral lipids are mostly incorporated into membranes that reside either as outer envelopes or membranes inside an icosahedral capsid. Mechanisms for the membrane acquisition seem to be similar to those of viruses infecting other host organisms. There are indications that also some proteins of archaeal viruses are lipid modified. Further studies on the characterization of lipids in archaeal viruses as well as on their role in virion assembly and infectivity require not only highly purified viral material but also, for example, constant evaluation of the adaptability of emerging technologies for their analysis. Biological membranes contain proteins and membranes of archaeal viruses are not an exception. Archaeal viruses as relatively simple systems can be used as excellent tools for studying the lipid protein interactions in archaeal membranes. PMID:23049284

Structural studies of the Sputnik virophage.

PubMed

Sun, Siyang; La Scola, Bernard; Bowman, Valorie D; Ryan, Christopher M; Whitelegge, Julian P; Raoult, Didier; Rossmann, Michael G

2010-01-01

The virophage Sputnik is a satellite virus of the giant mimivirus and is the only satellite virus reported to date whose propagation adversely affects its host virus' production. Genome sequence analysis showed that Sputnik has genes related to viruses infecting all three domains of life. Here, we report structural studies of Sputnik, which show that it is about 740 A in diameter, has a T=27 icosahedral capsid, and has a lipid membrane inside the protein shell. Structural analyses suggest that the major capsid protein of Sputnik is likely to have a double jelly-roll fold, although sequence alignments do not show any detectable similarity with other viral double jelly-roll capsid proteins. Hence, the origin of Sputnik's capsid might have been derived from other viruses prior to its association with mimivirus.

Structural Studies of the Sputnik Virophage▿

PubMed Central

Sun, Siyang; La Scola, Bernard; Bowman, Valorie D.; Ryan, Christopher M.; Whitelegge, Julian P.; Raoult, Didier; Rossmann, Michael G.

2010-01-01

The virophage Sputnik is a satellite virus of the giant mimivirus and is the only satellite virus reported to date whose propagation adversely affects its host virus' production. Genome sequence analysis showed that Sputnik has genes related to viruses infecting all three domains of life. Here, we report structural studies of Sputnik, which show that it is about 740 Å in diameter, has a T=27 icosahedral capsid, and has a lipid membrane inside the protein shell. Structural analyses suggest that the major capsid protein of Sputnik is likely to have a double jelly-roll fold, although sequence alignments do not show any detectable similarity with other viral double jelly-roll capsid proteins. Hence, the origin of Sputnik's capsid might have been derived from other viruses prior to its association with mimivirus. PMID:19889775

Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lok, Shee-Mei; Kostyuchenko, Victor; Nybakken, Grant E.

The monoclonal antibody 1A1D-2 has been shown to strongly neutralize dengue virus serotypes 1, 2 and 3, primarily by inhibiting attachment to host cells. A crystal structure of its antigen binding fragment (Fab) complexed with domain III of the viral envelope glycoprotein, E, showed that the epitope would be partially occluded in the known structure of the mature dengue virus. Nevertheless, antibody could bind to the virus at 37 degrees C, suggesting that the virus is in dynamic motion making hidden epitopes briefly available. A cryo-electron microscope image reconstruction of the virus:Fab complex showed large changes in the organization ofmore » the E protein that exposed the epitopes on two of the three E molecules in each of the 60 icosahedral asymmetric units of the virus. The changes in the structure of the viral surface are presumably responsible for inhibiting attachment to cells.« less

Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

PubMed

Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

2018-05-01

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. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

Mechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery

PubMed Central

Peralta, Bibiana; Gil-Carton, David; Castaño-Díez, Daniel; Bertin, Aurelie; Boulogne, Claire; Oksanen, Hanna M.; Bamford, Dennis H.; Abrescia, Nicola G. A.

2013-01-01

In internal membrane-containing viruses, a lipid vesicle enclosed by the icosahedral capsid protects the genome. It has been postulated that this internal membrane is the genome delivery device of the virus. Viruses built with this architectural principle infect hosts in all three domains of cellular life. Here, using a combination of electron microscopy techniques, we investigate bacteriophage PRD1, the best understood model for such viruses, to unveil the mechanism behind the genome translocation across the cell envelope. To deliver its double-stranded DNA, the icosahedral protein-rich virus membrane transforms into a tubular structure protruding from one of the 12 vertices of the capsid. We suggest that this viral nanotube exits from the same vertex used for DNA packaging, which is biochemically distinct from the other 11. The tube crosses the capsid through an aperture corresponding to the loss of the peripentonal P3 major capsid protein trimers, penton protein P31 and membrane protein P16. The remodeling of the internal viral membrane is nucleated by changes in osmolarity and loss of capsid-membrane interactions as consequence of the de-capping of the vertices. This engages the polymerization of the tail tube, which is structured by membrane-associated proteins. We have observed that the proteo-lipidic tube in vivo can pierce the gram-negative bacterial cell envelope allowing the viral genome to be shuttled to the host cell. The internal diameter of the tube allows one double-stranded DNA chain to be translocated. We conclude that the assembly principles of the viral tunneling nanotube take advantage of proteo-lipid interactions that confer to the tail tube elastic, mechanical and functional properties employed also in other protein-membrane systems. PMID:24086111

Mechanisms of Virus Assembly

PubMed Central

Perlmutter, Jason D.; Hagan, Michael F.

2015-01-01

Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid, and in some cases surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which capsids assembles within their host cells and in vitro. We describe the thermodynamics and kinetics for assembly of protein subunits into icosahedral capsid shells, and how these are modified in cases where the capsid assembles around a nucleic acid or on a lipid bilayer. We present experimental and theoretical techniques that have been used to characterize capsid assembly, and we highlight aspects of virus assembly which are likely to receive significant attention in the near future. PMID:25532951

Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208.

PubMed

Nissimov, Jozef I; Worthy, Charlotte A; Rooks, Paul; Napier, Johnathan A; Kimmance, Susan A; Henn, Matthew R; Ogata, Hiroyuki; Allen, Michael J

2012-03-01

The Coccolithoviridae are a group of viruses which infect the marine coccolithophorid microalga Emiliania huxleyi. The Emiliania huxleyi viruses (known as EhVs) described herein have 160- to 180-nm diameter icosahedral structures, have genomes of approximately 400 kbp, and consist of more than 450 predicted coding sequences (CDSs). Here, we describe the genomic features of four newly sequenced coccolithoviruses (EhV-88, EhV-201, EhV-207, and EhV-208) together with their draft genome sequences and their annotations, highlighting the homology and heterogeneity of these genomes to the EhV-86 model reference genome.

Membrane-containing virus particles exhibit the mechanics of a composite material for genome protection.

PubMed

Azinas, S; Bano, F; Torca, I; Bamford, D H; Schwartz, G A; Esnaola, J; Oksanen, H M; Richter, R P; Abrescia, N G

2018-04-26

The protection of the viral genome during extracellular transport is an absolute requirement for virus survival and replication. In addition to the almost universal proteinaceous capsids, certain viruses add a membrane layer that encloses their double-stranded (ds) DNA genome within the protein shell. Using the membrane-containing enterobacterial virus PRD1 as a prototype, and a combination of nanoindentation assays by atomic force microscopy and finite element modelling, we show that PRD1 provides a greater stability against mechanical stress than that achieved by the majority of dsDNA icosahedral viruses that lack a membrane. We propose that the combination of a stiff and brittle proteinaceous shell coupled with a soft and compliant membrane vesicle yields a tough composite nanomaterial well-suited to protect the viral DNA during extracellular transport.

Ultrastructure of Lymphocystis Virus

PubMed Central

Zwillenberg, Lutz O.; Wolf, Ken

1968-01-01

Lymphocystis virus obtained from bluegills (Lepomis macrochirus) was cultured in the permanent bluegill cell line BF-2 and examined by electron microscopy in ultrathin sections of cell cultures and in negative-contrast preparations from cells and from centrifuged culture medium. According to negative-contrast preparations, the icosahedral virions have an overall diameter close to but not exceeding 300 mμ. Delicate filaments seem to issue from the vertices. In collapsed virions, an ordered array of morphological units was seen. Positively contrasted virions in ultrathin sections show a shell with three dark (heavy metal-stained) layers alternating with and separated by two clear layers. The acquisition of an additional outer membrane during release from the cell, as found in African swine fever virus, was never seen. Morphologically, lymphocystis virus is considered to be closely related to Tipula iridescent virus. Images PMID:4986903

Viral video: Live imaging of virus-host encounters

NASA Astrophysics Data System (ADS)

Son, Kwangmin; Guasto, Jeffrey S.; Cubillos-Ruiz, Andres; Chisholm, Sallie W.; Sullivan, Matthew B.; Stocker, Roman

2014-11-01

Viruses are non-motile infectious agents that rely on Brownian motion to encounter and subsequently adsorb to their hosts. Paradoxically, the viral adsorption rate is often reported to be larger than the theoretical limit imposed by the virus-host encounter rate, highlighting a major gap in the experimental quantification of virus-host interactions. Here we present the first direct quantification of the viral adsorption rate, obtained using live imaging of individual host cells and viruses for thousands of encounter events. The host-virus pair consisted of Prochlorococcus MED4, a 800 nm small non-motile bacterium that dominates photosynthesis in the oceans, and its virus PHM-2, a myovirus that has a 80 nm icosahedral capsid and a 200 nm long rigid tail. We simultaneously imaged hosts and viruses moving by Brownian motion using two-channel epifluorescent microscopy in a microfluidic device. This detailed quantification of viral transport yielded a 20-fold smaller adsorption efficiency than previously reported, indicating the need for a major revision in infection models for marine and likely other ecosystems.

Presence of Panulirus argus virus 1 (PaV1) in juvenile spiny lobsters Panulirus argus from the Caribbean coast of Mexico.

PubMed

Huchin-Mian, Juan Pablo; Rodríguez-Canul, Rossanna; Arias-Bañuelos, Efrain; Simá-Alvarez, Raúl; Pérez-Vega, Juan A; Briones-Fourzán, Patricia; Lozano-Alvarez, Enrique

2008-04-01

Macroscopic evidence, histological sections, transmission electron microscopy (TEM) evaluation, and PCR analyses of 25 apparently diseased juvenile spiny lobsters Panulirus argus from the reef lagoon of Puerto Morelos, Mexico, showed the presence of Panulirus argus Virus 1 (PaV1). Cowdry Type A intranuclear viral inclusions were observed in histological analyses, icosahedral viral particles were observed by TEM, and PCR using specific primers for PaV1 amplified a fragment of 499 bp. This is the first report of PaV1 infecting P. argus outside the Florida Keys, USA.

Morphogenesis of mimivirus and its viral factories: an atomic force microscopy study of infected cells.

PubMed

Kuznetsov, Yuri G; Klose, Thomas; Rossmann, Michael; McPherson, Alexander

2013-10-01

Amoebas infected with mimivirus were disrupted at sequential stages of virus production and were visualized by atomic force microscopy. The development of virus factories proceeded over 3 to 4 h postinfection and resulted from the coalescence of 0.5- to 2-μm vesicles, possibly bearing nucleic acid, derived from either the nuclear membrane or the closely associated rough endoplasmic reticulum. Virus factories actively producing virus capsids on their surfaces were imaged, and this allowed the morphogenesis of the capsids to be delineated. The first feature to appear on a virus factory surface when a new capsid is born is the center of a stargate, which is a pentameric protein oligomer. As the arms of the stargate grow from the pentamer, a rough disk the diameter of a capsid thickens around it. This marks the initial emergence of a protein-coated membrane vesicle. The capsid self-assembles on the vesicle. Hillocks capped by different pentameric proteins spontaneously appear on the emerging vesicle at positions that are ultimately occupied by 5-fold icosahedral vertices. A lattice of coat protein nucleates at each of the 5-fold vertices, but not at the stargate, and then spreads outward from the vertices over the surface, merging seamlessly to complete the icosahedral capsid. Filling with DNA and associated proteins occurs by the transfer of nucleic acid from the interior of the virus factory into the nearly completed capsids. The portal, through which the DNA enters, is sealed by a plug of protein having a diameter of about 40 nm. A layer of integument protein that anchors the surface fibers is acquired by the passage of capsids through a membrane enriched in the protein. The coating of surface fibers is similarly acquired when the integument protein-coated capsids pass through a second membrane that has a forest of surface fibers embedded on one side.

Morphogenesis of Mimivirus and Its Viral Factories: an Atomic Force Microscopy Study of Infected Cells

PubMed Central

Kuznetsov, Yuri G.; Klose, Thomas; Rossmann, Michael

2013-01-01

Amoebas infected with mimivirus were disrupted at sequential stages of virus production and were visualized by atomic force microscopy. The development of virus factories proceeded over 3 to 4 h postinfection and resulted from the coalescence of 0.5- to 2-μm vesicles, possibly bearing nucleic acid, derived from either the nuclear membrane or the closely associated rough endoplasmic reticulum. Virus factories actively producing virus capsids on their surfaces were imaged, and this allowed the morphogenesis of the capsids to be delineated. The first feature to appear on a virus factory surface when a new capsid is born is the center of a stargate, which is a pentameric protein oligomer. As the arms of the stargate grow from the pentamer, a rough disk the diameter of a capsid thickens around it. This marks the initial emergence of a protein-coated membrane vesicle. The capsid self-assembles on the vesicle. Hillocks capped by different pentameric proteins spontaneously appear on the emerging vesicle at positions that are ultimately occupied by 5-fold icosahedral vertices. A lattice of coat protein nucleates at each of the 5-fold vertices, but not at the stargate, and then spreads outward from the vertices over the surface, merging seamlessly to complete the icosahedral capsid. Filling with DNA and associated proteins occurs by the transfer of nucleic acid from the interior of the virus factory into the nearly completed capsids. The portal, through which the DNA enters, is sealed by a plug of protein having a diameter of about 40 nm. A layer of integument protein that anchors the surface fibers is acquired by the passage of capsids through a membrane enriched in the protein. The coating of surface fibers is similarly acquired when the integument protein-coated capsids pass through a second membrane that has a forest of surface fibers embedded on one side. PMID:23926353

Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus

PubMed Central

Mangala Prasad, Vidya

2017-01-01

Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway. PMID:28575072

Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.

PubMed

Mangala Prasad, Vidya; Klose, Thomas; Rossmann, Michael G

2017-06-01

Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.

Structure of a Venezuelan equine encephalitis virus assembly intermediate isolated from infected cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lamb, Kristen; Lokesh, G.L.; Sherman, Michael

2010-10-25

Venezuelan equine encephalitis virus (VEEV) is a prototypical enveloped ssRNA virus of the family Togaviridae. To better understand alphavirus assembly, we analyzed newly formed nucleocapsid particles (termed pre-viral nucleocapsids) isolated from infected cells. These particles were intermediates along the virus assembly pathway, and ultimately bind membrane-associated viral glycoproteins to bud as mature infectious virus. Purified pre-viral nucleocapsids were spherical with a unimodal diameter distribution. The structure of one class of pre-viral nucleocapsids was determined with single particle reconstruction of cryo-electron microscopy images. These studies showed that pre-viral nucleocapsids assembled into an icosahedral structure with a capsid stoichiometry similar to themore » mature nucleocapsid. However, the individual capsomers were organized significantly differently within the pre-viral and mature nucleocapsids. The pre-viral nucleocapsid structure implies that nucleocapsids are highly plastic and undergo glycoprotein and/or lipid-driven rearrangements during virus self-assembly. This mechanism of self-assembly may be general for other enveloped viruses.« less

[Plant-infecting reoviruses].

PubMed

Sasaya, Takahide

2014-01-01

The family Reoviridae separates two subfamilies and consists of 15 genera. Fourteen viruses in three genera (Phytoreovirus, Oryzavirus, and Fijivirus) infect plants. The outbreaks of the plant-infecting reoviruses cause sometime the serious yield loss of rice and maize, and are a menace to safe and efficient food production in the Southeast Asia.　The plant-infecting reoviruses are double-shelled icosahedral particles, from 50 to 80nm in diameter, and include from 10 to 12 segmented double-stranded genomic RNAs depending on the viruses. These viruses are transmitted in a persistent manner by the vector insects and replicated in both plants and in their vectors. This review provides a brief overview of the plant-infecting reoviruses and their recent research progresses including the strategy for viral controls using transgenic rice plants.

RNA-dependent RNA polymerases of dsRNA bacteriophages.

PubMed

Makeyev, Eugene V; Grimes, Jonathan M

2004-04-01

Genome replication and transcription of riboviruses are catalyzed by an RNA-dependent RNA polymerase (RdRP). RdRPs are normally associated with other virus- or/and host-encoded proteins that modulate RNA polymerization activity and template specificity. The polymerase complex of double-stranded dsRNA viruses is a large icosahedral particle (inner core) containing RdRP as a minor constituent. In phi6 and other dsRNA bacteriophages from the Cystoviridae family, the inner core is composed of four virus-specific proteins. Of these, protein P2, or Pol subunit, has been tentatively identified as RdRP by sequence comparisons, but the role of this protein in viral RNA synthesis has not been studied until recently. Here, we overview the work on the Pol subunits of phi6 and related viruses from the standpoints of function, structure and evolution.

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

NASA Astrophysics Data System (ADS)

Kurta, Ruslan P.; Donatelli, Jeffrey J.; Yoon, Chun Hong; Berntsen, Peter; Bielecki, Johan; Daurer, Benedikt J.; DeMirci, Hasan; Fromme, Petra; Hantke, Max Felix; Maia, Filipe R. N. C.; Munke, Anna; Nettelblad, Carl; Pande, Kanupriya; Reddy, Hemanth K. N.; Sellberg, Jonas A.; Sierra, Raymond G.; Svenda, Martin; van der Schot, Gijs; Vartanyants, Ivan A.; Williams, Garth J.; Xavier, P. Lourdu; Aquila, Andrew; Zwart, Peter H.; Mancuso, Adrian P.

2017-10-01

We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.

Molecular characterization of birnaviruses isolated from wild marine fishes at the Flemish Cap (Newfoundland)

USGS Publications Warehouse

Romero-Brey, I.; Batts, W.N.; Bandin, I.; Winton, J.R.; Dopazo, C.P.

2004-01-01

Several isolates of aquatic birnaviruses were recovered from different species of wild fish caught in the Flemish Cap, a Newfoundland fishery close to the Atlantic coast of Canada. The nucleotide sequence of a region of the NS gene was identical among the isolates and was most similar to the Dry Mills and West Buxton reference strains of infectious pancreatic necrosis virus (IPNV). Phylogenetic analysis of the sequence of a region of the VP2 gene demonstrated that the isolates were most closely aligned with the American strains of IPNV serotype Al. Electron microscopy of virus structures clarified and concentrated from cultures of infected chinook salmon embryo (CHSE-214) cells revealed a majority of typical IPNV-like icosahedral particles, as well as a low proportion of type I tubules having a diameter of approximately 55 nm and a variable length of up to 2 ??m. The tubules could be propagated in cell cultures, but always in the presence of low proportions of icosahedral particles. Cloning of selected isolates by serial dilution yielded preparations with a high proportion of the tubular structures with a density in CsCl gradients of approximately 1.30 g cm-3. Polyacrylamide gel electrophoresis revealed the material in the band was composed of the IPNV pVP2 and VP2 proteins.

Comparison of the structures of three circoviruses: chicken anemia virus, porcine circovirus type 2, and beak and feather disease virus.

PubMed

Crowther, R A; Berriman, J A; Curran, W L; Allan, G M; Todd, D

2003-12-01

Circoviruses are small, nonenveloped icosahedral animal viruses characterized by circular single-stranded DNA genomes. Their genomes are the smallest possessed by animal viruses. Infections with circoviruses, which can lead to economically important diseases, frequently result in virus-induced damage to lymphoid tissue and immunosuppression. Within the family Circoviridae, different genera are distinguished by differences in genomic organization. Thus, Chicken anemia virus is in the genus Gyrovirus, while porcine circoviruses and Beak and feather disease virus belong to the genus CIRCOVIRUS: Little is known about the structures of circoviruses. Accordingly, we investigated the structures of these three viruses with a view to determining whether they are related. Three-dimensional maps computed from electron micrographs showed that all three viruses have a T=1 organization with capsids formed from 60 subunits. Porcine circovirus type 2 and beak and feather disease virus show similar capsid structures with flat pentameric morphological units, whereas chicken anemia virus has stikingly different protruding pentagonal trumpet-shaped units. It thus appears that the structures of viruses in the same genus are related but that those of viruses in different genera are unrelated.

Time-resolved spectroscopy of self-assembly of CCMV protein capsids

NASA Astrophysics Data System (ADS)

Moore, Jelyn; Aronzon, Dina; Manoharan, V. N.

2008-10-01

In order to gain a deeper understanding of the process a virus undergoes to assemble; the purpose of this study to time resolve the self-assembly of a virus. Cowpea Chlorotic Mottle virus (CCMV), an icosahedral type virus, can assemble without its genetic code (RNA) depending on its chemical and physical surroundings. The surface plasmon resonance (SPR) of colloidal gold particles is known to display a shift when the gold interacts with the proteins of a virus. Surface plasmon resonance is the free electron oscillation occurring at the surface of the gold particle resulting in a characteristic peak location at maximal absorbance and peak width. The shift results from the change in the refractive index of the particles as induced by the presence of the proteins. We hope to detect this shift through total internal reflection microscopy (TIRM). The accomplishments of this research are the completion of the TIR setup and the purification of the virus and its proteins.

Structural Comparison of Different Antibodies Interacting with Parvovirus Capsids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hafenstein, Susan; Bowman, Valorie D.; Sun, Tao

2009-05-13

The structures of canine parvovirus (CPV) and feline parvovirus (FPV) complexed with antibody fragments from eight different neutralizing monoclonal antibodies were determined by cryo-electron microscopy (cryoEM) reconstruction to resolutions varying from 8.5 to 18 {angstrom}. The crystal structure of one of the Fab molecules and the sequence of the variable domain for each of the Fab molecules have been determined. The structures of Fab fragments not determined crystallographically were predicted by homology modeling according to the amino acid sequence. Fitting of the Fab and virus structures into the cryoEM densities identified the footprints of each antibody on the viral surface.more » As anticipated from earlier analyses, the Fab binding sites are directed to two epitopes, A and B. The A site is on an exposed part of the surface near an icosahedral threefold axis, whereas the B site is about equidistant from the surrounding five-, three-, and twofold axes. One antibody directed to the A site binds CPV but not FPV. Two of the antibodies directed to the B site neutralize the virus as Fab fragments. The differences in antibody properties have been linked to the amino acids within the antibody footprints, the position of the binding site relative to the icosahedral symmetry elements, and the orientation of the Fab structure relative to the surface of the virus. Most of the exposed surface area was antigenic, although each of the antibodies had a common area of overlap that coincided with the positions of the previously mapped escape mutations.« less

Viral Uncoating Is Directional: Exit of the Genomic RNA in a Common Cold Virus Starts with the Poly-(A) Tail at the 3′-End

PubMed Central

Sedivy, Arthur; Subirats, Xavier; Kowalski, Heinrich; Köhler, Gottfried; Blaas, Dieter

2013-01-01

Upon infection, many RNA viruses reorganize their capsid for release of the genome into the host cell cytosol for replication. Often, this process is triggered by receptor binding and/or by the acidic environment in endosomes. In the genus Enterovirus, which includes more than 150 human rhinovirus (HRV) serotypes causing the common cold, there is persuasive evidence that the viral RNA exits single-stranded through channels formed in the protein shell. We have determined the time-dependent emergence of the RNA ends from HRV2 on incubation of virions at 56°C using hybridization with specific oligonucleotides and detection by fluorescence correlation spectroscopy. We report that psoralen UV crosslinking prevents complete RNA release, allowing for identification of the sequences remaining inside the capsid. We also present the structure of uncoating intermediates in which parts of the RNA are condensed and take the form of a rod that is directed roughly towards a two-fold icosahedral axis, the presumed RNA exit point. Taken together, in contrast to schemes frequently depicted in textbooks and reviews, our findings demonstrate that exit of the RNA starts from the 3′-end. This suggests that packaging also occurs in an ordered manner resulting in the 3′-poly-(A) tail becoming located close to a position of pore formation during conversion of the virion into a subviral particle. This directional genome release may be common to many icosahedral non-enveloped single-stranded RNA viruses. PMID:23592991

A virus of hyperthermophilic archaea with a unique architecture among DNA viruses.

PubMed

Rensen, Elena Ilka; Mochizuki, Tomohiro; Quemin, Emmanuelle; Schouten, Stefan; Krupovic, Mart; Prangishvili, David

2016-03-01

Viruses package their genetic material in diverse ways. Most known strategies include encapsulation of nucleic acids into spherical or filamentous virions with icosahedral or helical symmetry, respectively. Filamentous viruses with dsDNA genomes are currently associated exclusively with Archaea. Here, we describe a filamentous hyperthermophilic archaeal virus, Pyrobaculum filamentous virus 1 (PFV1), with a type of virion organization not previously observed in DNA viruses. The PFV1 virion, 400 ± 20 × 32 ± 3 nm, contains an envelope and an inner core consisting of two structural units: a rod-shaped helical nucleocapsid formed of two 14-kDa major virion proteins and a nucleocapsid-encompassing protein sheath composed of a single major virion protein of 18 kDa. The virion organization of PFV1 is superficially similar to that of negative-sense RNA viruses of the family Filoviridae, including Ebola virus and Marburg virus. The linear dsDNA of PFV1 carries 17,714 bp, including 60-bp-long terminal inverted repeats, and contains 39 predicted ORFs, most of which do not show similarities to sequences in public databases. PFV1 is a lytic virus that completely disrupts the host cell membrane at the end of the infection cycle.

A biodistribution study of two differently shaped plant virus nanoparticles reveals new peculiar traits.

PubMed

Lico, Chiara; Giardullo, Paola; Mancuso, Mariateresa; Benvenuto, Eugenio; Santi, Luca; Baschieri, Selene

2016-12-01

Self-assembling plant virus nanoparticles (pVNPs) have started to be explored as nanometre-sized objects for biomedical applications, such as vaccine or drug delivery and imaging. Plant VNPs may be ideal tools in terms of biocompatibility and biodegradability endowed with a wide diversity of symmetries and dimensions, easy chemical/biological engineering, and rapid production in plants. Recently, we defined that icosahedral Tomato bushy stunt virus (TBSV) and filamentous Potato virus X (PVX) are neither toxic nor teratogenic. We report here the results of an interdisciplinary study aimed to define for the first time the biodistribution of unlabelled, unpegylated, underivatized TBSV and PVX by proved detecting antibodies. These data add new insights on the in vivo behaviour of these nano-objects and demonstrate that the pVNPs under scrutiny are each intrinsically endowed with peculiar properties foreshadowing different applications in molecular medicine. Copyright © 2016 Elsevier B.V. All rights reserved.

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

DOE PAGES

Kurta, Ruslan P.; Donatelli, Jeffrey J.; Yoon, Chun Hong; ...

2017-10-12

We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates frommore » the expected perfect icosahedral symmetry. Lastly, our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.« less

Assembly/disassembly of a complex icosahedral virus to incorporate heterologous nucleic acids

NASA Astrophysics Data System (ADS)

Pascual, Elena; Mata, Carlos P.; Carrascosa, José L.; Castón, José R.

2017-12-01

Hollow protein containers are widespread in nature, and include virus capsids as well as eukaryotic and bacterial complexes. Protein cages are studied extensively for applications in nanotechnology, nanomedicine and materials science. Their inner and outer surfaces can be modified chemically or genetically, and the internal cavity can be used to template, store and/or arrange molecular cargos. Virus capsids and virus-like particles (VLP, noninfectious particles) provide versatile platforms for nanoscale bioengineering. Study of capsid protein self-assembly into monodispersed particles, and of VLP structure and biophysics is necessary not only to understand natural processes, but also to infer how these platforms can be redesigned to furnish novel functional VLP. Here we address the assembly dynamics of infectious bursal disease virus (IBDV), a complex icosahedral virus. IBDV has a ~70 nm-diameter T  =  13 capsid with VP2 trimers as the only structural subunits. During capsid assembly, VP2 is synthesized as a precursor (pVP2) whose C terminus is cleaved. The pVP2 C terminus has an amphipathic helix that controls VP2 polymorphism. In the absence of the VP3 scaffolding protein, necessary for control of assembly, 466/456-residue pVP2 intermediates bearing this helix assemble into VLP only when expressed with an N-terminal His6 tag (the HT-VP2-466 protein). HT-VP2-466 capsids are optimal for genetic insertion of proteins (cargo space ~78 000 nm3). We established an in vitro assembly/disassembly system of HT-VP2-466-based VLP for heterologous nucleic acid packaging and/or encapsulation of drugs and other molecules. HT-VP2-466 (empty) capsids were disassembled and reassembled by dialysis against low-salt/basic pH and high-salt/acid pH buffers, respectively, thus illustrating the reversibility in vitro of IBDV capsid assembly. HT-VP2-466 VLP also packed heterologous DNA by non-specific confinement during assembly. These and previous results establish the bases for biotechnological applications based on the IBDV capsid and its ability to incorporate exogenous proteins and nucleic acids.

Differential segregation of nodaviral coat protein and RNA into progeny virions during mixed infection with FHV and NoV

PubMed Central

Gopal, Radhika; Venter, P. Arno; Schneemann, Anette

2014-01-01

Nodaviruses are icosahedral viruses with a bipartite, positive-sense RNA genome. The two RNAs are packaged into a single virion by a poorly understood mechanism. We chose two distantly related nodaviruses, Flock House virus and Nodamura virus, to explore formation of viral reassortants as a means to further understand genome recognition and encapsidation. In mixed infections, the viruses were incompatible at the level of RNA replication and their coat proteins segregated into separate populations of progeny particles. RNA packaging, on the other hand, was indiscriminate as all four viral RNAs were detectable in each progeny population. Consistent with the trans-encapsidation phenotype, fluorescence in situ hybridization of viral RNA revealed that the genomes of the two viruses co-localized throughout the cytoplasm. Our results imply that nodaviral RNAs lack rigorously defined packaging signals and that coencapsidation of the viral RNAs does not require a pair of cognate RNA1 and RNA2. PMID:24725955

Highly specific salt bridges govern bacteriophage P22 icosahedral capsid assembly: identification of the site in coat protein responsible for interaction with scaffolding protein.

PubMed

Cortines, Juliana R; Motwani, Tina; Vyas, Aashay A; Teschke, Carolyn M

2014-05-01

Icosahedral virus assembly requires a series of concerted and highly specific protein-protein interactions to produce a proper capsid. In bacteriophage P22, only coat protein (gp5) and scaffolding protein (gp8) are needed to assemble a procapsid-like particle, both in vivo and in vitro. In scaffolding protein's coat binding domain, residue R293 is required for procapsid assembly, while residue K296 is important but not essential. Here, we investigate the interaction of scaffolding protein with acidic residues in the N-arm of coat protein, since this interaction has been shown to be electrostatic. Through site-directed mutagenesis of genes 5 and 8, we show that changing coat protein N-arm residue 14 from aspartic acid to alanine causes a lethal phenotype. Coat protein residue D14 is shown by cross-linking to interact with scaffolding protein residue R293 and, thus, is intimately involved in proper procapsid assembly. To a lesser extent, coat protein N-arm residue E18 is also implicated in the interaction with scaffolding protein and is involved in capsid size determination, since a cysteine mutation at this site generated petite capsids. The final acidic residue in the N-arm that was tested, E15, is shown to only weakly interact with scaffolding protein's coat binding domain. This work supports growing evidence that surface charge density may be the driving force of virus capsid protein interactions. Bacteriophage P22 infects Salmonella enterica serovar Typhimurium and is a model for icosahedral viral capsid assembly. In this system, coat protein interacts with an internal scaffolding protein, triggering the assembly of an intermediate called a procapsid. Previously, we determined that there is a single amino acid in scaffolding protein required for P22 procapsid assembly, although others modulate affinity. Here, we identify partners in coat protein. We show experimentally that relatively weak interactions between coat and scaffolding proteins are capable of driving correctly shaped and sized procapsids and that the lack of these proper protein-protein interfaces leads to aberrant structures. The present work represents an important contribution supporting the hypothesis that virus capsid assembly is governed by seemingly simple interactions. The highly specific nature of the subunit interfaces suggests that these could be good targets for antivirals.

Many-molecule encapsulation by an icosahedral shell

PubMed Central

Perlmutter, Jason D; Mohajerani, Farzaneh; Hagan, Michael F

2016-01-01

We computationally study how an icosahedral shell assembles around hundreds of molecules. Such a process occurs during the formation of the carboxysome, a bacterial microcompartment that assembles around many copies of the enzymes ribulose 1,5-bisphosphate carboxylase/ oxygenase and carbonic anhydrase to facilitate carbon fixation in cyanobacteria. Our simulations identify two classes of assembly pathways leading to encapsulation of many-molecule cargoes. In one, shell assembly proceeds concomitantly with cargo condensation. In the other, the cargo first forms a dense globule; then, shell proteins assemble around and bud from the condensed cargo complex. Although the model is simplified, the simulations predict intermediates and closure mechanisms not accessible in experiments, and show how assembly can be tuned between these two pathways by modulating protein interactions. In addition to elucidating assembly pathways and critical control parameters for microcompartment assembly, our results may guide the reengineering of viruses as nanoreactors that self-assemble around their reactants. DOI: http://dx.doi.org/10.7554/eLife.14078.001 PMID:27166515

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

PubMed Central

Munke, Anna; Andreasson, Jakob; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Bean, Richard J.; Berntsen, Peter; Bielecki, Johan; Boutet, Sébastien; Bucher, Maximilian; Chapman, Henry N.; Daurer, Benedikt J.; DeMirci, Hasan; Elser, Veit; Fromme, Petra; Hajdu, Janos; Hantke, Max F.; Higashiura, Akifumi; Hogue, Brenda G.; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A.; Reddy, Hemanth K.N.; Lan, Ti-Yen; Larsson, Daniel S.D.; Liu, Haiguang; Loh, N. Duane; Maia, Filipe R.N.C.; Mancuso, Adrian P.; Mühlig, Kerstin; Nakagawa, Atsushi; Nam, Daewoong; Nelson, Garrett; Nettelblad, Carl; Okamoto, Kenta; Ourmazd, Abbas; Rose, Max; van der Schot, Gijs; Schwander, Peter; Seibert, M. Marvin; Sellberg, Jonas A.; Sierra, Raymond G.; Song, Changyong; Svenda, Martin; Timneanu, Nicusor; Vartanyants, Ivan A.; Westphal, Daniel; Wiedorn, Max O.; Williams, Garth J.; Xavier, Paulraj Lourdu; Yoon, Chun Hong; Zook, James

2016-01-01

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here. PMID:27478984

Flavivirus structural heterogeneity: implications for cell entry.

PubMed

Rey, Félix A; Stiasny, Karin; Heinz, Franz X

2017-06-01

The explosive spread of Zika virus is the most recent example of the threat imposed to human health by flaviviruses. High-resolution structures are available for several of these arthropod-borne viruses, revealing alternative icosahedral organizations of immature and mature virions. Incomplete proteolytic maturation, however, results in a cloud of highly heterogeneous mosaic particles. This heterogeneity is further expanded by a dynamic behavior of the viral envelope glycoproteins. The ensemble of heterogeneous and dynamic infectious particles circulating in infected hosts offers a range of alternative possible receptor interaction sites at their surfaces, potentially contributing to the broad flavivirus host-range and variation in tissue tropism. The potential synergy between heterogeneous particles in the circulating cloud thus provides an additional dimension to understand the unanticipated properties of Zika virus in its recent outbreaks. Copyright © 2017 Elsevier B.V. All rights reserved.

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

DOE PAGES

Munke, Anna; Andreasson, Jakob; Aquila, Andrew; ...

2016-08-01

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. Here, the diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB)more » as a resource for algorithm development, the contents of which are described here.« less

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source.

PubMed

Munke, Anna; Andreasson, Jakob; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Bean, Richard J; Berntsen, Peter; Bielecki, Johan; Boutet, Sébastien; Bucher, Maximilian; Chapman, Henry N; Daurer, Benedikt J; DeMirci, Hasan; Elser, Veit; Fromme, Petra; Hajdu, Janos; Hantke, Max F; Higashiura, Akifumi; Hogue, Brenda G; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A; Reddy, Hemanth K N; Lan, Ti-Yen; Larsson, Daniel S D; Liu, Haiguang; Loh, N Duane; Maia, Filipe R N C; Mancuso, Adrian P; Mühlig, Kerstin; Nakagawa, Atsushi; Nam, Daewoong; Nelson, Garrett; Nettelblad, Carl; Okamoto, Kenta; Ourmazd, Abbas; Rose, Max; van der Schot, Gijs; Schwander, Peter; Seibert, M Marvin; Sellberg, Jonas A; Sierra, Raymond G; Song, Changyong; Svenda, Martin; Timneanu, Nicusor; Vartanyants, Ivan A; Westphal, Daniel; Wiedorn, Max O; Williams, Garth J; Xavier, Paulraj Lourdu; Yoon, Chun Hong; Zook, James

2016-08-01

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.

Icosahedral and decagonal quasicrystals of intermetallic compounds are multiple twins of cubic or orthorhombic crystals composed of very large atomic complexes with icosahedral point-group symmetry in cubic close packing or body-centered packing: Structure of decagonal Al6Pd

PubMed Central

Pauling, Linus

1989-01-01

A doubly icosahedral complex involves roughly spherical clusters of atoms with icosahedral point-group symmetry, which are themselves, in parallel orientation, icosahedrally packed. These complexes may form cubic crystallites; three structures of this sort have been identified. Analysis of electron diffraction photographs of the decagonal quasicrystal Al6Pd has led to its description as involving pentagonal twinning of an orthorhombic crystal with a = 51.6 Å, b = 37.6 Å, and c = 33.24 Å, with about 4202 atoms in the unit, comprising two 1980-atom doubly icosahedral complexes, each involving icosahedral packing of 45 44-atom icosahedral complexes (at 0 0 0 and 1/2 1/2 1/2) and 242 interstitial atoms. The complexes and clusters are oriented with one of their fivefold axes in the c-axis direction. Images PMID:16594092

Icosahedral and decagonal quasicrystals of intermetallic compounds are multiple twins of cubic or orthorhombic crystals composed of very large atomic complexes with icosahedral point-group symmetry in cubic close packing or body-centered packing: Structure of decagonal Al(6)Pd.

PubMed

Pauling, L

1989-12-01

A doubly icosahedral complex involves roughly spherical clusters of atoms with icosahedral point-group symmetry, which are themselves, in parallel orientation, icosahedrally packed. These complexes may form cubic crystallites; three structures of this sort have been identified. Analysis of electron diffraction photographs of the decagonal quasicrystal Al(6)Pd has led to its description as involving pentagonal twinning of an orthorhombic crystal with a = 51.6 A, b = 37.6 A, and c = 33.24 A, with about 4202 atoms in the unit, comprising two 1980-atom doubly icosahedral complexes, each involving icosahedral packing of 45 44-atom icosahedral complexes (at 0 0 0 and 1/2 1/2 1/2) and 242 interstitial atoms. The complexes and clusters are oriented with one of their fivefold axes in the c-axis direction.

Halophilic viruses with varying biochemical and biophysical properties are amenable to purification with asymmetrical flow field-flow fractionation.

PubMed

Eskelin, Katri; Lampi, Mirka; Meier, Florian; Moldenhauer, Evelin; Bamford, Dennis H; Oksanen, Hanna M

2017-11-01

Viruses come in various shapes and sizes, and a number of viruses originate from extremities, e.g. high salinity or elevated temperature. One challenge for studying extreme viruses is to find efficient purification conditions where viruses maintain their infectivity. Asymmetrical flow field-flow fractionation (AF4) is a gentle native chromatography-like technique for size-based separation. It does not have solid stationary phase and the mobile phase composition is readily adjustable according to the sample needs. Due to the high separation power of specimens up to 50 µm, AF4 is suitable for virus purification. Here, we applied AF4 for extremophilic viruses representing four morphotypes: lemon-shaped, tailed and tailless icosahedral, as well as pleomorphic enveloped. AF4 was applied to input samples of different purity: crude supernatants of infected cultures, polyethylene glycol-precipitated viruses and viruses purified by ultracentrifugation. All four virus morphotypes were successfully purified by AF4. AF4 purification of culture supernatants or polyethylene glycol-precipitated viruses yielded high recoveries, and the purities were comparable to those obtained by the multistep ultracentrifugation purification methods. In addition, we also demonstrate that AF4 is a rapid monitoring tool for virus production in slowly growing host cells living in extreme conditions.

Icosahedral quasicrystals of intermetallic compounds are icosahedral twins of cubic crystals of three kinds, consisting of large (about 5000 atoms) icosahedral complexes in either a cubic body-centered or a cubic face-centered arrangement or smaller (about 1350 atoms) icosahedral complexes in the β-tungsten arrangement

PubMed Central

Pauling, Linus

1989-01-01

The twofold-axis electron-diffraction photographs of icosahedral quasicrystals are of three kinds, reflecting three different structures of the cubic crystals that by icosahedral twinning form the quasicrystals. The first kind, represented by Al13Cu4Fe3, contains two very large icosahedral complexes, each of about 4680 atoms, in the body-centered arrangement, with six smaller icosahedral complexes (104 atoms each) in the principal interstices. The second kind, represented by Al5Mn, contains four of the very large complexes in the face-centered arrangement (cubic close packing), with four of the smaller clusters in the interstices. The third kind, represented by Al6CuLi3, contains eight icosahedral complexes, each of about 1350 atoms, in the β-W arrangement. The supporting evidence for these cubic structures is discussed as well as other evidence showing that the simple quasicrystal theory, which states that quasicrystals do not involve any translational identity operations, has to be modified. Images PMID:16594078

Expanding the host range of small insect RNA viruses: Providence virus (Carmotetraviridae) infects and replicates in a human tissue culture cell line.

PubMed

Jiwaji, Meesbah; Short, James Roswell; Dorrington, Rosemary Ann

2016-10-01

Tetraviruses are small, positive (+ve)-sense ssRNA viruses that infect the midgut cells of lepidopteran larvae. Providence virus (PrV) is the only member of the family Carmotetraviridae (previously Tetraviridae). PrV particles exhibit the characteristic tetraviral T=4 icosahedral symmetry, but PrV is distinct from other tetraviruses with respect to genome organization and viral non-structural proteins. Currently, PrV is the only tetravirus known to infect and replicate in lepidopteran cell culture lines. In this report we demonstrate, using immunofluorescence microscopy, that PrV infects and replicates in a human tissue culture cell line (HeLa), producing infectious virus particles. We also provide evidence for PrV replication in vitro in insect, mammalian and plant cell-free systems. This study challenges the long-held view that tetraviruses have a narrow host range confined to one or a few lepidopteran species and highlights the need to consider the potential for apparently non-infectious viruses to be transferred to new hosts in the laboratory.

A novel totivirus-like virus isolated from bat guano.

PubMed

Yang, Xinglou; Zhang, Yunzhi; Ge, Xingyi; Yuan, Junfa; Shi, Zhengli

2012-06-01

Previous metagenomic analysis indicated that numerous insect viruses exist in bat guano. In this study, we isolated a novel double-stranded RNA virus, a tentative member of the family Totiviridae, designated Tianjin totivirus (ToV-TJ), from bat feces. The virus is an icosahedral particle with a diameter of 40-43 nm, and it causes cytopathic effect in Sf9, Hz, and C6/36 cell lines. Full-length genomic sequence analysis showed that ToV-TJ shares high similarity with the totivirus OMRV-AK4, which was recently isolated from mosquitoes in Japan. The full-length genome of the ToV-TJ was 7611 bp and contained two predicted non-overlapping open reading frames (ORFs): ORF1, encoding the capsid protein (CP), and ORF2, encoding an RNA-dependent RNA polymerase. Bioassay of ToV-TJ by feeding on the larvae of Spodoptera exigua and Helicoverpa armigera (Hubner) suggests that this virus is not infectious for these two larvae in vivo. Sequences similar to that of ToV-TJ have been detected in bat feces sampled in Yunnan and Hainan Provinces, suggesting that this virus is widely distributed.

Microscopic Characterization of the Brazilian Giant Samba Virus.

PubMed

Schrad, Jason R; Young, Eric J; Abrahão, Jônatas S; Cortines, Juliana R; Parent, Kristin N

2017-02-14

Prior to the discovery of the mimivirus in 2003, viruses were thought to be physically small and genetically simple. Mimivirus, with its ~750-nm particle size and its ~1.2-Mbp genome, shattered these notions and changed what it meant to be a virus. Since this discovery, the isolation and characterization of giant viruses has exploded. One of the more recently discovered giant viruses, Samba virus, is a Mimivirus that was isolated from the Rio Negro in the Brazilian Amazon. Initial characterization of Samba has revealed some structural information, although the preparation techniques used are prone to the generation of structural artifacts. To generate more native-like structural information for Samba, we analyzed the virus through cryo-electron microscopy, cryo-electron tomography, scanning electron microscopy, and fluorescence microscopy. These microscopy techniques demonstrated that Samba particles have a capsid diameter of ~527 nm and a fiber length of ~155 nm, making Samba the largest Mimivirus yet characterized. We also compared Samba to a fiberless mimivirus variant. Samba particles, unlike those of mimivirus, do not appear to be rigid, and quasi-icosahedral, although the two viruses share many common features, including a multi-layered capsid and an asymmetric nucleocapsid, which may be common amongst the Mimiviruses .

Microscopic Characterization of the Brazilian Giant Samba Virus

PubMed Central

Schrad, Jason R.; Young, Eric J.; Abrahão, Jônatas S.; Cortines, Juliana R.; Parent, Kristin N.

2017-01-01

Prior to the discovery of the mimivirus in 2003, viruses were thought to be physically small and genetically simple. Mimivirus, with its ~750-nm particle size and its ~1.2-Mbp genome, shattered these notions and changed what it meant to be a virus. Since this discovery, the isolation and characterization of giant viruses has exploded. One of the more recently discovered giant viruses, Samba virus, is a Mimivirus that was isolated from the Rio Negro in the Brazilian Amazon. Initial characterization of Samba has revealed some structural information, although the preparation techniques used are prone to the generation of structural artifacts. To generate more native-like structural information for Samba, we analyzed the virus through cryo-electron microscopy, cryo-electron tomography, scanning electron microscopy, and fluorescence microscopy. These microscopy techniques demonstrated that Samba particles have a capsid diameter of ~527 nm and a fiber length of ~155 nm, making Samba the largest Mimivirus yet characterized. We also compared Samba to a fiberless mimivirus variant. Samba particles, unlike those of mimivirus, do not appear to be rigid, and quasi-icosahedral, although the two viruses share many common features, including a multi-layered capsid and an asymmetric nucleocapsid, which may be common amongst the Mimiviruses. PMID:28216551

Morphological and molecular diagnostics of Phytoseiulus persimilis and Phytoseiulus macropilis (Acari: Phytoseiidae).

PubMed

Okassa, Mireille; Tixier, Marie-Stéphane; Kreiter, Serge

2010-11-01

This study focuses on the diagnostics of two natural enemy species, belonging to the genus Phytoseiulus in the family Phytoseiidae (sub-family Amblyseiinae): P. macropilis and P. persimilis. These two species are of primary importance in biological control all over the world. However, they are morphologically very similar and specific diagnostics is difficult. This study utilizes mitochondrial molecular markers (12S rRNA and Cytb mtDNA) to differentiate these two species. Morphological analyses showed significant differences between P. persimilis and P. macropilis for 17 morphological characters of the 32 considered. However, despite these significant differences, the ranges of all characters overlap. Only the serration of the macroseta on the basitarsus (StIV) allows the differentiation between P. persimilis and P. macropilis. Despite these small morphological differences, molecular results, for both mitochondrial DNA fragments considered (rRNA and Cytb mtDNA), showed a clear delineation between the specimens of P. macropilis and P. persimilis. This study emphasizes (i) that only one morphological character (serration of the seta StIV) clearly separates these two species, and (ii) the usefulness of an automatical molecular and simple diagnostic tool for accurate differentiation of the two species and ensure the morphological diagnostics. Further studies are proposed, including more DNA sequences especially for P. macropilis.

Simulating Self-Assembly with Simple Models

NASA Astrophysics Data System (ADS)

Rapaport, D. C.

Results from recent molecular dynamics simulations of virus capsid self-assembly are described. The model is based on rigid trapezoidal particles designed to form polyhedral shells of size 60, together with an atomistic solvent. The underlying bonding process is fully reversible. More extensive computations are required than in previous work on icosahedral shells built from triangular particles, but the outcome is a high yield of closed shells. Intermediate clusters have a variety of forms, and bond counts provide a useful classification scheme

Estimating contrast transfer function and associated parameters by constrained non-linear optimization.

PubMed

Yang, C; Jiang, W; Chen, D-H; Adiga, U; Ng, E G; Chiu, W

2009-03-01

The three-dimensional reconstruction of macromolecules from two-dimensional single-particle electron images requires determination and correction of the contrast transfer function (CTF) and envelope function. A computational algorithm based on constrained non-linear optimization is developed to estimate the essential parameters in the CTF and envelope function model simultaneously and automatically. The application of this estimation method is demonstrated with focal series images of amorphous carbon film as well as images of ice-embedded icosahedral virus particles suspended across holes.

Simulations of curved assemblies in soft matter and biological systems

NASA Astrophysics Data System (ADS)

Qiao, Cong

Viruses are small infectious agents that replicate only inside living cells of other organisms. In the viral life cycle, the self-assembly of the outer protein shell (capsid) is an essential step. We study this process in the hope of shedding light on development of antiviral drugs, gene therapy and other virus-related technologies that can benefit the humankind. More fundamentally, learning about the process of viral capsid assembly can elucidate the assembly mechanisms of a wide range of complex structures. In this work, we use molecular dynamics simulations and coarse-grained computational models to study viral capsid assembly in several situations where geometric constraints play a role in dictating assembly outcomes. We first focus on icosahedral viruses with single-stranded RNA genomes, in which case the capsid usually assembles around the genomic RNA. It is consistently observed in experiments that such viral particles are ''overcharged'', meaning the net negative charge on the viral genome is greater than the net positive charge on the viral capsid. We computationally investigate the mechanisms that lead to ``overcharging'', and more broadly, how the encapsidated genome length is influenced by the capsid. We perform both dynamical simulations of the assembly process and equilibrium calculations to determine the optimal genome length (meaning that which maximizes the assembly yield and/or minimizes the free energy of the assembled virus). We find that the optimal genome length is determined by the interplay between capsid size, net capsid charge, distribution of capsid charge and nucleic acid structures. Our simulations demonstrate that overcharging results from a combination of electrostatic screening and the geometric constraints associated with encapsulating a nucleic acid inside of a spherical virus. We then study the assembly of the immature HIV. In contrast to icosahedral viruses, the immature HIV forms an asymmetric particle, consisting of continuous regularly packed regions with local hexagonal order and vacancies. A similar lattice structure has been observed in experiments in which mutually attractive colloidal particles pack on the surface of a spherical droplet (G. Meng, J. Paulose, D. R. Nelson, and V. N. Manoharan, ''Elastic instability of a crystal growing on a curved surface'', Science 343, 634-637 (2014).), suggesting that the two systems experience a similar form of geometric frustration. We therefore study the adsorption and packing of spherical particles on a spherical template, as a function of the strength and range of interparticle attractions, as well as the radius of the spherical template. We observe that the adsorbed particles form two different classes of packing arrangements, one with icosahedrally ordered topological defects, and the other with highly disordered defects and vacancies. The latter regime is consistent with experiments on colloidal packing on spherical droplets and the immature HIV lattice. Our results suggest that the transition between these regimes is controlled by the range of the interparticle attractions. In the last chapter, we study a model for the assembly and budding of a capsid on a membrane, such as occurs during the exit of the immature HIV virus from a cell. We use a coarse-grained subunit model to represent the capsid proteins, and a fluid membrane model to represent the cell membrane. We find that the size and structure of the assembled capsid depends sensitively on the timescale of budding.

Structure of Bombyx mori densovirus 1, a silkworm pathogen.

PubMed

Kaufmann, Bärbel; El-Far, Mohamed; Plevka, Pavel; Bowman, Valorie D; Li, Yi; Tijssen, Peter; Rossmann, Michael G

2011-05-01

Bombyx mori densovirus 1 (BmDNV-1), a major pathogen of silkworms, causes significant losses to the silk industry. The structure of the recombinant BmDNV-1 virus-like particle has been determined at 3.1-Å resolution using X-ray crystallography. It is the first near-atomic-resolution structure of a virus-like particle within the genus Iteravirus. The particles consist of 60 copies of the 55-kDa VP3 coat protein. The capsid protein has a β-barrel "jelly roll" fold similar to that found in many diverse icosahedral viruses, including archaeal, bacterial, plant, and animal viruses, as well as other parvoviruses. Most of the surface loops have little structural resemblance to other known parvovirus capsid proteins. In contrast to vertebrate parvoviruses, the N-terminal β-strand of BmDNV-1 VP3 is positioned relative to the neighboring 2-fold related subunit in a "domain-swapped" conformation, similar to findings for other invertebrate parvoviruses, suggesting domain swapping is an evolutionarily conserved structural feature of the Densovirinae.

Reverse genetics of Mononegavirales: How they work, new vaccines, and new cancer therapeutics

PubMed Central

Pfaller, Christian K.; Cattaneo, Roberto; Schnell, Matthias J.

2015-01-01

The order Mononegavirales includes five families: Bornaviridae, Filoviridae, Nyamaviridae, Paramyxoviridae, and Rhabdoviridae. The genome of these viruses is one molecule of negative-sense single strand RNA coding for five to ten genes in a conserved order. The RNA is not infectious until packaged by the nucleocapsid protein and transcribed by the polymerase and co-factors. Reverse genetics approaches have answered fundamental questions about the biology of Mononegavirales. The lack of icosahedral symmetry and modular organization in the genome of these viruses has facilitated engineering of viruses expressing fluorescent proteins, and these fluorescent proteins have provided important insights about the molecular and cellular basis of tissue tropism and pathogenesis. Studies have assessed the relevance for virulence of different receptors and the interactions with cellular proteins governing the innate immune responses. Research has also analyzed the mechanisms of attenuation. Based on these findings, ongoing clinical trials are exploring new live attenuated vaccines and the use of viruses re-engineered as cancer therapeutics. PMID:25702088

Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae

PubMed Central

Sõmera, Merike; Sarmiento, Cecilia; Truve, Erkki

2015-01-01

The genus Sobemovirus, unassigned to any family, consists of viruses with single-stranded plus-oriented single-component RNA genomes and small icosahedral particles. Currently, 14 species within the genus have been recognized by the International Committee on Taxonomy of Viruses (ICTV) but several new species are to be recognized in the near future. Sobemovirus genomes are compact with a conserved structure of open reading frames and with short untranslated regions. Several sobemoviruses are important pathogens. Moreover, over the last decade sobemoviruses have become important model systems to study plant virus evolution. In the current review we give an overview of the structure and expression of sobemovirus genomes, processing and functions of individual proteins, particle structure, pathology and phylogenesis of sobemoviruses as well as of satellite RNAs present together with these viruses. Based on a phylogenetic analysis we propose that a new family Sobemoviridae should be recognized including the genera Sobemovirus and Polemovirus. Finally, we outline the future perspectives and needs for the research focusing on sobemoviruses. PMID:26083319

Induced Förster resonance energy transfer by encapsulation of DNA-scaffold based probes inside a plant virus based protein cage

NASA Astrophysics Data System (ADS)

de Ruiter, Mark V.; Overeem, Nico J.; Singhai, Gaurav; Cornelissen, Jeroen J. L. M.

2018-05-01

Insight into the assembly and disassembly of viruses can play a crucial role in developing cures for viral diseases. Specialized fluorescent probes can benefit the study of interactions within viruses, especially during cell studies. In this work, we developed a strategy based on Förster resonance energy transfer (FRET) to study the assembly of viruses without labeling the exterior of viruses. Instead, we exploit their encapsulation of nucleic cargo, using three different fluorescent ATTO dyes linked to single-stranded DNA oligomers, which are hybridised to a longer DNA strand. FRET is induced upon assembly of the cowpea chlorotic mottle virus, which forms monodisperse icosahedral particles of about 22 nm, thereby increasing the FRET efficiency by a factor of 8. Additionally, encapsulation of the dyes in virus-like particles induces a two-step FRET. When the formed constructs are disassembled, this FRET signal is fully reduced to the value before encapsulation. This reversible behavior makes the system a good probe for studying viral assembly and disassembly. It, furthermore, shows that multi-component supramolecular materials are stabilized in the confinement of a protein cage.

Three-dimensional structure and function of the Paramecium bursaria chlorella virus capsid.

PubMed

Zhang, Xinzheng; Xiang, Ye; Dunigan, David D; Klose, Thomas; Chipman, Paul R; Van Etten, James L; Rossmann, Michael G

2011-09-06

A cryoelectron microscopy 8.5 Å resolution map of the 1,900 Å diameter, icosahedral, internally enveloped Paramecium bursaria chlorella virus was used to interpret structures of the virus at initial stages of cell infection. A fivefold averaged map demonstrated that two minor capsid proteins involved in stabilizing the capsid are missing in the vicinity of the unique vertex. Reconstruction of the virus in the presence of host chlorella cell walls established that the spike at the unique vertex initiates binding to the cell wall, which results in the enveloped nucleocapsid moving closer to the cell. This process is concurrent with the release of the internal viral membrane that was linked to the capsid by many copies of a viral membrane protein in the mature infectous virus. Simultaneously, part of the trisymmetrons around the unique vertex disassemble, probably in part because two minor capsid proteins are absent, causing Paramecium bursaria chlorella virus and the cellular contents to merge, possibly as a result of enzyme(s) within the spike assembly. This may be one of only a few recordings of successive stages of a virus while infecting a eukaryotic host in pseudoatomic detail in three dimensions.

Three-dimensional structure and function of the Paramecium bursaria chlorella virus capsid

PubMed Central

Zhang, Xinzheng; Xiang, Ye; Dunigan, David D.; Klose, Thomas; Chipman, Paul R.; Van Etten, James L.; Rossmann, Michael G.

2011-01-01

A cryoelectron microscopy 8.5 Å resolution map of the 1,900 Å diameter, icosahedral, internally enveloped Paramecium bursaria chlorella virus was used to interpret structures of the virus at initial stages of cell infection. A fivefold averaged map demonstrated that two minor capsid proteins involved in stabilizing the capsid are missing in the vicinity of the unique vertex. Reconstruction of the virus in the presence of host chlorella cell walls established that the spike at the unique vertex initiates binding to the cell wall, which results in the enveloped nucleocapsid moving closer to the cell. This process is concurrent with the release of the internal viral membrane that was linked to the capsid by many copies of a viral membrane protein in the mature infectous virus. Simultaneously, part of the trisymmetrons around the unique vertex disassemble, probably in part because two minor capsid proteins are absent, causing Paramecium bursaria chlorella virus and the cellular contents to merge, possibly as a result of enzyme(s) within the spike assembly. This may be one of only a few recordings of successive stages of a virus while infecting a eukaryotic host in pseudoatomic detail in three dimensions. PMID:21873222

DOE Office of Scientific and Technical Information (OSTI.GOV)

Munke, Anna; Andreasson, Jakob; Aquila, Andrew

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. Here, the diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB)more » as a resource for algorithm development, the contents of which are described here.« less

Fine Structure of Reovirus Type 2

PubMed Central

Loh, Philip C.; Hohl, H. R.; Soergel, M.

1965-01-01

Loh, Philip C. (University of Hawaii, Honolulu), H. R. Hohl, and M. Soergel. Fine structure of reovirus type 2. J. Bacteriol. 89:1140–1144. 1965.—The fine structure reovirus type 2 was studied by electron microscopy with the negative-staining method. The virus has a mean diameter of 772 A and shows evidence of icosahedral shape and 5:3:2 symmetry. The particle is composed of a core, an inner layer, and a capsid composed of 92 elongated hollow capsomeres. These capsomeres have mean dimensions of 116 A × 110 A and a central hole 48 A in diameter. In size and architecture, reovirus type 2 is very similar to the other members (reoviruses types 1 and 3) of this group of animal viruses. Images PMID:14276109

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 7

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quesada, Odayme; Gurda, Brittney; Govindasamy, Lakshmanan

2007-12-01

Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids have been produced which diffract X-rays to ∼3.0 Å resolution. Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids diffract X-rays to ∼3.0 Å resolution. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = 252.4, c = 591.2 Å in the hexagonal setting. The diffraction data were processed and reduced to an overall completeness of 79.0% and an R{sub merge} of 12.0%. There are three viral capsids in the unit cell. The icosahedral threefold axis is coincident with the crystallographic threefold axis, resulting in one third of amore » capsid (20 monomers) per crystallographic asymmetric unit. The orientation of the viral capsid has been determined by rotation-function searches and is positioned at (0, 0, 0) by packing considerations.« less

Magic-angle spinning NMR of intact bacteriophages: Insights into the capsid, DNA and their interface

NASA Astrophysics Data System (ADS)

Abramov, Gili; Morag, Omry; Goldbourt, Amir

2015-04-01

Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses.

The Expanding Family of Virophages.

PubMed

Bekliz, Meriem; Colson, Philippe; La Scola, Bernard

2016-11-23

Virophages replicate with giant viruses in the same eukaryotic cells. They are a major component of the specific mobilome of mimiviruses. Since their discovery in 2008, five other representatives have been isolated, 18 new genomes have been described, two of which being nearly completely sequenced, and they have been classified in a new viral family, Lavidaviridae . Virophages are small viruses with approximately 35-74 nm large icosahedral capsids and 17-29 kbp large double-stranded DNA genomes with 16-34 genes, among which a very small set is shared with giant viruses. Virophages have been isolated or detected in various locations and in a broad range of habitats worldwide, including the deep ocean and inland. Humans, therefore, could be commonly exposed to virophages, although currently limited evidence exists of their presence in humans based on serology and metagenomics. The distribution of virophages, the consequences of their infection and the interactions with their giant viral hosts within eukaryotic cells deserve further research.

Towards the modeling of nanoindentation of virus shells: Do substrate adhesion and geometry matter?

NASA Astrophysics Data System (ADS)

Bousquet, Arthur; Dragnea, Bogdan; Tayachi, Manel; Temam, Roger

2016-12-01

Soft nanoparticles adsorbing at surfaces undergo deformation and buildup of elastic strain as a consequence of interfacial adhesion of similar magnitude with constitutive interactions. An example is the adsorption of virus particles at surfaces, a phenomenon of central importance for experiments in virus nanoindentation and for understanding of virus entry. The influence of adhesion forces and substrate corrugation on the mechanical response to indentation has not been studied. This is somewhat surprising considering that many single-stranded RNA icosahedral viruses are organized by soft intermolecular interactions while relatively strong adhesion forces are required for virus immobilization for nanoindentation. This article presents numerical simulations via finite elements discretization investigating the deformation of a thick shell in the context of slow evolution linear elasticity and in presence of adhesion interactions with the substrate. We study the influence of the adhesion forces in the deformation of the virus model under axial compression on a flat substrate by comparing the force-displacement curves for a shell having elastic constants relevant to virus capsids with and without adhesion forces derived from the Lennard-Jones potential. Finally, we study the influence of the geometry of the substrate in two-dimensions by comparing deformation of the virus model adsorbed at the cusp between two cylinders with that on a flat surface.

Diversity in virus assembly: biology makes things complicated

NASA Astrophysics Data System (ADS)

Zlotnick, Adam

2008-03-01

Icosahedral viruses have an elegance of geometry that implies a general path of assembly. However, structure alone provides insufficient information. Cowpea Chlorotic Mottle Virus (CCMV), an important system for studying virus assembly, consists of 90 coat protein (CP) homodimers condensed around an RNA genome. The crystal structure (Speir et al, 1995) reveals that assembly causes burial of hydrophobic surface and formation of β hexamers, the intertwining of N-termini of the CPs surrounding a quasi-sixfold. This structural view leads to reasonable and erroneous predictions: (i) CCMV capsids are extremely stable, and (ii) β hexamer formation is critical to assembly. Experimentally, we have found that capsids are based on a network of extremely weak (4-5 kT) pairwise interactions and that pentamer formation is the critical step in assembly kinetics. Because of the fragility of CP-Cp interaction, we can redirect assembly to generate and dissociate tubular nanostructures. The dynamic behavior of CCMV reflects the requirements and peculiarities of an evolved biological system; it does not necessarily reflect the behavior predicted from a more static picture of the virus.

Human papilloma virus: Apprehending the link with carcinogenesis and unveiling new research avenues (Review)

PubMed Central

Ilie, Mihaela Adriana; Caruntu, Constantin; Zurac, Sabina; Neagu, Monica; Constantin, Carolina; Branisteanu, Daciana Elena; Voiculescu, Vlad; Mamoulakis, Charalampos; Tzanakakis, George; Spandidos, Demetrios A.

2018-01-01

Human papilloma viruses (HPV) are a small group of non-enveloped viruses belonging to the Papillomaviridae family with strong similarities to polyoma viruses. The viral particles consist of a genome in the form of a circular double-stranded DNA, encompassing eight open reading frames, as well as a non-enveloped icosahedral capsid. HPV infection is considered the most common sexually transmitted disease in both sexes and is strongly implicated in the pathogenesis of different types of cancer. ‘High-risk’ mucosal HPV types, predominantly types 16, 18, 31, 33 and 35, are associated with most cervical, penile, vulvar, vaginal, anal, oropharyngeal cancers and pre-cancers. Screening for HPV is necessary for the prognosis and for determining treatment strategies for cancer. Novel HPV markers, including proteomic and genomic markers, as well as anti-papillomavirus vaccines are currently available. The aim of this comprehensive review was to thoroughly present the updated information on virus development, cancer occurrence, treatment and prevention strategies, in an attempt to shed further light into the field, including novel research avenues. PMID:29393378

Satellite Tobacco Mosaic Virus (STMV)

NASA Technical Reports Server (NTRS)

2000-01-01

The structure of the Satellite Tobacco Mosaic Virus (STMV)--one of the smallest viruses known--has been successfully deduced using STMV crystals grown aboard the Space Shuttle in 1992 and 1994. The STMV crystals were up to 30 times the volume of any seen in the laboratory. At the same time they gave the best resolution data ever obtained on any virus crystal. STMV is a small icosahedral plant virus, consisting of a protein shell made up of 60 identical protein subunits of molecular weight 17,500. Particularly noteworthy is the fact that, in contrast to the crystal grown on Earth, the crystals grown under microgravity conditions were viusally perfect, with no striations or clumping of crystals. Furthermore, the X-ray diffraction data obtained from the space-grown crystals was of a much higher quality than the best data available at that time from ground-based crystals. This computer model shows the external coating or capsid. STMV is used because it is a simple protein to work with; studies are unrelated to tobacco. Credit: Dr. Alex McPherson, Univeristy of California at Irvin.

Allosteric Control of Icosahedral Capsid Assembly

PubMed Central

Lazaro, Guillermo R.

2017-01-01

During the lifecycle of a virus, viral proteins and other components self-assemble to form an ordered protein shell called a capsid. This assembly process is subject to multiple competing constraints, including the need to form a thermostable shell while avoiding kinetic traps. It has been proposed that viral assembly satisfies these constraints through allosteric regulation, including the interconversion of capsid proteins among conformations with different propensities for assembly. In this article we use computational and theoretical modeling to explore how such allostery affects the assembly of icosahedral shells. We simulate assembly under a wide range of protein concentrations, protein binding affinities, and two different mechanisms of allosteric control. We find that, above a threshold strength of allosteric control, assembly becomes robust over a broad range of subunit binding affinities and concentrations, allowing the formation of highly thermostable capsids. Our results suggest that allostery can significantly shift the range of protein binding affinities that lead to successful assembly, and thus should be accounted for in models that are used to estimate interaction parameters from experimental data. PMID:27117092

Components of Adenovirus Genome Packaging

PubMed Central

Ahi, Yadvinder S.; Mittal, Suresh K.

2016-01-01

Adenoviruses (AdVs) are icosahedral viruses with double-stranded DNA (dsDNA) genomes. Genome packaging in AdV is thought to be similar to that seen in dsDNA containing icosahedral bacteriophages and herpesviruses. Specific recognition of the AdV genome is mediated by a packaging domain located close to the left end of the viral genome and is mediated by the viral packaging machinery. Our understanding of the role of various components of the viral packaging machinery in AdV genome packaging has greatly advanced in recent years. Characterization of empty capsids assembled in the absence of one or more components involved in packaging, identification of the unique vertex, and demonstration of the role of IVa2, the putative packaging ATPase, in genome packaging have provided compelling evidence that AdVs follow a sequential assembly pathway. This review provides a detailed discussion on the functions of the various viral and cellular factors involved in AdV genome packaging. We conclude by briefly discussing the roles of the empty capsids, assembly intermediates, scaffolding proteins, portal vertex and DNA encapsidating enzymes in AdV assembly and packaging. PMID:27721809

Isolation and characterization of a virus infecting the freshwater algae Chrysochromulina parva

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mirza, S.F.; Staniewski, M.A.; Short, C.M.

Water samples from Lake Ontario, Canada were tested for lytic activity against the freshwater haptophyte algae Chrysochromulina parva. A filterable lytic agent was isolated and identified as a virus via transmission electron microscopy and molecular methods. The virus, CpV-BQ1, is icosahedral, ca. 145 nm in diameter, assembled within the cytoplasm, and has a genome size of ca. 485 kb. Sequences obtained through PCR-amplification of DNA polymerase (polB) genes clustered among sequences from the family Phycodnaviridae, whereas major capsid protein (MCP) sequences clustered among sequences from either the Phycodnaviridae or Mimiviridae. Based on quantitative molecular assays, C. parva's abundance in Lakemore » Ontario was relatively stable, yet CpV-BQ1's abundance was variable suggesting complex virus-host dynamics. This study demonstrates that CpV-BQ1 is a member of the proposed order Megavirales with characteristics of both phycodnaviruses and mimiviruses indicating that, in addition to its complex ecological dynamics, it also has a complex evolutionary history. - Highlights: • A virus infecting the algae C. parva was isolated from Lake Ontario. • Virus characteristics demonstrated that this novel virus is an NCLDV. • The virus's polB sequence suggests taxonomic affiliation with the Phycodnaviridae. • The virus's capsid protein sequences also suggest Mimiviridae ancestry. • Surveys of host and virus natural abundances revealed complex host–virus dynamics.« less

Isolation and characterization of a ranavirus from koi, Cyprinus carpio L., experiencing mass mortalities in India.

PubMed

George, M R; John, K R; Mansoor, M M; Saravanakumar, R; Sundar, P; Pradeep, V

2015-04-01

We investigated mass mortalities of koi, Cyprinus carpio Linnaeus, 1758, experienced in South Indian fish farms by virus isolation, electron microscopy, PCR detection, sequencing of capsid protein gene and transmission studies. Samples of moribund koi brought to the laboratory suffered continuous mortality exhibiting swimming abnormalities, intermittent surfacing and skin darkening. Irido-like virus was isolated from the infected fish in the indigenous snakehead kidney cell line (SNKD2a). Icosahedral virus particles of 100 to 120 nm were observed in the infected cell cultures, budding from the cell membrane. Virus transmission and pathogenicity studies revealed that horizontal transmission occurred associated with mortality. PCR analysis of infected fish and cell cultures confirmed the presence of Ranavirus capsid protein sequences. Sequence analysis of the major capsid protein gene showed an identity of 99.9% to that of largemouth bass virus isolated from North America. Detection and successful isolation of this viral agent becomes the first record of isolation of a virus resembling Santee-Cooper Ranavirus from a koi and from India. We propose the name koi ranavirus to this agent. © 2014 John Wiley & Sons Ltd.

Icosahedral quasicrystals as twins of cubic crystals containing large icosahedral clusters of atoms: The 1012-atom primitive cubic structure of Al(6)CuLi(3), the C-phase Al(37)Cu(3)Li(21)Mg(3), and GaMg(2)Zn(3).

PubMed

Pauling, L

1988-06-01

Single-grain precession x-ray diffraction photographs of Al(6)CuLi(3) have been successfully indexed on the basis of icosahedral twinning of cubic crystals with a 1012-atom primitive cubic unit with edge 25.70 A, giving support to the proposal that the so-called icosahedral quasicrystals are twins of crystals containing eight large icosahedral clusters in the beta-W arrangement. In this compound two of the clusters consist of 104 atoms and six consist of 136 atoms, with 24 atoms shared. The same structure is assigned to the C-phase, Al(37)Cu(3)Li(21)Mg(3), and to GaMg(2)Zn(3). A theory of icosahedral quasicrystals and amorphous metals is described.

Icosahedral quasicrystals as twins of cubic crystals containing large icosahedral clusters of atoms: The 1012-atom primitive cubic structure of Al6CuLi3, the C-phase Al37Cu3Li21Mg3, and GaMg2Zn3

PubMed Central

Pauling, Linus

1988-01-01

Single-grain precession x-ray diffraction photographs of Al6CuLi3 have been successfully indexed on the basis of icosahedral twinning of cubic crystals with a 1012-atom primitive cubic unit with edge 25.70 Å, giving support to the proposal that the so-called icosahedral quasicrystals are twins of crystals containing eight large icosahedral clusters in the β-W arrangement. In this compound two of the clusters consist of 104 atoms and six consist of 136 atoms, with 24 atoms shared. The same structure is assigned to the C-phase, Al37Cu3Li21Mg3, and to GaMg2Zn3. A theory of icosahedral quasicrystals and amorphous metals is described. PMID:16593929

Nanobody-mediated resistance to Grapevine fanleaf virus in plants.

PubMed

Hemmer, Caroline; Djennane, Samia; Ackerer, Léa; Hleibieh, Kamal; Marmonier, Aurélie; Gersch, Sophie; Garcia, Shahinez; Vigne, Emmanuelle; Komar, Véronique; Perrin, Mireille; Gertz, Claude; Belval, Lorène; Berthold, François; Monsion, Baptiste; Schmitt-Keichinger, Corinne; Lemaire, Olivier; Lorber, Bernard; Gutiérrez, Carlos; Muyldermans, Serge; Demangeat, Gérard; Ritzenthaler, Christophe

2018-02-01

Since their discovery, single-domain antigen-binding fragments of camelid-derived heavy-chain-only antibodies, also known as nanobodies (Nbs), have proven to be of outstanding interest as therapeutics against human diseases and pathogens including viruses, but their use against phytopathogens remains limited. Many plant viruses including Grapevine fanleaf virus (GFLV), a nematode-transmitted icosahedral virus and causal agent of fanleaf degenerative disease, have worldwide distribution and huge burden on crop yields representing billions of US dollars of losses annually, yet solutions to combat these viruses are often limited or inefficient. Here, we identified a Nb specific to GFLV that confers strong resistance to GFLV upon stable expression in the model plant Nicotiana benthamiana and also in grapevine rootstock, the natural host of the virus. We showed that resistance was effective against a broad range of GFLV isolates independently of the inoculation method including upon nematode transmission but not against its close relative, Arabis mosaic virus. We also demonstrated that virus neutralization occurs at an early step of the virus life cycle, prior to cell-to-cell movement. Our findings will not only be instrumental to confer resistance to GFLV in grapevine, but more generally they pave the way for the generation of novel antiviral strategies in plants based on Nbs. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

CHLORELLA VIRUSES

PubMed Central

Yamada, Takashi; Onimatsu, Hideki; Van Etten, James L.

2007-01-01

Chlorella viruses or chloroviruses are large, icosahedral, plaque‐forming, double‐stranded‐DNA—containing viruses that replicate in certain strains of the unicellular green alga Chlorella. DNA sequence analysis of the 330‐kbp genome of Paramecium bursaria chlorella virus 1 (PBCV‐1), the prototype of this virus family (Phycodnaviridae), predict ∼366 protein‐encoding genes and 11 tRNA genes. The predicted gene products of ∼50% of these genes resemble proteins of known function, including many that are completely unexpected for a virus. In addition, the chlorella viruses have several features and encode many gene products that distinguish them from most viruses. These products include: (1) multiple DNA methyltransferases and DNA site‐specific endonucleases, (2) the enzymes required to glycosylate their proteins and synthesize polysaccharides such as hyaluronan and chitin, (3) a virus‐encoded K+ channel (called Kcv) located in the internal membrane of the virions, (4) a SET domain containing protein (referred to as vSET) that dimethylates Lys27 in histone 3, and (5) PBCV‐1 has three types of introns; a self‐splicing intron, a spliceosomal processed intron, and a small tRNA intron. Accumulating evidence indicates that the chlorella viruses have a very long evolutionary history. This review mainly deals with research on the virion structure, genome rearrangements, gene expression, cell wall degradation, polysaccharide synthesis, and evolution of PBCV‐1 as well as other related viruses. PMID:16877063

Preliminary X-ray data analysis of crystalline hibiscus chlorotic ringspot virus

PubMed Central

Cheng, Ao; Speir, Jeffrey A.; Yuan, Y. Adam; Johnson, John E.; Wong, Sek-Man

2009-01-01

Hibiscus chlorotic ringspot virus (HCRSV) is a positive-sense monopartite single-stranded RNA virus that belongs to the Carmovirus genus of the Tombusviridae family, which includes carnation mottle virus (CarMV). The HCRSV virion has a 30 nm diameter icosahedral capsid with T = 3 quasi-symmetry containing 180 copies of a 38 kDa coat protein (CP) and encapsidates a full-length 3.9 kb genomic RNA. Authentic virus was harvested from infected host kenaf leaves and was purified by saturated ammonium sulfate precipitation, sucrose density-gradient centrifugation and anion-exchange chromatography. Virus crystals were grown in multiple conditions; one of the crystals diffracted to 3.2 Å resolution and allowed the collection of a partial data set. The crystal belonged to space group R32, with unit-cell parameters a = b = 336.4, c = 798.5 Å. Packing considerations and rotation-function analysis determined that there were three particles per unit cell, all of which have the same orientation and fixed positions, and resulted in tenfold noncrystallography symmetry for real-space averaging. The crystals used for the structure determination of southern bean mosaic virus (SBMV) have nearly identical characteristics. Together, these findings will greatly aid the high-resolution structure determination of HCRSV. PMID:19478438

Preliminary X-ray Data Analysis of Crystalline Hibiscus Chlorotic Ringspot Virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, A.; Speir, J; Yuan, Y

Hibiscus chlorotic ringspot virus (HCRSV) is a positive-sense monopartite single-stranded RNA virus that belongs to the Carmovirus genus of the Tombusviridae family, which includes carnation mottle virus (CarMV). The HCRSV virion has a 30 nm diameter icosahedral capsid with T = 3 quasi-symmetry containing 180 copies of a 38 kDa coat protein (CP) and encapsidates a full-length 3.9 kb genomic RNA. Authentic virus was harvested from infected host kenaf leaves and was purified by saturated ammonium sulfate precipitation, sucrose density-gradient centrifugation and anion-exchange chromatography. Virus crystals were grown in multiple conditions; one of the crystals diffracted to 3Synchrotron .2 Amore » resolution and allowed the collection of a partial data set. The crystal belonged to space group R32, with unit-cell parameters a = b = 336.4, c = 798.5 . Packing considerations and rotation-function analysis determined that there were three particles per unit cell, all of which have the same orientation and fixed positions, and resulted in tenfold noncrystallography symmetry for real-space averaging. The crystals used for the structure determination of southern bean mosaic virus (SBMV) have nearly identical characteristics. Together, these findings will greatly aid the high-resolution structure determination of HCRSV.« less

Molecular packing in virus crystals: geometry, chemistry, and biology.

PubMed

Natarajan, P; Johnson, J E

1998-01-01

An automated procedure was developed to determine the geometrical and chemical interactions of crystalline virus particles using the crystal parameters, particle position, orientation, and atomic coordinates for an icosahedral asymmetric unit. Two applications of the program are reported: (1) An analysis of a novel pseudo-rhombohedral (R32) symmetry present in the monoclinic crystal lattices of both Nodamura Virus (NOV) and Coxsackie virus B3 (CVB3). The study shows that in both cases the interactions between particles is substantially increased by minor deviations from exact R32 symmetry and that only particles with the proper ratio of dimensions along twofold and fivefold symmetry axes (such as southern bean mosaic virus) can achieve comparable buried surface area in the true R32 space group. (2) An attempt was made to correlate biological function with remarkably conserved interparticle contact regions found in different crystal forms of three members of the nodavirus family, NOV, Flock House Virus (FHV), and Black Beetle Virus (BBV). Mutational evidence implicates the quasi-threefold region on the viral surface in receptor binding in nodaviruses and this region is dominant in particle contacts in all three virus crystals. Examination of particle contacts in numerous crystal structures of viruses in the picornavirus super-family showed that portions of the capsid surface known to interact with a receptor or serve as an epitope for monoclonal antibodies frequently stabilize crystal contacts.

A Novel Virus Causes Scale Drop Disease in Lates calcarifer

PubMed Central

de Groof, Ad; Guelen, Lars; Deijs, Martin; van der Wal, Yorick; Miyata, Masato; Ng, Kah Sing; van Grinsven, Lotte; Simmelink, Bartjan; Biermann, Yvonne; Grisez, Luc; van Lent, Jan; de Ronde, Anthony; Chang, Siow Foong; Schrier, Carla; van der Hoek, Lia

2015-01-01

From 1992 onwards, outbreaks of a previously unknown illness have been reported in Asian seabass (Lates calcarifer) kept in maricultures in Southeast Asia. The most striking symptom of this emerging disease is the loss of scales. It was referred to as scale drop syndrome, but the etiology remained enigmatic. By using a next-generation virus discovery technique, VIDISCA-454, sequences of an unknown virus were detected in serum of diseased fish. The near complete genome sequence of the virus was determined, which shows a unique genome organization, and low levels of identity to known members of the Iridoviridae. Based on homology of a series of putatively encoded proteins, the virus is a novel member of the Megalocytivirus genus of the Iridoviridae family. The virus was isolated and propagated in cell culture, where it caused a cytopathogenic effect in infected Asian seabass kidney and brain cells. Electron microscopy revealed icosahedral virions of about 140 nm, characteristic for the Iridoviridae. In vitro cultured virus induced scale drop syndrome in Asian seabass in vivo and the virus could be reisolated from these infected fish. These findings show that the virus is the causative agent for the scale drop syndrome, as each of Koch’s postulates is fulfilled. We have named the virus Scale Drop Disease Virus. Vaccines prepared from BEI- and formalin inactivated virus, as well as from E. coli produced major capsid protein provide efficacious protection against scale drop disease. PMID:26252390

Orientation relationship between the T structure and the icosahedral quasicrystal in the Zn-Mg-Al alloy system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakayama, Kei, E-mail: k.n@aoni.waseda.jp; Watanabe, Junya; Koyama, Yasumasa, E-mail: ykoyama@waseda.jp

2016-08-26

To understand the crystallographic relation between the Bergman-type icosahedral quasicrystal and its approximant-T structure, we have investigated the crystallographic features of prepared Zn-Mg-Al alloy samples, mainly by transmission electron microscopy. It was found that there existed three kinds of regions: that is, C14-Laves, approximant-T, and icosahedral-quasicrystal regions, in Zn-Mg-Al alloy samples with the composition of Zn-36at.%Mg-9at.%Al. Among these regions, in particular, we tried to determine an orientation relationship between neighboring icosahedral-quasicrystal and approximant-T regions. Based on the determined relationship, for instance, four threefold rotatory-inversion axes in the T structure were found to be parallel to four of ten threefold rotatory-inversionmore » axes in the icosahedral quasicrystal. It was thus understood that the atomic arrangements of the Bergman-type icosahedral quasicrystal and its approximant-T structure are likely to resemble each other.« less

Structure of Bombyx mori Densovirus 1, a Silkworm Pathogen▿‡

PubMed Central

Kaufmann, Bärbel; El-Far, Mohamed; Plevka, Pavel; Bowman, Valorie D.; Li, Yi; Tijssen, Peter; Rossmann, Michael G.

2011-01-01

Bombyx mori densovirus 1 (BmDNV-1), a major pathogen of silkworms, causes significant losses to the silk industry. The structure of the recombinant BmDNV-1 virus-like particle has been determined at 3.1-Å resolution using X-ray crystallography. It is the first near-atomic-resolution structure of a virus-like particle within the genus Iteravirus. The particles consist of 60 copies of the 55-kDa VP3 coat protein. The capsid protein has a β-barrel “jelly roll” fold similar to that found in many diverse icosahedral viruses, including archaeal, bacterial, plant, and animal viruses, as well as other parvoviruses. Most of the surface loops have little structural resemblance to other known parvovirus capsid proteins. In contrast to vertebrate parvoviruses, the N-terminal β-strand of BmDNV-1 VP3 is positioned relative to the neighboring 2-fold related subunit in a “domain-swapped” conformation, similar to findings for other invertebrate parvoviruses, suggesting domain swapping is an evolutionarily conserved structural feature of the Densovirinae. PMID:21367906

Microgravity

NASA Image and Video Library

2000-05-01

The structure of the Satellite Tobacco Mosaic Virus (STMV)--one of the smallest viruses known--has been successfully deduced using STMV crystals grown aboard the Space Shuttle in 1992 and 1994. The STMV crystals were up to 30 times the volume of any seen in the laboratory. At the same time they gave the best resolution data ever obtained on any virus crystal. STMV is a small icosahedral plant virus, consisting of a protein shell made up of 60 identical protein subunits of molecular weight 17,500. Particularly noteworthy is the fact that, in contrast to the crystal grown on Earth, the crystals grown under microgravity conditions were viusally perfect, with no striations or clumping of crystals. Furthermore, the X-ray diffraction data obtained from the space-grown crystals was of a much higher quality than the best data available at that time from ground-based crystals. This computer model shows the external coating or capsid. STMV is used because it is a simple protein to work with; studies are unrelated to tobacco. Credit: Dr. Alex McPherson, Univeristy of California at Irvin.

Satellite Tobacco Mosaic Virus Structure

NASA Technical Reports Server (NTRS)

2000-01-01

The structure of the Satellite Tobacco Mosaic Viurus (STMV)--one of the smallest viruses known--has been successfully reduced using STMV crystals grown aboard the Space Shuttle in 1992 and 1994. The STMV crystals were up to 30 times the volume of any seen in the laboratory. At the time they gave the best resolution data ever obtained on any virus crystal. STMV is a small icosahedral plant virus, consisting of a protein shell made up of 60 identical protein subunits of molecular weight 17,500. Particularly noteworthy is the fact that, in contrast to the crystals grown on Earth, the crystals grown under microgravity conditions were visually perfect, with no striations or clumping of crystals. Furthermore, the x-ray diffraction data obtained from the space-grown crystals was of a much higher quality than the best data available at that time from ground-based crystals. This stylized ribbon model shows the protein coat in white and the nucleic acid in yellow. STMV is used because it is a simple protein to work with; studies are unrelated to tobacco. Credit: Dr. Alex McPherson, University of California at Irvin.

Visualization of the herpes simplex virus portal in situ by cryo-electron tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardone, Giovanni; Winkler, Dennis C.; Trus, Benes L.

2007-05-10

Herpes simplex virus type 1 (HSV-1), the prototypical herpesvirus, has an icosahedral nucleocapsid surrounded by a proteinaceous tegument and a lipoprotein envelope. As in tailed bacteriophages, the icosahedral symmetry of the capsid is broken at one of the 12 vertices, which is occupied by a dodecameric ring of portal protein, UL6, instead of a pentamer of the capsid protein, UL19. The portal ring serves as a conduit for DNA entering and exiting the capsid. From a cryo-EM reconstruction of capsids immuno-gold-labeled with anti-UL6 antibodies, we confirmed that UL6 resides at a vertex. To visualize the portal in the context ofmore » the assembled capsid, we used cryo-electron tomography to determine the three-dimensional structures of individual A-capsids (empty, mature capsids). The similarity in size and overall shape of the portal and a UL19 pentamer - both are cylinders of {approx} 800 kDa - combined with residual noise in the tomograms, prevented us from identifying the portal vertices directly; however, this was accomplished by a computational classification procedure. Averaging the portal-containing subtomograms produced a structure that tallies with the isolated portal, as previously reconstructed by cryo-EM. The portal is mounted on the outer surface of the capsid floor layer, with its narrow end pointing outwards. This disposition differs from that of known phage portals in that the bulk of its mass lies outside, not inside, the floor. This distinction may be indicative of divergence at the level of portal-related functions other than its role as a DNA channel.« less

Magic-angle spinning NMR of intact bacteriophages: insights into the capsid, DNA and their interface.

PubMed

Abramov, Gili; Morag, Omry; Goldbourt, Amir

2015-04-01

Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses. Copyright © 2015 Elsevier Inc. All rights reserved.

Improved cell disruption of Pichia pastoris utilizing aminopropyl magnesium phyllosilicate (AMP) clay.

PubMed

Kim, Sun-Il; Wu, Yuanzheng; Kim, Ka-Lyun; Kim, Geun-Joong; Shin, Hyun-Jae

2013-06-01

An efficient method for Pichia cell disruption that employs an aminopropyl magnesium phyllosilicate (AMP) clay-assisted glass beads mill is presented. AMP clay is functionalized nanocomposite resembling the talc parent structure Si8Mg6O20(OH)4 that has been proven to permeate the bacterial membrane and cause cell lysis. The recombinant capsid protein of cowpea chlorotic mottle virus (CCMV) expressed in Pichia pastoris GS115 was used as demonstration system for their ability of self-assembly into icosahedral virus-like particles (VLPs). The total protein concentration reached 4.24 mg/ml after 4 min treatment by glass beads mill combined with 0.2 % AMP clay, which was 11.2 % higher compared to glass beads mill only and the time was half shortened. The stability of purified CCMV VLPs illustrated AMP clay had no influence on virus assembly process. Considering the tiny amount added and simple approach of AMP clay, it could be a reliable method for yeast cell disruption.

Structure-dependent efficacy of infectious bursal disease virus (IBDV) recombinant vaccines.

PubMed

Martinez-Torrecuadrada, Jorge L; Saubi, Narciís; Pagès-Manté, Albert; Castón, José R; Espuña, Enric; Casal, J Ignacio

2003-07-04

The immunogenicity and protective capability of several baculovirus-expressed infectious bursal disease virus (IBDV)-derived assemblies as VP2 capsids, VPX tubules and polyprotein (PP)-derived mixed structures, were tested. Four-week-old chickens were immunised subcutaneously with one dose of each particulate antigen. VP2 icosahedral capsids induced the highest neutralising response, followed by PP-derived structures and then VPX tubules. All vaccinated animals were protected when challenged with a very virulent IBDV (vvIBDV) isolate, however the degree of protection is directly correlated with the levels of neutralising antibodies. VP2 capsids elicited stronger protective immunity than tubular structures and 3 micrograms of them were sufficient to confer a total protection comparable to that induced by an inactivated vaccine. Therefore, VP2 capsids represent a suitable candidate recombinant vaccine instead of virus-like particles (VLPs) for IBDV infections. Our results also provide clear evidence that the recombinant IBDV-derived antigens are structure-dependent in order to be efficient as vaccine components.

Structure-dependent efficacy of infectious bursal disease virus (IBDV) recombinant vaccines.

PubMed

Martinez-Torrecuadrada, Jorge L; Saubi, Narcis; Pagès-Manté, Albert; Castón, José R; Espuña, Enric; Casal, J Ignacio

2003-05-16

The immunogenicity and protective capability of several baculovirus-expressed infectious bursal disease virus (IBDV)-derived assemblies as VP2 capsids, VPX tubules and polyprotein (PP)-derived mixed structures, were tested. Four-week-old chickens were immunised subcutaneously with one dose of each particulate antigen. VP2 icosahedral capsids induced the highest neutralising response, followed by PP-derived structures and then VPX tubules. All vaccinated animals were protected when challenged with a very virulent IBDV (vvIBDV) isolate, however the degree of protection is directly correlated with the levels of neutralising antibodies. VP2 capsids elicited stronger protective immunity than tubular structures and 3& mgr;g of them were sufficient to confer a total protection comparable to that induced by an inactivated vaccine. Therefore, VP2 capsids represent a suitable candidate recombinant vaccine instead of virus-like particles (VLPs) for IBDV infections. Our results also provide clear evidence that the recombinant IBDV-derived antigens are structure-dependent in order to be efficient as vaccine components.

The Expanding Family of Virophages

PubMed Central

Bekliz, Meriem; Colson, Philippe; La Scola, Bernard

2016-01-01

Virophages replicate with giant viruses in the same eukaryotic cells. They are a major component of the specific mobilome of mimiviruses. Since their discovery in 2008, five other representatives have been isolated, 18 new genomes have been described, two of which being nearly completely sequenced, and they have been classified in a new viral family, Lavidaviridae. Virophages are small viruses with approximately 35–74 nm large icosahedral capsids and 17–29 kbp large double-stranded DNA genomes with 16–34 genes, among which a very small set is shared with giant viruses. Virophages have been isolated or detected in various locations and in a broad range of habitats worldwide, including the deep ocean and inland. Humans, therefore, could be commonly exposed to virophages, although currently limited evidence exists of their presence in humans based on serology and metagenomics. The distribution of virophages, the consequences of their infection and the interactions with their giant viral hosts within eukaryotic cells deserve further research. PMID:27886075

Induction of apoptosis in a flounder gill cell line by lymphocystis disease virus infection.

PubMed

Hu, G-B; Cong, R-S; Fan, T-J; Mei, X-G

2004-11-01

Lymphocystis disease virus (LCDV), a large icosahedral DNA virus classified to the iridovirus family, is the causative agent of lymphocystis, a disease which occurs in marine and freshwater fish species and is characterized by formation of papilloma-like lesions on the surface of the skin. In vitro, LCDV infection causes flounder gill cells, an adherent cell line, to exhibit an obvious cytopathic effect (CPE). In order to test whether apoptosis is responsible for the observed CPE, cells infected with LCDV at a multiplicity of infection (m.o.i.) of 5 PFU per cell were examined at various time intervals for the appearance of apoptotic signs. Nuclear fragmentation, DNA laddering and caspase activation were observed in the infected cells at the time (i.e. 10 days post-infection) when an intensive CPE was observed. These findings demonstrate that LCDV is capable of inducing apoptosis in vitro, which is different from the result of LCDV infection in vivo, and consequently suggest an intricate LCDV-host interaction.

Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types

PubMed Central

Swanson, Maud M.; Dawson, Lorna; Freitag, Thomas E.; Singh, Brajesh K.; Torrance, Lesley; Mushegian, Arcady R.

2015-01-01

The potential dependence of virus populations on soil types was examined by electron microscopy, and the total abundance of virus particles in four soil types was similar to that previously observed in soil samples. The four soil types examined differed in the relative abundances of four morphological groups of viruses. Machair, a unique type of coastal soil in western Scotland and Ireland, differed from the others tested in having a higher proportion of tailed bacteriophages. The other soils examined contained predominantly spherical and thin filamentous virus particles, but the Machair soil had a more even distribution of the virus types. As the first step in looking at differences in populations in detail, virus sequences from Machair and brown earth (agricultural pasture) soils were examined by metagenomic sequencing after enriching for circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) virus genomes. Sequences from the family Microviridae (icosahedral viruses mainly infecting bacteria) of CRESS-DNA viruses were predominant in both soils. Phylogenetic analysis of Microviridae major coat protein sequences from the Machair viruses showed that they spanned most of the diversity of the subfamily Gokushovirinae, whose members mainly infect obligate intracellular parasites. The brown earth soil had a higher proportion of sequences that matched the morphologically similar family Circoviridae in BLAST searches. However, analysis of putative replicase proteins that were similar to those of viruses in the Circoviridae showed that they are a novel clade of Circoviridae-related CRESS-DNA viruses distinct from known Circoviridae genera. Different soils have substantially different taxonomic biodiversities even within ssDNA viruses, which may be driven by physicochemical factors. PMID:25841004

Strategies for the crystallization of viruses: using phase diagrams and gels to produce 3D crystals of Grapevine fanleaf virus.

PubMed

Schellenberger, Pascale; Demangeat, Gérard; Lemaire, Olivier; Ritzenthaler, Christophe; Bergdoll, Marc; Oliéric, Vincent; Sauter, Claude; Lorber, Bernard

2011-05-01

The small icosahedral plant RNA nepovirus Grapevine fanleaf virus (GFLV) is specifically transmitted by a nematode and causes major damage to vineyards worldwide. To elucidate the molecular mechanisms underlying the recognition between the surface of its protein capsid and cellular components of its vector, host and viral proteins synthesized upon infection, the wild type GFLV strain F13 and a natural mutant (GFLV-TD) carrying a Gly₂₉₇Asp mutation were purified, characterized and crystallized. Subsequently, the geometry and volume of their crystals was optimized by establishing phase diagrams. GFLV-TD was twice as soluble as the parent virus in the crystallization solution and its crystals diffracted X-rays to a resolution of 2.7 Å. The diffraction limit of GFLV-F13 crystals was extended from 5.5 to 3 Å by growth in agarose gel. Preliminary crystallographic analyses indicate that both types of crystals are suitable for structure determination. Keys for the successful production of GFLV crystals include the rigorous quality control of virus preparations, crystal quality improvement using phase diagrams, and crystal lattice reinforcement by growth in agarose gel. These strategies are applicable to the production of well-diffracting crystals of other viruses and macromolecular assemblies. Copyright © 2011 Elsevier Inc. All rights reserved.

Replication of Chilo iridescent virus in the cotton boll weevil, Anthonomus grandis, and development of an infectivity assay.

PubMed

Henderson, C W; Johnson, C L; Lodhi, S A; Bilimoria, S L

2001-01-01

The boll weevil, Anthonomus grandis Boheman, is a devastating pest of cotton. Chemical pesticides are problematic due to relative lack of target specificity and resistance. Microbial pesticides may provide viable alternatives because of their narrow host range. Chilo iridescent virus (CIV) is the type species for genus Iridovirus, family Iridoviridae: large, icosahedral cytoplasmic viruses containing a double-stranded DNA genome. Earlier work suggested that CIV replicated in the boll weevil; however, efficiency or production of infectious virus was not established. We showed that CIV undergoes a productive cycle in A. grandis. CIV DNA levels in boll weevil pupae increased significantly from 0 to 3 days post infection. Moreover, virogenic stromata and complete virus particles were observed in the cytoplasm by 7 days. An endpoint dilution assay using viral DNA replication as indicator suggested a 10(5)-fold increase in infectious virus titer over 7 days. This is the first such demonstration in larval infections with genus Iridovirus. Our study establishes that CIV undergoes a productive cycle in the boll weevil and provides an important and useful model system for replication at the organismal level. These results have important implications for the potential of CIV and its components in boll weevil control.

The Connection Between Local Icosahedral Order in Metallic Liquids and the Nucleation Behavior of Ordered Phases

NASA Technical Reports Server (NTRS)

Kelton, K. F.; Gangopadhyay, A. K.; Lee, G. W.; Hyers, R. W.; Rathz, T. J.; Rogers, J. R.; Robinson, M. B.; Schenk, T.; Simonet, V.

2003-01-01

Over fifty years ago, David Turnbull showed that the temperature of many metallic liquids could be decreased far below their equilibrium melting temperature before crystallization occurred. To explain those surprising results, Charles Frank hypothesized that the local structures of undercooled metallic liquids are different from those of crystal phases, containing a significant degree of icosahedral order that is incompatible with extended periodicity. Such structural differences must create a barrier to the formation crystal phases, explaining the observed undercooling behavior. If true, the nucleation from the liquid of phases with extended icosahedral order should be easier. Icosahedral order is often favored in small clusters, as observed recently in liquid-like clusters of pure Pb on the (111) surface of Si[3], for example. However, it has never been shown that an increasing preference for icosahedral phase formation can be directly linked with the development of icosahedral order in the undercooled liquid. Owing to the combination of very recent advances in levitation techniques and the availability of synchrotron x-ray and high flux neutron facilities, this is shown here.

The Connection Between Local Icosahedral Order in Metallic Liquids and the Nucleation of Ordered Phases

NASA Technical Reports Server (NTRS)

Curreri, Peter A. (Technical Monitor); Kelton, K. F.; Gangopadhyay, A.; Lee, G. W.; Hyers, R. W.; Rathz, R. J.; Rogers, J.; Schenk, T.; Simonet, V.; Holland-Moritz, D.

2003-01-01

Over fifty years ago, David Turnbull showed that the temperature of many metallic liquids could be decreased far below their equilibrium melting temperature before crystallization occurred. To explain those surprising results, Charles Frank hypothesized that the local structures of undercooled metallic liquids are different from those of crystal phases, containing a significant degree of icosahedral order that is incompatible with extended periodicity. Such structural differences must create a barrier to the formation crystal phases, explaining the observed undercooling behavior. If true, the nucleation from the liquid of phases with extended icosahedral order should be easier. Icosahedral order is often favored in small clusters, as observed recently in liquid-like clusters of pure Pb on the (111) surface of Si, for example. However, it has never been shown that an increasing preference for icosahedral phase formation can be directly linked with the development of icosahedral order in the undercooled liquid. Owing to the combination of very recent advances in levitation techniques and the availability of synchrotron x-ray and high flux neutron facilities, this is shown here.

The Connection Between Local Icosahedral Order in Metallic Liquids and the Nucleation of Ordered Phases

NASA Technical Reports Server (NTRS)

Kelton, K. F.; Gangopadhyay, A. K.; Lee, G. W.; Hyers, R. W.; Rathz, T. J.; Rogers, J. R.; Robinson, M. B.; Schenk, T.; Simonet, V.; Holland-Moritz, D.;

Zika Virus: An Emergent Neuropathological Agent

PubMed Central

White, Martyn K.; Wollebo, Hassen S.; Beckham, J. David; Tyler, Kenneth L.; Khalili, Kamel

2016-01-01

The emergence of Zika virus in the Americas has followed a pattern that is familiar from earlier epidemics of other viruses, where a new disease is introduced into a human population and then spreads rapidly with important public health consequences. In the case of Zika virus, an accumulating body of recent evidence implicates the virus in the etiology of serious pathologies of the human nervous system, that is, the occurrence of microcephaly in neonates and Guillain–Barré syndrome in adults. Zika virus is an arbovirus (arthropod-borne virus) and a member of the family Flaviviridae, genus Flavivirus. Zika virions are enveloped and icosahedral, and contain a nonsegmented, single-stranded, positive-sense RNA genome, which encodes 3 structural and 7 nonstructural proteins that are expressed as a single polyprotein that undergoes cleavage. Zika genomic RNA replicates in the cytoplasm of infected host cells. Zika virus was first detected in 1947 in the blood of a febrile monkey in Uganda’s Zika Forest and in crushed suspensions of the Aedes mosquito, which is one of the vectors for Zika virus. The virus remained obscure, with a few human cases confined to Africa and Asia. There are two lineages of the Zika virus, African and Asian, with the Asian strain causing outbreaks in Micronesia in 2007 and French Polynesia in 2013–2014. From here, the virus spread to Brazil with the first report of autochthonous Zika transmission in the Americas in March 2015. The rapid advance of the virus in the Americas and its likely association with microcephaly and Guillain–Barré syndrome make Zika an urgent public health concern. PMID:27464346

Structural Insights into the Coupling of Virion Assembly and Rotavirus Replication

PubMed Central

Trask, Shane D.; McDonald, Sarah M.; Patton, John T.

2013-01-01

Preface Viral replication is rapid and robust, but it is far from a chaotic process. Instead, successful production of infectious progeny requires that events occur in the correct place and at the correct time. Rotavirus, a segmented double-stranded RNA virus of the Reoviridae family, seems to govern its replication through ordered disassembly and assembly of a triple-layered icosahedral capsid. In recent years, high-resolution structural data have provided unprecedented insight into these events. In this Review, we explore the current understanding of rotavirus replication and how it compares to other Reoviridae family members. PMID:22266782

Quasiperiodic oscillation and possible Second Law violation in a nanosystem

NASA Astrophysics Data System (ADS)

Quick, R.; Singharoy, A.; Ortoleva, P.

2013-05-01

Simulation of a virus-like particle reveals persistent oscillation about a free-energy minimizing structure. For an icosahedral structure of 12 human papillomavirus (HPV) L1 protein pentamers, the period is about 70 picoseconds and has amplitude of about 4 Å at 300 K and pH 7. The pentamers move radially and out-of-phase with their neighbors. As temperature increases the amplitude and period decrease. Since the dynamics are shown to be friction-dominated and free-energy driven, the oscillations are noninertial. These anomalous oscillations are an apparent violation of the Second Law mediated by fluctuations accompanying nanosystem behavior.

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

PubMed Central

Dolja, Valerian V.

2014-01-01

SUMMARY Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus “self” that defines the identity of deep, ancient viral lineages. However, several other widespread viral “hallmark genes” encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host. PMID:24847023

The virophage as a unique parasite of the giant mimivirus.

PubMed

La Scola, Bernard; Desnues, Christelle; Pagnier, Isabelle; Robert, Catherine; Barrassi, Lina; Fournous, Ghislain; Merchat, Michèle; Suzan-Monti, Marie; Forterre, Patrick; Koonin, Eugene; Raoult, Didier

2008-09-04

Viruses are obligate parasites of Eukarya, Archaea and Bacteria. Acanthamoeba polyphaga mimivirus (APMV) is the largest known virus; it grows only in amoeba and is visible under the optical microscope. Mimivirus possesses a 1,185-kilobase double-stranded linear chromosome whose coding capacity is greater than that of numerous bacteria and archaea1, 2, 3. Here we describe an icosahedral small virus, Sputnik, 50 nm in size, found associated with a new strain of APMV. Sputnik cannot multiply in Acanthamoeba castellanii but grows rapidly, after an eclipse phase, in the giant virus factory found in amoebae co-infected with APMV4. Sputnik growth is deleterious to APMV and results in the production of abortive forms and abnormal capsid assembly of the host virus. The Sputnik genome is an 18.343-kilobase circular double-stranded DNA and contains genes that are linked to viruses infecting each of the three domains of life Eukarya, Archaea and Bacteria. Of the 21 predicted protein-coding genes, eight encode proteins with detectable homologues, including three proteins apparently derived from APMV, a homologue of an archaeal virus integrase, a predicted primase-helicase, a packaging ATPase with homologues in bacteriophages and eukaryotic viruses, a distant homologue of bacterial insertion sequence transposase DNA-binding subunit, and a Zn-ribbon protein. The closest homologues of the last four of these proteins were detected in the Global Ocean Survey environmental data set5, suggesting that Sputnik represents a currently unknown family of viruses. Considering its functional analogy with bacteriophages, we classify this virus as a virophage. The virophage could be a vehicle mediating lateral gene transfer between giant viruses.

Unified structure theory of icosahedral quasicrystals: Evidence from neutron powder diffraction patterns that AlCrFeMnSi, AlCuLiMg, and TiNiFeSi icosahedral quasicrystals are twins of cubic crystals containing about 820 or 1012 atoms in a primitive unit cube

PubMed Central

Pauling, Linus

1988-01-01

A unified structure theory of icosahedral quasicrystals, combining the twinned-cubic-crystal theory and the Penrose-tiling-six-dimensional-projection theory, is described. Values of the primitive-cubic lattice constant for several quasicrystals are evaluated from x-ray and neutron diffraction data. The fact that the low-angle diffraction maxima can be indexed with cubic unit cells provides additional support for the twinned-cubic-crystal theory of icosahedral quasicrystals. PMID:16593990

Structural Studies of Adeno-Associated Virus Serotype 8 Capsid Transitions Associated with Endosomal Trafficking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nam, Hyun-Joo; Gurda, Brittney L.; McKenna, Robert

2012-09-17

The single-stranded DNA (ssDNA) parvoviruses enter host cells through receptor-mediated endocytosis, and infection depends on processing in the early to late endosome as well as in the lysosome prior to nuclear entry for replication. However, the mechanisms of capsid endosomal processing, including the effects of low pH, are poorly understood. To gain insight into the structural transitions required for this essential step in infection, the crystal structures of empty and green fluorescent protein (GFP) gene-packaged adeno-associated virus serotype 8 (AAV8) have been determined at pH values of 6.0, 5.5, and 4.0 and then at pH 7.5 after incubation at pHmore » 4.0, mimicking the conditions encountered during endocytic trafficking. While the capsid viral protein (VP) topologies of all the structures were similar, significant amino acid side chain conformational rearrangements were observed on (i) the interior surface of the capsid under the icosahedral 3-fold axis near ordered nucleic acid density that was lost concomitant with the conformational change as pH was reduced and (ii) the exterior capsid surface close to the icosahedral 2-fold depression. The 3-fold change is consistent with DNA release from an ordering interaction on the inside surface of the capsid at low pH values and suggests transitions that likely trigger the capsid for genome uncoating. The surface change results in disruption of VP-VP interface interactions and a decrease in buried surface area between VP monomers. This disruption points to capsid destabilization which may (i) release VP1 amino acids for its phospholipase A2 function for endosomal escape and nuclear localization signals for nuclear targeting and (ii) trigger genome uncoating.« less

In silico analysis of surface structure variation of PCV2 capsid resulting from loop mutations of its capsid protein (Cap)

PubMed Central

Wang, Aibing; Zhang, Lijie; Khayat, Reza

2016-01-01

Outbreaks of porcine circovirus (PCV) type 2 (PCV2)-associated diseases have caused substantial economic losses worldwide in the last 20 years. The PCV capsid protein (Cap) is the sole structural protein and main antigenic determinant of this virus. In this study, not only were phylogenetic trees reconstructed, but variations of surface structure of the PCV capsid were analysed in the course of evolution. Unique surface patterns of the icosahedral fivefold axes of the PCV2 capsid were identified and characterized, all of which were absent in PCV type 1 (PCV1). Icosahedral fivefold axes, decorated with Loops BC, HI and DE, were distinctly different between PCV2 and PCV1. Loops BC, determining the outermost surface around the fivefold axes of PCV capsids, had limited homology between Caps of PCV1 and PCV2. A conserved tyrosine phosphorylation motif in Loop HI that might be recognized by non-receptor tyrosine kinase(s) in vivo was present only in PCV2. Particularly, the concurrent presence of 60 pairs of the conserved tyrosine and a canonical PXXP motif on the PCV2 capsid surface could be a mechanism for PXXP motif binding to and activation of an SH3-domain-containing tyrosine kinase in host cells. Additionally, a conserved cysteine in Loop DE of the PCV2 Cap was substituted by an arginine in PCV1, indicating potentially distinct assembly mechanisms of the capsid in vitro between PCV1 and PCV2. Therefore, these unique patterns on the PCV2 capsid surface, absent in PCV1 isolates, might be related to cell entry, virus function and pathogenesis. PMID:27902320

In silico analysis of surface structure variation of PCV2 capsid resulting from loop mutations of its capsid protein (Cap).

PubMed

Wang, Naidong; Zhan, Yang; Wang, Aibing; Zhang, Lijie; Khayat, Reza; Yang, Yi

2016-12-01

Outbreaks of porcine circovirus (PCV) type 2 (PCV2)-associated diseases have caused substantial economic losses worldwide in the last 20 years. The PCV capsid protein (Cap) is the sole structural protein and main antigenic determinant of this virus. In this study, not only were phylogenetic trees reconstructed, but variations of surface structure of the PCV capsid were analysed in the course of evolution. Unique surface patterns of the icosahedral fivefold axes of the PCV2 capsid were identified and characterized, all of which were absent in PCV type 1 (PCV1). Icosahedral fivefold axes, decorated with Loops BC, HI and DE, were distinctly different between PCV2 and PCV1. Loops BC, determining the outermost surface around the fivefold axes of PCV capsids, had limited homology between Caps of PCV1 and PCV2. A conserved tyrosine phosphorylation motif in Loop HI that might be recognized by non-receptor tyrosine kinase(s) in vivo was present only in PCV2. Particularly, the concurrent presence of 60 pairs of the conserved tyrosine and a canonical PXXP motif on the PCV2 capsid surface could be a mechanism for PXXP motif binding to and activation of an SH3-domain-containing tyrosine kinase in host cells. Additionally, a conserved cysteine in Loop DE of the PCV2 Cap was substituted by an arginine in PCV1, indicating potentially distinct assembly mechanisms of the capsid in vitro between PCV1 and PCV2. Therefore, these unique patterns on the PCV2 capsid surface, absent in PCV1 isolates, might be related to cell entry, virus function and pathogenesis.

Investigating the thermal dissociation of viral capsid by lattice model

NASA Astrophysics Data System (ADS)

Chen, Jingzhi; Chevreuil, Maelenn; Combet, Sophie; Lansac, Yves; Tresset, Guillaume

2017-11-01

The dissociation of icosahedral viral capsids was investigated by a homogeneous and a heterogeneous lattice model. In thermal dissociation experiments with cowpea chlorotic mottle virus and probed by small-angle neutron scattering, we observed a slight shrinkage of viral capsids, which can be related to the strengthening of the hydrophobic interaction between subunits at increasing temperature. By considering the temperature dependence of hydrophobic interaction in the homogeneous lattice model, we were able to give a better estimate of the effective charge. In the heterogeneous lattice model, two sets of lattice sites represented different capsid subunits with asymmetric interaction strengths. In that case, the dissociation of capsids was found to shift from a sharp one-step transition to a gradual two-step transition by weakening the hydrophobic interaction between AB and CC subunits. We anticipate that such lattice models will shed further light on the statistical mechanics underlying virus assembly and disassembly.

An alphavirus temperature-sensitive capsid mutant reveals stages of nucleocapsid assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Yan, E-mail: yzheng15@students.kgi.edu; Kielian, Margaret, E-mail: margaret.kielian@einstein.yu.edu

2015-10-15

Alphaviruses have a nucleocapsid core composed of the RNA genome surrounded by an icosahedral lattice of capsid protein. An insertion after position 186 in the capsid protein produced a strongly temperature-sensitive growth phenotype. Even when the structural proteins were synthesized at the permissive temperature (28 °C), subsequent incubation of the cells at the non-permissive temperature (37 °C) dramatically decreased mutant capsid protein stability and particle assembly. Electron microscopy confirmed the presence of cytoplasmic nucleocapsids in mutant-infected cells cultured at the permissive temperature, but these nucleocapsids were not stable to sucrose gradient separation. In contrast, nucleocapsids isolated from mutant virus particlesmore » had similar stability to that of wildtype virus. Our data support a model in which cytoplasmic nucleocapsids go through a maturation step during packaging into virus particles. The insertion site lies in the interface between capsid proteins in the assembled nucleocapsid, suggesting the region where such a stabilizing transition occurs. - Highlights: • We characterize an alphavirus capsid insertion mutation. • These capsid mutants are highly temperature sensitive for growth. • The insertion affects nucleocapsid stability. • Results suggest that the nucleocapsid is stabilized during virus budding.« less

Tomato bushy stunt virus (TBSV), a versatile platform for polyvalent display of antigenic epitopes and vaccine design.

PubMed

Kumar, Shantanu; Ochoa, Wendy; Singh, Pratik; Hsu, Catherine; Schneemann, Anette; Manchester, Marianne; Olson, Mark; Reddy, Vijay

2009-05-25

Viruses-like particles (VLPs) are frequently being used as platforms for polyvalent display of foreign epitopes of interest on their capsid surface to improve their presentation enhancing the antigenicity and host immune response. In the present study, we used the VLPs of Tomato bushy stunt virus (TBSV), an icosahedral plant virus, as a platform to display 180 copies of 16 amino acid epitopes of ricin toxin fused to the C-terminal end of a modified TBSV capsid protein (NDelta52). Expression of the chimeric recombinant protein in insect cells resulted in spontaneous assembly of VLPs displaying the ricin epitope. Cryo-electron microscopy and image reconstruction of the chimeric VLPs at 22 A resolution revealed the locations and orientation of the ricin epitope exposed on the TBSV capsid surface. Furthermore, injection of chimeric VLPs into mice generated antisera that detected the native ricin toxin. The ease of fusing of short peptides of 15-20 residues and their ability to form two kinds (T=1, T=3) of bio-nanoparticles that result in the display of 60 or 180 copies of less constrained and highly exposed antigenic epitopes makes TBSV an attractive and versatile display platform for vaccine design.

Envelope lipid-packing as a critical factor for the biological activity and stability of alphavirus particles isolated from mammalian and mosquito cells.

PubMed

Sousa, Ivanildo P; Carvalho, Carlos A M; Ferreira, Davis F; Weissmüller, Gilberto; Rocha, Gustavo M; Silva, Jerson L; Gomes, Andre M O

2011-01-21

Alphaviruses are enveloped arboviruses. The viral envelope is derived from the host cell and is positioned between two icosahedral protein shells (T = 4). Because the viral envelope contains glycoproteins involved in cell recognition and entry, the integrity of the envelope is critical for the success of the early events of infection. Differing levels of cholesterol in different hosts leads to the production of alphaviruses with distinct levels of this sterol loaded in the envelope. Using Mayaro virus, a New World alphavirus, we investigated the role of cholesterol on the envelope of alphavirus particles assembled in either mammalian or mosquito cells. Our results show that although quite different in their cholesterol content, Mayaro virus particles obtained from both cells share a similar high level of lateral organization in their envelopes. This organization, as well as viral stability and infectivity, is severely compromised when cholesterol is depleted from the envelope of virus particles isolated from mammalian cells, but virus particles isolated from mosquito cells are relatively unaffected by cholesterol depletion. We suggest that it is not cholesterol itself, but rather the organization of the viral envelope, that is critical for the biological activity of alphaviruses.

Isolation and characterization of Nylanderia fulva virus 1, a positive-sense, single-stranded RNA virus infecting the tawny crazy ant, Nylanderia fulva

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valles, Steven M., E-mail: steven.valles@ars.usda.gov; Oi, David H.; Becnel, James J.

We report the discovery of Nylanderia fulva virus 1 (NfV-1), the first virus identified and characterized from the ant, Nylanderia fulva. The NfV-1 genome (GenBank accession KX024775) is 10,881 nucleotides in length, encoding one large open reading frame (ORF). Helicase, protease, RNA-dependent RNA polymerase, and jelly-roll capsid protein domains were recognized within the polyprotein. Phylogenetic analysis placed NfV-1 in an unclassified clade of viruses. Electron microscopic examination of negatively stained samples revealed particles with icosahedral symmetry with a diameter of 28.7±1.1 nm. The virus was detected by RT-PCR in larval, pupal, worker and queen developmental stages. However, the replicative strandmore » of NfV-1 was only detected in larvae. Vertical transmission did not appear to occur, but horizontal transmission was facile. The inter-colonial field prevalence of NfV-1 was 52±35% with some local infections reaching 100%. NfV-1 was not detected in limited samples of other Nylanderia species or closely related ant species. - Highlights: • A new positive-strand RNA virus was discovered in the ant, Nylanderia fulva. • The Nylanderia fulva virus 1 genome was comprised of 10,881 nucleotides. • NfV-1 was detected in larval, pupal, queen and worker ants, but not eggs. • Replication of NfV-1 appeared to be limited to the larval stage.« less

Insights into bunyavirus architecture from electron cryotomography of Uukuniemi virus

PubMed Central

Överby, A. K.; Pettersson, R. F.; Grünewald, K.; Huiskonen, J. T.

2008-01-01

Bunyaviridae is a large family of viruses that have gained attention as “emerging viruses” because many members cause serious disease in humans, with an increasing number of outbreaks. These negative-strand RNA viruses possess a membrane envelope covered by glycoproteins. The virions are pleiomorphic and thus have not been amenable to structural characterization using common techniques that involve averaging of electron microscopic images. Here, we determined the three-dimensional structure of a member of the Bunyaviridae family by using electron cryotomography. The genome, incorporated as a complex with the nucleoprotein inside the virions, was seen as a thread-like structure partially interacting with the viral membrane. Although no ordered nucleocapsid was observed, lateral interactions between the two membrane glycoproteins determine the structure of the viral particles. In the most regular particles, the glycoprotein protrusions, or “spikes,” were seen to be arranged on an icosahedral lattice, with T = 12 triangulation. This arrangement has not yet been proven for a virus. Two distinctly different spike conformations were observed, which were shown to depend on pH. This finding is reminiscent of the fusion proteins of alpha-, flavi-, and influenza viruses, in which conformational changes occur in the low pH of the endosome to facilitate fusion of the viral and host membrane during viral entry. PMID:18272496

ADENOVIRUS INTERACTION WITH ITS CELLULAR RECEPTOR CAR.

DOE Office of Scientific and Technical Information (OSTI.GOV)

HOWITT,J.; ANDERSON,C.W.; FREIMUTH,P.

The mechanism of adenovirus attachment to the host cell plasma membrane has been revealed in detail by research over the past 10 years. It has long been known that receptor binding activity is associated with the viral fibers, trimeric spike proteins that protrude radially from the vertices of the icosahedral capsid (Philipson et al. 1968). In some adenovirus serotypes, fiber and other virus structural proteins are synthesized in excess and accumulate in the cell nucleus during late stages of infection. Fiber protein can be readily purified from lysates of cells infected with subgroup C viruses, for example Ad2 and Ad5more » (Boulanger and Puvion 1973). Addition of purified fiber protein to virus suspensions during adsorption strongly inhibits infection, indicating that fiber and intact virus particles compete for binding sites on host cells (Philipson et al. 1968; Hautala et al. 1998). Cell binding studies using purified radiolabeled fiber demonstrated that fiber binds specifically and with high affinity to the cell plasma membrane, and that cell lines typically used for laboratory propagation of adenovirus have approximately 10{sup 4} high-affinity receptor sites per cell (Persson et al. 1985; Freimuth 1996). Similar numbers of high-affinity binding sites for radiolabeled intact virus particles also were observed (Seth et al. 1994).« less

Turnip Yellow Mosaic Virus

NASA Technical Reports Server (NTRS)

2000-01-01

The bumpy exterior of the turnip yellow mosaic virus (TYMV) protein coat, or capsid, was defined in detail by Dr. Alexander McPherson of the University of California, Irvin using proteins crystallized in space for analysis on Earth. TYMV is an icosahedral virus constructed from 180 copies of the same protein arranged into 12 clusters of five proteins (pentamers), and 20 clusters of six proteins (hexamers). The final TYMV structure led to the unexpected hypothesis that the virus releases its RNA by essentially chemical-mechanical means. Most viruses have fairly flat coats, but in TYNV, the fold in each protein, called the jellyroll, is clustered at the points where the protein pentamers and hexamers join. The jellyrolls are almost standing on end, producing a bumpy surface with knobs at all of the pentamers and hexamers. At the inside surface of the pentamers is a void that is not present at the hexamers. The coating had been seen in early stuties of TYMV, but McPherson's atomic structure shows much more detail. The inside surface is strikingly, and unexpectedly, different than the outside. While the pentamers contain a central void on the inside, the hexameric units contain peptides linked to each other, forming a ring or, more accurately, rings to fill the void. Credit: Dr. Alexander McPherson, University of California, Irvine

Turnip Yellow Mosaic Virus Structure

NASA Technical Reports Server (NTRS)

2000-01-01

The bumpy exterior of the turnip yellow mosaic virus (TYMV) protein coat, or capsid, was defined in detail by Dr. Alexander McPherson of the University of California, Irvin using protein crystallized in space for analysis on Earth. TYMV is an icosahedral virus constructed from 180 copies of the same protein arranged into 12 clusters of five proteins (pentamers), and 20 clusters of six proteins (hexamers). The final TYMV structure led to the enexpected hypothesis that the virus release its RNA by essentially chemical-mechanical means. Most viruses have farly flat coats, but in TYMV, the fold in each protein, called the jellyroll, is clustered at the points where the protein pentamers and hexamers join. The jellyrolls are almost standing on end, producing a bumpy surface with knobs at all of the pentamers and hexamers. At the inside surface of the pentamers is a void that is not present at the hexamers. The coating had been seen in early studies of TYMV, but McPhereson's atomic structure shows much more detail. The inside surface is strikingly, and unexpectedly, different than the outside. While the pentamers contain a central viod on the inside, the hexameric units contain peptides liked to each other, forming a ring or, more accurately, rings to fill the voild. Credit: Dr. Alexander McPherson, University of California, Irvine.

Structure of the Triatoma virus capsid.

PubMed

Squires, Gaëlle; Pous, Joan; Agirre, Jon; Rozas-Dennis, Gabriela S; Costabel, Marcelo D; Marti, Gerardo A; Navaza, Jorge; Bressanelli, Stéphane; Guérin, Diego M A; Rey, Felix A

2013-06-01

The members of the Dicistroviridae family are non-enveloped positive-sense single-stranded RNA (+ssRNA) viruses pathogenic to beneficial arthropods as well as insect pests of medical importance. Triatoma virus (TrV), a member of this family, infects several species of triatomine insects (popularly named kissing bugs), which are vectors for human trypanosomiasis, more commonly known as Chagas disease. The potential use of dicistroviruses as biological control agents has drawn considerable attention in the past decade, and several viruses of this family have been identified, with their targets covering honey bees, aphids and field crickets, among others. Here, the crystal structure of the TrV capsid at 2.5 Å resolution is reported, showing that as expected it is very similar to that of Cricket paralysis virus (CrPV). Nevertheless, a number of distinguishing structural features support the introduction of a new genus (Triatovirus; type species TrV) under the Dicistroviridae family. The most striking differences are the absence of icosahedrally ordered VP4 within the infectious particle and the presence of prominent projections that surround the fivefold axis. Furthermore, the structure identifies a second putative autoproteolytic DDF motif in protein VP3, in addition to the conserved one in VP1 which is believed to be responsible for VP0 cleavage during capsid maturation. The potential meaning of these new findings is discussed.

Varieties of charge distributions in coat proteins of ssRNA+  viruses

NASA Astrophysics Data System (ADS)

Lošdorfer Božič, Anže; Podgornik, Rudolf

2018-01-01

A major part of the interactions involved in the assembly and stability of icosahedral, positive-sense single-stranded RNA (ssRNA+) viruses is electrostatic in nature, as can be inferred from the strong pH- and salt-dependence of their assembly phase diagrams. Electrostatic interactions do not act only between the capsid coat proteins (CPs), but just as often provide a significant contribution to the interactions of the CPs with the genomic RNA, mediated to a large extent by positively charged, flexible N-terminal tails of the CPs. In this work, we provide two clear and complementary definitions of an N-terminal tail of a protein, and use them to extract the tail sequences of a large number of CPs of ssRNA+  viruses. We examine the pH-dependent interplay of charge on both tails and CPs alike, and show that—in contrast to the charge on the CPs—the net positive charge on the N-tails persists even to very basic pH values. In addition, we note a limit to the length of the wild-type genomes of those viruses which utilize positively charged tails, when compared to viruses without charged tails and similar capsid size. At the same time, we observe no clear connection between the charge on the N-tails and the genome lengths of the viruses included in our study.

Raman effect in icosahedral boron-rich solids

PubMed Central

Werheit, Helmut; Filipov, Volodymyr; Kuhlmann, Udo; Schwarz, Ulrich; Armbrüster, Marc; Leithe-Jasper, Andreas; Tanaka, Takaho; Higashi, Iwami; Lundström, Torsten; Gurin, Vladimir N; Korsukova, Maria M

2010-01-01

We present Raman spectra of numerous icosahedral boron-rich solids having the structure of α-rhombohedral, β-rhombohedral, α-tetragonal, β-tetragonal, YB66, orthorhombic or amorphous boron. The spectra were newly measured and, in some cases, compared with reported data and discussed. We emphasize the importance of a high signal-to-noise ratio in the Raman spectra for detecting weak effects evoked by the modification of compounds, accommodation of interstitial atoms and other structural defects. Vibrations of the icosahedra, occurring in all the spectra, are interpreted using the description of modes in α-rhombohedral boron by Beckel et al. The Raman spectrum of boron carbide is largely clarified. Relative intra- and inter-icosahedral bonding forces are estimated for the different structural groups and for vanadium-doped β-rhombohedral boron. The validity of Badger's rule is demonstrated for the force constants of inter-icosahedral B–B bonds, whereas the agreement is less satisfactory for the intra-icosahedral B–B bonds. PMID:27877328

Characterisation of a Novel Retrovirus and a dsDNA Virus Infecting the Coral Algal Endosymbiont, Symbiodinium sp.

NASA Astrophysics Data System (ADS)

Weynberg, K. D.; Neave, M. J.; Clode, P. L.; Voolstra, C. R.; Brownlee, C.; Laffy, P.; Webster, N.; Levin, R.; Wood-Charlson, E.; van Oppen, M. J.

2016-02-01

Research into viruses associated with coral reefs is a newly emerging field. Corals form an important symbiotic relationship with the dinoflagellate species Symbiodinium, which the coral relies heavily upon for nutrients and calcification. Coral bleaching is the result of disruption of this symbiosis when the algae and/or its photosynthetic pigments are lost from the coral tissues. Environmental stressors, including elevated sea surface temperatures and increased UV light exposure, have been implicated in coral bleaching. We set out to test the hypothesis that Symbiodinium in culture plays host to a latent virus that switches to a lytic infection under stress, such as UV exposure or elevated temperature. Analysis of Symbiodinium cultures (isolated from corals on the Great Barrier Reef) using flow cytometry and transmission electron microscopy (TEM), revealed an active viral infection was ongoing, regardless of experimental conditions. Morphological analysis using TEM revealed filamentous and icosahedral virus-like particles associated with Symbiodinium cultures. We present genomic data of the virus assemblages isolated from cultured Symbiodinium cells that indicate this dinoflagellate is targeted by both a dsDNA virus, related to members of the Nucleo-Cytoplasmic Large dsDNA Virus family (NCLDV), and a novel ssRNA virus related to the Orthoretrovirinae. Further investigations are underway to detect viruses in freshly isolated Symbiodinium from reef corals and to compare these with viruses observed in laboratory cultures of this symbiotic alga. We aim to develop molecular diagnostic probes to detect viruses in field samples to help monitor and assess the impact of viruses in coral bleaching and other climate change-related events, which have huge implications for the health of coral reefs to future global climate scenarios.

The 2.3-Angstrom Structure of Porcine Circovirus 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khayat, Reza; Brunn, Nicholas; Speir, Jeffrey A.

Porcine circovirus 2 (PCV2) is a T = 1 nonenveloped icosahedral virus that has had severe impact on the swine industry. Here we report the crystal structure of an N-terminally truncated PCV2 virus-like particle at 2.3-{angstrom} resolution, and the cryo-electron microscopy (cryo-EM) image reconstruction of a full-length PCV2 virus-like particle at 9.6-{angstrom} resolution. This is the first atomic structure of a circovirus. The crystal structure revealed that the capsid protein fold is a canonical viral jelly roll. The loops connecting the strands of the jelly roll define the limited features of the surface. Sulfate ions interacting with the surface andmore » electrostatic potential calculations strongly suggest a heparan sulfate binding site that allows PCV2 to gain entry into the cell. The crystal structure also allowed previously determined epitopes of the capsid to be visualized. The cryo-EM image reconstruction showed that the location of the N terminus, absent in the crystal structure, is inside the capsid. As the N terminus was previously shown to be antigenic, it may externalize through viral 'breathing'.« less

Microgravity

NASA Image and Video Library

2000-05-01

The structure of the Satellite Tobacco Mosaic Viurus (STMV)--one of the smallest viruses known--has been successfully reduced using STMV crystals grown aboard the Space Shuttle in 1992 and 1994. The STMV crystals were up to 30 times the volume of any seen in the laboratory. At the time they gave the best resolution data ever obtained on any virus crystal. STMV is a small icosahedral plant virus, consisting of a protein shell made up of 60 identical protein subunits of molecular weight 17,500. Particularly noteworthy is the fact that, in contrast to the crystals grown on Earth, the crystals grown under microgravity conditions were visually perfect, with no striations or clumping of crystals. Furthermore, the x-ray diffraction data obtained from the space-grown crystals was of a much higher quality than the best data available at that time from ground-based crystals. This stylized ribbon model shows the protein coat in white and the nucleic acid in yellow. STMV is used because it is a simple protein to work with; studies are unrelated to tobacco. Credit: Dr. Alex McPherson, University of California at Irvin.

Templated Formation of Luminescent Virus-like Particles by Tailor-Made Pt(II) Amphiphiles

PubMed Central

2018-01-01

Virus-like particles (VLPs) have been created from luminescent Pt(II) complex amphiphiles, able to form supramolecular structures in water solutions, that can be encapsulated or act as templates of cowpea chlorotic mottle virus capsid proteins. By virtue of a bottom-up molecular design, icosahedral and nonicosahedral (rod-like) VLPs have been constructed through diverse pathways, and a relationship between the molecular structure of the complexes and the shape and size of the VLPs has been observed. A deep insight into the mechanism for the templated formation of the differently shaped VLPs was achieved, by electron microscopy measurements (TEM and STEM) and bulk analysis (FPLC, DLS, photophysical investigations). Interestingly, the obtained VLPs can be visualized by their intense emission at room temperature, generated by the self-assembly of the Pt(II) complexes. The encapsulation of the luminescent species is further verified by their higher emission quantum yields inside the VLPs, which is due to the confinement effect of the protein cage. These hybrid materials demonstrate the potential of tailor-made supramolecular systems able to control the assembly of biological building blocks. PMID:29357236

Templated Formation of Luminescent Virus-like Particles by Tailor-Made Pt(II) Amphiphiles.

PubMed

Sinn, Stephan; Yang, Liulin; Biedermann, Frank; Wang, Di; Kübel, Christian; Cornelissen, Jeroen J L M; De Cola, Luisa

2018-02-14

Virus-like particles (VLPs) have been created from luminescent Pt(II) complex amphiphiles, able to form supramolecular structures in water solutions, that can be encapsulated or act as templates of cowpea chlorotic mottle virus capsid proteins. By virtue of a bottom-up molecular design, icosahedral and nonicosahedral (rod-like) VLPs have been constructed through diverse pathways, and a relationship between the molecular structure of the complexes and the shape and size of the VLPs has been observed. A deep insight into the mechanism for the templated formation of the differently shaped VLPs was achieved, by electron microscopy measurements (TEM and STEM) and bulk analysis (FPLC, DLS, photophysical investigations). Interestingly, the obtained VLPs can be visualized by their intense emission at room temperature, generated by the self-assembly of the Pt(II) complexes. The encapsulation of the luminescent species is further verified by their higher emission quantum yields inside the VLPs, which is due to the confinement effect of the protein cage. These hybrid materials demonstrate the potential of tailor-made supramolecular systems able to control the assembly of biological building blocks.

Evidence for the role of basic amino acids in the coat protein arm region of Cucumber necrosis virus in particle assembly and selective encapsidation of viral RNA.

PubMed

Alam, Syed Benazir; Reade, Ron; Theilmann, Jane; Rochon, D'Ann

2017-12-01

Cucumber necrosis virus (CNV) is a T = 3 icosahedral virus with a (+)ssRNA genome. The N-terminal CNV coat protein arm contains a conserved, highly basic sequence ("KGRKPR"), which we postulate is involved in RNA encapsidation during virion assembly. Seven mutants were constructed by altering the CNV "KGRKPR" sequence; the four basic residues were mutated to alanine individually, in pairs, or in total. Virion accumulation and vRNA encapsidation were significantly reduced in mutants containing two or four substitutions and virion morphology was also affected, where both T = 1 and intermediate-sized particles were produced. Mutants with two or four substitutions encapsidated significantly greater levels of truncated RNA than that of WT, suggesting that basic residues in the "KGRKPR" sequence are important for encapsidation of full-length CNV RNA. Interestingly, "KGRKPR" mutants also encapsidated relatively higher levels of host RNA, suggesting that the "KGRKPR" sequence also contributes to selective encapsidation of CNV RNA. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

The novel asymmetric entry intermediate of a picornavirus captured with nanodiscs

PubMed Central

Lee, Hyunwook; Shingler, Kristin L.; Organtini, Lindsey J.; Ashley, Robert E.; Makhov, Alexander M.; Conway, James F.; Hafenstein, Susan

2016-01-01

Many nonenveloped viruses engage host receptors that initiate capsid conformational changes necessary for genome release. Structural studies on the mechanisms of picornavirus entry have relied on in vitro approaches of virus incubated at high temperatures or with excess receptor molecules to trigger the entry intermediate or A-particle. We have induced the coxsackievirus B3 entry intermediate by triggering the virus with full-length receptors embedded in lipid bilayer nanodiscs. These asymmetrically formed A-particles were reconstructed using cryo-electron microscopy and a direct electron detector. These first high-resolution structures of a picornavirus entry intermediate captured at a membrane with and without imposing icosahedral symmetry (3.9 and 7.8 Å, respectively) revealed a novel A-particle that is markedly different from the classical A-particles. The asymmetric receptor binding triggers minimal global capsid expansion but marked local conformational changes at the site of receptor interaction. In addition, viral proteins extrude from the capsid only at the site of extensive protein remodeling adjacent to the nanodisc. Thus, the binding of the receptor triggers formation of a unique site in preparation for genome release. PMID:27574701

Self-assembling Polypeptide Nanoparticles: Design, Synthesis, Biophysical Characterization and Biomedical Applications

NASA Astrophysics Data System (ADS)

Araujo Pereira Falcao Pimentel, Tais de

Inspired by the architecture of icosahedral viruses, self-assembling polypeptide nanoparticles (SAPN) with icosahedral symmetry were developed. The building block for the SAPN was a single polypeptide chain. Similarly, the capsid of quite a few small viruses are built from one single peptide chain. The polypeptide chain of the SAPN consists of a pentameric coiled-coil domain at the N-terminus joined by a short linker segment to a trimeric coiled-coil domain at the C-terminus. Here we have studied factors governing self-assembly of the SAPN such as linker constitution and trimer length. The interdomain linker 2i88 afforded the most homogenous nanoparticles as verified by TEM and DLS. Furthermore, AUC and STEM analyses suggest that the nanoparticles formed using the linker 2i88 have a T=3-like architecture confirming computer modeling predictions. As for trimer length, we have shown that it is possible to synthesize SAPN with a trimer that is as short as only 17 amino acids. Given that the N-terminus and C-terminus of the SAPN can be extended to include epitopes and give rise to a repetitive antigen display system, vaccine applications of the SAPN were also investigated here. We grafted parts of the SARS virus' spike protein onto our SAPN to repetitively display this B-cell epitope. Biophysical characterization showed that single nanoparticles of the expected size range were formed. Immunization experiments in mice at University of Colorado Denver revealed that the antibodies elicited were conformation-specific. Moreover, the antibodies significantly inhibited SARS virus infection of Vero E6 cells. SAPN were also functionalized at the C-terminus with a B-cell epitope from the circumsporozoite protein (CSP) of the malaria parasite Plasmodium falciparum and at the N-terminus with CTL epitopes from CSP. The trimeric coiled-coil domains of these malaria SAPN were modified to include a HTL epitope. Even will all these modifications, self-assembly occurred as confirmed by TEM and DLS. In immunization experiments performed at WRAIR good immune responses were obtained. Another biomedical application of SAPN is the development of a peptide-based serodiagnostic assay for tuberculosis (Tb). In an ELISA format, Tb-SAPN showed modest responses in serodiagnosis of Tb.

Detection of Intermediates And Kinetic Control During Assembly of Bacteriophage P22 Procapsid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuma, R.; Tsuruta, H.; French, K.H.

2009-05-26

Bacteriophage P22 serves as a model for the assembly and maturation of other icosahedral double-stranded DNA viruses. P22 coat and scaffolding proteins assemble in vitro into an icosahedral procapsid, which then expands during DNA packaging (maturation). Efficient in vitro assembly makes this system suitable for design and production of monodisperse spherical nanoparticles (diameter {approx} 50 nm). In this work, we explore the possibility of controlling the outcome of assembly by scaffolding protein engineering. The scaffolding protein exists in monomer-dimer-tetramer equilibrium. We address the role of monomers and dimers in assembly by using three different scaffolding proteins with altered monomer-dimer equilibriummore » (weak dimer, covalent dimer, monomer). The progress and outcome of assembly was monitored by time-resolved X-ray scattering, which allowed us to distinguish between closed shells and incomplete assembly intermediates. Binding of scaffolding monomer activates the coat protein for assembly. Excess dimeric scaffolding protein resulted in rapid nucleation and kinetic trapping yielding incomplete shells. Addition of monomeric wild-type scaffold with excess coat protein completed these metastable shells. Thus, the monomeric scaffolding protein plays an essential role in the elongation phase by activating the coat and effectively lowering its critical concentration for assembly.« less

Structure, function and dynamics in adenovirus maturation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mangel, Walter F.; San Martín, Carmen

2014-11-21

Here we review the current knowledge on maturation of adenovirus, a non-enveloped icosahedral eukaryotic virus. The adenovirus dsDNA genome fills the capsid in complex with a large amount of histone-like viral proteins, forming the core. Maturation involves proteolytic cleavage of several capsid and core precursor proteins by the viral protease (AVP). AVP uses a peptide cleaved from one of its targets as a “molecular sled” to slide on the viral genome and reach its substrates, in a remarkable example of one-dimensional chemistry. Immature adenovirus containing the precursor proteins lacks infectivity because of its inability to uncoat. The immature core ismore » more compact and stable than the mature one, due to the condensing action of unprocessed core polypeptides; shell precursors underpin the vertex region and the connections between capsid and core. Maturation makes the virion metastable, priming it for stepwise uncoating by facilitating vertex release and loosening the condensed genome and its attachment to the icosahedral shell. The packaging scaffold protein L1 52/55k is also a substrate for AVP. Proteolytic processing of L1 52/55k disrupts its interactions with other virion components, providing a mechanism for its removal during maturation. In conclusion, possible roles for maturation of the terminal protein are discussed.« less

Evidence from electron micrographs that icosahedral quasicrystals are icosahedral twins of cubic crystals.

PubMed

Pauling, L

1990-10-01

An analysis of electron micrographs of Al5Mn quasicrystals obtained by rapidly cooling a molten alloy with composition Al17Mn and removing the Al matrix by electrosolution, revealing aggregates of 20 microcrystals at the corners of a pentagonal dodecahedron, supports the proposal that these microcrystals are cubic crystals twinned about an icosahedral seed, with each cubic microcrystal sharing a threefold axis and three symmetry planes with the seed.

Virus world as an evolutionary network of viruses and capsidless selfish elements.

PubMed

Koonin, Eugene V; Dolja, Valerian V

2014-06-01

Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus "self" that defines the identity of deep, ancient viral lineages. However, several other widespread viral "hallmark genes" encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Speckle in the diffraction patterns of Hendricks-Teller and icosahedral glass models

NASA Technical Reports Server (NTRS)

Garg, Anupam; Levine, Dov

1988-01-01

It is shown that the X-ray diffraction patterns from the Hendricks-Teller model for layered systems and the icosahedral glass models for the icosahedral phases show large fluctuations between nearby scattering wave vectors and from sample to sample, that are quite analogous to laser speckle. The statistics of these fluctuations are studied analytically for the first model and via computer simulations for the second. The observability of these effects is discussed briefly.

Additional evidence from x-ray powder diffraction patterns that icosahedral quasi-crystals of intermetallic compounds are twinned cubic crystals

PubMed Central

Pauling, Linus

1988-01-01

Analysis of the measured values of Q for the weak peaks (small maxima, usually considered to be background fluctuations, “noise”) on the x-ray powder diffraction curves for 17 rapidly quenched alloys leads directly to the conclusion that they are formed by an 820-atom or 1012-atom primitive cubic structure that by icosahedral twinning produces the so-called icosahedral quasi-crystals. PMID:16593948

Biochemical Requirements of Virus Wrapping by the Endoplasmic Reticulum: Involvement of ATP and Endoplasmic Reticulum Calcium Store during Envelopment of African Swine Fever Virus

PubMed Central

Cobbold, Christian; Brookes, Sharon M.; Wileman, Thomas

2000-01-01

Enwrapment by membrane cisternae has emerged recently as a mechanism of envelopment for large enveloped DNA viruses, such as herpesviruses, poxviruses, and African swine fever (ASF) virus. For both ASF virus and the poxviruses, wrapping is a multistage process initiated by the recruitment of capsid proteins onto membrane cisternae of the endoplasmic reticulum (ER) or associated ER-Golgi intermediate membrane compartments. Capsid assembly induces progressive bending of membrane cisternae into the characteristic shape of viral particles, and envelopment provides virions with two membranes in one step. We have used biochemical assays for ASF virus capsid recruitment, assembly, and envelopment to define the cellular processes important for the enwrapment of viruses by membrane cisternae. Capsid assembly on the ER membrane, and envelopment by ER cisternae, were inhibited when cells were depleted of ATP or depleted of calcium by incubation with A23187 and EDTA or the ER calcium ATPase inhibitor, thapsigargin. Electron microscopy analysis showed that cells depleted of calcium were unable to assemble icosahedral particles. Instead, assembly sites contained crescent-shaped and bulbous structures and, in rare cases, empty closed five-sided particles. Interestingly, recruitment of the capsid protein from the cytosol onto the ER membrane did not require ATP or an intact ER calcium store. The results show that following recruitment of the virus capsid protein onto the ER membrane, subsequent stages of capsid assembly and enwrapment are dependent on ATP and are regulated by the calcium gradients present across the ER membrane cisternae. PMID:10666244

Impact of virus surface characteristics on removal mechanisms within membrane bioreactors.

PubMed

Chaudhry, Rabia M; Holloway, Ryan W; Cath, Tzahi Y; Nelson, Kara L

2015-11-01

In this study we investigated the removal of viruses with similar size and shape but with different external surface capsid proteins by a bench-scale membrane bioreactor (MBR). The goal was to determine which virus removal mechanisms (retention by clean backwashed membrane, retention by cake layer, attachment to biomass, and inactivation) were most impacted by differences in the virus surface properties. Seven bench-scale MBR experiments were performed using mixed liquor wastewater sludge that was seeded with three lab-cultured bacteriophages with icosahedral capsids of ∼30 nm diameter (MS2, phiX174, and fr). The operating conditions were designed to simulate those at a reference, full-scale MBR facility. The virus removal mechanism most affected by virus type was attachment to biomass (removals of 0.2 log for MS2, 1.2 log for phiX174, and 3 log for fr). These differences in removal could not be explained by electrostatic interactions, as the three viruses had similar net negative charge when suspended in MBR permeate. Removals by the clean backwashed membrane (less than 1 log) and cake layer (∼0.6 log) were similar for the three viruses. A comparison between the clean membrane removals seen at the bench-scale using a virgin membrane (∼1 log), and the full-scale using 10-year old membranes (∼2-3 logs) suggests that irreversible fouling, accumulated on the membrane over years of operation that cannot be removed by cleaning, also contributes towards virus removal. This study enhances the current mechanistic understanding of virus removal in MBRs and will contribute to more reliable treatment for water reuse applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Synthesis of icosahedral gold nanocrystals: a thermal process strategy.

PubMed

Zhou, Min; Chen, Shenhao; Zhao, Shiyong

2006-03-16

We demonstrate a one-step thermal process route to the synthesis of icosahedral gold nanocrystals. By regulating the concentrations of poly(vinyl pyrrolidone) (PVP) and HAuCl4 or changing the temperature, we can readily access the shapes of icosahedral nanocrystals with good uniformity. These gold nanostructures, with unique geometrical shapes, might find use in areas that include photonics, optoelectronics, and optical sensing. We also observed that these gold nanocrystals have a strong tendency to be immobilized spontaneously on the glass substrate.

Encapsidation of Linear Polyelectrolyte in a Viral Nanocontainer

NASA Astrophysics Data System (ADS)

Hu, Yufang

2005-03-01

We present the results from a combined experimental and theoretical study on the self-assembly of a model icosahedral virus, Cowpea Chlorotic Mottle Virus (CCMV). The formation of native CCMV capsids is believed to be driven primarily by the electrostatic interactions between the viral RNA and the positively charged capsid interior, as well as by the hydrophobic interactions between capsid protein subunits. To probe these molecular interactions, in vitro self-assembly reactions are carried out using the CCMV capsid protein and a synthetic linear polyelectrolyte, sodium polystyrene sulfonate (NaPSS), which functions as the analog of viral RNA. Under appropriate solutions conditions, NaPSS is encapsidated by the viral capsid. The molecular weight of NaPSS is systematically varied and the resulting average capsid size, size distribution, and particle morphology are measured by transmission electron microscopy. The correlation between capsid size and packaged cargo size, as well as the upper limit of capsid packaging capacity, are characterized. To elucidate the physical role played by the encapsidated polyelectrolyte in determining the preferred size of spherical viruses, we have used a mean-field approach to calculate the free energy of the virus-like particle as a function of chain length (and of the strength of chain/capsid attractive interaction). We find good agreement with our analytical calculations and experimental results.

Microgravity

NASA Image and Video Library

2000-05-01

The bumpy exterior of the turnip yellow mosaic virus (TYMV) protein coat, or capsid, was defined in detail by Dr. Alexander McPherson of the University of California, Irvin using protein crystallized in space for analysis on Earth. TYMV is an icosahedral virus constructed from 180 copies of the same protein arranged into 12 clusters of five proteins (pentamers), and 20 clusters of six proteins (hexamers). The final TYMV structure led to the enexpected hypothesis that the virus release its RNA by essentially chemical-mechanical means. Most viruses have farly flat coats, but in TYMV, the fold in each protein, called the jellyroll, is clustered at the points where the protein pentamers and hexamers join. The jellyrolls are almost standing on end, producing a bumpy surface with knobs at all of the pentamers and hexamers. At the inside surface of the pentamers is a void that is not present at the hexamers. The coating had been seen in early studies of TYMV, but McPhereson's atomic structure shows much more detail. The inside surface is strikingly, and unexpectedly, different than the outside. While the pentamers contain a central viod on the inside, the hexameric units contain peptides liked to each other, forming a ring or, more accurately, rings to fill the voild. Credit: Dr. Alexander McPherson, University of California, Irvine.

Microgravity

NASA Image and Video Library

2000-05-01

The bumpy exterior of the turnip yellow mosaic virus (TYMV) protein coat, or capsid, was defined in detail by Dr. Alexander McPherson of the University of California, Irvin using proteins crystallized in space for analysis on Earth. TYMV is an icosahedral virus constructed from 180 copies of the same protein arranged into 12 clusters of five proteins (pentamers), and 20 clusters of six proteins (hexamers). The final TYMV structure led to the unexpected hypothesis that the virus releases its RNA by essentially chemical-mechanical means. Most viruses have fairly flat coats, but in TYNV, the fold in each protein, called the jellyroll, is clustered at the points where the protein pentamers and hexamers join. The jellyrolls are almost standing on end, producing a bumpy surface with knobs at all of the pentamers and hexamers. At the inside surface of the pentamers is a void that is not present at the hexamers. The coating had been seen in early stuties of TYMV, but McPherson's atomic structure shows much more detail. The inside surface is strikingly, and unexpectedly, different than the outside. While the pentamers contain a central void on the inside, the hexameric units contain peptides linked to each other, forming a ring or, more accurately, rings to fill the void. Credit: Dr. Alexander McPherson, University of California, Irvine

Tomato bushy stunt virus (TBSV), a versatile platform for polyvalent display of antigenic epitopes and vaccine design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Shantanu; Ochoa, Wendy; Singh, Pratik

2009-05-25

Viruses-like particles (VLPs) are frequently being used as platforms for polyvalent display of foreign epitopes of interest on their capsid surface to improve their presentation enhancing the antigenicity and host immune response. In the present study, we used the VLPs of Tomato bushy stunt virus (TBSV), an icosahedral plant virus, as a platform to display 180 copies of 16 amino acid epitopes of ricin toxin fused to the C-terminal end of a modified TBSV capsid protein (NDELTA52). Expression of the chimeric recombinant protein in insect cells resulted in spontaneous assembly of VLPs displaying the ricin epitope. Cryo-electron microscopy and imagemore » reconstruction of the chimeric VLPs at 22 A resolution revealed the locations and orientation of the ricin epitope exposed on the TBSV capsid surface. Furthermore, injection of chimeric VLPs into mice generated antisera that detected the native ricin toxin. The ease of fusing of short peptides of 15-20 residues and their ability to form two kinds (T = 1, T = 3) of bio-nanoparticles that result in the display of 60 or 180 copies of less constrained and highly exposed antigenic epitopes makes TBSV an attractive and versatile display platform for vaccine design.« less

Mechanisms of Entry and Endosomal Pathway of African Swine Fever Virus

PubMed Central

G. Sánchez, Elena; Pérez-Núñez, Daniel; Revilla, Yolanda

2017-01-01

African Swine Fever Virus (ASFV) causes a serious swine disease that is endemic in Africa and Sardinia and presently spreading in Russia and neighboring countries, including Poland and recently, the Czech Republic. This uncontrolled dissemination is a world-wide threat, as no specific protection or vaccine is available. ASFV is a very complex icosahedral, enveloped virus about 200 nm in diameter, which infects several members of pigs. The virus enters host cells by receptor-mediated endocytosis that depends on energy, vacuolar pH and temperature. The specific receptor(s) and attachment factor(s) involved in viral entry are still unknown, although macropinocytosis and clathrin-dependent mechanisms have been proposed. After internalization, ASFV traffics through the endolysosomal system. The capsid and inner envelope are found in early endosomes or macropinosomes early after infection, colocalizing with EEA1 and Rab5, while at later times they co-localize with markers of late endosomes and lysosomes, such as Rab7 or Lamp 1. A direct relationship has been established between the maturity of the endosomal pathway and the progression of infection in the cell. Finally, ASFV uncoating first involves the loss of the outer capsid layers, and later fusion of the inner membrane with endosomes, releasing the nude core into the cytosol. PMID:29117102

Role of dynamic capsomere supply for viral capsid self-assembly

NASA Astrophysics Data System (ADS)

Boettcher, Marvin A.; Klein, Heinrich C. R.; Schwarz, Ulrich S.

2015-02-01

Many viruses rely on the self-assembly of their capsids to protect and transport their genomic material. For many viral systems, in particular for human viruses like hepatitis B, adeno or human immunodeficiency virus, that lead to persistent infections, capsomeres are continuously produced in the cytoplasm of the host cell while completed capsids exit the cell for a new round of infection. Here we use coarse-grained Brownian dynamics simulations of a generic patchy particle model to elucidate the role of the dynamic supply of capsomeres for the reversible self-assembly of empty T1 icosahedral virus capsids. We find that for high rates of capsomere influx only a narrow range of bond strengths exists for which a steady state of continuous capsid production is possible. For bond strengths smaller and larger than this optimal value, the reaction volume becomes crowded by small and large intermediates, respectively. For lower rates of capsomere influx a broader range of bond strengths exists for which a steady state of continuous capsid production is established, although now the production rate of capsids is smaller. Thus our simulations suggest that the importance of an optimal bond strength for viral capsid assembly typical for in vitro conditions can be reduced by the dynamic influx of capsomeres in a cellular environment.

Preparation of (Ga1−xZnx)(N1−xOx) Photocatalysts from the Reaction of NH3 with Ga2O3/ZnO and ZnGa2O4: In Situ Time-Resolved XRD and XAFS Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, H.; Wen , W; Wang, Q

Hibiscus chlorotic ringspot virus (HCRSV) is a positive-sense monopartite single-stranded RNA virus that belongs to the Carmovirus genus of the Tombusviridae family, which includes carnation mottle virus (CarMV). The HCRSV virion has a 30 nm diameter icosahedral capsid with T = 3 quasi-symmetry containing 180 copies of a 38 kDa coat protein (CP) and encapsidates a full-length 3.9 kb genomic RNA. Authentic virus was harvested from infected host kenaf leaves and was purified by saturated ammonium sulfate precipitation, sucrose density-gradient centrifugation and anion-exchange chromatography. Virus crystals were grown in multiple conditions; one of the crystals diffracted to 3.2 A resolutionmore » Ad allowed the collection of a partial data set. The crystal belonged to space group R32, with unit-cell parameters a = b = 336.4, c = 798.5 A. Packing considerations and rotation-function analysis determined that there were three particles per unit cell, all of which have the same orientation and fixed positions, and resulted in tenfold noncrystallography symmetry for real-space averaging. The crystals used for the structure determination of southern bean mosaic virus (SBMV) have nearly identical characteristics. Together, these findings will greatly aid the high-resolution structure determination of HCRSV.« less

High-level systemic expression of conserved influenza epitope in plants on the surface of rod-shaped chimeric particles.

PubMed

Petukhova, Natalia V; Gasanova, Tatiana V; Ivanov, Peter A; Atabekov, Joseph G

2014-04-21

Recombinant viruses based on the cDNA copy of the tobacco mosaic virus (TMV) genome carrying different versions of the conserved M2e epitope from influenza virus A cloned into the coat protein (CP) gene were obtained and partially characterized by our group previously; cysteines in the human consensus M2e sequence were changed to serine residues. This work intends to show some biological properties of these viruses following plant infections. Agroinfiltration experiments on Nicotiana benthamiana confirmed the efficient systemic expression of M2e peptides, and two point amino acid substitutions in recombinant CPs significantly influenced the symptoms and development of viral infections. Joint expression of RNA interference suppressor protein p19 from tomato bushy stunt virus (TBSV) did not affect the accumulation of CP-M2e-ser recombinant protein in non-inoculated leaves. RT-PCR analysis of RNA isolated from either infected leaves or purified TMV-M2e particles proved the genetic stability of TMV‑based viral vectors. Immunoelectron microscopy of crude plant extracts demonstrated that foreign epitopes are located on the surface of chimeric virions. The rod‑shaped geometry of plant-produced M2e epitopes is different from the icosahedral or helical filamentous arrangement of M2e antigens on the carrier virus-like particles (VLP) described earlier. Thereby, we created a simple and efficient system that employs agrobacteria and plant viral vectors in order to produce a candidate broad-spectrum flu vaccine.

A rapid and quantitative assay for measuring antibody-mediated neutralization of West Nile virus infection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pierson, Theodore C.; Sanchez, Melissa D.; Puffer, Bridget A.

2006-03-01

West Nile virus (WNV) is a neurotropic flavivirus within the Japanese encephalitis antigenic complex that is responsible for causing West Nile encephalitis in humans. The surface of WNV virions is covered by a highly ordered icosahedral array of envelope proteins that is responsible for mediating attachment and fusion with target cells. These envelope proteins are also primary targets for the generation of neutralizing antibodies in vivo. In this study, we describe a novel approach for measuring antibody-mediated neutralization of WNV infection using virus-like particles that measure infection as a function of reporter gene expression. These reporter virus particles (RVPs) aremore » produced by complementation of a sub-genomic replicon with WNV structural proteins provided in trans using conventional DNA expression vectors. The precision and accuracy of this approach stem from an ability to measure the outcome of the interaction between antibody and viral antigens under conditions that satisfy the assumptions of the law of mass action as applied to virus neutralization. In addition to its quantitative strengths, this approach allows the production of WNV RVPs bearing the prM-E proteins of different WNV strains and mutants, offering considerable flexibility for the study of the humoral immune response to WNV in vitro. WNV RVPs are capable of only a single round of infection, can be used under BSL-2 conditions, and offer a rapid and quantitative approach for detecting virus entry and its inhibition by neutralizing antibody.« less

Metal-organic framework materials based on icosahedral boranes and carboranes

DOEpatents

Mirkin, Chad A.; Hupp, Joseph T.; Farha, Omar K.; Spokoyny, Alexander M.; Mulfort, Karen L.

2010-11-02

Disclosed herein are metal-organic frameworks of metals and boron rich ligands, such as carboranes and icosahedral boranes. Methods of synthesizing and using these materials in gas uptake are disclosed.

Icosahedral (A5) family symmetry and the golden ratio prediction for solar neutrino mixing

NASA Astrophysics Data System (ADS)

Everett, Lisa L.; Stuart, Alexander J.

2009-04-01

We investigate the possibility of using icosahedral symmetry as a family symmetry group in the lepton sector. The rotational icosahedral group, which is isomorphic to A5, the alternating group of five elements, provides a natural context in which to explore (among other possibilities) the intriguing hypothesis that the solar neutrino mixing angle is governed by the golden ratio, ϕ=(1+5)/2. We present a basic toolbox for model building using icosahedral symmetry, including explicit representation matrices and tensor product rules. As a simple application, we construct a minimal model at tree level in which the solar angle is related to the golden ratio, the atmospheric angle is maximal, and the reactor angle vanishes to leading order. The approach provides a rich setting in which to investigate the flavor puzzle of the standard model.

From Glass Formation to Icosahedral Ordering by Curving Three-Dimensional Space.

PubMed

Turci, Francesco; Tarjus, Gilles; Royall, C Patrick

2017-05-26

Geometric frustration describes the inability of a local molecular arrangement, such as icosahedra found in metallic glasses and in model atomic glass formers, to tile space. Local icosahedral order, however, is strongly frustrated in Euclidean space, which obscures any causal relationship with the observed dynamical slowdown. Here we relieve frustration in a model glass-forming liquid by curving three-dimensional space onto the surface of a 4-dimensional hypersphere. For sufficient curvature, frustration vanishes and the liquid "freezes" in a fully icosahedral structure via a sharp "transition." Frustration increases upon reducing the curvature, and the transition to the icosahedral state smoothens while glassy dynamics emerge. Decreasing the curvature leads to decoupling between dynamical and structural length scales and the decrease of kinetic fragility. This sheds light on the observed glass-forming behavior in Euclidean space.

Highly diverse population of Picornaviridae and other members of the Picornavirales, in Cameroonian fruit bats.

PubMed

Yinda, Claude Kwe; Zell, Roland; Deboutte, Ward; Zeller, Mark; Conceição-Neto, Nádia; Heylen, Elisabeth; Maes, Piet; Knowles, Nick J; Ghogomu, Stephen Mbigha; Van Ranst, Marc; Matthijnssens, Jelle

2017-03-23

The order Picornavirales represents a diverse group of positive-stranded RNA viruses with small non-enveloped icosahedral virions. Recently, bats have been identified as an important reservoir of several highly pathogenic human viruses. Since many members of the Picornaviridae family cause a wide range of diseases in humans and animals, this study aimed to characterize members of the order Picornavirales in fruit bat populations located in the Southwest region of Cameroon. These bat populations are frequently in close contact with humans due to hunting, selling and eating practices, which provides ample opportunity for interspecies transmissions. Fecal samples from 87 fruit bats (Eidolon helvum and Epomophorus gambianus), were combined into 25 pools and analyzed using viral metagenomics. In total, Picornavirales reads were found in 19 pools, and (near) complete genomes of 11 picorna-like viruses were obtained from 7 of these pools. The picorna-like viruses possessed varied genomic organizations (monocistronic or dicistronic), and arrangements of gene cassettes. Some of the viruses belonged to established families, including the Picornaviridae, whereas others clustered distantly from known viruses and most likely represent novel genera and families. Phylogenetic and nucleotide composition analyses suggested that mammals were the likely host species of bat sapelovirus, bat kunsagivirus and bat crohivirus, whereas the remaining viruses (named bat iflavirus, bat posalivirus, bat fisalivirus, bat cripavirus, bat felisavirus, bat dicibavirus and bat badiciviruses 1 and 2) were most likely diet-derived. The existence of a vast genetic variability of picorna-like viruses in fruit bats may increase the probability of spillover infections to humans especially when humans and bats have direct contact as the case in this study site. However, further screening for these viruses in humans will fully indicate their zoonotic potential.

Mysteries of icosahedral quasicrystals: how are the atoms arranged?

PubMed

Ishimasa, Tsutomu

2016-07-01

Higher-dimensional structure analysis of quasicrystals is now possible. Yamada et al. [IUCrJ (2016), 3, 247-258] have solved the atomic structure of icosahedral ScZn7.33 including the characteristic imperfections.

Stability of Cucumber Necrosis Virus at the Quasi-6-Fold Axis Affects Zoospore Transmission.

PubMed

Sherman, Michael B; Kakani, Kishore; Rochon, D'Ann; Jiang, Wen; Voss, Neil R; Smith, Thomas J

2017-10-01

Cucumber necrosis virus (CNV) is a member of the genus Tombusvirus and has a monopartite positive-sense RNA genome. CNV is transmitted in nature via zoospores of the fungus Olpidium bornovanus As with other members of the Tombusvirus genus, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation blocks the virus from zoospore transmission while not significantly affecting replication in plants (K. Kakani, R. Reade, and D. Rochon, J Mol Biol 338:507-517, 2004, https://doi.org/10.1016/j.jmb.2004.03.008). P73 lies immediately adjacent to a putative zinc binding site (M. Li et al., J Virol 87:12166-12175, 2013, https://doi.org/10.1128/JVI.01965-13) that is formed by three icosahedrally related His residues in the N termini of the C subunit at the quasi-6-fold axes. To better understand how this buried residue might affect vector transmission, we determined the cryo-electron microscopy structure of wild-type CNV in the native and swollen state and of the transmission-defective mutant, P73G, under native conditions. With the wild-type CNV, the swollen structure demonstrated the expected expansion of the capsid. However, the zinc binding region at the quasi-6-fold at the β-annulus axes remained intact. By comparison, the zinc binding region of the P73G mutant, even under native conditions, was markedly disordered, suggesting that the β-annulus had been disrupted and that this could destabilize the capsid. This was confirmed with pH and urea denaturation experiments in conjunction with electron microscopy analysis. We suggest that the P73G mutation affects the zinc binding and/or the β-annulus, making it more fragile under neutral/basic pH conditions. This, in turn, may affect zoospore transmission. IMPORTANCE Cucumber necrosis virus (CNV), a member of the genus Tombusvirus , is transmitted in nature via zoospores of the fungus Olpidium bornovanus While a number of plant viruses are transmitted via insect vectors, little is known at the molecular level as to how the viruses are recognized and transmitted. As with many spherical plant viruses, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation that lies inside the capsid immediately adjacent to a putative zinc binding site (Li et al., J Virol 87:12166-12175, 2013, https://doi.org/10.1128/JVI.01965-13) blocks the virus from zoospore transmission while not significantly affecting replication in plants (K. Kakani, R. Reade, and D. Rochon, J Mol Biol 338:507-517, 2004, https://doi.org/10.1016/j.jmb.2004.03.008). Here, we show that the P73G mutant is less stable than the wild type, and this appears to be correlated with destabilization of the β-annulus at the icosahedral 3-fold axes. Therefore, the β-annulus appears not to be essential for particle assembly but is necessary for interactions with the transmission vector. Copyright © 2017 American Society for Microbiology.

Stability of Cucumber Necrosis Virus at the Quasi-6-Fold Axis Affects Zoospore Transmission

PubMed Central

Sherman, Michael B.; Kakani, Kishore; Rochon, D'Ann; Jiang, Wen; Voss, Neil R.

2017-01-01

ABSTRACT Cucumber necrosis virus (CNV) is a member of the genus Tombusvirus and has a monopartite positive-sense RNA genome. CNV is transmitted in nature via zoospores of the fungus Olpidium bornovanus. As with other members of the Tombusvirus genus, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation blocks the virus from zoospore transmission while not significantly affecting replication in plants (K. Kakani, R. Reade, and D. Rochon, J Mol Biol 338:507–517, 2004, https://doi.org/10.1016/j.jmb.2004.03.008). P73 lies immediately adjacent to a putative zinc binding site (M. Li et al., J Virol 87:12166–12175, 2013, https://doi.org/10.1128/JVI.01965-13) that is formed by three icosahedrally related His residues in the N termini of the C subunit at the quasi-6-fold axes. To better understand how this buried residue might affect vector transmission, we determined the cryo-electron microscopy structure of wild-type CNV in the native and swollen state and of the transmission-defective mutant, P73G, under native conditions. With the wild-type CNV, the swollen structure demonstrated the expected expansion of the capsid. However, the zinc binding region at the quasi-6-fold at the β-annulus axes remained intact. By comparison, the zinc binding region of the P73G mutant, even under native conditions, was markedly disordered, suggesting that the β-annulus had been disrupted and that this could destabilize the capsid. This was confirmed with pH and urea denaturation experiments in conjunction with electron microscopy analysis. We suggest that the P73G mutation affects the zinc binding and/or the β-annulus, making it more fragile under neutral/basic pH conditions. This, in turn, may affect zoospore transmission. IMPORTANCE Cucumber necrosis virus (CNV), a member of the genus Tombusvirus, is transmitted in nature via zoospores of the fungus Olpidium bornovanus. While a number of plant viruses are transmitted via insect vectors, little is known at the molecular level as to how the viruses are recognized and transmitted. As with many spherical plant viruses, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation that lies inside the capsid immediately adjacent to a putative zinc binding site (Li et al., J Virol 87:12166–12175, 2013, https://doi.org/10.1128/JVI.01965-13) blocks the virus from zoospore transmission while not significantly affecting replication in plants (K. Kakani, R. Reade, and D. Rochon, J Mol Biol 338:507–517, 2004, https://doi.org/10.1016/j.jmb.2004.03.008). Here, we show that the P73G mutant is less stable than the wild type, and this appears to be correlated with destabilization of the β-annulus at the icosahedral 3-fold axes. Therefore, the β-annulus appears not to be essential for particle assembly but is necessary for interactions with the transmission vector. PMID:28724762

Beta cell device using icosahedral boride compounds

DOEpatents

Aselage, Terrence L.; Emin, David

2002-01-01

A beta cell for converting beta-particle energies into electrical energy having a semiconductor junction that incorporates an icosahedral boride compound selected from B.sub.12 As.sub.2, B.sub.12 P.sub.2, elemental boron having an .alpha.-rhombohedral structure, elemental boron having a .beta.-rhombohedral structure, and boron carbides of the chemical formula B.sub.12-x C.sub.3-x, where 0.15

Screening for the Location of RNA using the Chloride Ion Distribution in Simulations of Virus Capsids.

PubMed

Larsson, Daniel S D; van der Spoel, David

2012-07-10

The complete structure of the genomic material inside a virus capsid remains elusive, although a limited amount of symmetric nucleic acid can be resolved in the crystal structure of 17 icosahedral viruses. The negatively charged sugar-phosphate backbone of RNA and DNA as well as the large positive charge of the interior surface of the virus capsids suggest that electrostatic complementarity is an important factor in the packaging of the genomes in these viruses. To test how much packing information is encoded by the electrostatic and steric envelope of the capsid interior, we performed extensive all-atom molecular dynamics (MD) simulations of virus capsids with explicit water molecules and solvent ions. The model systems were two small plant viruses in which significant amounts of RNA has been observed by X-ray crystallography: satellite tobacco mosaic virus (STMV, 62% RNA visible) and satellite tobacco necrosis virus (STNV, 34% RNA visible). Simulations of half-capsids of these viruses with no RNA present revealed that the binding sites of RNA correlated well with regions populated by chloride ions, suggesting that it is possible to screen for the binding sites of nucleic acids by determining the equilibrium distribution of negative ions. By including the crystallographically resolved RNA in addition to ions, we predicted the localization of the unresolved RNA in the viruses. Both viruses showed a hot-spot for RNA binding at the 5-fold symmetry axis. The MD simulations were compared to predictions of the chloride density based on nonlinear Poisson-Boltzmann equation (PBE) calculations with mobile ions. Although the predictions are superficially similar, the PBE calculations overestimate the ion concentration close to the capsid surface and underestimate it far away, mainly because protein dynamics is not taken into account. Density maps from chloride screening can be used to aid in building atomic models of packaged virus genomes. Knowledge of the principles of genome packaging might be exploited for both antiviral therapy and technological applications.

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling

PubMed Central

Baker, Matthew L.; Hryc, Corey F.; Zhang, Qinfen; Wu, Weimin; Jakana, Joanita; Haase-Pettingell, Cameron; Afonine, Pavel V.; Adams, Paul D.; King, Jonathan A.; Jiang, Wen; Chiu, Wah

2013-01-01

High-resolution structures of viruses have made important contributions to modern structural biology. Bacteriophages, the most diverse and abundant organisms on earth, replicate and infect all bacteria and archaea, making them excellent potential alternatives to antibiotics and therapies for multidrug-resistant bacteria. Here, we improved upon our previous electron cryomicroscopy structure of Salmonella bacteriophage epsilon15, achieving a resolution sufficient to determine the tertiary structures of both gp7 and gp10 protein subunits that form the T = 7 icosahedral lattice. This study utilizes recently established best practice for near-atomic to high-resolution (3–5 Å) electron cryomicroscopy data evaluation. The resolution and reliability of the density map were cross-validated by multiple reconstructions from truly independent data sets, whereas the models of the individual protein subunits were validated adopting the best practices from X-ray crystallography. Some sidechain densities are clearly resolved and show the subunit–subunit interactions within and across the capsomeres that are required to stabilize the virus. The presence of the canonical phage and jellyroll viral protein folds, gp7 and gp10, respectively, in the same virus suggests that epsilon15 may have emerged more recently relative to other bacteriophages. PMID:23840063

Cryo-EM maps reveal five-fold channel structures and their modification by gatekeeper mutations in the parvovirus minute virus of mice (MVM) capsid.

PubMed

Subramanian, Suriyasri; Organtini, Lindsey J; Grossman, Alec; Domeier, Phillip P; Cifuente, Javier O; Makhov, Alexander M; Conway, James F; D'Abramo, Anthony; Cotmore, Susan F; Tattersall, Peter; Hafenstein, Susan

2017-10-01

In minute virus of mice (MVM) capsids, icosahedral five-fold channels serve as portals mediating genome packaging, genome release, and the phased extrusion of viral peptides. Previous studies suggest that residues L172 and V40 are essential for channel function. The structures of MVMi wildtype, and mutant L172T and V40A virus-like particles (VLPs) were solved from cryo-EM data. Two constriction points, termed the mid-gate and inner-gate, were observed in the channels of wildtype particles, involving residues L172 and V40 respectively. While the mid-gate of V40A VLPs appeared normal, in L172T adjacent channel walls were altered, and in both mutants there was major disruption of the inner-gate, demonstrating that direct L172:V40 bonding is essential for its structural integrity. In wildtype particles, residues from the N-termini of VP2 map into claw-like densities positioned below the channel opening, which become disordered in the mutants, implicating both L172 and V40 in the organization of VP2 N-termini. Copyright © 2017 Elsevier Inc. All rights reserved.

Swelling and Softening of the Cowpea Chlorotic Mottle Virus in Response to pH Shifts

PubMed Central

Wilts, Bodo D.; Schaap, Iwan A.T.; Schmidt, Christoph F.

2015-01-01

Cowpea chlorotic mottle virus (CCMV) forms highly elastic icosahedral protein capsids that undergo a characteristic swelling transition when the pH is raised from 5 to 7. Here, we performed nano-indentation experiments using an atomic force microscope to track capsid swelling and measure the shells’ Young’s modulus at the same time. When we chelated Ca2+ ions and raised the pH, we observed a gradual swelling of the RNA-filled capsids accompanied by a softening of the shell. Control experiments with empty wild-type virus and a salt-stable mutant revealed that the softening was not strictly coupled to the swelling of the protein shells. Our data suggest that a pH increase and Ca2+ chelation lead primarily to a loosening of contacts within the protein shell, resulting in a softening of the capsid. This appears to render the shell metastable and make swelling possible when repulsive forces among the capsid proteins become large enough, which is known to be followed by capsid disassembly at even higher pH. Thus, softening and swelling are likely to play a role during inoculation. PMID:25992732

Neutralization of West Nile virus by cross-linking of its surface proteins with Fab fragments of the human monoclonal antibody CR4354

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaufmann, Bärbel; Vogt, Matthew R.; Goudsmit, Jaap

2010-11-15

Many flaviviruses are significant human pathogens, with the humoral immune response playing an essential role in restricting infection and disease. CR4354, a human monoclonal antibody isolated from a patient, neutralizes West Nile virus (WNV) infection at a postattachment stage in the viral life-cycle. Here, we determined the structure of WNV complexed with Fab fragments of CR4354 using cryoelectron microscopy. The outer glycoprotein shell of a mature WNV particle is formed by 30 rafts of three homodimers of the viral surface protein E. CR4354 binds to a discontinuous epitope formed by protein segments from two neighboring E molecules, but does notmore » cause any detectable structural disturbance on the viral surface. The epitope occurs at two independent positions within an icosahedral asymmetric unit, resulting in 120 binding sites on the viral surface. The cross-linking of the six E monomers within one raft by four CR4354 Fab fragments suggests that the antibody neutralizes WNV by blocking the pH-induced rearrangement of the E protein required for virus fusion with the endosomal membrane.« less

Atomic force microscopy investigation of Mason-Pfizer monkey virus and human immunodeficiency virus type 1 reassembled particles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuznetsov, Yu. G.; Ulbrich, P.; Institute of Molecular Genetics, Czech Academy of Sciences, 166 10 Prague

2007-04-10

Particles of {delta}ProCANC, a fusion of capsid (Canada) and nucleocapsid (NC) protein of Mason-Pfizer monkey virus (M-PMV), which lacks the amino terminal proline, were reassembled in vitro and visualized by atomic force microscopy (AFM). The particles, of 83-84 nm diameter, exhibited ordered domains based on trigonal arrays of prominent rings with center to center distances of 8.7 nm. Imperfect closure of the lattice on the spherical surface was affected by formation of discontinuities. The lattice is consistent only with plane group p3 where one molecule is shared between contiguous rings. There are no pentameric clusters nor evidence that the particlesmore » are icosahedral. Tubular structures were also reassembled, in vitro, from two HIV fusion proteins, {delta}ProCANC and CANC. The tubes were uniform in diameter, 40 nm, but varied in length to a maximum of 600 nm. They exhibited left handed helical symmetry based on a p6 hexagonal net. The organization of HIV fusion proteins in the tubes is significantly different than for the protein units in the particles of M-PMV {delta}ProCANC.« less

Metallic-covalent bonding conversion and thermoelectric properties of Al-based icosahedral quasicrystals and approximants.

PubMed

Takagiwa, Yoshiki; Kimura, Kaoru

2014-08-01

In this article, we review the characteristic features of icosahedral cluster solids, metallic-covalent bonding conversion (MCBC), and the thermoelectric properties of Al-based icosahedral quasicrystals and approximants. MCBC is clearly distinguishable from and closely related to the well-known metal-insulator transition. This unique bonding conversion has been experimentally verified in 1/1-AlReSi and 1/0-Al 12 Re approximants by the maximum entropy method and Rietveld refinement for powder x-ray diffraction data, and is caused by a central atom inside the icosahedral clusters. This helps to understand pseudogap formation in the vicinity of the Fermi energy and establish a guiding principle for tuning the thermoelectric properties. From the electron density distribution analysis, rigid heavy clusters weakly bonded with glue atoms are observed in the 1/1-AlReSi approximant crystal, whose physical properties are close to icosahedral Al-Pd-TM (TM: Re, Mn) quasicrystals. They are considered to be an intermediate state among the three typical solids: metals, covalently bonded networks (semiconductor), and molecular solids. Using the above picture and detailed effective mass analysis, we propose a guiding principle of weakly bonded rigid heavy clusters to increase the thermoelectric figure of merit ( ZT ) by optimizing the bond strengths of intra- and inter-icosahedral clusters. Through element substitutions that mainly weaken the inter-cluster bonds, a dramatic increase of ZT from less than 0.01 to 0.26 was achieved. To further increase ZT , materials should form a real gap to obtain a higher Seebeck coefficient.

Pseudo-icosahedral Cr55Al232 -δ as a high-temperature protective material

NASA Astrophysics Data System (ADS)

Rosa, R.; Bhattacharya, S.; Pabla, J.; He, H.; Misuraca, J.; Nakajima, Y.; Bender, A. D.; Antonacci, A. K.; Adrip, W.; McNally, D. E.; Zebro, A.; Kamenov, P.; Geschwind, G.; Ghose, S.; Dooryhee, E.; Ibrahim, A.; Tritt, T. M.; Aronson, M. C.; Simonson, J. W.

2018-03-01

We report here a course of basic research into the potential suitability of a pseudo-icosahedral Cr aluminide as a material for high-temperature protective coatings. Cr55Al232 -δ [ δ =2.70 (6 ) ] exhibits high hardness at room temperature as well as low thermal conductivity and excellent oxidation resistance at 973 K, with an oxidation rate comparable to those of softer, denser benchmark materials. The origin of these promising properties can be traced to competing long-range and short-range symmetries within the pseudo-icosahedral crystal structure, suggesting new criteria for future materials research.

Collisions in outer space produced an icosahedral phase in the Khatyrka meteorite never observed previously in the laboratory.

PubMed

Bindi, Luca; Lin, Chaney; Ma, Chi; Steinhardt, Paul J

2016-12-08

We report the first occurrence of an icosahedral quasicrystal with composition Al 62.0(8) Cu 31.2(8) Fe 6.8(4) , outside the measured equilibrium stability field at standard pressure of the previously reported Al-Cu-Fe quasicrystal (Al x Cu y Fe z , with x between 61 and 64, y between 24 and 26, z between 12 and 13%). The new icosahedral mineral formed naturally and was discovered in the Khatyrka meteorite, a recently described CV3 carbonaceous chondrite that experienced shock metamorphism, local melting (with conditions exceeding 5 GPa and 1,200 °C in some locations), and rapid cooling, all of which likely resulted from impact-induced shock in space. This is the first example of a quasicrystal composition discovered in nature prior to being synthesized in the laboratory. The new composition was found in a grain that has a separate metal assemblage containing icosahedrite (Al 63 Cu 24 Fe 13 ), currently the only other known naturally occurring mineral with icosahedral symmetry (though the latter composition had already been observed in the laboratory prior to its discovery in nature). The chemistry of both the icosahedral phases was characterized by electron microprobe, and the rotational symmetry was confirmed by means of electron backscatter diffraction.

Analysis of boron carbides' electronic structure

NASA Technical Reports Server (NTRS)

Howard, Iris A.; Beckel, Charles L.

1986-01-01

The electronic properties of boron-rich icosahedral clusters were studied as a means of understanding the electronic structure of the icosahedral borides such as boron carbide. A lower bound was estimated on bipolaron formation energies in B12 and B11C icosahedra, and the associated distortions. While the magnitude of the distortion associated with bipolaron formation is similar in both cases, the calculated formation energies differ greatly, formation being much more favorable on B11C icosahedra. The stable positions of a divalent atom relative to an icosahedral borane was also investigated, with the result that a stable energy minimum was found when the atom is at the center of the borane, internal to the B12 cage. If incorporation of dopant atoms into B12 cages in icosahedral boride solids is feasible, novel materials might result. In addition, the normal modes of a B12H12 cluster, of the C2B10 cage in para-carborane, and of a B12 icosahedron of reduced (D sub 3d) symmetry, such as is found in the icosahedral borides, were calculated. The nature of these vibrational modes will be important in determining, for instance, the character of the electron-lattice coupling in the borides, and in analyzing the lattice contribution to the thermal conductivity.

Collisions in outer space produced an icosahedral phase in the Khatyrka meteorite never observed previously in the laboratory

PubMed Central

Bindi, Luca; Lin, Chaney; Ma, Chi; Steinhardt, Paul J.

2016-01-01

We report the first occurrence of an icosahedral quasicrystal with composition Al62.0(8)Cu31.2(8)Fe6.8(4), outside the measured equilibrium stability field at standard pressure of the previously reported Al-Cu-Fe quasicrystal (AlxCuyFez, with x between 61 and 64, y between 24 and 26, z between 12 and 13%). The new icosahedral mineral formed naturally and was discovered in the Khatyrka meteorite, a recently described CV3 carbonaceous chondrite that experienced shock metamorphism, local melting (with conditions exceeding 5 GPa and 1,200 °C in some locations), and rapid cooling, all of which likely resulted from impact-induced shock in space. This is the first example of a quasicrystal composition discovered in nature prior to being synthesized in the laboratory. The new composition was found in a grain that has a separate metal assemblage containing icosahedrite (Al63Cu24Fe13), currently the only other known naturally occurring mineral with icosahedral symmetry (though the latter composition had already been observed in the laboratory prior to its discovery in nature). The chemistry of both the icosahedral phases was characterized by electron microprobe, and the rotational symmetry was confirmed by means of electron backscatter diffraction. PMID:27929519

Structure of the Triatoma virus capsid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Squires, Gaëlle; Pous, Joan; Agirre, Jon

The crystallographic structure of TrV shows specific morphological and functional features that clearly distinguish it from the type species of the Cripavirus genus, CrPV. The members of the Dicistroviridae family are non-enveloped positive-sense single-stranded RNA (+ssRNA) viruses pathogenic to beneficial arthropods as well as insect pests of medical importance. Triatoma virus (TrV), a member of this family, infects several species of triatomine insects (popularly named kissing bugs), which are vectors for human trypanosomiasis, more commonly known as Chagas disease. The potential use of dicistroviruses as biological control agents has drawn considerable attention in the past decade, and several viruses ofmore » this family have been identified, with their targets covering honey bees, aphids and field crickets, among others. Here, the crystal structure of the TrV capsid at 2.5 Å resolution is reported, showing that as expected it is very similar to that of Cricket paralysis virus (CrPV). Nevertheless, a number of distinguishing structural features support the introduction of a new genus (Triatovirus; type species TrV) under the Dicistroviridae family. The most striking differences are the absence of icosahedrally ordered VP4 within the infectious particle and the presence of prominent projections that surround the fivefold axis. Furthermore, the structure identifies a second putative autoproteolytic DDF motif in protein VP3, in addition to the conserved one in VP1 which is believed to be responsible for VP0 cleavage during capsid maturation. The potential meaning of these new findings is discussed.« less

Identification of a Novel RNA Virus Lethal to Tilapia

PubMed Central

Eyngor, Marina; Zamostiano, Rachel; Kembou Tsofack, Japhette Esther; Berkowitz, Asaf; Bercovier, Hillel; Tinman, Simon; Lev, Menachem; Hurvitz, Avshalom; Galeotti, Marco; Eldar, Avi

2014-01-01

Tilapines are important for the sustainability of ecological systems and serve as the second most important group of farmed fish worldwide. Significant mortality of wild and cultured tilapia has been observed recently in Israel. The etiological agent of this disease, a novel RNA virus, is described here, and procedures allowing its isolation and detection are revealed. The virus, denominated tilapia lake virus (TiLV), was propagated in primary tilapia brain cells or in an E-11 cell line, and it induced a cytopathic effect at 5 to 10 days postinfection. Electron microscopy revealed enveloped icosahedral particles of 55 to 75 nm. Low-passage TiLV, injected intraperitoneally in tilapia, induced a disease resembling the natural disease, which typically presents with lethargy, ocular alterations, and skin erosions, with >80% mortality. Histological changes included congestion of the internal organs (kidneys and brain) with foci of gliosis and perivascular cuffing of lymphocytes in the brain cortex; ocular inflammation included endophthalmitis and cataractous changes of the lens. The cohabitation of healthy and diseased fish demonstrated that the disease is contagious and that mortalities (80 to 100%) occur within a few days. Fish surviving the initial mortality were immune to further TiLV infections, suggesting the mounting of a protective immune response. Screening cDNA libraries identified a TiLV-specific sequence, allowing the design of a PCR-based diagnostic test. This test enables the specific identification of TiLV in tilapines and should help control the spread of this virus worldwide. PMID:25232154

ULTRASTRUCTURAL CHARACTERIZATION OF THE LYTIC CYCLE OF AN INTRANUCLEAR VIRUS INFECTING THE DIATOM CHAETOCEROS CF. WIGHAMII(BACILLARIOPHYCEAE) FROM CHESAPEAKE BAY, USA(1).

PubMed

Eissler, Yoanna; Wang, Kui; Chen, Feng; Eric Wommack, K; Wayne Coats, D

2009-08-01

Numerous microalgal species are infected by viruses that have the potential to control phytoplankton dynamics by reducing host populations, preventing bloom formation, or causing the collapse of blooms. Here we describe a virus infecting the diatom Chaetoceros cf. wighamii Brightw. from the Chesapeake Bay. To characterize the morphology and lytic cycle of this virus, we conducted a time-course experiment, sampling every 4 h over 72 h following viral inoculation. In vivo fluorescence began to decline 16 h after inoculation and was reduced to <19% of control cultures by the end of experiment. TEM confirmed infection within the first 8 h of inoculation, as indicated by the presence of virus-like particles (VLP) in the nuclei. VLP were present in two different arrangements: rod-like structures that appeared in cross-section as paracrystalline arrays of hexagonal-shaped profiles measuring 12 ± 2 nm in diameter and uniformly electron-dense hexagonal-shaped particles measuring ∼ 22-28 nm in diameter. Nuclei containing paracrystalline arrays were most prevalent early in the infection cycle, while cells containing VLP increased and then declined toward the end of the cycle. The proportion of nuclei containing both paracrystalline arrays and VLP remained relatively constant. This pattern suggests that rod-like paracrystalline arrays fragmented to produce icosahedral VLP. C. cf. wighamii nuclear inclusion virus (CwNIV) is characterized by a high burst size (averaged 26,400 viruses per infected cell) and fast generation time that could have ecological implications on C. cf. wighamii population control. © 2009 Phycological Society of America.

Pseudo-icosahedral Cr 55 Al 232 - δ as a high-temperature protective material

DOE PAGES

Rosa, R.; Bhattacharya, S.; Pabla, J.; ...

2018-03-19

In this paper, we report here a course of basic research into the potential suitability of a pseudo-icosahedral Cr aluminide as a material for high temperature protective coatings. Cr 55Al 232-δ [δ = 2.70(6)] exhibits high hardness at room temperature as well as low thermal conductivity and excellent oxidation resistance at 973 K, with an oxidation rate comparable to those of softer, denser benchmark materials. Lastly, the origin of these promising properties can be traced to competing long-range and short-range symmetries within the pseudo-icosahedral crystal structure, suggesting new criteria for future materials research.

Pseudo-icosahedral Cr 55 Al 232 - δ as a high-temperature protective material

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosa, R.; Bhattacharya, S.; Pabla, J.

In this paper, we report here a course of basic research into the potential suitability of a pseudo-icosahedral Cr aluminide as a material for high temperature protective coatings. Cr 55Al 232-δ [δ = 2.70(6)] exhibits high hardness at room temperature as well as low thermal conductivity and excellent oxidation resistance at 973 K, with an oxidation rate comparable to those of softer, denser benchmark materials. Lastly, the origin of these promising properties can be traced to competing long-range and short-range symmetries within the pseudo-icosahedral crystal structure, suggesting new criteria for future materials research.

Description of an as yet unclassified DNA virus from diseased Cyprinus carpio species.

PubMed

Hutoran, Marina; Ronen, Ariel; Perelberg, Ayana; Ilouze, Maya; Dishon, Arnon; Bejerano, Izhak; Chen, Nissim; Kotler, Moshe

2005-02-01

Numerous deaths of koi and common carp (Cyprinus carpio) were observed on many farms throughout Israel, resulting in severe financial losses. The lethal viral disease observed is highly contagious and extremely virulent, but morbidity and mortality are restricted to koi and common carp populations. Diseased fish exhibit fatigue and gasping movements in shallow water. Infected fish had interstitial nephritis and gill necrosis as well as petechial hemorrhages in the liver and other symptoms that were not consistent with viral disease, suggesting a secondary infection. Here we report the isolation of carp nephritis and gill necrosis virus (CNGV), which is the etiologic agent of this disease. The virus propagates and induces severe cytopathic effects by 5 days postinfection in fresh koi or carp fin cell cultures (KFC and CFC, respectively), but not in epithelioma papillosum cyprini cells. The virus harvested from KFC cultures induced the same clinical signs, with a mortality of 75 to 95%, upon inoculation into naive koi and common carp. Using PCR, we provide final proof that the isolated virus is indeed the etiologic agent of food and ornamental carp mortalities in fish husbandry. Electron microscopy revealed viral cores with icosahedral morphology of 100 to 110 nm that resembled herpesviruses. Electron micrographs of purified pelleted CNGV sections, together with viral sensitivities to ether and Triton X-100, suggested that it is an enveloped virus. However, the genome of the isolated virus is a double-stranded DNA (dsDNA) molecule of 270 to 290 kbp, which is larger than known herpesviruses. The viral DNA seems highly divergent and bears only small fragments (16 to 45 bp) that are similar to the genomes of several DNA viruses. Nevertheless, amino acid sequences encoded by CNGV DNA fragments bear similarities primarily to members of the Poxviridae and Herpesviridae and to other large dsDNA viruses. We suggest, therefore, that the etiologic agent of this disease may represent an as yet unclassified virus species that is endemic in C. carpio (carp).

Description of an as Yet Unclassified DNA Virus from Diseased Cyprinus carpio Species

PubMed Central

Hutoran, Marina; Ronen, Ariel; Perelberg, Ayana; Ilouze, Maya; Dishon, Arnon; Bejerano, Izhak; Chen, Nissim; Kotler, Moshe

2005-01-01

Numerous deaths of koi and common carp (Cyprinus carpio) were observed on many farms throughout Israel, resulting in severe financial losses. The lethal viral disease observed is highly contagious and extremely virulent, but morbidity and mortality are restricted to koi and common carp populations. Diseased fish exhibit fatigue and gasping movements in shallow water. Infected fish had interstitial nephritis and gill necrosis as well as petechial hemorrhages in the liver and other symptoms that were not consistent with viral disease, suggesting a secondary infection. Here we report the isolation of carp nephritis and gill necrosis virus (CNGV), which is the etiologic agent of this disease. The virus propagates and induces severe cytopathic effects by 5 days postinfection in fresh koi or carp fin cell cultures (KFC and CFC, respectively), but not in epithelioma papillosum cyprini cells. The virus harvested from KFC cultures induced the same clinical signs, with a mortality of 75 to 95%, upon inoculation into naive koi and common carp. Using PCR, we provide final proof that the isolated virus is indeed the etiologic agent of food and ornamental carp mortalities in fish husbandry. Electron microscopy revealed viral cores with icosahedral morphology of 100 to 110 nm that resembled herpesviruses. Electron micrographs of purified pelleted CNGV sections, together with viral sensitivities to ether and Triton X-100, suggested that it is an enveloped virus. However, the genome of the isolated virus is a double-stranded DNA (dsDNA) molecule of 270 to 290 kbp, which is larger than known herpesviruses. The viral DNA seems highly divergent and bears only small fragments (16 to 45 bp) that are similar to the genomes of several DNA viruses. Nevertheless, amino acid sequences encoded by CNGV DNA fragments bear similarities primarily to members of the Poxviridae and Herpesviridae and to other large dsDNA viruses. We suggest, therefore, that the etiologic agent of this disease may represent an as yet unclassified virus species that is endemic in C. carpio (carp). PMID:15681400

Diphosphine-protected ultrasmall gold nanoclusters: opened icosahedral Au 13 and heart-shaped Au 8 clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Shan-Shan; Feng, Lei; Senanayake, Ravithree D.

Two ultrasmall gold clusters, Au 13 and Au 8 , were identified as a distorted I h icosahedral Au 13 and edge-shared “core + 4 exo ” structure Au 8 S 2 cores, respectively. They showed interesting luminescence and electrochemical properties.

Diphosphine-protected ultrasmall gold nanoclusters: opened icosahedral Au 13 and heart-shaped Au 8 clusters

DOE PAGES

Zhang, Shan-Shan; Feng, Lei; Senanayake, Ravithree D.; ...

2018-01-01

Two ultrasmall gold clusters, Au 13 and Au 8 , were identified as a distorted I h icosahedral Au 13 and edge-shared “core + 4 exo ” structure Au 8 S 2 cores, respectively. They showed interesting luminescence and electrochemical properties.

Structural transitions in Cowpea chlorotic mottle virus (CCMV)

NASA Astrophysics Data System (ADS)

Liepold, Lars O.; Revis, Jennifer; Allen, Mark; Oltrogge, Luke; Young, Mark; Douglas, Trevor

2005-12-01

Viral capsids act as molecular containers for the encapsulation of genomic nucleic acid. These protein cages can also be used as constrained reaction vessels for packaging and entrapment of synthetic cargos. The icosahedral Cowpea chlorotic mottle virus (CCMV) is an excellent model for understanding the encapsulation and packaging of both genomic and synthetic materials. High-resolution structural information of the CCMV capsid has been invaluable for evaluating structure-function relationships in the assembled capsid but does not allow insight into the capsid dynamics. The dynamic nature of the CCMV capsid might play an important role in the biological function of the virus. The CCMV capsid undergoes a pH and metal ion dependent reversible structural transition where 60 separate pores in the capsid open or close, exposing the interior of the protein cage to the bulk medium. In addition, the highly basic N-terminal domain of the capsid, which is disordered in the crystal structure, plays a significant role in packaging the viral cargo. Interestingly, in limited proteolysis and mass spectrometry experiments the N-terminal domain is the first part of the subunit to be cleaved, confirming its dynamic nature. Based on our fundamental understanding of the capsid dynamics in CCMV, we have utilized these aspects to direct packaging of a range of synthetic materials including drugs and inorganic nanoparticles.

RNA encapsidation by SV40-derived nanoparticles follows a rapid two-state mechanism

PubMed Central

Kler, Stanislav; Asor, Roi; Li, Chenglei; Ginsburg, Avi; Harries, Daniel; Oppenheim, Ariella; Zlotnick, Adam; Raviv, Uri

2012-01-01

Remarkably, uniform virus-like particles self-assemble in a process that appears to follow a rapid kinetic mechanism. The mechanisms by which spherical viruses assemble from hundreds of capsid proteins around nucleic acid, however, are yet unresolved. Using Time-Resolved Small-Angle X-ray Scattering (TR-SAXS) we have been able to directly visualize SV40 VP1 pentamers encapsidating short RNA molecules (500 mers). This assembly process yields T = 1 icosahedral particles comprised of 12 pentamers and one RNA molecule. The reaction is nearly 1/3 complete within 35 milliseconds, following a two–state kinetic process with no detectable intermediates. Theoretical analysis of kinetics, using a master equation, shows that the assembly process nucleates at the RNA and continues by a cascade of elongation reactions in which one VP1 pentamer is added at a time, with a rate of approximately 109 M−1 s−1. The reaction is highly robust and faster than the predicted diffusion limit. The emerging molecular mechanism, which appears to be general to viruses that assemble around nucleic acids, implicates long-ranged electrostatic interactions. The model proposes that the growing nucleo-protein complex acts as an electrostatic antenna that attracts other capsid subunits for the encapsidation process. PMID:22329660

Direct typing of Canine parvovirus (CPV) from infected dog faeces by rapid mini sequencing technique.

PubMed

V, Pavana Jyothi; S, Akila; Selvan, Malini K; Naidu, Hariprasad; Raghunathan, Shwethaa; Kota, Sathish; Sundaram, R C Raja; Rana, Samir Kumar; Raj, G Dhinakar; Srinivasan, V A; Mohana Subramanian, B

2016-12-01

Canine parvovirus (CPV) is a non-enveloped single stranded DNA virus with an icosahedral capsid. Mini-sequencing based CPV typing was developed earlier to detect and differentiate all the CPV types and FPV in a single reaction. This technique was further evaluated in the present study by performing the mini-sequencing directly from fecal samples which avoided tedious virus isolation steps by cell culture system. Fecal swab samples were collected from 84 dogs with enteritis symptoms, suggestive of parvoviral infection from different locations across India. Seventy six of these samples were positive by PCR; the subsequent mini-sequencing reaction typed 74 of them as type 2a virus, and 2 samples as type 2b. Additionally, 25 of the positive samples were typed by cycle sequencing of PCR products. Direct CPV typing from fecal samples using mini-sequencing showed 100% correlation with CPV typing by cycle sequencing. Moreover, CPV typing was achieved by mini-sequencing even with faintly positive PCR amplicons which was not possible by cycle sequencing. Therefore, the mini-sequencing technique is recommended for regular epidemiological follow up of CPV types, since the technique is rapid, highly sensitive and high capacity method for CPV typing. Copyright © 2016. Published by Elsevier B.V.

A Vertically Flow-Following, Icosahedral Grid Model for Medium-Range and Seasonal Prediction. Part 1: Model Description

NASA Technical Reports Server (NTRS)

Bleck, Rainer; Bao, Jian-Wen; Benjamin, Stanley G.; Brown, John M.; Fiorino, Michael; Henderson, Thomas B.; Lee, Jin-Luen; MacDonald, Alexander E.; Madden, Paul; Middlecoff, Jacques;

Structure of Penaeus stylirostris Densovirus, a Shrimp Pathogen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaufmann, Bärbel; Bowman, Valorie D.; Li, Yi

Penaeus stylirostris densovirus (PstDNV), a pathogen of penaeid shrimp, causes significant damage to farmed and wild shrimp populations. In contrast to other parvoviruses, PstDNV probably has only one type of capsid protein that lacks the phospholipase A2 activity that has been implicated as a requirement during parvoviral host cell infection. The structure of recombinant virus-like particles, composed of 60 copies of the 37.5-kDa coat protein, the smallest parvoviral capsid protein reported thus far, was determined to 2.5-{angstrom} resolution by X-ray crystallography. The structure represents the first near-atomic resolution structure within the genus Brevidensovirus. The capsid protein has a {beta}-barrel 'jellymore » roll' motif similar to that found in many icosahedral viruses, including other parvoviruses. The N-terminal portion of the PstDNV coat protein adopts a 'domain-swapped' conformation relative to its twofold-related neighbor similar to the insect parvovirus Galleria mellonella densovirus (GmDNV) but in stark contrast to vertebrate parvoviruses. However, most of the surface loops have little structural resemblance to any of the known parvoviral capsid proteins.« less

Intrinsically-disordered N-termini in human parechovirus 1 capsid proteins bind encapsidated RNA.

PubMed

Shakeel, Shabih; Evans, James D; Hazelbaker, Mark; Kao, C Cheng; Vaughan, Robert C; Butcher, Sarah J

2018-04-11

Human parechoviruses (HPeV) are picornaviruses with a highly-ordered RNA genome contained within icosahedrally-symmetric capsids. Ordered RNA structures have recently been shown to interact with capsid proteins VP1 and VP3 and facilitate virus assembly in HPeV1. Using an assay that combines reversible cross-linking, RNA affinity purification and peptide mass fingerprinting (RCAP), we mapped the RNA-interacting regions of the capsid proteins from the whole HPeV1 virion in solution. The intrinsically-disordered N-termini of capsid proteins VP1 and VP3, and unexpectedly, VP0, were identified to interact with RNA. Comparing these results to those obtained using recombinantly-expressed VP0 and VP1 confirmed the virion binding regions, and revealed unique RNA binding regions in the isolated VP0 not previously observed in the crystal structure of HPeV1. We used RNA fluorescence anisotropy to confirm the RNA-binding competency of each of the capsid proteins' N-termini. These findings suggests that dynamic interactions between the viral RNA and the capsid proteins modulate virus assembly, and suggest a novel role for VP0.

Transmission electron microscopy in molecular structural biology: A historical survey.

PubMed

Harris, J Robin

2015-09-01

In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

Isolation of a reovirus from coho salmon (Oncorhynchus kisutch) in Oregon, USA

USGS Publications Warehouse

Winton, J.R.; Arakawa, C.N.; Lannan, C.N.; Fryer, J.L.

1989-01-01

Reoviruses isolated from aquatic animals share certain common characteristics: (1) a typical reovirus-like morphology which shows an icosahedral particle with a double capsid that is approximately 75 nm in diameter; (2) a genome with eleven segments of double-stranded RNA (dsRNA) distributed as three large, three medium and five small segments with a total molecular weight of approximately 15 x 106; (3) a virion composed of five major and several minor structural proteins that range in molecular weight from 32,000 to 137,000; and (4) form plaque-like syncytia in monolayer cultures of fish cells. Intact virus particles have buoyant densities in CsCl of 1.34 to 1.36 g/ml. The viruses have been isolated from fish and shellfish collected in both the marine and freshwater environments and will replicate in several fish cell lines (Plumb et al., 1979; Meyers and Hirai, 1980; Winton et al., 1981; Nagabayashi and Mori, 1983; Hedrick et al., 1984; Chen and Jiang, 1984). The original four aquatic reovirus isolates have been compared by Winton et al., 1987.

Atomic clusters and atomic surfaces in icosahedral quasicrystals.

PubMed

Quiquandon, Marianne; Portier, Richard; Gratias, Denis

2014-05-01

This paper presents the basic tools commonly used to describe the atomic structures of quasicrystals with a specific focus on the icosahedral phases. After a brief recall of the main properties of quasiperiodic objects, two simple physical rules are discussed that lead one to eventually obtain a surprisingly small number of atomic structures as ideal quasiperiodic models for real quasicrystals. This is due to the fact that the atomic surfaces (ASs) used to describe all known icosahedral phases are located on high-symmetry special points in six-dimensional space. The first rule is maximizing the density using simple polyhedral ASs that leads to two possible sets of ASs according to the value of the six-dimensional lattice parameter A between 0.63 and 0.79 nm. The second rule is maximizing the number of complete orbits of high symmetry to construct as large as possible atomic clusters similar to those observed in complex intermetallic structures and approximant phases. The practical use of these two rules together is demonstrated on two typical examples of icosahedral phases, i-AlMnSi and i-CdRE (RE = Gd, Ho, Tm).

A stretch of 11 amino acids in the betaB-betaC loop of the coat protein of grapevine fanleaf virus is essential for transmission by the nematode Xiphinema index.

PubMed

Schellenberger, Pascale; Andret-Link, Peggy; Schmitt-Keichinger, Corinne; Bergdoll, Marc; Marmonier, Aurélie; Vigne, Emmanuelle; Lemaire, Olivier; Fuchs, Marc; Demangeat, Gérard; Ritzenthaler, Christophe

2010-08-01

Grapevine fanleaf virus (GFLV) and Arabis mosaic virus (ArMV) from the genus Nepovirus, family Secoviridae, cause a severe degeneration of grapevines. GFLV and ArMV have a bipartite RNA genome and are transmitted specifically by the ectoparasitic nematodes Xiphinema index and Xiphinema diversicaudatum, respectively. The transmission specificity of both viruses maps to their respective RNA2-encoded coat protein (CP). To further delineate the GFLV CP determinants of transmission specificity, three-dimensional (3D) homology structure models of virions and CP subunits were constructed based on the crystal structure of Tobacco ringspot virus, the type member of the genus Nepovirus. The 3D models were examined to predict amino acids that are exposed at the external virion surface, highly conserved among GFLV isolates but divergent between GFLV and ArMV. Five short amino acid stretches that matched these topographical and sequence conservation criteria were selected and substituted in single and multiple combinations by their ArMV counterparts in a GFLV RNA2 cDNA clone. Among the 21 chimeric RNA2 molecules engineered, transcripts of only three of them induced systemic plant infection in the presence of GFLV RNA1. Nematode transmission assays of the three viable recombinant viruses showed that swapping a stretch of (i) 11 residues in the betaB-betaC loop near the icosahedral 3-fold axis abolished transmission by X. index but was insufficient to restore transmission by X. diversicaudatum and (ii) 7 residues in the betaE-alphaB loop did not interfere with transmission by the two Xiphinema species. This study provides new insights into GFLV CP determinants of nematode transmission.

Immunodominance and Functional Activities of Antibody Responses to Inactivated West Nile Virus and Recombinant Subunit Vaccines in Mice▿

PubMed Central

Zlatkovic, Juergen; Stiasny, Karin; Heinz, Franz X.

2011-01-01

Factors controlling the dominance of antibody responses to specific sites in viruses and/or protein antigens are ill defined but can be of great importance for the induction of potent immune responses to vaccines. West Nile virus and other related important human-pathogenic flaviviruses display the major target of neutralizing antibodies, the E protein, in an icosahedral shell at the virion surface. Potent neutralizing antibodies were shown to react with the upper surface of domain III (DIII) of this protein. Using the West Nile virus system, we conducted a study on the immunodominance and functional quality of E-specific antibody responses after immunization of mice with soluble protein E (sE) and isolated DIII in comparison to those after immunization with inactivated whole virions. With both virion and sE, the neutralizing response was dominated by DIII-specific antibodies, but the functionality of these antibodies was almost four times higher after virion immunization. Antibodies induced by the isolated DIII had an at least 15-fold lower specific neutralizing activity than those induced by the virion, and only 50% of these antibodies were able to bind to virus particles. Our results suggest that immunization with the tightly packed E in virions focuses the DIII antibody response to the externally exposed sites of this domain which are the primary targets for virus neutralization, different from sE and isolated DIII, which also display protein surfaces that are cryptic in the virion. Despite its low potency for priming, DIII was an excellent boosting antigen, suggesting novel vaccination strategies that strengthen and focus the antibody response to critical neutralizing sites in DIII. PMID:21147919

Identification of a novel RNA virus lethal to tilapia.

PubMed

Eyngor, Marina; Zamostiano, Rachel; Kembou Tsofack, Japhette Esther; Berkowitz, Asaf; Bercovier, Hillel; Tinman, Simon; Lev, Menachem; Hurvitz, Avshalom; Galeotti, Marco; Bacharach, Eran; Eldar, Avi

2014-12-01

Tilapines are important for the sustainability of ecological systems and serve as the second most important group of farmed fish worldwide. Significant mortality of wild and cultured tilapia has been observed recently in Israel. The etiological agent of this disease, a novel RNA virus, is described here, and procedures allowing its isolation and detection are revealed. The virus, denominated tilapia lake virus (TiLV), was propagated in primary tilapia brain cells or in an E-11 cell line, and it induced a cytopathic effect at 5 to 10 days postinfection. Electron microscopy revealed enveloped icosahedral particles of 55 to 75 nm. Low-passage TiLV, injected intraperitoneally in tilapia, induced a disease resembling the natural disease, which typically presents with lethargy, ocular alterations, and skin erosions, with >80% mortality. Histological changes included congestion of the internal organs (kidneys and brain) with foci of gliosis and perivascular cuffing of lymphocytes in the brain cortex; ocular inflammation included endophthalmitis and cataractous changes of the lens. The cohabitation of healthy and diseased fish demonstrated that the disease is contagious and that mortalities (80 to 100%) occur within a few days. Fish surviving the initial mortality were immune to further TiLV infections, suggesting the mounting of a protective immune response. Screening cDNA libraries identified a TiLV-specific sequence, allowing the design of a PCR-based diagnostic test. This test enables the specific identification of TiLV in tilapines and should help control the spread of this virus worldwide. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

pH-Induced Stability Switching of the Bacteriophage HK97 Maturation Pathway

PubMed Central

2015-01-01

Many viruses undergo large-scale conformational changes during their life cycles. Blocking the transition from one stage of the life cycle to the next is an attractive strategy for the development of antiviral compounds. In this work, we have constructed an icosahedrally symmetric, low-energy pathway for the maturation transition of bacteriophage HK97. By conducting constant-pH molecular dynamics simulations on this pathway, we identify which residues are contributing most significantly to shifting the stability between the states along the pathway under differing pH conditions. We further analyze these data to establish the connection between critical residues and important structural motifs which undergo reorganization during maturation. We go on to show how DNA packaging can induce spontaneous reorganization of the capsid during maturation. PMID:24495192

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xing, L.; Wall, J.; Li, T.-C.

Hepatitis E virus (HEV) induces acute hepatitis in humans with a high fatality rate in pregnant women. There is a need for anti-HEV research to understand the assembly process of HEV native capsid. Here, we produced a large virion-sized and a small T=1 capsid by expressing the HEV capsid protein in insect cells with and without the N-terminal 111 residues, respectively, for comparative structural analysis. The virion-sized capsid demonstrates a T=3 icosahedral lattice and contains RNA fragment in contrast to the RNA-free T=1 capsid. However, both capsids shared common decameric organization. The in vitro assembly further demonstrated that HEV capsidmore » protein had the intrinsic ability to form decameric intermediate. Our data suggest that RNA binding is the extrinsic factor essential for the assembly of HEV native capsids.« less

Crystallography of decahedral and icosahedral particles. II - High symmetry orientations

NASA Technical Reports Server (NTRS)

Yang, C. Y.; Yacaman, M. J.; Heinemann, K.

1979-01-01

Based on the exact crystal structure of decahedral and icosahedral particles, high energy electron diffraction patterns and image profiles have been derived for various high symmetry orientations of the particles with respect to the incident beam. These results form a basis for the identification of small metal particle structures with advanced methods of transmission electron microscopy.

On the kinetic and equilibrium shapes of icosahedral Al 71Pd 19Mn 10 quasicrystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Senabulya, Nancy; Xiao, Xianghui; Han, Insung

The dynamics of growth and relaxation of icosahedral single quasicrystals in a liquid phase were investigated using in situ synchrotron-based X-ray tomography. Here, our 4D studies (i.e., space- and time-resolved) provide direct evidence that indicates the growth process of an Al 71Pd 19Mn 10 quasicrystal is governed predominantly by bulk transport rather than attachment kinetics. This work is in agreement with theoretical predictions, which show that the pentagonal dodecahedron is not the minimum energy structure in Al-Pd-Mn icosahedral quasicrystals, but merely a growth shape characterized by non-zero anisotropic velocity. This transient shape transforms into a truncated dodecahedral Archimedian polyhedron oncemore » equilibrium has been attained.« less

On the kinetic and equilibrium shapes of icosahedral Al 71Pd 19Mn 10 quasicrystals

DOE PAGES

Senabulya, Nancy; Xiao, Xianghui; Han, Insung; ...

2018-03-06

The dynamics of growth and relaxation of icosahedral single quasicrystals in a liquid phase were investigated using in situ synchrotron-based X-ray tomography. Here, our 4D studies (i.e., space- and time-resolved) provide direct evidence that indicates the growth process of an Al 71Pd 19Mn 10 quasicrystal is governed predominantly by bulk transport rather than attachment kinetics. This work is in agreement with theoretical predictions, which show that the pentagonal dodecahedron is not the minimum energy structure in Al-Pd-Mn icosahedral quasicrystals, but merely a growth shape characterized by non-zero anisotropic velocity. This transient shape transforms into a truncated dodecahedral Archimedian polyhedron oncemore » equilibrium has been attained.« less

Why are Buckyonions Round?

NASA Technical Reports Server (NTRS)

Bates, Kevin R.; Scuseria, Gustavo E.

1998-01-01

Multi-layered round carbon particles (onions) containing tens to hundreds of thousands of atoms form during electron irradiation of graphite. However. theoretical models or large icosahedral fullerenes predict highly faceted shapes for molecules with more than a few hundred atoms. This discrepancy in shape may be explained by the presence of defects during the formation of carbon onions. Here, we use the semi-empirical tight-binding method for carbon to simulate the incorporation of pentagon-heptagon defects on to the surface of large icosahedral fullerenes. We show a simple mechanism that results in energetically competitive derivative structures and a global change in molecular shape from faceted to round. Our results provide a plausible explanation of the apparent discrepancy between experimental observations or round buckyonions and theoretical predictions of faceted icosahedral fullerenes.

Tomato chocolate spot virus, a member of a new torradovirus species that causes a necrosis-associated disease of tomato in Guatemala.

PubMed

Batuman, O; Kuo, Y-W; Palmieri, M; Rojas, M R; Gilbertson, R L

2010-06-01

Tomatoes in Guatemala have been affected by a new disease, locally known as "mancha de chocolate" (chocolate spot). The disease is characterized by distinct necrotic spots on leaves, stems and petioles that eventually expand and cause a dieback of apical tissues. Samples from symptomatic plants tested negative for infection by tomato spotted wilt virus, tobacco streak virus, tobacco etch virus and other known tomato-infecting viruses. A virus-like agent was sap-transmitted from diseased tissue to Nicotiana benthamiana and, when graft-transmitted to tomato, this agent induced chocolate spot symptoms. This virus-like agent also was sap-transmitted to Datura stramonium and Nicotiana glutinosa, but not to a range of non-solanaceous indicator plants. Icosahedral virions approximately 28-30 nm in diameter were purified from symptomatic N. benthamiana plants. When rub-inoculated onto leaves of N. benthamiana plants, these virions induced symptoms indistinguishable from those in N. benthamiana plants infected with the sap-transmissible virus associated with chocolate spot disease. Tomatoes inoculated with sap or grafted with shoots from N. benthamiana plants infected with purified virions developed typical chocolate spot symptoms, consistent with this virus being the causal agent of the disease. Analysis of nucleic acids associated with purified virions of the chocolate-spot-associated virus, revealed a genome composed of two single-stranded RNAs of approximately 7.5 and approximately 5.1 kb. Sequence analysis of these RNAs revealed a genome organization similar to recently described torradoviruses, a new group of picorna-like viruses causing necrosis-associated diseases of tomatoes in Europe [tomato torrado virus (ToTV)] and Mexico [tomato apex necrosis virus (ToANV) and tomato marchitez virus (ToMarV)]. Thus, the approximately 7.5 kb and approximately 5.1 kb RNAs of the chocolate-spot-associated virus corresponded to the torradovirus RNA1 and RNA2, respectively; however, sequence comparisons revealed 64-83% identities with RNA1 and RNA2 sequences of ToTV, ToANV and ToMarV. Together, these results indicate that the chocolate-spot-associated virus is a member of a distinct torradovirus species and, thus, another member of the recently established genus Torradovirus in the family Secoviridae. The name tomato chocolate spot virus is proposed.

In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus.

PubMed

Dai, Xinghong; Li, Zhihai; Lai, Mason; Shu, Sara; Du, Yushen; Zhou, Z Hong; Sun, Ren

2017-01-05

Packaging of the genome into a protein capsid and its subsequent delivery into a host cell are two fundamental processes in the life cycle of a virus. Unlike double-stranded DNA viruses, which pump their genome into a preformed capsid, single-stranded RNA (ssRNA) viruses, such as bacteriophage MS2, co-assemble their capsid with the genome; however, the structural basis of this co-assembly is poorly understood. MS2 infects Escherichia coli via the host 'sex pilus' (F-pilus); it was the first fully sequenced organism and is a model system for studies of translational gene regulation, RNA-protein interactions, and RNA virus assembly. Its positive-sense ssRNA genome of 3,569 bases is enclosed in a capsid with one maturation protein monomer and 89 coat protein dimers arranged in a T = 3 icosahedral lattice. The maturation protein is responsible for attaching the virus to an F-pilus and delivering the viral genome into the host during infection, but how the genome is organized and delivered is not known. Here we describe the MS2 structure at 3.6 Å resolution, determined by electron-counting cryo-electron microscopy (cryoEM) and asymmetric reconstruction. We traced approximately 80% of the backbone of the viral genome, built atomic models for 16 RNA stem-loops, and identified three conserved motifs of RNA-coat protein interactions among 15 of these stem-loops with diverse sequences. The stem-loop at the 3' end of the genome interacts extensively with the maturation protein, which, with just a six-helix bundle and a six-stranded β-sheet, forms a genome-delivery apparatus and joins 89 coat protein dimers to form a capsid. This atomic description of genome-capsid interactions in a spherical ssRNA virus provides insight into genome delivery via the host sex pilus and mechanisms underlying ssRNA-capsid co-assembly, and inspires speculation about the links between nucleoprotein complexes and the origins of viruses.

Stochastic dynamics of virus capsid formation: direct versus hierarchical self-assembly

PubMed Central

2012-01-01

Background In order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually assume that the bonds leading to cluster formation have constant reactivity over the time course of assembly (direct assembly). In some cases, however, binding sites between the capsomers have been reported to be activated during the self-assembly process (hierarchical assembly). Results In order to study possible advantages of such hierarchical schemes for icosahedral virus capsid assembly, we use Brownian dynamics simulations of a patchy particle model that allows us to switch binding sites on and off during assembly. For T1 viruses, we implement a hierarchical assembly scheme where inter-capsomer bonds become active only if a complete pentamer has been assembled. We find direct assembly to be favorable for reversible bonds allowing for repeated structural reorganizations, while hierarchical assembly is favorable for strong bonds with small dissociation rate, as this situation is less prone to kinetic trapping. However, at the same time it is more vulnerable to monomer starvation during the final phase. Increasing the number of initial monomers does have only a weak effect on these general features. The differences between the two assembly schemes become more pronounced for more complex virus geometries, as shown here for T3 viruses, which assemble through homogeneous pentamers and heterogeneous hexamers in the hierarchical scheme. In order to complement the simulations for this more complicated case, we introduce a master equation approach that agrees well with the simulation results. Conclusions Our analysis shows for which molecular parameters hierarchical assembly schemes can outperform direct ones and suggests that viruses with high bond stability might prefer hierarchical assembly schemes. These insights increase our physical understanding of an essential biological process, with many interesting potential applications in medicine and materials science. PMID:23244740

Analysis of pulsed-neutron powder diffraction patterns of the icosahedral quasicrystals Pd3Siu and AlCuLiMg (three alloys) as twinned cubic crystals with large units.

PubMed Central

Pauling, L

1991-01-01

The low-Q peaks on three pulsed-neutron powder patterns (total, U differential, and Pd differential) of the icosahedral quasicrystal Pd3SiU have been indexed on the basis of an assumed cubic structure of the crystals that by icosahedral twinning form the quasicrystal. The primitive unit cube is found to have edge length 56.20 A and to contain approximately 12,100 atoms. Similar analyses of pulsed-neutron patterns of Al55Cu10Li35, Al55Cu10Li30Mg5, and Al510Cu125Li235Mg130 give values of the cube edge length 58.3, 58.5, and 58.4 A, respectively, with approximately 11,650 atoms in the unit cube. It is suggested that the unit contains eight complexes in the beta-W positions, plus some small interstitial groups of atoms, with each complex consisting of a centered icosahedron of 13 clusters, each of 116 atoms with the icosahedral structure found in the body-centered cubic crystal Mg32(Al,Zn)49. PMID:11607201

Analysis of pulsed-neutron powder diffraction patterns of the icosahedral quasicrystals Pd3Siu and AlCuLiMg (three alloys) as twinned cubic crystals with large units.

PubMed

Pauling, L

1991-08-01

The low-Q peaks on three pulsed-neutron powder patterns (total, U differential, and Pd differential) of the icosahedral quasicrystal Pd3SiU have been indexed on the basis of an assumed cubic structure of the crystals that by icosahedral twinning form the quasicrystal. The primitive unit cube is found to have edge length 56.20 A and to contain approximately 12,100 atoms. Similar analyses of pulsed-neutron patterns of Al55Cu10Li35, Al55Cu10Li30Mg5, and Al510Cu125Li235Mg130 give values of the cube edge length 58.3, 58.5, and 58.4 A, respectively, with approximately 11,650 atoms in the unit cube. It is suggested that the unit contains eight complexes in the beta-W positions, plus some small interstitial groups of atoms, with each complex consisting of a centered icosahedron of 13 clusters, each of 116 atoms with the icosahedral structure found in the body-centered cubic crystal Mg32(Al,Zn)49.

Controlling the Growth of Au on Icosahedral Seeds of Pd by Manipulating the Reduction Kinetics

DOE PAGES

Lv, Tian; Yang, Xuan; Zheng, Yiqun; ...

2016-03-29

This article reports a systematic study of how Au atoms nucleate and grow on Pd icosahedral seeds with a multiply twinned structure. By manipulating the reduction kinetics, we obtained Pd–Au bimetallic nanocrystals with two distinct shapes and structures. Specifically, Pd@Au core–shell icosahedra were formed when a relatively fast reduction rate was used for the HAuCl 4 precursor. At a slow reduction rate, in contrast, the nucleation and growth of Au atoms were mainly confined to one of the vertices of a Pd icosahedral seed, resulting in the formation of a Au icosahedron by sharing five adjacent faces with the Pdmore » seed. The same growth pattern was observed for Pd icosahedral seeds with both sizes of 32 and 20 nm. Also, we have also investigated the effects of other kinetic parameters, including the concentration of reducing agent and reaction temperature, on the growth pathway undertaken by the Au atoms. In conclusion, we believe that the mechanistic insights obtained from this study can be extended to other systems, including the involvement of different metals and/or seeds with different morphologies.« less

Structural evolutions and hereditary characteristics of icosahedral nano-clusters formed in Mg70Zn30 alloys during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liang, Yong-Chao; Liu, Rang-Su; Xie, Quan; Tian, Ze-An; Mo, Yun-Fei; Zhang, Hai-Tao; Liu, Hai-Rong; Hou, Zhao-Yang; Zhou, Li-Li; Peng, Ping

2017-02-01

To investigate the structural evolution and hereditary mechanism of icosahedral nano-clusters formed during rapid solidification, a molecular dynamics (MD) simulation study has been performed for a system consisting of 107 atoms of liquid Mg70Zn30 alloy. Adopting Honeycutt-Anderson (HA) bond-type index method and cluster type index method (CTIM-3) to analyse the microstructures in the system it is found that for all the nano-clusters including 2~8 icosahedral clusters in the system, there are 62 kinds of geometrical structures, and those can be classified, by the configurations of the central atoms of basic clusters they contained, into four types: chain-like, triangle-tailed, quadrilateral-tailed and pyramidal-tailed. The evolution of icosahedral nano-clusters can be conducted by perfect heredity and replacement heredity, and the perfect heredity emerges when temperature is slightly less than Tm then increase rapidly and far exceeds the replacement heredity at Tg; while for the replacement heredity, there are three major modes: replaced by triangle (3-atoms), quadrangle (4-atoms) and pentagonal pyramid (6-atoms), rather than by single atom step by step during rapid solidification processes.

Au13(8e): A secondary block for describing a special group of liganded gold clusters containing icosahedral Au13 motifs

NASA Astrophysics Data System (ADS)

Xu, Wen Wu; Zeng, Xiao Cheng; Gao, Yi

2017-05-01

A grand unified model (GUM) has been proposed recently to understand structure anatomy and evolution of liganded gold clusters. In this work, besides the two types of elementary blocks (triangular Au3(2e) and tetrahedral Au4(2e)), we introduce a secondary block, namely, the icosahedral Au13 with 8e valence electrons, noted as Au13(8e). Using this secondary block, structural anatomy and evolution of a special group of liganded gold nanoclusters containing icosahedral Au13 motifs can be conveniently analyzed. In addition, a new ligand-protected cluster Au49(PR3)10(SR)15Cl2 is predicted to exhibit high chemical and thermal stability, suggesting likelihood of its synthesis in the laboratory.

Why Are Buckyonions Round?

NASA Technical Reports Server (NTRS)

Bates, Kevin R.; Scuseria, Gustavo E.

1997-01-01

Multi-layered round carbon particles (onions) containing tens to hundreds of thousands of atoms form during electron irradiation of graphite carbon. However, theoretical models of large icosahedral fullerenes predict highly faceted shapes for molecules with more than a few hundred atoms. This discrepancy in shape may be explained by the presence of defects during the formation of carbon onions. Here, we use the semi-empirical tight-binding method for carbon to simulate the incorporation of pentagon-heptagon defects on to the surface of large icosahedral fullerenes. We show a simple mechanism that results in energetically competitive derivative structures and a global change in molecular shape from faceted to round. Our results provide a plausible explanation of the apparent discrepancy between experimental observations of round buckyonions and theoretical predictions of faceted icosahedral fullerenes.

Dynamic stabilities of icosahedral-like clusters and their ability to form quasicrystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liang, Xiaogang; Hamid, Ilyar; Duan, Haiming, E-mail: dhm@xju.edu.cn

2016-06-15

The dynamic stabilities of the icosahedral-like clusters containing up to 2200 atoms are investigated for 15 metal elements. The clusters originate from five different initial structures (icosahedron, truncated decahedron, octahedron, closed-shell fragment of an HCP structure, and non-closed-shell fragment of an HCP structure). The obtained order of the dynamic stabilities of the icosahedral-like clusters can be assigned to three groups, from stronger to weaker, according to the size ranges involved: (Zr, Al, Ti) > (Cu, Fe, Co, Ni, Mg, Ag) > (Pb, Au, Pd, Pt, Rh, Ir), which correspond to the predicted formation ability of the quasicrystals. The differences ofmore » the sequences can be explained by analyzing the parameters of the Gupta-type many-body inter-atomic potentials.« less

Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes.

PubMed

Faulkner, Matthew; Rodriguez-Ramos, Jorge; Dykes, Gregory F; Owen, Siân V; Casella, Selene; Simpson, Deborah M; Beynon, Robert J; Liu, Lu-Ning

2017-08-03

Carboxysomes are proteinaceous organelles that play essential roles in enhancing carbon fixation in cyanobacteria and some proteobacteria. These self-assembling organelles encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase using a protein shell structurally resembling an icosahedral viral capsid. The protein shell serves as a physical barrier to protect enzymes from the cytosol and a selectively permeable membrane to mediate transport of enzyme substrates and products. The structural and mechanical nature of native carboxysomes remain unclear. Here, we isolate functional β-carboxysomes from the cyanobacterium Synechococcus elongatus PCC7942 and perform the first characterization of the macromolecular architecture and inherent physical mechanics of single β-carboxysomes using electron microscopy, atomic force microscopy (AFM) and proteomics. Our results illustrate that the intact β-carboxysome comprises three structural domains, a single-layered icosahedral shell, an inner layer and paracrystalline arrays of interior Rubisco. We also observe the protein organization of the shell and partial β-carboxysomes that likely serve as the β-carboxysome assembly intermediates. Furthermore, the topography and intrinsic mechanics of functional β-carboxysomes are determined in native conditions using AFM and AFM-based nanoindentation, revealing the flexible organization and soft mechanical properties of β-carboxysomes compared to rigid viruses. Our study provides new insights into the natural characteristics of β-carboxysome organization and nanomechanics, which can be extended to diverse bacterial microcompartments and are important considerations for the design and engineering of functional carboxysomes in other organisms to supercharge photosynthesis. It offers an approach for inspecting the structural and mechanical features of synthetic metabolic organelles and protein scaffolds in bioengineering.

Barley yellow dwarf virus: Luteoviridae or Tombusviridae?

PubMed

Miller, W Allen; Liu, Sijun; Beckett, Randy

2002-07-01

Summary Barley yellow dwarf virus (BYDV), the most economically important virus of small grains, features highly specialised relationships with its aphid vectors, a plethora of novel translation mechanisms mediated by long-distance RNA interactions, and an ambiguous taxonomic status. The structural and movement proteins of BYDV that confer aphid transmission and phloem-limitation properties resemble those of the Luteoviridae, the family in which BYDV is classified. In contrast, many genes and cis-acting signals involved in replication and gene expression most closely resemble those of the Tombusviridae. BYDV is in genus Luteovirus, family Luteoviridae. BYDV includes at least two serotypes or viruses: BYDV-PAV and BYDV-MAV. The former BYDV-RPV is now Cereal yellow dwarf virus-RPV (CYDV-RPV). CYDV is in genus Polerovirus, family Luteoviridae. Genus Luteovirus shares many features with family Tombusviridae. Physical properties: approximately 25 nm icosahedral (T = 3) virions. One major (22 kDa) and one minor (50-55 kDa) coat protein. 5.6-5.8 kb positive sense RNA genome with no 5'-cap and no poly(A) tail. Most grasses. Most important in oats, barley and wheat. Also infects maize and rice. Yellowing and dwarfing in barley, stunting in wheat; reddening, yellowing and blasting in oats. Some isolates cause leaf notching and curling. Key attractions: Model for the study of circulative transmission of aphid-transmitted viruses. Plethora of unusual translation mechanisms. Evidence of recombination in recent evolutionary history creates taxonomic ambiguity. Economically important virus of wheat, barley and oats, worldwide. Useful websites/meetings: International symposium: 'Barley Yellow Dwarf Disease: Recent Advances and Future Strategies', CIMMYT, El Batan, Mexico, 1-5 September 2002, http://www.cimmyt.cgiar.org/Research/wheat/Conf_BYD_02/invitation.htm http://www.cimmyt.org/Research/wheat/BYDVNEWS/htm/BYDVNEWS.htm Aphid transmission animation: http://www.ppws.vt.edu/~sforza/tmv/bydv_aph.html.

Preliminary crystallographic analysis of the major capsid protein P2 of the lipid-containing bacteriophage PM2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abrescia, Nicola G. A.; Kivelä, Hanna M.; Grimes, Jonathan M.

2005-08-01

The viral capsid protein P2 of bacteriophage PM2 has been crystallized. Preliminary X-ray analysis demonstrates the position and orientation of the two trimers in the asymmetric unit. PM2 (Corticoviridae) is a dsDNA bacteriophage which contains a lipid membrane beneath its icosahedral capsid. In this respect it resembles bacteriophage PRD1 (Tectiviridae), although it is not known whether the similarity extends to the detailed molecular architecture of the virus, for instance the fold of the major coat protein P2. Structural analysis of PM2 has been initiated and virus-derived P2 has been crystallized by sitting-nanodrop vapour diffusion. Crystals of P2 have been obtainedmore » in space group P2{sub 1}2{sub 1}2, with two trimers in the asymmetric unit and unit-cell parameters a = 171.1, b = 78.7, c = 130.1 Å. The crystals diffract to 4 Å resolution at the ESRF BM14 beamline (Grenoble, France) and the orientation of the non-crystallographic threefold axes, the spatial relationship between the two trimers and the packing of the trimers within the unit cell have been determined. The trimers form tightly packed layers consistent with the crystal morphology, possibly recapitulating aspects of the arrangement of subunits in the virus.« less

Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction.

PubMed

Pittman, Nikéa; Misseldine, Adam; Geilen, Lorena; Halder, Sujata; Smith, J Kennon; Kurian, Justin; Chipman, Paul; Janssen, Mandy; Mckenna, Robert; Baker, Timothy S; D'Abramo, Anthony; Cotmore, Susan; Tattersall, Peter; Agbandje-McKenna, Mavis

2017-10-30

LuIII, a protoparvovirus pathogenic to rodents, replicates in human mitotic cells, making it applicable for use to kill cancer cells. This virus group includes H-1 parvovirus (H-1PV) and minute virus of mice (MVM). However, LuIII displays enhanced oncolysis compared to H-1PV and MVM, a phenotype mapped to the major capsid viral protein 2 (VP2). This suggests that within LuIII VP2 are determinants for improved tumor lysis. To investigate this, the structure of the LuIII virus-like-particle was determined using single particle cryo-electron microscopy and image reconstruction to 3.17 Å resolution, and compared to the H-1PV and MVM structures. The LuIII VP2 structure, ordered from residue 37 to 587 (C-terminal), had the conserved VP topology and capsid morphology previously reported for other protoparvoviruses. This includes a core β-barrel and α-helix A, a depression at the icosahedral 2-fold and surrounding the 5-fold axes, and a single protrusion at the 3-fold axes. Comparative analysis identified surface loop differences among LuIII, H-1PV, and MVM at or close to the capsid 2- and 5-fold symmetry axes, and the shoulder of the 3-fold protrusions. The 2-fold differences cluster near the previously identified MVM sialic acid receptor binding pocket, and revealed potential determinants of protoparvovirus tumor tropism.

Porites white patch syndrome: associated viruses and disease physiology

NASA Astrophysics Data System (ADS)

Lawrence, S. A.; Davy, J. E.; Wilson, W. H.; Hoegh-Guldberg, O.; Davy, S. K.

2015-03-01

In recent decades, coral reefs worldwide have undergone significant changes in response to various environmental and anthropogenic impacts. Among the numerous causes of reef degradation, coral disease is one factor that is to a large extent still poorly understood. Here, we characterize the physiology of white patch syndrome (WPS), a disease affecting poritid corals on the Great Barrier Reef. WPS manifests as small, generally discrete patches of tissue discolouration. Physiological analysis revealed that chlorophyll a content was significantly lower in lesions than in healthy tissues, while host protein content remained constant, suggesting that host tissue is not affected by WPS. This was confirmed by transmission electron microscope (TEM) examination, which showed intact host tissue within lesions. TEM also revealed that Symbiodinium cells are lost from the host gastrodermis with no apparent harm caused to the surrounding host tissue. Also present in the electron micrographs were numerous virus-like particles (VLPs), in both coral and Symbiodinium cells. Small (<50 nm diameter) icosahedral VLPs were significantly more abundant in coral tissue taken from diseased colonies, and there was an apparent, but not statistically significant, increase in abundance of filamentous VLPs in Symbiodinium cells from diseased colonies. There was no apparent increase in prokaryotic or eukaryotic microbial abundance in diseased colonies. Taken together, these results suggest that viruses infecting the coral and/or its resident Symbiodinium cells may be the causative agents of WPS.

Structure of acidic pH dengue virus showing the fusogenic glycoprotein trimers.

PubMed

Zhang, Xinzheng; Sheng, Ju; Austin, S Kyle; Hoornweg, Tabitha E; Smit, Jolanda M; Kuhn, Richard J; Diamond, Michael S; Rossmann, Michael G

2015-01-01

Flaviviruses undergo large conformational changes during their life cycle. Under acidic pH conditions, the mature virus forms transient fusogenic trimers of E glycoproteins that engage the lipid membrane in host cells to initiate viral fusion and nucleocapsid penetration into the cytoplasm. However, the dynamic nature of the fusogenic trimer has made the determination of its structure a challenge. Here we have used Fab fragments of the neutralizing antibody DV2-E104 to stop the conformational change of dengue virus at an intermediate stage of the fusion process. Using cryo-electron microscopy, we show that in this intermediate stage, the E glycoproteins form 60 trimers that are similar to the predicted "open" fusogenic trimer. The structure of a dengue virus has been captured during the formation of fusogenic trimers. This was accomplished by binding Fab fragments of the neutralizing antibody DV2-E104 to the virus at neutral pH and then decreasing the pH to 5.5. These trimers had an "open" conformation, which is distinct from the "closed" conformation of postfusion trimers. Only two of the three E proteins within each spike are bound by a Fab molecule at domain III. Steric hindrance around the icosahedral 3-fold axes prevents binding of a Fab to the third domain III of each E protein spike. Binding of the DV2-E104 Fab fragments prevents domain III from rotating by about 130° to the postfusion orientation and thus precludes the stem region from "zipping" together the three E proteins along the domain II boundaries into the "closed" postfusion conformation, thus inhibiting fusion. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Visualizing Herpesvirus Procapsids in Living Cells.

PubMed

Maier, Oana; Sollars, Patricia J; Pickard, Gary E; Smith, Gregory A

2016-11-15

A complete understanding of herpesvirus morphogenesis requires studies of capsid assembly dynamics in living cells. Although fluorescent tags fused to the VP26 and pUL25 capsid proteins are available, neither of these components is present on the initial capsid assembly, the procapsid. To make procapsids accessible to live-cell imaging, we made a series of recombinant pseudorabies viruses that encoded green fluorescent protein (GFP) fused in frame to the internal capsid scaffold and maturation protease. One recombinant, a GFP-VP24 fusion, maintained wild-type propagation kinetics in vitro and approximated wild-type virulence in vivo The fusion also proved to be well tolerated in herpes simplex virus. Viruses encoding GFP-VP24, along with a traditional capsid reporter fusion (pUL25/mCherry), demonstrated that GFP-VP24 was a reliable capsid marker and revealed that the protein remained capsid associated following entry into cells and upon nuclear docking. These dual-fluorescent viruses made possible the discrimination of procapsids during infection and monitoring of capsid shell maturation kinetics. The results demonstrate the feasibility of imaging herpesvirus procapsids and their morphogenesis in living cells and indicate that the encapsidation machinery does not substantially help coordinate capsid shell maturation. The family Herpesviridae consists of human and veterinary pathogens that cause a wide range of diseases in their respective hosts. These viruses share structurally related icosahedral capsids that encase the double-stranded DNA (dsDNA) viral genome. The dynamics of capsid assembly and maturation have been inaccessible to examination in living cells. This study has overcome this technical hurdle and provides new insights into this fundamental stage of herpesvirus infection. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Classification of capped tubular viral particles in the family of Papovaviridae

NASA Astrophysics Data System (ADS)

Keef, T.; Taormina, A.; Twarock, R.

2006-04-01

A vital constituent of a virus is its protein shell, called the viral capsid, that encapsulates and hence provides protection for the viral genome. Viral capsids are usually spherical, and for a significant number of viruses they exhibit overall icosahedral symmetry. The corresponding surface lattices, that encode the locations of the capsid proteins and intersubunit bonds, can be modelled by viral tiling theory. It has been shown in vitro that under a variation of the experimental boundary conditions, such as the pH value and salt concentration, tubular particles may appear instead of, or in addition to, spherical ones. In order to develop models that describe the simultaneous assembly of both spherical and tubular variants, and hence study the possibility of triggering tubular malformations as a means of interference with the replication mechanism, viral tiling theory has to be extended to include tubular lattices with end caps. We focus here on the case of Papovaviridae, which play a distinguished role from the viral structural point of view as they correspond to all pentamer lattices, i.e. lattices formed from clusters of five protein subunits throughout. These results pave the way for a generalization of recently developed assembly models.

Crystal Structure of the Japanese Encephalitis Virus Envelope Protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luca, Vincent C.; AbiMansour, Jad; Nelson, Christopher A.

2012-03-13

Japanese encephalitis virus (JEV) is the leading global cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion and is the primary target of neutralizing antibodies. We have determined the 2.1-{angstrom} resolution crystal structure of the JEV E ectodomain refolded from bacterial inclusion bodies. The E protein possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies onto the structure reveals determinants that correspond to the domain I lateral ridge, fusion loop, domain III lateral ridge, and domain I-II hinge. While monomeric in solution, JEV E assembles as an antiparallel dimermore » in the crystal lattice organized in a highly similar fashion as seen in cryo-electron microscopy models of mature flavivirus virions. The dimer interface, however, is remarkably small and lacks many of the domain II contacts observed in other flavivirus E homodimers. In addition, uniquely conserved histidines within the JEV serocomplex suggest that pH-mediated structural transitions may be aided by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation in dimer structure and stability may significantly influence the assembly, receptor interaction, and uncoating of virions.« less

Crystal structure of the Japanese encephalitis virus envelope protein.

PubMed

Luca, Vincent C; AbiMansour, Jad; Nelson, Christopher A; Fremont, Daved H

2012-02-01

Japanese encephalitis virus (JEV) is the leading global cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion and is the primary target of neutralizing antibodies. We have determined the 2.1-Å resolution crystal structure of the JEV E ectodomain refolded from bacterial inclusion bodies. The E protein possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies onto the structure reveals determinants that correspond to the domain I lateral ridge, fusion loop, domain III lateral ridge, and domain I-II hinge. While monomeric in solution, JEV E assembles as an antiparallel dimer in the crystal lattice organized in a highly similar fashion as seen in cryo-electron microscopy models of mature flavivirus virions. The dimer interface, however, is remarkably small and lacks many of the domain II contacts observed in other flavivirus E homodimers. In addition, uniquely conserved histidines within the JEV serocomplex suggest that pH-mediated structural transitions may be aided by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation in dimer structure and stability may significantly influence the assembly, receptor interaction, and uncoating of virions.

Essential role of the unordered VP2 n-terminal domain of the parvovirus MVM capsid in nuclear assembly and endosomal enlargement of the virion fivefold channel for cell entry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanchez-Martinez, Cristina; Grueso, Esther; Carroll, Miles

The unordered N-termini of parvovirus capsid proteins (Nt) are translocated through a channel at the icosahedral five-fold axis to serve for virus traffick. Heterologous peptides were genetically inserted at the Nt of MVM to study their functional tolerance to manipulations. Insertion of a 5T4-single-chain antibody at VP2-Nt (2Nt) yielded chimeric capsid subunits failing to enter the nucleus. The VEGFR2-binding peptide (V1) inserted at both 2Nt and VP1-Nt efficiently assembled in virions, but V1 disrupted VP1 and VP2 entry functions. The VP2 defect correlated with restricted externalization of V1-2Nt out of the coat. The specific infectivity of MVM and wtVP-pseudotyped mosaicmore » MVM-V1 virions, upon heating and/or partial 2Nt cleavage, demonstrated that some 2Nt domains become intracellularly translocated out of the virus shell and cleaved to initiate entry. The V1 insertion defines a VP2-driven endosomal enlargement of the channel as an essential structural rearrangement performed by the MVM virion to infect.« less

Crystallography of decahedral and icosahedral particles. I - Geometry of twinning

NASA Technical Reports Server (NTRS)

Yang, C. Y.

1979-01-01

The crystal structure of the tetrahedral twins in multiply-twinned particles with decahedral and icosahedral point group symmetries has been examined and correlated with the face-centered cubic structure. Details on the crystal structure as well as the geometrical relationships among twins in each particle are presented. These crystallographic facts serve as a basis for the interpretation of small particle images obtained with advanced methods of transmission electron microscopy.

Crystal Structure of the Human Astrovirus Capsid Protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toh, Yukimatsu; Harper, Justin; Dryden, Kelly A.

Human astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. HAstV is a nonenveloped virus with a T=3 capsid and a positive-sense RNA genome. The capsid protein (CP) of HAstV is synthesized as a 90-kDa precursor (VP90) that can be divided into three linear domains: a conserved N-terminal domain, a hypervariable domain, and an acidic C-terminal domain. Maturation of HAstV requires proteolytic processing of the astrovirus CP both inside and outside the host cell, resulting in the removal of the C-terminal domain and the breakdown of the rest of the CP into three predominantmore » protein species with molecular masses of ~34, 27/29, and 25/26 kDa, respectively. We have now solved the crystal structure of VP90 71–415(amino acids [aa] 71 to 415 of VP90) of human astrovirus serotype 8 at a 2.15-Å resolution. VP90 71–415encompasses the conserved N-terminal domain of VP90 but lacks the hypervariable domain, which forms the capsid surface spikes. The structure of VP90 71–415is comprised of two domains: an S domain, which adopts the typical jelly-roll β-barrel fold, and a P1 domain, which forms a squashed β-barrel consisting of six antiparallel β-strands similar to what was observed in the hepatitis E virus (HEV) capsid structure. Fitting of the VP90 71–415structure into the cryo-electron microscopy (EM) maps of HAstV produced an atomic model for a continuous, T=3 icosahedral capsid shell. Our pseudoatomic model of the human HAstV capsid shell provides valuable insights into intermolecular interactions required for capsid assembly and trypsin-mediated proteolytic maturation needed for virus infectivity. Such information has potential applications in the development of a virus-like particle (VLP) vaccine as well as small-molecule drugs targeting astrovirus assembly/maturation. IMPORTANCEHuman astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. As a nonenveloped virus, HAstV exhibits an intriguing feature in that its maturation requires extensive proteolytic processing of the astrovirus capsid protein (CP) both inside and outside the host cell. Mature HAstV contains three predominant protein species, but the mechanism for acquired infectivity upon maturation is unclear. We have solved the crystal structure of VP90 71–415of human astrovirus serotype 8. VP90 71–415encompasses the conserved N-terminal domain of the viral CP. Fitting of the VP90 71–415structure into the cryo-EM maps of HAstV produced an atomic model for the T=3 icosahedral capsid. Our model of the HAstV capsid provides valuable insights into intermolecular interactions required for capsid assembly and trypsin-mediated proteolytic maturation. Such information has potential applications in the development of a VLP vaccine as well as small-molecule drugs targeting astrovirus assembly/maturation.« less

Isolation and characterization of a reovirus from common eiders (Somateria mollissima) from Finland

USGS Publications Warehouse

Hollmen, T.; Franson, J. Christian; Kilpi, Mikael; Docherty, D.E.; Hansen, W.R.; Hario, Martti

2002-01-01

Samples of brain, intestine, liver, lung, spleen, and bursa of Fabricius were collected from five common eider (Somateria mollissima) duckling carcasses during a die-off in the western Gulf of Finland (59°50′N, 23°15′E) in June 1996. No viral activity was observed in specific-pathogen-free chicken embryos inoculated with tissue suspensions, but samples of bursa of Fabricius from three birds were positive when inoculated into Muscovy duck (Cairina moschata) embryo fibroblasts. The isolates were characterized as nonenveloped RNA viruses and possessed several characteristics of the genus Orthoreovirus. Virus particles were icosahedral with a mean diameter of 72 nm and were stable at pH 3.0; their genome was separated into 10 segments by polyacrylamide gel electrophoresis. Mallard (Anas platyrhynchos) ducklings experimentally infected with the eider reovirus showed elevated serum activities of aspartate aminotransferase, creatine kinase, and lactate dehydrogenase enzymes and focal hemorrhages in the liver, spleen, and bursa of Fabricius. During 1997–99, the prevalence of neutralizing antibodies to the isolated virus ranged from 0 to 86% in 302 serum samples collected from incubating eider hens at three nesting areas along coastal Finland. The highest seroprevalence was found in Hanko in 1999, just weeks before reports of an uninvestigated mortality event resulting in the death of an estimated 98% of ducklings at that location. These findings raise the question of potential involvement of the virus in poor duckling survival and eider population declines observed in several breeding areas along coastal Finland since the mid-1980s.

An orphan viral TNF receptor superfamily member identified in lymphocystis disease virus.

PubMed

Pontejo, Sergio M; Sánchez, Carolina; Martín, Rocío; Mulero, Victoriano; Alcami, Antonio; Alejo, Alí

2013-06-07

Lymphocystis disease virus (LCDV) is a large icosahedral dsDNA-containing virus of the Lymphocystivirus genus within the Iridoviridae family that can cause disease in more than 140 marine and freshwater fish species. While several isolates have been charcaterized and classified into distinct genotypes the complete genomic sequence is currently only available from two species, the LCDV-1, isolated from flounder (Platichtys flesus) in Europe and the LCDV-C, isolated from Japanese cultured flounder (Paralichthys olivaceus) in China. Analysis of the genome of LCDV-C showed it to encode a protein named LDVICp016 with similarities to the Tumour necrosis factor receptor (TNFR) superfamily with immunomodulatory potential. We have expressed and purified the recombinant protein LDVICp016 and screened for potential interaction partners using surface plasmon resonance. Commercially available human and mouse members of the TNF superfamily (TNFSF), along with a representative set of fish-derived TNFSF were tested.We have found the LDVICp016 protein to be secreted and we have identified a second viral TNFR encoded by ORF 095 of the same virus. None of the 42 tested proteins were found to interact with LDVICp016. We show that LDVICp016 is a secreted protein belonging to the TNF receptor family that may be part of a larger gene family in Lymphocystiviruses. While the ligand of this protein remains unknown, possibly due to the species specific nature of this interaction, further investigations into the potential role of this protein in the blockade of immune responses in its fish host are required.

An orphan viral TNF receptor superfamily member identified in lymphocystis disease virus

PubMed Central

2013-01-01

Background Lymphocystis disease virus (LCDV) is a large icosahedral dsDNA-containing virus of the Lymphocystivirus genus within the Iridoviridae family that can cause disease in more than 140 marine and freshwater fish species. While several isolates have been charcaterized and classified into distinct genotypes the complete genomic sequence is currently only available from two species, the LCDV-1, isolated from flounder (Platichtys flesus) in Europe and the LCDV-C, isolated from Japanese cultured flounder (Paralichthys olivaceus) in China. Analysis of the genome of LCDV-C showed it to encode a protein named LDVICp016 with similarities to the Tumour necrosis factor receptor (TNFR) superfamily with immunomodulatory potential. Findings We have expressed and purified the recombinant protein LDVICp016 and screened for potential interaction partners using surface plasmon resonance. Commercially available human and mouse members of the TNF superfamily (TNFSF), along with a representative set of fish-derived TNFSF were tested. We have found the LDVICp016 protein to be secreted and we have identified a second viral TNFR encoded by ORF 095 of the same virus. None of the 42 tested proteins were found to interact with LDVICp016. Conclusions We show that LDVICp016 is a secreted protein belonging to the TNF receptor family that may be part of a larger gene family in Lymphocystiviruses. While the ligand of this protein remains unknown, possibly due to the species specific nature of this interaction, further investigations into the potential role of this protein in the blockade of immune responses in its fish host are required. PMID:23758704

PREFACE The physics of virus assembly The physics of virus assembly

NASA Astrophysics Data System (ADS)

Stockley, Peter G.; Twarock, Reidun

2010-12-01

Viruses are pathogens in every kingdom of life and are major causes of human disease and suffering. They are known to encompass a size range that overlaps with that of the smallest bacterial cells, and the largest viruses now seem to be hosts of their own viral pathogens. Recent genomic sequencing efforts show that many organisms have genes that are likely to be descended in evolution from viral progenitors. Even more astonishingly, analysis of the world's oceans has shown that some of the simplest viruses, the tailed dsDNA phages, are the most common biological entities on the planet, with estimates of their numbers ranging up to 1031, with ~ 1021 infection events every second, leading to a turnover of around 20% of the biomass in the sea every few days. These cycles of infection and lysis of oceanic bacteria and algae provide the nutrients for the smallest organisms lying at the bottom of the food chain. Without viruses, therefore, life on Earth would probably not be sustainable. These are remarkable facts for systems that are non-living in the strict sense, and are composed of simple materials—nucleic acids, proteins and lipids. Many viruses consist of little more than a protective protein coat surrounding their genomic nucleic acids, which can be either DNA or RNA. Their simplicity leads to highly symmetrical structures with protein containers based on helical or icosahedral lattices. Many simple viruses self-assemble rapidly and with great fidelity, and many groups are busy trying to exploit these properties to make virus-like particles for a wide range of applications, including targeted drug-delivery, medical imaging and even novel materials. This issue of Physical Biology contains a series of papers describing some of the latest experimental and theoretical research on viruses, their structures and assembly, as well as their regulated disassembly during infection. These range from a dissection of the in vivo assembly mechanism of a filamentous virus, through structure determination using cryo-electron microscopy, to entirely in silico modelling of assembly pathways. This selection illustrates the interdisciplinarity of modern virus research which interests an ever widening community including physicists, mathematicians and engineers, and is reflected by the recent appearance of international conferences and workshops in physical and mathematical virology. We hope this selection of papers gives the readers of Physical Biology an impression of the exciting developments in this field.

Formation of fivefold axes in the FCC-metal nanoclusters

NASA Astrophysics Data System (ADS)

Myasnichenko, Vladimir S.; Starostenkov, Mikhail D.

2012-11-01

Formation of atomistic structures of metallic Cu, Au, Ag clusters and bimetallic Cu-Au clusters was studied with the help of molecular dynamics using the many-body tight-binding interatomic potential. The simulation of the crystallization process of clusters with the number of atoms ranging from 300 to 1092 was carried out. The most stable configurations of atoms in the system, corresponding to the minimum of potential energy, was found during super-fast cooling from 1000 K. Atoms corresponding to fcc, hcp, and Ih phases were identified by the method of common neighbor analysis. Incomplete icosahedral core can be discovered at the intersection of one of the Ih axes with the surface of monometallic cluster. The decahedron-shaped structure of bimetallic Cu-Au cluster with seven completed icosahedral cores was obtained. The principles of the construction of small bimetallic clusters with icosahedral symmetry and increased fractal dimensionality were offered.

Morphological evidence for phages in Xylella fastidiosa

PubMed Central

Chen, Jianchi; Civerolo, Edwin L

2008-01-01

Presumptive phage particles associated with Xylella fastidiosa strain Temecula-1 grown in PW broth were observed by transmission electron microscopy (TEM) in ultrathin sections of bacterial cell-containing low speed centrifugation pellets and in partially purified preparations from CsCl equilibrium centrifugation density gradients. Ultrathin-sectioned cell pellets contained icosahedral particles of about 45 nm in diameter. Samples collected from CsCl density gradients revealed mostly non-tailed icosahedral but also tailed particles. The icosahedral particles could be divided into two types: a large type (about 45 nm) and a small type (about 30 nm). Filamentous phage-like particles (17 × 120 to 6,300 nm) were also observed. The presence of different types of phage-like particles resembling to those in several bacteriophage families provides new physical evidence, in addition to X. fastidiosa genomic information, that X. fastidiosa possesses active phages. This is the first report of phage particles released in X. fastidiosa cultures. PMID:18538030

Forging Unsupported Metal-Boryl Bonds with Icosahedral Carboranes.

PubMed

Saleh, Liban M A; Dziedzic, Rafal M; Khan, Saeed I; Spokoyny, Alexander M

2016-06-13

In contrast to the plethora of metal-catalyzed cross-coupling methods available for the installation of functional groups on aromatic hydrocarbons, a comparable variety of methods are currently not available for icosahedral carboranes, which are boron-rich three-dimensional aromatic analogues of aryl groups. Part of this is due to the limited understanding of the elementary steps for cross-coupling involving carboranes. Here, we report our efforts in isolating metal-boryl complexes to further our understanding of one of these elementary steps, oxidative addition. Structurally characterized examples of group 10 M-B bonds featuring icosahedral carboranes are completely unknown. Use of mercurocarboranes as a reagent to deliver M-B bonds saw divergent reactivity for platinum and palladium, with a Pt-B bond being isolated for the former, and a rare Pd-Hg bond being formed for the latter. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interface of physics and biology: engineering virus-based nanoparticles for biophotonics.

PubMed

Wen, Amy M; Infusino, Melissa; De Luca, Antonio; Kernan, Daniel L; Czapar, Anna E; Strangi, Giuseppe; Steinmetz, Nicole F

2015-01-21

Virus-based nanoparticles (VNPs) have been used for a wide range of applications, spanning basic materials science and translational medicine. Their propensity to self-assemble into precise structures that offer a three-dimensional scaffold for functionalization has led to their use as optical contrast agents and related biophotonics applications. A number of fluorescently labeled platforms have been developed and their utility in optical imaging demonstrated, yet their optical properties have not been investigated in detail. In this study, two VNPs of varying architectures were compared side-by-side to determine the impact of dye density, dye localization, conjugation chemistry, and microenvironment on the optical properties of the probes. Dyes were attached to icosahedral cowpea mosaic virus (CPMV) and rod-shaped tobacco mosaic virus (TMV) through a range of chemistries to target particular side chains displayed at specific locations around the virus. The fluorescence intensity and lifetime of the particles were determined, first using photochemical experiments on the benchtop, and second in imaging experiments using tissue culture experiments. The virus-based optical probes were found to be extraordinarily robust under ultrashort, pulsed laser light conditions with a significant amount of excitation energy, maintaining structural and chemical stability. The most effective fluorescence output was achieved through dye placement at optimized densities coupled to the exterior surface avoiding conjugated ring systems. Lifetime measurements indicate that fluorescence output depends not only on spacing the fluorophores, but also on dimer stacking and configurational changes leading to radiationless relaxation-and these processes are related to the conjugation chemistry and nanoparticle shape. For biological applications, the particles were also examined in tissue culture, from which it was found that the optical properties differed from those found on the benchtop due to effects from cellular processes and uptake kinetics. Data indicate that fluorescent cargos are released in the endolysosomal compartment of the cell targeted by the virus-based optical probes. These studies provide insight into the optical properties and fates of fluorescent proteinaceous imaging probes. The cellular release of cargo has implications not only for virus-based optical probes, but also for drug delivery and release systems.

Dynamics and asymmetry in the dimer of the norovirus major capsid protein.

PubMed

Tubiana, Thibault; Boulard, Yves; Bressanelli, Stéphane

2017-01-01

Noroviruses are the major cause of non-bacterial acute gastroenteritis in humans and livestock worldwide, despite being physically among the simplest animal viruses. The icosahedral capsid encasing the norovirus RNA genome is made of 90 dimers of a single ca 60-kDa polypeptide chain, VP1, arranged with T = 3 icosahedral symmetry. Here we study the conformational dynamics of this main building block of the norovirus capsid. We use molecular modeling and all-atom molecular dynamics simulations of the VP1 dimer for two genogroups with 50% sequence identity. We focus on the two points of flexibility in VP1 known from the crystal structure of the genogroup I (GI, human) capsid and from subsequent cryo-electron microscopy work on the GII capsid (also human). First, with a homology model of the GIII (bovine) VP1 dimer subjected to simulated annealing then classical molecular dynamics simulations, we show that the N-terminal arm conformation seen in the GI crystal structure is also favored in GIII VP1 but depends on the protonation state of critical residues. Second, simulations of the GI dimer show that the VP1 spike domain will not keep the position found in the GII electron microscopy work. Our main finding is a consistent propensity of the VP1 dimer to assume prominently asymmetric conformations. In order to probe this result, we obtain new SAXS data on GI VP1 dimers. These data are not interpretable as a population of symmetric dimers, but readily modeled by a highly asymmetric dimer. We go on to discuss possible implications of spontaneously asymmetric conformations in the successive steps of norovirus capsid assembly. Our work brings new lights on the surprising conformational range encoded in the norovirus major capsid protein.

About the atomic structures of icosahedral quasicrystals

NASA Astrophysics Data System (ADS)

Quiquandon, Marianne; Gratias, Denis

2014-01-01

This paper is a survey of the crystallographic methods that have been developed these last twenty five years to decipher the atomic structures of the icosahedral stable quasicrystals since their discovery in 1982 by D. Shechtman. After a brief recall of the notion of quasiperiodicity and the natural description of Z-modules in 3-dim as projection of regular lattices in N>3-dim spaces, we give the basic geometrical ingredients useful to describe icosahedral quasicrystals as irrational 3-dim cuts of ordinary crystals in 6-dim space. Atoms are described by atomic surfaces (ASs) that are bounded volumes in the internal (or perpendicular) 3-dim space and the intersections of which with the physical space are the actual atomic positions. The main part of the paper is devoted to finding the major properties of quasicrystalline icosahedral structures. As experimentally demonstrated, they can be described with a surprisingly few high symmetry ASs located at high symmetry special points in 6-dim space. The atomic structures are best described by aggregations and intersections of high symmetry compact interpenetrating atomic clusters. We show here that the experimentally relevant clusters are derived from one generic cluster made of two concentric triacontahedra scaled by τ and an external icosidodecahedron. Depending on which ones of the orbits of this cluster are eventually occupied by atoms, the actual atomic clusters are of type Bergman, Mackay, Tsai and others….

Variable rainfall intensity and tillage effects on runoff, sediment, and carbon losses from a loamy sand under simulated rainfall.

PubMed

Truman, C C; Strickland, T C; Potter, T L; Franklin, D H; Bosch, D D; Bednarz, C W

2007-01-01

The low-carbon, intensively cropped Coastal Plain soils of Georgia are susceptible to runoff, soil loss, and drought. Reduced tillage systems offer the best management tool for sustained row crop production. Understanding runoff, sediment, and chemical losses from conventional and reduced tillage systems is expected to improve if the effect of a variable rainfall intensity storm was quantified. Our objective was to quantify and compare effects of a constant (Ic) intensity pattern and a more realistic, observed, variable (Iv) rainfall intensity pattern on runoff (R), sediment (E), and carbon losses (C) from a Tifton loamy sand cropped to conventional-till (CT) and strip-till (ST) cotton (Gossypium hirsutum L.). Four treatments were evaluated: CT-Ic, CT-Iv, ST-Ic, and ST-Iv, each replicated three times. Field plots (n=12), each 2 by 3 m, were established on each treatment. Each 6-m2 field plot received simulated rainfall at a constant (57 mm h(-1)) or variable rainfall intensity pattern for 70 min (12-run ave.=1402 mL; CV=3%). The Iv pattern represented the most frequent occurring intensity pattern for spring storms in the region. Compared with CT, ST decreased R by 2.5-fold, E by 3.5-fold, and C by 7-fold. Maximum runoff values for Iv events were 1.6-fold higher than those for Ic events and occurred 38 min earlier. Values for Etot and Ctot for Iv events were 19-36% and 1.5-fold higher than corresponding values for Ic events. Values for Emax and Cmax for Iv events were 3-fold and 4-fold higher than corresponding values for Ic events. Carbon enrichment ratios (CER) were or=1.0 for CT plots (except for first 20 min). Maximum CER for CT-Ic, CT-Iv, ST-Ic, and ST-Iv were 2.0, 2.2, 1.0, and 1.2, respectively. Transport of sediment, carbon, and agrichemicals would be better understood if variable rainfall intensity patterns derived from natural rainfall were used in rainfall simulations to evaluate their fate and transport from CT and ST systems.

Genome Analysis of the First Marseilleviridae Representative from Australia Indicates that Most of Its Genes Contribute to Virus Fitness

PubMed Central

Doutre, Gabriel; Philippe, Nadège

2014-01-01

ABSTRACT The family Marseilleviridae consists of Acanthamoeba-infecting large DNA viruses with icosahedral particles ∼0.2 μm in diameter and genome sizes in the 346- to 380-kb range. Since the isolation of Marseillevirus from a cooling tower in Paris (France) in 2009, the family Marseilleviridae has expanded rapidly, with representatives from Europe and Africa. Five members have been fully sequenced that are distributed among 3 emerging Marseilleviridae lineages. One comprises Marseillevirus and Cannes 8 virus, another one includes Insectomime virus and Tunisvirus, and the third one corresponds to the more distant Lausannevirus. We now report the genomic characterization of Melbournevirus, the first representative of the Marseilleviridae isolated from a freshwater pond in Melbourne, Australia. Despite the large distance separating this sampling point from France, Melbournevirus is remarkably similar to Cannes 8 virus and Marseillevirus, with most orthologous genes exhibiting more than 98% identical nucleotide sequences. We took advantage of this optimal evolutionary distance to evaluate the selection pressure, expressed as the ratio of nonsynonymous to synonymous mutations for various categories of genes. This ratio was found to be less than 1 for all of them, including those shared solely by the closest Melbournevirus and Cannes 8 virus isolates and absent from Lausannevirus. This suggests that most of the 403 protein-coding genes composing the large Melbournevirus genome are under negative/purifying selection and must thus significantly contribute to virus fitness. This conclusion contrasts with the more common view that many of the genes of the usually more diverse large DNA viruses might be (almost) dispensable. IMPORTANCE A pervasive view is that viruses are fast-evolving parasites and carry the smallest possible amount of genomic information required to highjack the host cell machinery and perform their replication. This notion, probably inherited from the study of RNA viruses, is being gradually undermined by the discovery of DNA viruses with increasingly large gene content. These viruses also encode a variety of DNA repair functions, presumably slowing down their evolution by preserving their genomes from random alterations. On the other hand, these viruses also encode a majority of proteins without cellular homologs, including many shared only between the closest members of the same family. One may thus question the actual contribution of these anonymous and/or quasi-orphan genes to virus fitness. Genomic comparisons of Marseilleviridae, including a new Marseillevirus isolated in Australia, demonstrate that most of their genes, irrespective of their functions and conservation across families, are evolving under negative selection. PMID:25275139

Physicochemical Study of Viral Nanoparticles at the Air/Water Interface.

PubMed

Torres-Salgado, Jose F; Comas-Garcia, Mauricio; Villagrana-Escareño, Maria V; Durán-Meza, Ana L; Ruiz-García, Jaime; Cadena-Nava, Ruben D

2016-07-07

The assembly of most single-stranded RNA (ssRNA) viruses into icosahedral nucleocapsids is a spontaneous process driven by protein-protein and RNA-protein interactions. The precise nature of these interactions results in the assembly of extremely monodisperse and structurally indistinguishable nucleocapsids. In this work, by using a ssRNA plant virus (cowpea chlorotic mottle virus [CCMV]) as a charged nanoparticle we show that the diffusion of these nanoparticles from the bulk solution to the air/water interface is an irreversible adsorption process. By using the Langmuir technique, we measured the diffusion and adsorption of viral nucleocapsids at the air/water interface at different pH conditions. The pH changes, and therefore in the net surface charge of the virions, have a great influence in the diffusion rate from the bulk solution to the air/water interface. Moreover, assembly of mesoscopic and microscopic viral aggregates at this interface depends on the net surface charge of the virions and the surface pressure. By using Brewster's angle microscopy we characterized these structures at the interface. Most common structures observed were clusters of virions and soap-frothlike micron-size structures. Furthermore, the CCMV films were compressed to form monolayers and multilayers from moderate to high surface pressures, respectively. After transferring the films from the air/water interface onto mica by using the Langmuir-Blodgett technique, their morphology was characterized by atomic force microscopy. These viral monolayers showed closed-packing nano- and microscopic arrangements.

Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction

PubMed Central

Misseldine, Adam; Geilen, Lorena; Halder, Sujata; Smith, J. Kennon; Kurian, Justin; Chipman, Paul; Janssen, Mandy; Mckenna, Robert; Baker, Timothy S.; D’Abramo, Anthony; Cotmore, Susan; Tattersall, Peter; Agbandje-McKenna, Mavis

2017-01-01

LuIII, a protoparvovirus pathogenic to rodents, replicates in human mitotic cells, making it applicable for use to kill cancer cells. This virus group includes H-1 parvovirus (H-1PV) and minute virus of mice (MVM). However, LuIII displays enhanced oncolysis compared to H-1PV and MVM, a phenotype mapped to the major capsid viral protein 2 (VP2). This suggests that within LuIII VP2 are determinants for improved tumor lysis. To investigate this, the structure of the LuIII virus-like-particle was determined using single particle cryo-electron microscopy and image reconstruction to 3.17 Å resolution, and compared to the H-1PV and MVM structures. The LuIII VP2 structure, ordered from residue 37 to 587 (C-terminal), had the conserved VP topology and capsid morphology previously reported for other protoparvoviruses. This includes a core β-barrel and α-helix A, a depression at the icosahedral 2-fold and surrounding the 5-fold axes, and a single protrusion at the 3-fold axes. Comparative analysis identified surface loop differences among LuIII, H-1PV, and MVM at or close to the capsid 2- and 5-fold symmetry axes, and the shoulder of the 3-fold protrusions. The 2-fold differences cluster near the previously identified MVM sialic acid receptor binding pocket, and revealed potential determinants of protoparvovirus tumor tropism. PMID:29084163

Fullerene-like organization of HIV gag-protein shell in virus-like particles produced by recombinant baculovirus.

PubMed

Nermut, M V; Hockley, D J; Jowett, J B; Jones, I M; Garreau, M; Thomas, D

1994-01-01

Virus-like particles produced by a recombinant baculovirus containing the HIV gag gene were examined by negative staining after delipidization. This technique demonstrated that the gag-protein shell consisted of radially arranged short rods which formed a network of ring-like structures. Similar structures were observed at the plasma membrane of infected cells which had been opened by wet-cleaving. Occasionally five or six subunits were observed forming a ring. These findings suggest that the gag-encoded precursor (pr55) is a rod-like molecule about 34 A in diameter and 85 A in length. A protein cylinder of such dimensions would have a molecular weight of 56K. The center-to-center distance of two neighboring rings formed by the rods was 66 +/- 8 A (N = 200) by direct measurements and 65 A as obtained from averaged images. This morphology and these dimensions indicate that the virus-like particles contain the gag precursor in the form of a near-spherical "fullerene-like" icosahedral shell. Our data indicate that the triangulation number of the rings equals 63. However, since one rod of pr55 is shared by two rings, the number of copies of the precursor will be 1890 as opposed to 2522 if the molecules were closely packed. The particle diameter of 102 nm deduced from the proposed model was close to the diameter obtained from thin sections of low-temperature-embedded specimens (103-108 nm).

Infectious rotavirus enters cells by direct cell membrane penetration, not by endocytosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaljot, K.T.; Shaw, R.D.; Greenberg, H.B.

1988-04-01

Rotaviruses are icosahedral viruses with a segmented, double-stranded RNA genome. They are the major cause of severe infantile infectious diarrhea. Rotavirus growth in tissue culture is markedly enhanced by pretreatment of virus with trypsin. Trypsin activation is associated with cleavage of the viral hemagglutinin (viral protein 3 (VP3); 88 kilodaltons) into two fragments (60 and 28 kilodaltons). The mechanism by which proteolytic cleavage leads to enhanced growth is unknown. To determine whether trypsin treatment affected rotavirus internalization, the authors studied the kinetics of entry of infectious rhesus rotavirus (RRV) into MA104 cells. Trypsin-activated RRV was internalized with a half-time ofmore » 3 to 5 min, while nonactivated virus disappeared from the cell surface with a half-time of 30 to 50 min. In contrast to trypsin-activated RRV, loss of nonactivated RRV from the cell surface did not result in the appearance of infection, as measured by plaque formation. Purified trypsin-activated RRV added to cell monolayers at pH 7.4 mediated {sup 51}Cr, ({sup 14}C)choline, and ({sup 3}H)inositol released from prelabeled MA104 cells. This release could be specifically blocked by neutralizing antibodies to VP3. These results suggest that MA104 cell infection follows the rapid entry of trypsin-activated RRV by direct cell membrane penetration. Cell membrane penetration of infectious RRV is initiated by trypsin cleavage of VP3. Neutralizing antibodies can inhibit this direct membrane penetration.« less

Structures of the Procapsid and Mature Virion of Enterovirus 71 Strain 1095

PubMed Central

Cifuente, Javier O.; Lee, Hyunwook; Yoder, Joshua D.; Shingler, Kristin L.; Carnegie, Michael S.; Yoder, Jennifer L.; Ashley, Robert E.; Makhov, Alexander M.; Conway, James F.

2013-01-01

Enterovirus 71 (EV71) is an important emerging human pathogen with a global distribution and presents a disease pattern resembling poliomyelitis with seasonal epidemics that include cases of severe neurological complications, such as acute flaccid paralysis. EV71 is a member of the Picornaviridae family, which consists of icosahedral, nonenveloped, single-stranded RNA viruses. Here we report structures derived from X-ray crystallography and cryoelectron microscopy (cryo-EM) for the 1095 strain of EV71, including a putative precursor in virus assembly, the procapsid, and the mature virus capsid. The cryo-EM map of the procapsid provides new structural information on portions of the capsid proteins VP0 and VP1 that are disordered in the higher-resolution crystal structures. Our structures solved from virus particles in solution are largely in agreement with those from prior X-ray crystallographic studies; however, we observe small but significant structural differences for the 1095 procapsid compared to a structure solved in a previous study (X. Wang, W. Peng, J. Ren, Z. Hu, J. Xu, Z. Lou, X. Li, W. Yin, X. Shen, C. Porta, T. S. Walter, G. Evans, D. Axford, R. Owen, D. J. Rowlands, J. Wang, D. I. Stuart, E. E. Fry, and Z. Rao, Nat. Struct. Mol. Biol. 19:424–429, 2012) for a different strain of EV71. For both EV71 strains, the procapsid is significantly larger in diameter than the mature capsid, unlike in any other picornavirus. Nonetheless, our results demonstrate that picornavirus capsid expansion is possible without RNA encapsidation and that picornavirus assembly may involve an inward radial collapse of the procapsid to yield the native virion. PMID:23637404

C Terminus of Infectious Bursal Disease Virus Major Capsid Protein VP2 Is Involved in Definition of the T Number for Capsid Assembly

PubMed Central

Castón, José R.; Martínez-Torrecuadrada, Jorge L.; Maraver, Antonio; Lombardo, Eleuterio; Rodríguez, José F.; Casal, J. Ignacio; Carrascosa, José L.

2001-01-01

Infectious bursal disease virus (IBDV), a member of the Birnaviridae family, is a double-stranded RNA virus. The IBDV capsid is formed by two major structural proteins, VP2 and VP3, which assemble to form a T=13 markedly nonspherical capsid. During viral infection, VP2 is initially synthesized as a precursor, called VPX, whose C end is proteolytically processed to the mature form during capsid assembly. We have computed three-dimensional maps of IBDV capsid and virus-like particles built up by VP2 alone by using electron cryomicroscopy and image-processing techniques. The IBDV single-shelled capsid is characterized by the presence of 260 protruding trimers on the outer surface. Five classes of trimers can be distinguished according to their different local environments. When VP2 is expressed alone in insect cells, dodecahedral particles form spontaneously; these may be assembled into larger, fragile icosahedral capsids built up by 12 dodecahedral capsids. Each dodecahedral capsid is an empty T=1 shell composed of 20 trimeric clusters of VP2. Structural comparison between IBDV capsids and capsids consisting of VP2 alone allowed the determination of the major capsid protein locations and the interactions between them. Whereas VP2 forms the outer protruding trimers, VP3 is found as trimers on the inner surface and may be responsible for stabilizing functions. Since elimination of the C-terminal region of VPX is correlated with the assembly of T=1 capsids, this domain might be involved (either alone or in cooperation with VP3) in the induction of different conformations of VP2 during capsid morphogenesis. PMID:11602723

In vitro and in silico studies reveal capsid-mutant Porcine circovirus 2b with novel cytopathogenic and structural characteristics.

PubMed

Cruz, Taís Fukuta; Magro, Angelo José; de Castro, Alessandra M M G; Pedraza-Ordoñez, Francisco J; Tsunemi, Miriam Harumi; Perahia, David; Araujo, João Pessoa

2018-06-02

Porcine circovirus 2 (PCV2) is an icosahedral, non-enveloped, and single-stranded circular DNA virus that belongs to the family Circoviridae, genus Circovirus, and is responsible for a complex of different diseases defined as porcine circovirus diseases (PCVDs). These diseases - including postweaning multisystemic wasting syndrome (PMWS), enteric disease, respiratory disease, porcine dermatitis and nephropathy syndrome (PDNS), and reproductive failure - are responsible for large economic losses in the pig industry. After serial passages in swine testicle (ST) cells of a wild-type virus isolated from an animal with PMWS, we identified three PCV2b viruses with capsid protein (known as Cap protein) cumulative mutations, including two novel mutants. The mutant viruses were introduced into new ST cell cultures for reisolation and showed, in comparison to the wild-type PCV2b, remarkable viral replication efficiency (> 10 11 DNA copies/ml) and cell death via necrosis, which were clearly related to the accretion of capsid protein mutations. The analysis of a Cap protein/capsid model showed that the mutated residues were located in solvent-accessible positions on the external PCV2b surface. Additionally, the mutated residues were found in linear epitopes and participated in pockets on the capsid surface, indicating that these residues could also be involved in antibody recognition. Taking into account the likely natural emergence of PCV2b variants, it is possible to consider that the results of this work increase knowledge of Circovirus biology and could help to prevent future serious cases of vaccine failure that could lead to heavy losses to the swine industry. Copyright © 2018 Elsevier B.V. All rights reserved.

Method of making an icosahedral boride structure

DOEpatents

Hersee, Stephen D.; Wang, Ronghua; Zubia, David; Aselage, Terrance L.; Emin, David

2005-01-11

A method for fabricating thin films of an icosahedral boride on a silicon carbide (SiC) substrate is provided. Preferably the icosahedral boride layer is comprised of either boron phosphide (B.sub.12 P.sub.2) or boron arsenide (B.sub.12 As.sub.2). The provided method achieves improved film crystallinity and lowered impurity concentrations. In one aspect, an epitaxially grown layer of B.sub.12 P.sub.2 with a base layer or substrate of SiC is provided. In another aspect, an epitaxially grown layer of B.sub.12 As.sub.2 with a base layer or substrate of SiC is provided. In yet another aspect, thin films of B.sub.12 P.sub.2 or B.sub.12 As.sub.2 are formed on SiC using CVD or other vapor deposition means. If CVD techniques are employed, preferably the deposition temperature is above 1050.degree. C., more preferably in the range of 1100.degree. C. to 1400.degree. C., and still more preferably approximately 1150.degree. C.

Cooling rate dependence and local structure in aluminum monatomic metallic glass

NASA Astrophysics Data System (ADS)

Kbirou, M.; Trady, S.; Hasnaoui, A.; Mazroui, M.

2017-10-01

The local atomic structure in aluminium monatomic metallic glass is studied using molecular dynamics simulations combined with the embedded atom method (EAM). We have used a variety of analytical methods to characterise the atomic configurations of our system: the Pair Distribution Function (PDF), the Common Neighbour Analysis (CNA) and the Voronoi Tessellation Analysis. CNA was used to investigate the order change from liquid to amorphous phases, recognising that the amount of icosahedral clusters increases with the decrease of temperature. The Voronoi analysis revealed that the icosahedral-like polyhedral are the predominant ones. It has been observed that the PDF function shows a splitting in the second peak, which cannot be attributed to the only ideal icosahedral polyhedron 〈0, 0, 12, 0〉, but also to the formation of other Voronoi polyhedra 〈0, 1, 10, 2〉 . Further, the PDFs were then integrated giving the cumulative coordination number in order to compute the fractal dimension (df).

Koi herpes virus: a review and risk assessment of Indian aquaculture.

PubMed

Rathore, Gaurav; Kumar, Gokhlesh; Raja Swaminathan, T; Swain, P

2012-09-01

Common carp (Cyprinus carpio) is a widely cultivated freshwater fish for human consumption, while koi carp, is a farmed colored sub species of common carp used for ornamental purposes. Since 1998, both common carp and koi carp are severely affected by a viral disease called as Koi herpes virus disease (KHVD). This disease is caused by Koi herpes virus (KHV), also known as cyprinid herpes virus-3. The virus causes interstitial nephritis and gill necrosis in carps, so it is also termed as carp interstitial nephritis and gill necrosis virus. KHV is a double stranded icosahedral DNA virus belonging to family Alloherpesviridae, with a genome size of 295 kbp, larger than any member of Herpesviridae. The viral genome encodes 156 potential protein coding open reading frames. Each virion consists of forty structural proteins, which are classified as capsid (3), envelope (13), tegument (2) and unclassified (22) structural proteins. Diagnosis of KHVD is mainly based on detection of viral DNA by polymerase chain reaction amplification using specific primers or loop mediated isothermal amplification. Temperature dependent latent infection is unique to KHV; and carrier fish are often not detected, thereby possibly resulting in spread of this pathogen to newer areas. The disease is now known to occur in, or has been recorded from at least 26 different countries of the world. Fortunately, KHVD has not been reported from India or from Indian major carps. To monitor the disease status of the country, a total of 254 fish samples collected from different parts of India were screened by PCR for the presence of KHV. None of the tested samples were found to be positive for KHV. These results demonstrate that tested samples from different parts of India were apparently free from KHV. Preliminary risk assessment of KHV suggest that in the event of unrestricted importation of koi carps into our country, there is a higher probability of risk to aquaculture as compared to natural waters. So there is strong need to develop diagnostic capabilities and launch surveillance programmes for KHV in India.

A 3-D Finite-Volume Non-hydrostatic Icosahedral Model (NIM)

NASA Astrophysics Data System (ADS)

Lee, Jin

2014-05-01

The Nonhydrostatic Icosahedral Model (NIM) formulates the latest numerical innovation of the three-dimensional finite-volume control volume on the quasi-uniform icosahedral grid suitable for ultra-high resolution simulations. NIM's modeling goal is to improve numerical accuracy for weather and climate simulations as well as to utilize the state-of-art computing architecture such as massive parallel CPUs and GPUs to deliver routine high-resolution forecasts in timely manner. NIM dynamic corel innovations include: * A local coordinate system remapped spherical surface to plane for numerical accuracy (Lee and MacDonald, 2009), * Grid points in a table-driven horizontal loop that allow any horizontal point sequence (A.E. MacDonald, et al., 2010), * Flux-Corrected Transport formulated on finite-volume operators to maintain conservative positive definite transport (J.-L, Lee, ET. Al., 2010), *Icosahedral grid optimization (Wang and Lee, 2011), * All differentials evaluated as three-dimensional finite-volume integrals around the control volume. The three-dimensional finite-volume solver in NIM is designed to improve pressure gradient calculation and orographic precipitation over complex terrain. NIM dynamical core has been successfully verified with various non-hydrostatic benchmark test cases such as internal gravity wave, and mountain waves in Dynamical Cores Model Inter-comparisons Projects (DCMIP). Physical parameterizations suitable for NWP are incorporated into NIM dynamical core and successfully tested with multimonth aqua-planet simulations. Recently, NIM has started real data simulations using GFS initial conditions. Results from the idealized tests as well as real-data simulations will be shown in the conference.

Design of a hyperstable 60-subunit protein icosahedron

NASA Astrophysics Data System (ADS)

Hsia, Yang; Bale, Jacob B.; Gonen, Shane; Shi, Dan; Sheffler, William; Fong, Kimberly K.; Nattermann, Una; Xu, Chunfu; Huang, Po-Ssu; Ravichandran, Rashmi; Yi, Sue; Davis, Trisha N.; Gonen, Tamir; King, Neil P.; Baker, David

2016-07-01

The icosahedron is the largest of the Platonic solids, and icosahedral protein structures are widely used in biological systems for packaging and transport. There has been considerable interest in repurposing such structures for applications ranging from targeted delivery to multivalent immunogen presentation. The ability to design proteins that self-assemble into precisely specified, highly ordered icosahedral structures would open the door to a new generation of protein containers with properties custom-tailored to specific applications. Here we describe the computational design of a 25-nanometre icosahedral nanocage that self-assembles from trimeric protein building blocks. The designed protein was produced in Escherichia coli, and found by electron microscopy to assemble into a homogenous population of icosahedral particles nearly identical to the design model. The particles are stable in 6.7 molar guanidine hydrochloride at up to 80 degrees Celsius, and undergo extremely abrupt, but reversible, disassembly between 2 molar and 2.25 molar guanidinium thiocyanate. The icosahedron is robust to genetic fusions: one or two copies of green fluorescent protein (GFP) can be fused to each of the 60 subunits to create highly fluorescent ‘standard candles’ for use in light microscopy, and a designed protein pentamer can be placed in the centre of each of the 20 pentameric faces to modulate the size of the entrance/exit channels of the cage. Such robust and customizable nanocages should have considerable utility in targeted drug delivery, vaccine design and synthetic biology.

Brome mosaic virus, good for an RNA virologist's basic needs.

PubMed

Kao, C C; Sivakumaran, K

2000-03-01

Abstract Taxonomic relationship: Type member of the Bromovirus genus, family Bromoviridae. A member of the alphavirus-like supergroup of positive-sense single-stranded RNA viruses. Physical properties: Virions are nonenveloped icosahedrals made up of 180 coat protein subunits (Fig. 1). The particles are 26 nm in diameter and contain 22% nucleic acid and 78% protein. The BMV genome is composed of three positive-sense, capped RNAs: RNA1 (3.2 kb), RNA2 (2.9 kb), RNA3 (2.1 kb) (Fig. 2). Viral proteins: RNA1 encodes protein 1a, containing capping and putative RNA helicase activities. RNA2 encodes protein 2a, a putative RNA-dependent RNA polymerase. RNA3 codes for two proteins: 3a, which is required for cell-to-cell movement, and the capsid protein. The capsid is translated from a subgenomic RNA, RNA4 (1.2 kb). Hosts: Monocots in the Poacea family, including Bromus inermis, Zea mays and Hordeum vulgare, in which BMV causes brown streaks. BMV can also infect the dicots Nicotiana benthamiana and several Chenopodium species. In N. benthamiana, the infection is asymptomatic while infection of Chenopodium can cause either necrotic or chlorotic lesions. Useful website:http://www4.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/10030001.htm.

Membrane Assembly during the Infection Cycle of the Giant Mimivirus

PubMed Central

Mutsafi, Yael; Shimoni, Eyal; Shimon, Amir; Minsky, Abraham

2013-01-01

Although extensively studied, the structure, cellular origin and assembly mechanism of internal membranes during viral infection remain unclear. By combining diverse imaging techniques, including the novel Scanning-Transmission Electron Microscopy tomography, we elucidate the structural stages of membrane biogenesis during the assembly of the giant DNA virus Mimivirus. We show that this elaborate multistage process occurs at a well-defined zone localized at the periphery of large viral factories that are generated in the host cytoplasm. Membrane biogenesis is initiated by fusion of multiple vesicles, ∼70 nm in diameter, that apparently derive from the host ER network and enable continuous supply of lipid components to the membrane-assembly zone. The resulting multivesicular bodies subsequently rupture to form large open single-layered membrane sheets from which viral membranes are generated. Membrane generation is accompanied by the assembly of icosahedral viral capsids in a process involving the hypothetical major capsid protein L425 that acts as a scaffolding protein. The assembly model proposed here reveals how multiple Mimivirus progeny can be continuously and efficiently generated and underscores the similarity between the infection cycles of Mimivirus and Vaccinia virus. Moreover, the membrane biogenesis process indicated by our findings provides new insights into the pathways that might mediate assembly of internal viral membranes in general. PMID:23737745

Essential role of the unordered VP2 n-terminal domain of the parvovirus MVM capsid in nuclear assembly and endosomal enlargement of the virion fivefold channel for cell entry.

PubMed

Sánchez-Martínez, Cristina; Grueso, Esther; Carroll, Miles; Rommelaere, Jean; Almendral, José M

2012-10-10

The unordered N-termini of parvovirus capsid proteins (Nt) are translocated through a channel at the icosahedral five-fold axis to serve for virus traffick. Heterologous peptides were genetically inserted at the Nt of MVM to study their functional tolerance to manipulations. Insertion of a 5T4-single-chain antibody at VP2-Nt (2Nt) yielded chimeric capsid subunits failing to enter the nucleus. The VEGFR2-binding peptide (V1) inserted at both 2Nt and VP1-Nt efficiently assembled in virions, but V1 disrupted VP1 and VP2 entry functions. The VP2 defect correlated with restricted externalization of V1-2Nt out of the coat. The specific infectivity of MVM and wtVP-pseudotyped mosaic MVM-V1 virions, upon heating and/or partial 2Nt cleavage, demonstrated that some 2Nt domains become intracellularly translocated out of the virus shell and cleaved to initiate entry. The V1 insertion defines a VP2-driven endosomal enlargement of the channel as an essential structural rearrangement performed by the MVM virion to infect. Copyright © 2012 Elsevier Inc. All rights reserved.

Application of the phase extension method in virus crystallography.

PubMed

Reddy, Vijay S

2016-01-01

The procedure for phase extension (PX) involves gradually extending the initial phases from low resolution (e.g., ~8Å) to the high-resolution limit of a diffraction data set. Structural redundancy present in the viral capsids that display icosahedral symmetry results in a high degree of non-crystallographic symmetry (NCS), which in turn translates into higher phasing power and is critical for improving and extending phases to higher resolution. Greater completeness of the diffraction data and determination of a molecular replacement solution, which entails accurately identifying the virus particle orientation(s) and position(s), are important for the smooth progression of the PX procedure. In addition, proper definition of a molecular mask (envelope) around the NCS-asymmetric unit has been found to be important for the success of density modification procedures, such as density averaging and solvent flattening. Regardless of the degree of NCS, the PX method appears to work well in all space groups, provided an accurate molecular mask is used along with reasonable initial phases. However, in the cases with space group P1, in addition to requiring a molecular mask, starting the phase extension at a higher resolution (e.g., 6Å) overcame the previously reported problems due to Babinet phases and phase flipping errors.

Functional Transplant of a Dengue Virus Serotype 3 (DENV3)-Specific Human Monoclonal Antibody Epitope into DENV1.

PubMed

Messer, William B; Yount, Boyd L; Royal, Scott R; de Alwis, Ruklanthi; Widman, Douglas G; Smith, Scott A; Crowe, James E; Pfaff, Jennifer M; Kahle, Kristen M; Doranz, Benjamin J; Ibarra, Kristie D; Harris, Eva; de Silva, Aravinda M; Baric, Ralph S

2016-05-15

The four dengue virus (DENV) serotypes, DENV1 through 4, are endemic throughout tropical and subtropical regions of the world. While first infection confers long-term protective immunity against viruses of the infecting serotype, a second infection with virus of a different serotype carries a greater risk of severe dengue disease, including dengue hemorrhagic fever and dengue shock syndrome. Recent studies demonstrate that humans exposed to DENV infections develop neutralizing antibodies that bind to quaternary epitopes formed by the viral envelope (E) protein dimers or higher-order assemblies required for the formation of the icosahedral viral envelope. Here we show that the quaternary epitope target of the human DENV3-specific neutralizing monoclonal antibody (MAb) 5J7 can be partially transplanted into a DENV1 strain by changing the core residues of the epitope contained within a single monomeric E molecule. MAb 5J7 neutralized the recombinant DENV1/3 strain in cell culture and was protective in a mouse model of infection with the DENV1/3 strain. However, the 5J7 epitope was only partially recreated by transplantation of the core residues because MAb 5J7 bound and neutralized wild-type (WT) DENV3 better than the DENV1/3 recombinant. Our studies demonstrate that it is possible to transplant a large number of discontinuous residues between DENV serotypes and partially recreate a complex antibody epitope, while retaining virus viability. Further refinement of this approach may lead to new tools for measuring epitope-specific antibody responses and new vaccine platforms. Dengue virus is the most important mosquito-borne pathogen of humans worldwide, with approximately one-half the world's population living in regions where dengue is endemic. Dengue immunity following infection is robust and thought to be conferred by antibodies raised against the infecting virus. However, the specific viral components that these antibodies recognize and how they neutralize the virus have been incompletely described. Here we map a region on dengue virus serotype 3 recognized by the human neutralizing antibody 5J7 and then test the functional significance of this region by transplanting it into a serotype 1 virus. Our studies demonstrate a region on dengue virus necessary for 5J7 binding and neutralization. Our work also demonstrates the technical feasibility of engineering dengue viruses to display targets of protective antibodies. This technology can be used to develop new dengue vaccines and diagnostic assays. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The Mammalian Cell Cycle Regulates Parvovirus Nuclear Capsid Assembly

PubMed Central

Riolobos, Laura; Domínguez, Carlos; Kann, Michael; Almendral, José M.

2015-01-01

It is unknown whether the mammalian cell cycle could impact the assembly of viruses maturing in the nucleus. We addressed this question using MVM, a reference member of the icosahedral ssDNA nuclear parvoviruses, which requires cell proliferation to infect by mechanisms partly understood. Constitutively expressed MVM capsid subunits (VPs) accumulated in the cytoplasm of mouse and human fibroblasts synchronized at G0, G1, and G1/S transition. Upon arrest release, VPs translocated to the nucleus as cells entered S phase, at efficiencies relying on cell origin and arrest method, and immediately assembled into capsids. In synchronously infected cells, the consecutive virus life cycle steps (gene expression, proteins nuclear translocation, capsid assembly, genome replication and encapsidation) proceeded tightly coupled to cell cycle progression from G0/G1 through S into G2 phase. However, a DNA synthesis stress caused by thymidine irreversibly disrupted virus life cycle, as VPs became increasingly retained in the cytoplasm hours post-stress, forming empty capsids in mouse fibroblasts, thereby impairing encapsidation of the nuclear viral DNA replicative intermediates. Synchronously infected cells subjected to density-arrest signals while traversing early S phase also blocked VPs transport, resulting in a similar misplaced cytoplasmic capsid assembly in mouse fibroblasts. In contrast, thymidine and density arrest signals deregulating virus assembly neither perturbed nuclear translocation of the NS1 protein nor viral genome replication occurring under S/G2 cycle arrest. An underlying mechanism of cell cycle control was identified in the nuclear translocation of phosphorylated VPs trimeric assembly intermediates, which accessed a non-conserved route distinct from the importin α2/β1 and transportin pathways. The exquisite cell cycle-dependence of parvovirus nuclear capsid assembly conforms a novel paradigm of time and functional coupling between cellular and virus life cycles. This junction may determine the characteristic parvovirus tropism for proliferative and cancer cells, and its disturbance could critically contribute to persistence in host tissues. PMID:26067441

[Investigation of West Nile virus RNA in blood donors by real-time RT-PCR].

PubMed

Sahiner, Fatih; Avcı, Ismail Yaşar; Bedir, Orhan; Koru, Ozgür; Sener, Kenan; Yapar, Mehmet; Kubar, Ayhan

2012-07-01

West Nile virus (WNV), a member of Flaviviridae family, is an enveloped, icosahedral symmetric RNA virus. Primary reservoir hosts of WNV are birds, but the virus can cause various infections in humans and other mammals. The most common and natural transmission way of WNV infections is mosquito bites, however, humans can be infected by different routes. The most important non-mosquito transmission route is contaminated blood and blood products. In this study, we aimed to investigate the risk of WNV transmission through blood and blood products in Ankara, Turkey. The presence of WNV RNA was investigated by in house real-time reverse transcriptase-polymerase chain reaction (RT-PCR) in serum samples obtained from 729 healthy blood donors (mean age: 27.7 years; 711 were male), regardless of the donor's seropositivity status since the virus can be transmitted at the early stages of infection when seroconversion has not yet developed. Serum samples were collected in August-September 2009, the period when these infections are more frequent due to mosquito activity. The vast majority of donors (n= 702, 96.3%) have been inhabiting in Ankara and 569 (78%) of donors have had risk factors for arboviral infections (e.g. outdoor activity, mosquito and tick bites). WNV RNA was not detected by real-time RT-PCR analysis in any serum sample included in this study. According to the results of our study, it can be said that the risk of WNV transmission through blood and blood products is low in Ankara. However, WNV seropositivity was detected within the range of 0.56 to 2.4% among blood donors in previous studies and probable and confirmed WNV infections have been reported in our region. In addition, WNV outbreaks have emerged in some countries neighbouring Turkey recently. Thus, the risk of WNV transmission through blood and blood products should not be ignored and blood donor questionnaires should be evaluated in detail.

Charge detection mass spectrometry: Instrumentation & applications to viruses

NASA Astrophysics Data System (ADS)

Pierson, Elizabeth E.

For over three decades, electrospray ionization (ESI) has been used to ionize non-covalent complexes and subsequently transfer the intact ion into the gas phase for mass spectrometry (MS) analysis. ESI generates a distribution of multiple charged ions, resulting in an m/z spectrum comprised of a series of peaks, known as a charge state envelope. To obtain mass information, the number of charges for each peak must be deduced. For smaller biological analytes like peptides, the charge states are sufficiently resolved and this process is straightforward. For macromolecular complexes exceeding ~100 kDa, this process is complicated by the broadening and shifting of charge states due to incomplete desolvation, salt adduction, and inherent mass heterogeneity. As the analyte mass approaches the MDa regime, the m/z spectrum is often comprised of a broad distribution of unresolved charge states. In such cases, mass determination is precluded. Charge detection mass spectrometry (CDMS) is an emerging MS technique for determining the masses of heterogeneous, macromolecular complexes. In CDMS, the m/z and z of single ions are measured concurrently so that mass is easily calculated. With this approach, deconvolution of an m/z spectrum is unnecessary. This measurement is carried out by passing macroions through a conductive cylinder. The induced image charge on the cylindrical detector provides information about m/z and z: the m/z is related to its time-of-flight through the detector, and the z is related to the intensity of the image charge. We have applied CDMS to study the self-assembly of virus capsids. Late-stage intermediates in the assembly of hepatitis B virus, a devastating human pathogen, have been identified. This is the first time that such intermediates have been detected and represent a significant advancement towards understanding virus capsid assembly. CDMS has also been used to identify oversized, non-icosahedral polymorphs in the assembly of woodchuck hepatitis virus capsids. Finally, CDMS has been used to characterize the purity of adeno-associated viral vectors for potential gene therapy applications.

Synthesis of boron suboxide from boron and boric acid under mild pressure and temperature conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiao, Xiaopeng; Jin, Hua; Ding, Zhanhui

2011-05-15

Graphical abstract: Well-crystallized and icosahedral B{sub 6}O crystals were prepared by reacting boron and boric acid at milder reaction conditions (1 GPa and 1300 {sup o}C for 2 h) as compared to previous work.. Research highlights: {yields} Well-crystallized icosahedral B{sub 6}O was synthesized by reacting boric acid and boron. {yields} The synthesis conditions (1 GPa and 1300 {sup o}C for 2 h) are milder in comparison with previous work. {yields} The more practical synthesis method may make B{sub 6}O as a potential substitute for diamond in industry. -- Abstract: Boron suboxide (B{sub 6}O) was synthesized by reacting boron and boricmore » acid (H{sub 3}BO{sub 3}) at pressures between 1 and 10 GPa, and at temperatures between 1300 and 1400 {sup o}C. The B{sub 6}O samples prepared were icosahedral with diameters ranging from 20 to 300 nm. Well-crystallized and icosahedral crystals with an average size of {approx}100 nm can be obtained at milder reaction conditions (1 GPa and 1300 {sup o}C for 2 h) as compared to previous work. The bulk B{sub 6}O sample was stable in air at 600 {sup o}C and then slowly oxidized up to 1000 {sup o}C. The relatively mild synthetic conditions developed in this study provide a more practical synthesis of B{sub 6}O, which may potentially be used as a substitute for diamond in industry as a new superhard material.« less

Science Using an Electrostatic Levitation Furnace in the MUCAT Sector at the APS

NASA Technical Reports Server (NTRS)

Goldman, A.; Kelton, K. F.; Rogers, J. R.

2004-01-01

The original motivation for the construction of the BESL prototype was to obtain the first proof of a 50-year-old hypothesis regarding the solidification of liquid metals. Since the 1950s it has been known that under proper conditions liquid metals can be cooled below their melting temperature (undercooled) without crystallizing to the stable solid phase. In 1952 Frank proposed that this was because the atoms in the metallic liquid were arranged with the symmetry of an icosahedron, a Platonic solid consisting of 20 tetrahedra (4-sided pyramid-shaped polyhedra) arranged around a common center. Since this local atomic order is incompatible with the long-range translational periodicity of crystal phases, a barrier is formed to the formation of small regions of the crystal phase, the nucleation barrier. A proof of Frank's hypothesis required a direct correlation between measured icosahedral order in the undercooled liquid and the nucleation barrier. The tendency of sample containers to catalyze nucleation obscured this relation, requiring containerless techniques. Combining containerless processing techniques for electrostatically levitated droplets (ESL) with x-ray synchrotron methods, a team from Washington University, St. Louis, MO, NASA Marshall Space Flight Center, and MUCAT at the APS demonstrated an increasing icosahedral order in TiZrNi liquids with decreasing temperature below the melting temperature. The increased icosahedral order caused the transformation of the liquid to a metastable icosahedral quasicrystal phase, instead of the stable tetrahedrally-coordinated crystal intermetallic, giving the first clear demonstration of the connection between the nucleation barrier and the local structure of the liquid, verifying Frank's hypothesis for this alloy.

Packaging of Polyelectrolytes in Viral Capsids: The Interplay Between Polymer Length and Capsid Size

NASA Astrophysics Data System (ADS)

Knobler, Charles

2008-03-01

Each particle of the Cowpea Chlorotic Mottle Virus (CCMV) has a very small ``parts list,'' consisting of two components: a molecule of single-stranded RNA and a 190-residue protein that makes up the 28-nm diameter icosahedral capsid. When purified viral RNA and capsid protein are mixed in solution at an appropriate pH and ionic strength, infectious wild-type viruses form spontaneously. Virus-like particles (VLPs) are formed when the protein self assembles around other anionic polymers such as poly(styrene sulfonate) (PSS). Under different pH and ionic strength conditions the capsid protein can assemble by itself into empty capsids, multishell structures, tubes and sheets. To explore the effect on virion size of the competition between the preferred curvature of the protein and the size of the packaged cargo we have examined the formation of VLPs around PSS polymers with molecular weights ranging from 400 kDa to 3.4 MDa. Two distinct sizes are observed -- 22 nm for the lower molecular weights, jumping to 27 nm at 2 MDa. While under given conditions the size of PSS in solution is directly determined by its molecular weight, the self-complementarity of RNA makes its solution structure dependent on the nucleotide sequence as well. We have therefore employed Small-Angle X-ray Scattering and Fluorescence Correlation Spectroscopy to examine the sizes of viral and non-viral RNAs of identical lengths. A model for the assembly that includes both the self-interactions of the polyelectrolyte and the capsid proteins and the interactions between them provides insight into the experimental results.

Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly.

PubMed

Wang, Xurong; Zhang, Fuxian; Su, Rui; Li, Xiaowu; Chen, Wenyuan; Chen, Qingxiu; Yang, Tao; Wang, Jiawei; Liu, Hongrong; Fang, Qin; Cheng, Lingpeng

2018-06-25

Most double-stranded RNA (dsRNA) viruses transcribe RNA plus strands within a common innermost capsid shell. This process requires coordinated efforts by RNA-dependent RNA polymerase (RdRp) together with other capsid proteins and genomic RNA. Here we report the near-atomic resolution structure of the RdRp protein VP2 in complex with its cofactor protein VP4 and genomic RNA within an aquareovirus capsid using 200-kV cryoelectron microscopy and symmetry-mismatch reconstruction. The structure of these capsid proteins enabled us to observe the elaborate nonicosahedral structure within the double-layered icosahedral capsid. Our structure shows that the RdRp complex is anchored at the inner surface of the capsid shell and interacts with genomic dsRNA and four of the five asymmetrically arranged N termini of the capsid shell proteins under the fivefold axis, implying roles for these N termini in virus assembly. The binding site of the RNA end at VP2 is different from the RNA cap binding site identified in the crystal structure of orthoreovirus RdRp λ3, although the structures of VP2 and λ3 are almost identical. A loop, which was thought to separate the RNA template and transcript, interacts with an apical domain of the capsid shell protein, suggesting a mechanism for regulating RdRp replication and transcription. A conserved nucleoside triphosphate binding site was localized in our RdRp cofactor protein VP4 structure, and interactions between the VP4 and the genomic RNA were identified.

Nonhydrostatic icosahedral atmospheric model (NICAM) for global cloud resolving simulations

NASA Astrophysics Data System (ADS)

Satoh, M.; Matsuno, T.; Tomita, H.; Miura, H.; Nasuno, T.; Iga, S.

2008-03-01

A new type of ultra-high resolution atmospheric global circulation model is developed. The new model is designed to perform "cloud resolving simulations" by directly calculating deep convection and meso-scale circulations, which play key roles not only in the tropical circulations but in the global circulations of the atmosphere. Since cores of deep convection have a few km in horizontal size, they have not directly been resolved by existing atmospheric general circulation models (AGCMs). In order to drastically enhance horizontal resolution, a new framework of a global atmospheric model is required; we adopted nonhydrostatic governing equations and icosahedral grids to the new model, and call it Nonhydrostatic ICosahedral Atmospheric Model (NICAM). In this article, we review governing equations and numerical techniques employed, and present the results from the unique 3.5-km mesh global experiments—with O(10 9) computational nodes—using realistic topography and land/ocean surface thermal forcing. The results show realistic behaviors of multi-scale convective systems in the tropics, which have not been captured by AGCMs. We also argue future perspective of the roles of the new model in the next generation atmospheric sciences.

Icosahedral quasicrystalline (Ti1.6V0.4Ni)100-xScx alloys: Synthesis, structure and their application in Ni-MH batteries

NASA Astrophysics Data System (ADS)

Hu, Wen; Yi, Jianhong; Zheng, Biju; Wang, Limin

2013-06-01

Thanks to the revolutionary discovery of 5-fold symmetry contributed by Shechtman, quasicrystal is now recognized as another solid-state existing form. As the second largest class of quasicrystals, titanium-based icosahedral quasicrystals are very promising for hydrogen storage applications owing to their inherent abundant interstitial sites and favorable hydrogen-metal chemistry. In this context, (Ti1.6V0.4Ni)100-xScx (x=0.5-6) quaternary icosahedral quasicrystals have been successfully synthesized via arc-melting and subsequent melt-spinning techniques, and then their electrochemical performance toward hydrogen is explored. When the molar ratio of Sc addition is under 1%, a maximum discharge capacity of about 270 mA h g-1 can be delivered. With further increasing Sc amount to 6%, good cycling stability as well as significantly retarded self-discharge rate (capacity retention 94% after 24 h relaxation) is observed. But meanwhile, the discharge capacities fall into 250-240 mA h g-1, and the electrocatalytic activity improvement is highly demanded.

Simulations of polymorphic icosahedral shells assembling around many cargo molecules

NASA Astrophysics Data System (ADS)

Mohajerani, Farzaneh; Perlmutter, Jason; Hagan, Michael

Bacterial microcompartments (BMCs) are large icosahedral shells that sequester the enzymes and reactants responsible for particular metabolic pathways in bacteria. Although different BMCs vary in size and encapsulate different cargoes, they are constructed from similar pentameric and hexameric shell proteins. Despite recent groundbreaking experiments which visualized the formation of individual BMCs, the detailed assembly pathways and the factors which control shell size remain unclear. In this talk, we describe theoretical and computational models that describe the dynamical encapsulation of hundreds of cargo molecules by self-assembling icosahedral shells. We present phase diagrams and analysis of dynamical simulation trajectories showing how the thermodynamics, assembly pathways, and emergent structures depend on the interactions among shell proteins and cargo molecules. Our model suggests a mechanism for controlling insertion of the 12 pentamers required for a closed shell topology, and the relationship between assembly pathway and BMC size polydispersity. In addition to elucidating how native BMCs assemble,our results establish principles for reengineering BMCs or viral capsids as customizable nanoreactors that can assemble around a programmable set of enzymes and reactants. Supported by NIH R01GM108021 and Brandeis MRSEC DMR-1420382.

Reduction of variance in spectral estimates for correction of ultrasonic aberration.

PubMed

Astheimer, Jeffrey P; Pilkington, Wayne C; Waag, Robert C

2006-01-01

A variance reduction factor is defined to describe the rate of convergence and accuracy of spectra estimated from overlapping ultrasonic scattering volumes when the scattering is from a spatially uncorrelated medium. Assuming that the individual volumes are localized by a spherically symmetric Gaussian window and that centers of the volumes are located on orbits of an icosahedral rotation group, the factor is minimized by adjusting the weight and radius of each orbit. Conditions necessary for the application of the variance reduction method, particularly for statistical estimation of aberration, are examined. The smallest possible value of the factor is found by allowing an unlimited number of centers constrained only to be within a ball rather than on icosahedral orbits. Computations using orbits formed by icosahedral vertices, face centers, and edge midpoints with a constraint radius limited to a small multiple of the Gaussian width show that a significant reduction of variance can be achieved from a small number of centers in the confined volume and that this reduction is nearly the maximum obtainable from an unlimited number of centers in the same volume.

Sigma-phase packing of icosahedral clusters in 780-atom tetragonal crystals of Cr5Ni3Si2 and V15Ni10Si that by twinning achieve 8-fold rotational point-group symmetry

PubMed Central

Pauling, Linus

1988-01-01

A 780-atom primitive tetragonal unit with edges 27.3, 27.3, and 12.6 Å is assigned to rapidly solidified Cu5Ni3Si2 and V15Ni10Si by analysis of electron diffraction photographs with the assumption that the crystals contain icosahedral clusters. There are thirty 26-atom clusters at the sigma-phase positions. Apparent 8-fold symmetry results from 45° twinning on the basal plane. PMID:16593915

Sigma-phase packing of icosahedral clusters in 780-atom tetragonal crystals of Cr(5)Ni(3)Si(2) and V(15)Ni(10)Si that by twinning achieve 8-fold rotational point-group symmetry.

PubMed

Pauling, L

1988-04-01

A 780-atom primitive tetragonal unit with edges 27.3, 27.3, and 12.6 A is assigned to rapidly solidified Cu(5)Ni(3)Si(2) and V(15)Ni(10)Si by analysis of electron diffraction photographs with the assumption that the crystals contain icosahedral clusters. There are thirty 26-atom clusters at the sigma-phase positions. Apparent 8-fold symmetry results from 45 degrees twinning on the basal plane.

Magnetism in icosahedral quasicrystals: current status and open questions

DOE PAGES

Goldman, Alan I.

2014-07-02

Progress in our understanding of the magnetic properties of R-containing icosahedral quasicrystals (R = rare earth element) from over 20 years of experimental effort is reviewed. This includes the much studied R-Mg-Zn and R-Mg-Cd ternary systems, as well as several magnetic quasicrystals that have been discovered and investigated more recently including Sc-Fe-Zn, R-Ag-In, Yb-Au-Al, the recently synthesized R-Cd binary quasicrystals, and their periodic approximants. In many ways, the magnetic properties among these quasicrystals are very similar. However, differences are observed that suggest new experiments and promising directions for future research.

Structural Conservation of the Myoviridae Phage Tail Sheath Protein Fold

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aksyuk, Anastasia A.; Kurochkina, Lidia P.; Fokine, Andrei

2012-02-21

Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 {angstrom} diameter icosahedral head and a 2000 {angstrom}-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 {angstrom} resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 {angstrom} resolution. Despite low sequence identity between these proteins, all ofmore » these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.« less

Mechanisms of DNA Packaging by Large Double-Stranded DNA Viruses

PubMed Central

Rao, Venigalla B.; Feiss, Michael

2016-01-01

Translocation of viral double-stranded DNA (dsDNA) into the icosahedral prohead shell is catalyzed by TerL, a motor protein that has ATPase, endonuclease, and translocase activities. TerL, following endonucleolytic cleavage of immature viral DNA concatemer recognized by TerS, assembles into a pentameric ring motor on the prohead’s portal vertex and uses ATP hydrolysis energy for DNA translocation. TerL’s N-terminal ATPase is connected by a hinge to the C-terminal endonuclease. Inchworm models propose that modest domain motions accompanying ATP hydrolysis are amplified, through changes in electrostatic interactions, into larger movements of the C-terminal domain bound to DNA. In phage φ29, four of the five TerL subunits sequentially hydrolyze ATP, each powering translocation of 2.5 bp. After one viral genome is encapsidated, the internal pressure signals termination of packaging and ejection of the motor. Current focus is on the structures of packaging complexes and the dynamics of TerL during DNA packaging, endonuclease regulation, and motor mechanics. PMID:26958920

The blood parasites of anurans from Costa Rica with reflections on the taxonomy of their trypanosomes.

PubMed

Desser, S S

2001-02-01

During May 1997, specimens of 7 species of anurans, that included 5 Phrynohyas venulosa Laurenti, 5 Rana forreri Boulenger, 7 Rana vaillanti Brucchi, 6 Eleutherodactylus fitzingeri Schimdt, 4 Smilisca baudinii Duméril and Bibron, 1 Leptodactylus melanonotus, and 3 Bufo marinus Linneaus, from the Guanacaste Conservation Area, Costa Rica were examined for blood parasites. Their hematozoan fauna included intraerythrocytic and intraleukocytic icosahedral viruses, a rickettsia (Aegyptianella sp.), 2 species of Hepatozoon, Lankesterella minima, 2 unknown species of apicomplexans, 9 morphologically distinct types of trypanosomes, and 2 species of microfilariae. Rana vaillanti, the most aquatic species of frog, harbored the most species of parasites. Recent evidence indicates that morphological changes in the highly pleomorphic trypanosomes of anurans from different geographical regions have not kept pace with biochemical (isozyme) and molecular (DNA sequence) changes. Describing new species based solely on bloodstream trypomastigotes is discouraged. Additional criteria described herein should be applied when naming new species of anuran trypanosomes.

Icosahedral quasicrystalline (Ti₁.₆V₀.₄Ni)₁₀₀₋xScx alloys: Synthesis, structure and their application in Ni-MH batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Wen; State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, CAS, Changchun 130022, Jilin; Yi, Jianhong

2013-06-01

Thanks to the revolutionary discovery of 5-fold symmetry contributed by Shechtman, quasicrystal is now recognized as another solid-state existing form. As the second largest class of quasicrystals, titanium-based icosahedral quasicrystals are very promising for hydrogen storage applications owing to their inherent abundant interstitial sites and favorable hydrogen-metal chemistry. In this context, (Ti₁.₆V₀.₄Ni)₁₀₀₋xScx (x=0.5–6) quaternary icosahedral quasicrystals have been successfully synthesized via arc-melting and subsequent melt-spinning techniques, and then their electrochemical performance toward hydrogen is explored. When the molar ratio of Sc addition is under 1%, a maximum discharge capacity of about 270 mA h g⁻¹ can be delivered. With furthermore » increasing Sc amount to 6%, good cycling stability as well as significantly retarded self-discharge rate (capacity retention 94% after 24 h relaxation) is observed. But meanwhile, the discharge capacities fall into 250-240 mA h g⁻¹, and the electrocatalytic activity improvement is highly demanded. - Graphical abstract: Quasicrystalline Ti–V–Ni–Sc hydrogen storage materials: Sc addition into Ti₁.₆V₀.₄Ni alloy forms the icosahedral phase (see picture). With optimal Sc dosage, the anodic cycling stability and self-discharge property are greatly enhanced. - Highlights: • Crystalline disallowed 5-fold symmetry is present in (Ti₁.₆V₀.₄Ni)₁₀₀₋xScx alloys. • Ti-based metastable quasicrystalline alloys can store hydrogen electrochemically. • A maximum discharge capacity of 270 mA h g⁻¹ can be delivered. • Advantageous cycle stability and self-discharge property benefit from Sc addition. • Ti and V dissolution is suppressed by an oxide layer resulting from Sc corrosion.« less

Molecular basis of endosomal-membrane association for the dengue virus envelope protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rogers, David M.; Kent, Michael S.; Rempe, Susan B.

Dengue virus is coated by an icosahedral shell of 90 envelope protein dimers that convert to trimers at low pH and promote fusion of its membrane with the membrane of the host endosome. We provide the first estimates for the free energy barrier and minimum for two key steps in this process: host membrane bending and protein–membrane binding. Both are studied using complementary membrane elastic, continuum electrostatics and all-atom molecular dynamics simulations. The predicted host membrane bending required to form an initial fusion stalk presents a 22–30 kcal/mol free energy barrier according to a constrained membrane elastic model. Combined continuummore » and molecular dynamics results predict a 15 kcal/mol free energy decrease on binding of each trimer of dengue envelope protein to a membrane with 30% anionic phosphatidylglycerol lipid. The bending cost depends on the preferred curvature of the lipids composing the host membrane leaflets, while the free energy gained for protein binding depends on the surface charge density of the host membrane. The fusion loop of the envelope protein inserts exactly at the level of the interface between the membrane's hydrophobic and head-group regions. As a result, the methods used in this work provide a means for further characterization of the structures and free energies of protein-assisted membrane fusion.« less

Molecular basis of endosomal-membrane association for the dengue virus envelope protein

DOE PAGES

Rogers, David M.; Kent, Michael S.; Rempe, Susan B.

2015-01-02

Dengue virus is coated by an icosahedral shell of 90 envelope protein dimers that convert to trimers at low pH and promote fusion of its membrane with the membrane of the host endosome. We provide the first estimates for the free energy barrier and minimum for two key steps in this process: host membrane bending and protein–membrane binding. Both are studied using complementary membrane elastic, continuum electrostatics and all-atom molecular dynamics simulations. The predicted host membrane bending required to form an initial fusion stalk presents a 22–30 kcal/mol free energy barrier according to a constrained membrane elastic model. Combined continuummore » and molecular dynamics results predict a 15 kcal/mol free energy decrease on binding of each trimer of dengue envelope protein to a membrane with 30% anionic phosphatidylglycerol lipid. The bending cost depends on the preferred curvature of the lipids composing the host membrane leaflets, while the free energy gained for protein binding depends on the surface charge density of the host membrane. The fusion loop of the envelope protein inserts exactly at the level of the interface between the membrane's hydrophobic and head-group regions. As a result, the methods used in this work provide a means for further characterization of the structures and free energies of protein-assisted membrane fusion.« less

Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus.

PubMed

Yoshimura, Masato; Chen, Nai Chi; Guan, Hong Hsiang; Chuankhayan, Phimonphan; Lin, Chien Chih; Nakagawa, Atsushi; Chen, Chun Jung

2016-07-01

Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures.

Rigid-Cluster Models of Conformational Transitions in Macromolecular Machines and Assemblies

PubMed Central

Kim, Moon K.; Jernigan, Robert L.; Chirikjian, Gregory S.

2005-01-01

We present a rigid-body-based technique (called rigid-cluster elastic network interpolation) to generate feasible transition pathways between two distinct conformations of a macromolecular assembly. Many biological molecules and assemblies consist of domains which act more or less as rigid bodies during large conformational changes. These collective motions are thought to be strongly related with the functions of a system. This fact encourages us to simply model a macromolecule or assembly as a set of rigid bodies which are interconnected with distance constraints. In previous articles, we developed coarse-grained elastic network interpolation (ENI) in which, for example, only Cα atoms are selected as representatives in each residue of a protein. We interpolate distance differences of two conformations in ENI by using a simple quadratic cost function, and the feasible conformations are generated without steric conflicts. Rigid-cluster interpolation is an extension of the ENI method with rigid-clusters replacing point masses. Now the intermediate conformations in an anharmonic pathway can be determined by the translational and rotational displacements of large clusters in such a way that distance constraints are observed. We present the derivation of the rigid-cluster model and apply it to a variety of macromolecular assemblies. Rigid-cluster ENI is then modified for a hybrid model represented by a mixture of rigid clusters and point masses. Simulation results show that both rigid-cluster and hybrid ENI methods generate sterically feasible pathways of large systems in a very short time. For example, the HK97 virus capsid is an icosahedral symmetric assembly composed of 60 identical asymmetric units. Its original Hessian matrix size for a Cα coarse-grained model is >(300,000)2. However, it reduces to (84)2 when we apply the rigid-cluster model with icosahedral symmetry constraints. The computational cost of the interpolation no longer scales heavily with the size of structures; instead, it depends strongly on the minimal number of rigid clusters into which the system can be decomposed. PMID:15833998

Internal Proteins of the Procapsid and Mature Capsids of Herpes Simplex Virus 1 Mapped by Bubblegram Imaging

PubMed Central

Wu, Weimin; Newcomb, William W.; Cheng, Naiqian; Aksyuk, Anastasia; Winkler, Dennis C.

2016-01-01

ABSTRACT The herpes simplex virus 1 (HSV-1) capsid is a huge assembly, ∼1,250 Å in diameter, and is composed of thousands of protein subunits with a combined mass of ∼200 MDa, housing a 100-MDa genome. First, a procapsid is formed through coassembly of the surface shell with an inner scaffolding shell; then the procapsid matures via a major structural transformation, triggered by limited proteolysis of the scaffolding proteins. Three mature capsids are found in the nuclei of infected cells. A capsids are empty, B capsids retain a shrunken scaffolding shell, and C capsids—which develop into infectious virions—are filled with DNA and ostensibly have expelled the scaffolding shell. The possible presence of other internal proteins in C capsids has been moot as, in cryo-electron microscopy (cryo-EM), they would be camouflaged by the surrounding DNA. We have used bubblegram imaging to map internal proteins in all four capsids, aided by the discovery that the scaffolding protein is exceptionally prone to radiation-induced bubbling. We confirmed that this protein forms thick-walled inner shells in the procapsid and the B capsid. C capsids generate two classes of bubbles: one occupies positions beneath the vertices of the icosahedral surface shell, and the other is distributed throughout its interior. A likely candidate is the viral protease. A subpopulation of C capsids bubbles particularly profusely and may represent particles in which expulsion of scaffold and DNA packaging are incomplete. Based on the procapsid structure, we propose that the axial channels of hexameric capsomers afford the pathway via which the scaffolding protein is expelled. IMPORTANCE In addition to DNA, capsids of tailed bacteriophages and their distant relatives, herpesviruses, contain internal proteins. These proteins are often essential for infectivity but are difficult to locate within the virion. A novel adaptation of cryo-EM based on detecting gas bubbles generated by radiation damage was used to localize internal proteins of HSV-1, yielding insights into how capsid maturation is regulated. The scaffolding protein, which forms inner shells in the procapsid and B capsid, is exceptionally bubbling-prone. In the mature DNA-filled C capsid, a previously undetected protein was found to underlie the icosahedral vertices: this is tentatively assigned as a storage form of the viral protease. We also observed a capsid species that appears to contain substantial amounts of scaffolding protein as well as DNA, suggesting that DNA packaging and expulsion of the scaffolding protein are coupled processes. PMID:26984725

Atomic Scale Investigation of Structural Properties and Glass Forming Ability of Ti100-x Al x Metallic Glasses

NASA Astrophysics Data System (ADS)

Tahiri, M.; Hasnaoui, A.; Sbiaai, K.

2018-03-01

In this work, we employed molecular dynamics (MD) simulations to study Ti-Al metallic glasses (MGs) using the embedded atom method (EAM) potential to model the atomic interaction with different compositions. The results showed evidence of the metallic glass formation induced by the split occurring in the second peak of the radial distribution function (RDF) curves implying both Ti and Al atoms. The common neighbor analysis (CNA) method confirmed the presence of the icosahedral clusters with a maximum amount observed for an alloy with 75 pct of Al. Analysis of coordination numbers (CNs) indicated that the total CNs are nearly unchanged in these systems. Finally, Voronoi tessellation analyses (VTA) showed a higher value of the number of icosahedral units at Ti25Al75 composition. This specific composition represents a nearby peritectic point localized at a low melting point in the Ti-Al binary phase diagram. The glass forming ability (GFA) becomes important when the fraction of Al increases by forming and connecting "icosahedral-like" clusters (12-coordinated <0, 0, 12, 0> and 13-coordinated <0, 1, 10, 2>) and by playing a main role in the structure stability of the Ti-Al MGs.

Atomic Scale Investigation of Structural Properties and Glass Forming Ability of Ti100- x Al x Metallic Glasses

NASA Astrophysics Data System (ADS)

Tahiri, M.; Hasnaoui, A.; Sbiaai, K.

2018-06-01

In this work, we employed molecular dynamics (MD) simulations to study Ti-Al metallic glasses (MGs) using the embedded atom method (EAM) potential to model the atomic interaction with different compositions. The results showed evidence of the metallic glass formation induced by the split occurring in the second peak of the radial distribution function (RDF) curves implying both Ti and Al atoms. The common neighbor analysis (CNA) method confirmed the presence of the icosahedral clusters with a maximum amount observed for an alloy with 75 pct of Al. Analysis of coordination numbers (CNs) indicated that the total CNs are nearly unchanged in these systems. Finally, Voronoi tessellation analyses (VTA) showed a higher value of the number of icosahedral units at Ti25Al75 composition. This specific composition represents a nearby peritectic point localized at a low melting point in the Ti-Al binary phase diagram. The glass forming ability (GFA) becomes important when the fraction of Al increases by forming and connecting "icosahedral-like" clusters (12-coordinated <0, 0, 12, 0> and 13-coordinated <0, 1, 10, 2>) and by playing a main role in the structure stability of the Ti-Al MGs.

Virus-like particle expression and assembly in plants: hepatitis B and Norwalk viruses.

PubMed

Huang, Zhong; Elkin, Galina; Maloney, Bryan J; Beuhner, Norene; Arntzen, Charles J; Thanavala, Yasmin; Mason, Hugh S

2005-03-07

Expression of vaccine antigens in plants and delivery via ingestion of transgenic plant material has shown promise in numerous pre-clinical animal studies and in a few clinical trials. A number of different viral antigens have been tested, and among the most promising are those that can assemble virus-like particles (VLP), which mimic the form of authentic virions and display neutralizing antibody epitopes. We have extensively studied plant expression, VLP assembly, and immunogenicity of hepatitis B surface antigen (HBsAg) and Norwalk virus capsid protein (NVCP). The HBsAg small protein (S protein) was found by TEM to assemble tubular membrane complexes derived from endoplasmic reticulum in suspension cultured cells of tobacco and soybean, and in potato leaf and tuber tissues. The potato material was immunogenic in mice upon delivery by ingestion. Here we describe the plant expression and immunogenicity of HBsAg middle protein (M protein or pre-S2 + S) which contains additional 55 amino acid pre-S2 region at N-terminus of the S protein. Plant-derived recombinant M protein provoked stronger serum antibody responses against HBsAg than did S protein when injected systemically in mice. We discuss implications for use of fusion proteins for enhanced immunogenicity and mucosal targeting of HBsAg, as well as delivery of heterologous fused antigens. NVCP expressed in plants assembled 38 nm virion-size icosahedral (T = 3) VLP, similar to those produced in insect cells. The VLP stimulated serum IgG and IgA responses in mice and humans when they were delivered by ingestion of fresh potato tuber. Here we show that freeze-drying of transgenic NVCP tomato fruit yielded stable preparations that stimulated excellent IgG and IgA responses against NVCP when fed to mice. However, the predominant VLP form in tomato fruit was the small 23 nm particle also observed in insect cell-derived NVCP.

Comparative Genomics of Chrysochromulina Ericina Virus and Other Microalga-Infecting Large DNA Viruses Highlights Their Intricate Evolutionary Relationship with the Established Mimiviridae Family.

PubMed

Gallot-Lavallée, Lucie; Blanc, Guillaume; Claverie, Jean-Michel

2017-07-15

Chrysochromulina ericina virus CeV-01B (CeV) was isolated from Norwegian coastal waters in 1998. Its icosahedral particle is 160 nm in diameter and encloses a 474-kb double-stranded DNA (dsDNA) genome. This virus, although infecting a microalga (the haptophyceae Haptolina ericina , formerly Chrysochromulina ericina ), is phylogenetically related to members of the Mimiviridae family, initially established with the acanthamoeba-infecting mimivirus and megavirus as prototypes. This family was later split into two genera ( Mimivirus and Cafeteriavirus ) following the characterization of a virus infecting the heterotrophic stramenopile Cafeteria roenbergensis (CroV). CeV, as well as two of its close relatives, which infect the unicellular photosynthetic eukaryotes Phaeocystis globosa (Phaeocystis globosa virus [PgV]) and Aureococcus anophagefferens (Aureococcus anophagefferens virus [AaV]), are currently unclassified by the International Committee on Viral Taxonomy (ICTV). The detailed comparative analysis of the CeV genome presented here confirms the phylogenetic affinity of this emerging group of microalga-infecting viruses with the Mimiviridae but argues in favor of their classification inside a distinct clade within the family. Although CeV, PgV, and AaV share more common features among them than with the larger Mimiviridae , they also exhibit a large complement of unique genes, attesting to their complex evolutionary history. We identified several gene fusion events and cases of convergent evolution involving independent lateral gene acquisitions. Finally, CeV possesses an unusual number of inteins, some of which are closely related despite being inserted in nonhomologous genes. This appears to contradict the paradigm of allele-specific inteins and suggests that the Mimiviridae are especially efficient in spreading inteins while enlarging their repertoire of homing genes. IMPORTANCE Although it infects the microalga Chrysochromulina ericina , CeV is more closely related to acanthamoeba-infecting viruses of the Mimiviridae family than to any member of the Phycodnaviridae , the ICTV-approved family historically including all alga-infecting large dsDNA viruses. CeV, as well as its relatives that infect the microalgae Phaeocystic globosa (PgV) and Aureococcus anophagefferens (AaV), remains officially unclassified and a source of confusion in the literature. Our comparative analysis of the CeV genome in the context of this emerging group of alga-infecting viruses suggests that they belong to a distinct clade within the established Mimiviridae family. The presence of a large number of unique genes as well as specific gene fusion events, evolutionary convergences, and inteins integrated at unusual locations document the complex evolutionary history of the CeV lineage. Copyright © 2017 American Society for Microbiology.

Evidence that Hsc70 Is Associated with Cucumber Necrosis Virus Particles and Plays a Role in Particle Disassembly

PubMed Central

Alam, Syed Benazir

2016-01-01

ABSTRACT Uncoating of a virus particle to expose its nucleic acid is a critical aspect of the viral multiplication cycle, as it is essential for the establishment of infection. In the present study, we investigated the role of plant HSP70 homologs in the uncoating process of Cucumber necrosis virus (CNV), a nonenveloped positive-sense single-stranded RNA [(+)ssRNA] virus having a T=3 icosahedral capsid. We have found through Western blot analysis and mass spectrometry that the HSP70 homolog Hsc70-2 copurifies with CNV particles. Virus overlay and immunogold labeling assays suggest that Hsc70-2 is physically bound to virions. Furthermore, trypsin digestion profiles suggest that the bound Hsc70-2 is partially protected by the virus, indicating an intimate association with particles. In investigating a possible role of Hsc70-2 in particle disassembly, we showed that particles incubated with Hsp70/Hsc70 antibody produce fewer local lesions than those incubated with prebleed control antibody on Chenopodium quinoa. In conjunction, CNV virions purified using CsCl and having undetectable amounts of Hsc70-2 produce fewer local lesions. We also have found that plants with elevated levels of HSP70/Hsc70 produce higher numbers of local lesions following CNV inoculation. Finally, incubation of recombinant Nicotiana benthamiana Hsc70-2 with virus particles in vitro leads to conformational changes or partial disassembly of capsids as determined by transmission electron microscopy, and particles are more sensitive to chymotrypsin digestion. This is the first report suggesting that a cellular Hsc70 chaperone is involved in disassembly of a plant virus. IMPORTANCE Virus particles must disassemble and release their nucleic acid in order to establish infection in a cell. Despite the importance of disassembly in the ability of a virus to infect its host, little is known about this process, especially in the case of nonenveloped spherical RNA viruses. Previous work has shown that host HSP70 homologs play multiple roles in the CNV infection cycle. We therefore examined the potential role of these cellular components in the CNV disassembly process. We show that the HSP70 family member Hsc70-2 is physically associated with CNV virions and that HSP70 antibody reduces the ability of CNV to establish infection. Statistically significantly fewer lesions are produced when virions having undetectable HSc70-2 are used as an inoculum. Finally incubation of Hsc70-2 with CNV particles results in conformational changes in particles. Taken together, our data point to an important role of the host factor Hsc70-2 in CNV disassembly. PMID:27807229

Electron cryo-tomographic structure of cystovirus phi 12.

PubMed

Hu, Guo-Bin; Wei, Hui; Rice, William J; Stokes, David L; Gottlieb, Paul

2008-03-01

Bacteriophage phi 12 is a member of the Cystoviridae virus family and contains a genome consisting of three segments of double-stranded RNA (dsRNA). This virus family contains eight identified members, of which four have been classified in regard to their complete genomic sequence and encoded viral proteins. A phospholipid envelope that contains the integral proteins P6, P9, P10, and P13 surrounds the viral particles. In species phi 6, host infection requires binding of a multimeric P3 complex to type IV pili. In species varphi8, phi 12, and phi 13, the attachment apparatus is a heteromeric protein assembly that utilizes the rough lipopolysaccharide (rlps) as a receptor. In phi 8 the protein components are designated P3a and P3b while in species phi 12 proteins P3a and P3c have been identified in the complex. The phospholipid envelope of the cystoviruses surrounds a nucleocapsid (NC) composed of two shells. The outer shell is composed of protein P8 with a T=13 icosahedral lattice while the primary component of the inner shell is a dodecahedral frame composed of dimeric protein P1. For the current study, the 3D architecture of the intact phi 12 virus was obtained by electron cryo-tomography. The nucleocapsid appears to be centered within the membrane envelope and possibly attached to it by bridging structures. Two types of densities were observed protruding from the membrane envelope. The densities of the first type were elongated, running parallel, and closely associated to the envelope outer surface. In contrast, the second density was positioned about 12 nm above the envelope connected to it by a flexible low-density stem. This second structure formed a torroidal structure termed "the donut" and appears to inhibit BHT-induced viral envelope fusion.

Different architectures in the assembly of infectious bursal disease virus capsid proteins expressed in insect cells.

PubMed

Martinez-Torrecuadrada, J L; Castón, J R; Castro, M; Carrascosa, J L; Rodriguez, J F; Casal, J I

2000-12-20

Infectious bursal disease virus (IBDV) capsid is formed by the processing of a large polyprotein and subsequent assembly of VPX/VP2 and VP3. To learn more about the processing of the polyprotein and factors affecting the correct assembly of the viral capsid in vitro, different constructs were made using two baculovirus transfer vectors, pFastBac and pAcYM1. Surprisingly, the expression of the capsid proteins gave rise to different types of particles in each system, as observed by electron microscopy and immunofluorescence. FastBac expression led to the production of only rigid tubular structures, similar to those described as type I in viral infection. Western blot analysis revealed that these rigid tubules are formed exclusively by VPX. These tubules revealed a hexagonal arrangement of units that are trimer clustered, similar to those observed in IBDV virions. In contrast, pAcYM1 expression led to the assembly of virus-like particles (VLPs), flexible tubules, and intermediate assembly products formed by icosahedral caps elongated in tubes, suggesting an aberrant morphogenesis. Processing of VPX to VP2 seems to be a crucial requirement for the proper morphogenesis and assembly of IBDV particles. After immunoelectron microscopy, VPX/VP2 was detected on the surface of tubules and VLPs. We also demonstrated that VP3 is found only on the inner surfaces of VLPs and caps of the tubular structures. In summary, assembly of VLPs requires the internal scaffolding of VP3, which seems to induce the closing of the tubular architecture into VLPs and, thereafter, the subsequent processing of VPX to VP2. Copyright 2000 Academic Press.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gupta, Arunava; Prevelige, Peter E

The primary goal of the project was to develop protein-templated approaches for the synthesis and directed assembly of semiconductor nanomaterials that are efficient for visible light absorption and hydrogen production. In general, visible-light-driven photocatalysis reactions exhibit low quantum efficiency for solar energy conversion primarily because of materials-related issues and limitations, such as the control of the band gap, band structure, photochemical stability, and available reactive surface area of the photocatalyst. Synthesis of multicomponent hierarchical nano-architectures, consisting of semiconductor nanoparticles (NPs) with desired optical properties fabricated to maximize spatial proximity for optimum electron and energy transfer represents an attractive route formore » addressing the problem. Virus capsids are highly symmetrical, self-assembling protein cage nanoparticles that exist in a range of sizes and symmetries. Selective deposition of inorganic, by design, at specific locations on virus capsids affords precise control over the size, spacing, and assembly of nanomaterials, resulting in uniform and reproducible nano-architectures. We utilized the self-assembling capabilities of the 420 subunit, 60 nm icosahedral, P22 virus capsid to direct the nucleation, growth, and proximity of a range of component materials. Controlled fabrication on the exterior of the temperature stable shell was achieved by genetically encoding specific binding peptides into an externally exposed loop which is displayed on each of the 420 coat protein subunits. Localization of complimentary materials to the interior of the particle was achieved through the use “scaffolding-fusion proteins. The scaffolding domain drives coat protein polymerization resulting in a coat protein shell surrounding a core of approximately 300 scaffolding/fusion molecules. The fusion domain comprises a peptide which specifically binds the semiconductor material of interest.« less

First-principles study of configurational disorder in B4C using a superatom-special quasirandom structure method

NASA Astrophysics Data System (ADS)

Ektarawong, A.; Simak, S. I.; Hultman, L.; Birch, J.; Alling, B.

2014-07-01

Configurationally disordered crystalline boron carbide, with the composition B4C, is studied using first-principles calculations. We investigate both dilute and high concentrations of carbon-boron substitutional defects. For the latter purpose, we suggest a superatom's picture of the complex structure and combine it with a special quasirandom structure approach for disorder. In this way, we model a random distribution of high concentrations of the identified low-energy defects: (1) bipolar defects and (2) rotation of icosahedral carbon among the three polar-up sites. Additionally, the substitutional disorder of the icosahedral carbon at all six polar sites, as previously discussed in the literature, is also considered. Two configurational phase transitions from the ordered to the disordered configurations are predicted to take place upon an increase in temperature using a mean-field approximation for the entropy. The first transition, at 870 K, induces substitutional disorder of the icosahedral carbon atoms among the three polar-up sites; meanwhile the second transition, at 2325 K, reveals the random substitution of the icosahedral carbon atoms at all six polar sites coexisting with bipolar defects. Already the first transition removes the monoclinic distortion existing in the ordered ground-state configuration and restore the rhombohedral system (R3m). The restoration of inversion symmetry yielding the full rhombohedral symmetry (R3¯m ) on average, corresponding to what is reported in the literature, is achieved after the second transition. Investigating the effects of high pressure on the configurational stability of the disordered B4C phases reveals a tendency to stabilize the ordered ground-state configuration as the configurationally ordering/disordering transition temperature increases with pressure exerted on B4C. The electronic density of states, obtained from the disordered phases, indicates a sensitivity of the band gap to the degree of configurational disorder in B4C.

3-dimensional indexation of the icosahedral diffraction pattern using the techniques of electron microscopy

NASA Astrophysics Data System (ADS)

Bourdillon, Antony

2012-11-01

The following facts about icosahedra need wider attention. 1) The golden section τ is as fundamental to the icosahedral structure (length /edge) as π is to the sphere (circumference /diameter). 2) The diffraction series are in restricted Fibonacci order because the ratio of adjacent terms fn/fn-1 does not vary, but is the constant τ. The series is therefore geometric. 3) Because of the tetragonal subgroup in the icosahedral point group symmetry, many axes in the icosahedral structure have identical orientation to axes in the face centered cubic matrix of Al6Mn [1] (e.g. [100] and [111]). On these bases, a three dimensional stereographic projection will be presented. 4) A quasi-Bragg law is derived that correctly represents the diffraction series in powers of τ [2]. Furthermore, by employing the normal conventions of electron microscopy, all diffraction patterns are completely indexed in three dimensions. These are the topic of this presentation. Significant consequences will be presented elsewhere: 1) The diffraction pattern intensities near all main axes are correctly simulated, and all atoms are located on a specimen image. 2) The quasi-Bragg law has a special metric. Atomic locations are consistently calculated for the first time. 3) Whereas the Bragg law transforms a crystal lattice in real space into a reciprocal lattice in diffraction space, the quasi-Bragg law transforms a geometric diffraction pattern into a hierarchic structure. 4) Hyperspatial indexation [3] is superceded. [1] Shechtman, D.; Blech, I.; Gratias, D.; Cahn, J.W., Metallic phase with long-range orientational order and no translational symmetry, Phys. Rev. Lett., 1984, 53, 1951-3. [2] Bourdillon, A. J., Nearly free electron band structures in a logarithmically periodic solid, Sol. State Comm. 2009, 149, 1221-1225. [3] Duneau, M., and Katz, A., Phys Rev Lett 54, 2688-2691

Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus

PubMed Central

Yoshimura, Masato; Chen, Nai-Chi; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Lin, Chien-Chih; Nakagawa, Atsushi; Chen, Chun-Jung

2016-01-01

Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380

Cutaneous HPV and skin cancer.

PubMed

Accardi, Rosita; Gheit, Tarik

2014-12-01

Papillomaviruses (HPVs) are small non-enveloped icosahedral viruses that infect the keratinocytes of skin and mucosa. The cutaneous HPV types are represented mainly by the beta and gamma genera, which are widely present in the skin of normal individuals. More than 40 beta-HPV types and 50 gamma-HPV types have been isolated, and these numbers are continuously growing. The main cause of non-melanoma skin cancer is exposure to ultraviolet radiation (UVR). However, cutaneous HPVs that belong to the beta genus may act as a co-carcinogen with UVR. The association between beta-HPVs and skin cancer was first reported in patients with epidermodysplasia verruciformis (EV), who frequently develop cutaneous squamous cell carcinoma (SCC) on sun-exposed areas. Isolation of HPVs from the lesions suggested that HPVs might act as a co-carcinogen with UVR in EV patients. Beta-HPVs may also play a role in cutaneous SCC in immunocompromised non-EV and in immunocompetent individuals. Several studies have reported an association of viral DNA and/or antibodies to beta HPV types with SCC. Interestingly, HPV prevalence and viral load decrease during skin carcinogenesis, being significantly higher in actinic keratosis than in SCC, suggesting that the virus may play a role in the early stages of tumour development (the "hit-and-run" hypothesis). Concordantly, in vivo and in vitro studies have shown that E6 and E7 from certain cutaneous HPV types display transforming activities, further confirming their potential role in carcinogenesis. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

The True Story and Advantages of RNA Phage Capsids as Nanotools.

PubMed

Pumpens, Paul; Renhofa, Regina; Dishlers, Andris; Kozlovska, Tatjana; Ose, Velta; Pushko, Peter; Tars, Kaspars; Grens, Elmars; Bachmann, Martin F

2016-01-01

RNA phages are often used as prototypes for modern recombinant virus-like particle (VLP) technologies. Icosahedral RNA phage VLPs can be formed from coat proteins (CPs) and are efficiently produced in bacteria and yeast. Both genetic fusion and chemical coupling have been successfully used for the production of numerous chimeras based on RNA phage VLPs. In this review, we describe advances in RNA phage VLP technology along with the history of the Leviviridae family, including its taxonomical organization, genomic structure, and important role in the development of molecular biology. Comparative 3D structures of different RNA phage VLPs are used to explain the level of VLP tolerance to foreign elements displayed on VLP surfaces. We also summarize data that demonstrate the ability of CPs to tolerate different organic (peptides, oligonucleotides, and carbohydrates) and inorganic (metal ions) compounds either chemically coupled or noncovalently added to the outer and/or inner surfaces of VLPs. Finally, we present lists of nanotechnological RNA phage VLP applications, such as experimental vaccines constructed by genetic fusion and chemical coupling methodologies, nanocontainers for targeted drug delivery, and bioimaging tools. © 2016 S. Karger AG, Basel.

Local rules simulation of the kinetics of virus capsid self-assembly.

PubMed

Schwartz, R; Shor, P W; Prevelige, P E; Berger, B

1998-12-01

A computer model is described for studying the kinetics of the self-assembly of icosahedral viral capsids. Solution of this problem is crucial to an understanding of the viral life cycle, which currently cannot be adequately addressed through laboratory techniques. The abstract simulation model employed to address this is based on the local rules theory of. Proc. Natl. Acad. Sci. USA. 91:7732-7736). It is shown that the principle of local rules, generalized with a model of kinetics and other extensions, can be used to simulate complicated problems in self-assembly. This approach allows for a computationally tractable molecular dynamics-like simulation of coat protein interactions while retaining many relevant features of capsid self-assembly. Three simple simulation experiments are presented to illustrate the use of this model. These show the dependence of growth and malformation rates on the energetics of binding interactions, the tolerance of errors in binding positions, and the concentration of subunits in the examples. These experiments demonstrate a tradeoff within the model between growth rate and fidelity of assembly for the three parameters. A detailed discussion of the computational model is also provided.

Al-centered icosahedral ordering in Cu46Zr46Al8 bulk metallic glass

NASA Astrophysics Data System (ADS)

Fang, H. Z.; Hui, X.; Chen, G. L.; Liu, Z. K.

2009-03-01

Icosahedral short-range order, of which Al atoms are caged in the center of icosahedra with Cu and Zr atoms being the vertices, has been evidenced in the Cu46Zr46Al8 glassy structure by ab initio molecular dynamics simulation. These Al-centered clusters distribute irregularly in the three-dimensional space and form a "backbone" structure of the Cu46Zr46Al8 glass alloy. It is suggested that this kind of local structural feature is attributed to the requirement of efficient dense packing and the chemical affinity between Zr-Zr, Zr-Al, and Cu-Zr atoms. Our calculated results are found to be in good agreement with the experimental data.

Variation of the Specificity of the Human Antibody Responses after Tick-Borne Encephalitis Virus Infection and Vaccination

PubMed Central

Jarmer, Johanna; Zlatkovic, Jürgen; Tsouchnikas, Georgios; Vratskikh, Oksana; Strauß, Judith; Aberle, Judith H.; Chmelik, Vaclav; Kundi, Michael; Stiasny, Karin

2014-01-01

ABSTRACT Tick-borne encephalitis (TBE) virus is an important human-pathogenic flavivirus endemic in large parts of Europe and Central and Eastern Asia. Neutralizing antibodies specific for the viral envelope protein E are believed to mediate long-lasting protection after natural infection and vaccination. To study the specificity and individual variation of human antibody responses, we developed immunoassays with recombinant antigens representing viral surface protein domains and domain combinations. These allowed us to dissect and quantify antibody populations of different fine specificities in sera of TBE patients and vaccinees. Postinfection and postvaccination sera both displayed strong individual variation of antibody titers as well as the relative proportions of antibodies to different domains of E, indicating that the immunodominance patterns observed were strongly influenced by individual-specific factors. The contributions of these antibody populations to virus neutralization were quantified by serum depletion analyses and revealed a significantly biased pattern. Antibodies to domain III, in contrast to what was found in mouse immunization studies with TBE and other flaviviruses, did not play any role in the human neutralizing antibody response, which was dominated by antibodies to domains I and II. Importantly, most of the neutralizing activity could be depleted from sera by a dimeric soluble form of the E protein, which is the building block of the icosahedral herringbone-like shell of flaviviruses, suggesting that antibodies to more complex quaternary epitopes involving residues from adjacent dimers play only a minor role in the total response to natural infection and vaccination in humans. IMPORTANCE Tick-borne encephalitis (TBE) virus is a close relative of yellow fever, dengue, Japanese encephalitis, and West Nile viruses and distributed in large parts of Europe and Central and Eastern Asia. Antibodies to the viral envelope protein E prevent viral attachment and entry into cells and thus mediate virus neutralization and protection from disease. However, the fine specificity and individual variation of neutralizing antibody responses are currently not known. We have therefore developed new in vitro assays for dissecting the antibody populations present in blood serum and determining their contribution to virus neutralization. In our analysis of human postinfection and postvaccination sera, we found an extensive variation of the antibody populations present in sera, indicating substantial influences of individual-specific factors that control the specificity of the antibody response. Our study provides new insights into the immune response to an important human pathogen that is of relevance for the design of novel vaccines. PMID:25253341

Variation of the specificity of the human antibody responses after tick-borne encephalitis virus infection and vaccination.

PubMed

Jarmer, Johanna; Zlatkovic, Jürgen; Tsouchnikas, Georgios; Vratskikh, Oksana; Strauß, Judith; Aberle, Judith H; Chmelik, Vaclav; Kundi, Michael; Stiasny, Karin; Heinz, Franz X

2014-12-01

Tick-borne encephalitis (TBE) virus is an important human-pathogenic flavivirus endemic in large parts of Europe and Central and Eastern Asia. Neutralizing antibodies specific for the viral envelope protein E are believed to mediate long-lasting protection after natural infection and vaccination. To study the specificity and individual variation of human antibody responses, we developed immunoassays with recombinant antigens representing viral surface protein domains and domain combinations. These allowed us to dissect and quantify antibody populations of different fine specificities in sera of TBE patients and vaccinees. Postinfection and postvaccination sera both displayed strong individual variation of antibody titers as well as the relative proportions of antibodies to different domains of E, indicating that the immunodominance patterns observed were strongly influenced by individual-specific factors. The contributions of these antibody populations to virus neutralization were quantified by serum depletion analyses and revealed a significantly biased pattern. Antibodies to domain III, in contrast to what was found in mouse immunization studies with TBE and other flaviviruses, did not play any role in the human neutralizing antibody response, which was dominated by antibodies to domains I and II. Importantly, most of the neutralizing activity could be depleted from sera by a dimeric soluble form of the E protein, which is the building block of the icosahedral herringbone-like shell of flaviviruses, suggesting that antibodies to more complex quaternary epitopes involving residues from adjacent dimers play only a minor role in the total response to natural infection and vaccination in humans. Tick-borne encephalitis (TBE) virus is a close relative of yellow fever, dengue, Japanese encephalitis, and West Nile viruses and distributed in large parts of Europe and Central and Eastern Asia. Antibodies to the viral envelope protein E prevent viral attachment and entry into cells and thus mediate virus neutralization and protection from disease. However, the fine specificity and individual variation of neutralizing antibody responses are currently not known. We have therefore developed new in vitro assays for dissecting the antibody populations present in blood serum and determining their contribution to virus neutralization. In our analysis of human postinfection and postvaccination sera, we found an extensive variation of the antibody populations present in sera, indicating substantial influences of individual-specific factors that control the specificity of the antibody response. Our study provides new insights into the immune response to an important human pathogen that is of relevance for the design of novel vaccines. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

The Large Marseillevirus Explores Different Entry Pathways by Forming Giant Infectious Vesicles.

PubMed

Arantes, Thalita Souza; Rodrigues, Rodrigo Araújo Lima; Dos Santos Silva, Ludmila Karen; Oliveira, Graziele Pereira; de Souza, Helton Luís; Khalil, Jacques Y B; de Oliveira, Danilo Bretas; Torres, Alice Abreu; da Silva, Luis Lamberti; Colson, Philippe; Kroon, Erna Geessien; da Fonseca, Flávio Guimarães; Bonjardim, Cláudio Antônio; La Scola, Bernard; Abrahão, Jônatas Santos

2016-06-01

Triggering the amoebal phagocytosis process is a sine qua non condition for most giant viruses to initiate their replication cycle and consequently to promote their progeny formation. It is well known that the amoebal phagocytosis process requires the recognition of particles of >500 nm, and most amoebal giant viruses meet this requirement, such as mimivirus, pandoravirus, pithovirus, and mollivirus. However, in the context of the discovery of amoebal giant viruses in the last decade, Marseillevirus marseillevirus (MsV) has drawn our attention, because despite its ability to successfully replicate in Acanthamoeba, remarkably it does not fulfill the >500-nm condition, since it presents an ∼250-nm icosahedrally shaped capsid. We deeply investigated the MsV cycle by using a set of methods, including virological, molecular, and microscopic (immunofluorescence, scanning electron microscopy, and transmission electron microscopy) assays. Our results revealed that MsV is able to form giant vesicles containing dozens to thousands of viral particles wrapped by membranes derived from amoebal endoplasmic reticulum. Remarkably, our results strongly suggested that these giant vesicles are able to stimulate amoebal phagocytosis and to trigger the MsV replication cycle by an acidification-independent process. Also, we observed that MsV entry may occur by the phagocytosis of grouped particles (without surrounding membranes) and by an endosome-stimulated pathway triggered by single particles. Taken together, not only do our data deeply describe the main features of MsV replication cycle, but this is the first time, to our knowledge, that the formation of giant infective vesicles related to a DNA virus has been described. Triggering the amoebal phagocytosis process is a sine qua non condition required by most giant viruses to initiate their replication cycle. This process requires the recognition of particles of >500 nm, and many giant viruses meet this requirement. However, MsV is unusual, as despite having particles of ∼250 nm it is able to replicate in Acanthamoeba Our results revealed that MsV is able to form giant vesicles, containing dozens to thousands of viral particles, wrapped in membranes derived from amoebal endoplasmic reticulum. Remarkably, our results strongly suggest that these giant vesicles are able to stimulate phagocytosis using an acidification-independent process. Our work not only describes the main features of the MsV replication cycle but also describes, for the first time to our knowledge, the formation of huge infective vesicles in a large DNA viruses. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Concurrence of Iridovirus, Polyomavirus, and a Unique Member of a New Group of Fish Papillomaviruses in Lymphocystis Disease-Affected Gilthead Sea Bream

PubMed Central

López-Bueno, Alberto; Mavian, Carla; Labella, Alejandro M.; Castro, Dolores; Borrego, Juan J.; Alcami, Antonio

2016-01-01

ABSTRACT Lymphocystis disease is a geographically widespread disease affecting more than 150 different species of marine and freshwater fish. The disease, provoked by the iridovirus lymphocystis disease virus (LCDV), is characterized by the appearance of papillomalike lesions on the skin of affected animals that usually self-resolve over time. Development of the disease is usually associated with several environmental factors and, more frequently, with stress conditions provoked by the intensive culture conditions present in fish farms. In gilthead sea bream (Sparus aurata), an economically important cultured fish species in the Mediterranean area, a distinct LCDV has been identified but not yet completely characterized. We have used direct sequencing of the virome of lymphocystis lesions from affected S. aurata fish to obtain the complete genome of a new LCDV-Sa species that is the largest vertebrate iridovirus sequenced to date. Importantly, this approach allowed us to assemble the full-length circular genome sequence of two previously unknown viruses belonging to the papillomaviruses and polyomaviruses, termed Sparus aurata papillomavirus 1 (SaPV1) and Sparus aurata polyomavirus 1 (SaPyV1), respectively. Epidemiological surveys showed that lymphocystis disease was frequently associated with the concurrent appearance of one or both of the new viruses. SaPV1 has unique characteristics, such as an intron within the L1 gene, and as the first member of the Papillomaviridae family described in fish, provides evidence for a more ancient origin of this family than previously thought. IMPORTANCE Lymphocystis disease affects marine and freshwater fish species worldwide. It is characterized by the appearance of papillomalike lesions on the skin that contain heavily enlarged cells (lymphocysts). The causative agent is the lymphocystis disease virus (LCDV), a large icosahedral virus of the family Iridoviridae. In the Mediterranean area, the gilthead sea bream (Sparus aurata), an important farmed fish, is frequently affected. Using next-generation sequencing, we have identified within S. aurata lymphocystis lesions the concurrent presence of an additional LCDV species (LCDV-Sa) as well as two novel viruses. These are members of polyomavirus and papillomavirus families, and here we report them to be frequently associated with the presence of lymphocysts in affected fish. Because papillomaviruses have not been described in fish before, these findings support a more ancient origin of this virus family than previously thought and evolutionary implications are discussed. PMID:27440877

Concurrence of Iridovirus, Polyomavirus, and a Unique Member of a New Group of Fish Papillomaviruses in Lymphocystis Disease-Affected Gilthead Sea Bream.

PubMed

López-Bueno, Alberto; Mavian, Carla; Labella, Alejandro M; Castro, Dolores; Borrego, Juan J; Alcami, Antonio; Alejo, Alí

2016-10-01

Lymphocystis disease is a geographically widespread disease affecting more than 150 different species of marine and freshwater fish. The disease, provoked by the iridovirus lymphocystis disease virus (LCDV), is characterized by the appearance of papillomalike lesions on the skin of affected animals that usually self-resolve over time. Development of the disease is usually associated with several environmental factors and, more frequently, with stress conditions provoked by the intensive culture conditions present in fish farms. In gilthead sea bream (Sparus aurata), an economically important cultured fish species in the Mediterranean area, a distinct LCDV has been identified but not yet completely characterized. We have used direct sequencing of the virome of lymphocystis lesions from affected S. aurata fish to obtain the complete genome of a new LCDV-Sa species that is the largest vertebrate iridovirus sequenced to date. Importantly, this approach allowed us to assemble the full-length circular genome sequence of two previously unknown viruses belonging to the papillomaviruses and polyomaviruses, termed Sparus aurata papillomavirus 1 (SaPV1) and Sparus aurata polyomavirus 1 (SaPyV1), respectively. Epidemiological surveys showed that lymphocystis disease was frequently associated with the concurrent appearance of one or both of the new viruses. SaPV1 has unique characteristics, such as an intron within the L1 gene, and as the first member of the Papillomaviridae family described in fish, provides evidence for a more ancient origin of this family than previously thought. Lymphocystis disease affects marine and freshwater fish species worldwide. It is characterized by the appearance of papillomalike lesions on the skin that contain heavily enlarged cells (lymphocysts). The causative agent is the lymphocystis disease virus (LCDV), a large icosahedral virus of the family Iridoviridae In the Mediterranean area, the gilthead sea bream (Sparus aurata), an important farmed fish, is frequently affected. Using next-generation sequencing, we have identified within S. aurata lymphocystis lesions the concurrent presence of an additional LCDV species (LCDV-Sa) as well as two novel viruses. These are members of polyomavirus and papillomavirus families, and here we report them to be frequently associated with the presence of lymphocysts in affected fish. Because papillomaviruses have not been described in fish before, these findings support a more ancient origin of this virus family than previously thought and evolutionary implications are discussed. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cameron, Maria K., E-mail: cameron@math.umd.edu

We develop computational tools for spectral analysis of stochastic networks representing energy landscapes of atomic and molecular clusters. Physical meaning and some properties of eigenvalues, left and right eigenvectors, and eigencurrents are discussed. We propose an approach to compute a collection of eigenpairs and corresponding eigencurrents describing the most important relaxation processes taking place in the system on its way to the equilibrium. It is suitable for large and complex stochastic networks where pairwise transition rates, given by the Arrhenius law, vary by orders of magnitude. The proposed methodology is applied to the network representing the Lennard-Jones-38 cluster created bymore » Wales's group. Its energy landscape has a double funnel structure with a deep and narrow face-centered cubic funnel and a shallower and wider icosahedral funnel. However, the complete spectrum of the generator matrix of the Lennard-Jones-38 network has no appreciable spectral gap separating the eigenvalue corresponding to the escape from the icosahedral funnel. We provide a detailed description of the escape process from the icosahedral funnel using the eigencurrent and demonstrate a superexponential growth of the corresponding eigenvalue. The proposed spectral approach is compared to the methodology of the Transition Path Theory. Finally, we discuss whether the Lennard-Jones-38 cluster is metastable from the points of view of a mathematician and a chemical physicist, and make a connection with experimental works.« less

Cooperative Formation of Icosahedral Proline Clusters from Dimers

NASA Astrophysics Data System (ADS)

Jacobs, Alexander D.; Jovan Jose, K. V.; Horness, Rachel; Raghavachari, Krishnan; Thielges, Megan C.; Clemmer, David E.

2018-01-01

Ion mobility spectrometry-mass spectrometry and Fourier transform infrared spectroscopy (FTIR) techniques were combined with quantum chemical calculations to examine the origin of icosahedral clusters of the amino acid proline. When enantiopure proline solutions are electrosprayed (using nanospray) from 100 mM ammonium acetate, only three peaks are observed in the mass spectrum across a concentration range of five orders of magnitude: a monomer [Pro+H]+ species, favored from 0.001 to 0.01 mM proline concentrations; a dimer [2Pro+H]+ species, the most abundant species for proline concentrations above 0.01 mM; and, the dimer and dodecamer [12Pro+2H]2+ for 1.0 mM and more concentrated proline solutions. Electrospraying racemic D/ L-proline solutions from 100 mM ammonium acetate leads to a monomer at low proline concentrations (0.001 to 0.1 mM), and a dimer at higher concentrations (>0.09 mM), as well as a very small population of 8 to 15 Pro clusters that comprise <0.1% of the total ion signals even at the highest proline concentration. Solution FTIR studies show unique features that increase in intensity in the enantiopure proline solutions, consistent with clustering, presumably from the icosahedral geometry in bulk solution. When normalized for the total proline, these results are indicative of a cooperative formation of the enantiopure 12Pro species from 2Pro. [Figure not available: see fulltext.

Effects of Al addition on atomic structure of Cu-Zr metallic glass

NASA Astrophysics Data System (ADS)

Li, Feng; Zhang, Huajian; Liu, Xiongjun; Dong, Yuecheng; Yu, Chunyan; Lu, Zhaoping

2018-02-01

The atomic structures of Cu52Zr48 and Cu45Zr48Al7 metallic glasses (MGs) have been studied by molecular dynamic simulations. The results reveal that the molar volume of the Cu45Zr48Al7 MG is smaller than that of the Cu52Zr48 MG, although the size of the Al atom is larger than that of the Cu atom, implying an enhanced atomic packing density achieved by introducing Al into the ternary MG. Bond shortening in unlike atomic pairs Zr-Al and Cu-Al is observed in the Cu45Zr48Al7 MG, which is attributed to strong interactions between Al and (Zr, Cu) atoms. Meanwhile, the atomic packing efficiency is enhanced by the minor addition of Al. Compared with the Cu52Zr48 binary MG, the potential energy of the ternary MG decreases and the glass transition temperature increases. Structural analyses indicate that more Cu- and Al-centered full icosahedral clusters emerge in the Cu45Zr48Al7 MG as some Cu atoms are substituted by Al. Furthermore, the addition of Al leads to more icosahedral medium-range orders in the ternary MG. The increase of full icosahedral clusters and the enhancement of the packing density are responsible for the improved glass-forming ability of Cu45Zr48Al7.

Shellwise Mackay transformation in iron nanoclusters.

PubMed

Rollmann, Georg; Gruner, Markus E; Hucht, Alfred; Meyer, Ralf; Entel, Peter; Tiago, Murilo L; Chelikowsky, James R

2007-08-24

Structure and magnetism of iron clusters with up to 641 atoms have been investigated by means of density functional theory calculations including full geometric optimizations. Body-centered cubic (bcc) isomers are found to be lowest in energy when the clusters contain more than about 100 atoms. In addition, another stable conformation has been identified for magic-number clusters, which lies well within the range of thermal energies as compared to the bcc isomers. Its structure is characterized by a close-packed particle core and an icosahedral surface, while intermediate shells are partially transformed along the Mackay path between icosahedral and cuboctahedral geometry. The gradual transformation results in a favorable bcc environment for the subsurface atoms. For Fe55, the shellwise Mackay-transformed morphology is a promising candidate for the ground state.

Assembly of viral capsids, buckling, and the Asaro-Grinfeld-Tiller instability

NASA Astrophysics Data System (ADS)

Morozov, Alexander Yu.; Bruinsma, Robijn F.

2010-04-01

Icosahedral viral shells are characterized by intrinsic elastic stress focused on the 12 structurally required pentamers. We show that, according to thin-shell theory, assembling icosahedral viral shells should be subject to the Asaro-Grinfeld-Tiller instability (AGTI). AGTIs are encountered in growing epitaxial films exposed to extrinsic elastic stress. For viral shells, the AGTI relieves intrinsic elastic stresses by generating corrugation along the perimeter of the assembling shell. The buckling transition of Lidmar, Mirny, and Nelson provides an alternative mechanism for stress release, which in principle would allow for avoidance of AGTIs. For system parameters appropriate for viral shells however, the AGTI appears to be unavoidable. The azimuthal stress condensation produced by the AGTI might actually assist assembly by providing a guiding mechanism for the insertion of pentamers during viral assembly.

Characterization of subunit-specific interactions in a double-stranded RNA virus: Raman difference spectroscopy of the phi6 procapsid.

PubMed

Benevides, James M; Juuti, Jarmo T; Tuma, Roman; Bamford, Dennis H; Thomas, George J

2002-10-08

The icosahedral core of a double-stranded (ds) RNA virus hosts RNA-dependent polymerase activity and provides the molecular machinery for RNA packaging. The stringent requirements of dsRNA metabolism may explain the similarities observed in core architecture among a broad spectrum of dsRNA viruses, from the mammalian rotaviruses to the Pseudomonas bacteriophage phi6. Although the structure of the assembled core has been described in atomic detail for Reoviridae (blue tongue virus and reovirus), the molecular mechanism of assembly has not been characterized in terms of conformational changes and key interactions of protein constituents. In the present study, we address such questions through the application of Raman spectroscopy to an in vitro core assembly system--the procapsid of phi6. The phi6 procapsid, which comprises multiple copies of viral proteins P1 (copy number 120), P2 (12), P4 (72), and P7 (60), represents a precursor of the core that is devoid of RNA. Raman signatures of the procapsid, its purified recombinant core protein components, and purified sub-assemblies lacking either one or two of the protein components have been obtained and interpreted. The major procapsid protein (P1), which forms the skeletal frame of the core, is an elongated and monomeric molecule of high alpha-helical content. The fold of the core RNA polymerase (P2) is also mostly alpha-helical. On the other hand, the folds of both the procapsid accessory protein (P7) and RNA-packaging ATPase (P4) are of the alpha/beta type. Raman difference spectra show that conformational changes occur upon interaction of P1 with either P4 or P7 in the procapsid. These changes involve substantial ordering of the polypeptide backbone. Conversely, conformations of procapsid subunits are not significantly affected by interactions with P2. An assembly model is proposed in which P1 induces alpha-helix in P4 during formation of the nucleation complex. Subsequently, the partially disordered P7 subunit is folded within the context of the procapsid shell.

Integrated Nanosystems Templated by Self-assembled Virus Capsids

NASA Astrophysics Data System (ADS)

Stephanopoulos, Nicholas

This dissertation presents the synthesis and modeling of multicomponent nanosystems templated by self-assembled virus capsids. The design principles, synthesis, analysis, and future directions for these capsid-based materials are presented. Chapter 1 gives an overview of the literature on the application of virus capsids in constructing nanomaterials. The uses of capsids in three main areas are considered: (1) as templates for inorganic materials or nanoparticles; (2) as vehicles for biological applications like medical imaging and treatment; and (3) as scaffolds for catalytic materials. In light of this introduction, an overview of the material in this dissertation is described. Chapters 2-4 all describe integrated nanosystems templated by bacteriophage MS2, a spherical icosahedral virus capsid. MS2 possesses an interior and exterior surface that can be modified orthogonally using bioconjugation chemistry to create multivalent, multicomponent constructs with precise localization of components attached to the capsid proteins. Chapter 2 describes the use of MS2 to synthesize a photocatalytic construct by modifying the internal surface with sensitizing chromophores and the external surface with a photocatalytic porphyrin. The chromophores absorbed energy that the porphyrin could not, and transferred it to the porphyrin via FRET through the protein shell. The porphyrin was then able to utilize the energy to carry out photocatalysis at new wavelengths. In Chapter 3, porphyrins were installed on the interior surface of MS2 and DNA aptamers specific for Jurkat leukemia T cells on the exterior surface. The dual-modified capsids were able to bind to Jurkat cells, and upon illumination the porphyrins generated singlet oxygen to kill them selectively over non-targeted cells. Chapter 4 explores integrating MS2 with DNA origami in order to arrange the capsids at larger length scales. Capsids modified with fluorescent dyes inside and single-stranded DNA outside were able to bind to origami tiles bearing complementary DNA probes. The tiles could then be used to arrange the capsids in a one-dimensional array with dimensions far exceeding those of individual MS2 particles. In Chapter 5, the use of a different capsid, that of the tobacco mosaic virus (TMV) is described. The defect tolerance of light harvesting systems built using TMV as a scaffold was investigated using a kinetic Monte Carlo model to simulate the energy transfer processes. The results of the simulation were used to understand and explain experimental results obtained from the system.

First-principles prediction of stabilities and instabilities of compounds and alloys in the ternary B-As-P system

NASA Astrophysics Data System (ADS)

Ektarawong, A.; Simak, S. I.; Alling, B.

2017-07-01

We examine the thermodynamic stability of compounds and alloys in the ternary B-As-P system theoretically using first-principles calculations. We demonstrate that the icosahedral B12As2 is the only stable compound in the binary B-As system, while the zinc-blende BAs is thermodynamically unstable with respect to B12As2 and the pure arsenic phase at 0 K, and increasingly so at higher temperature, suggesting that BAs may merely exist as a metastable phase. On the contrary, in the binary B-P system, both zinc-blende BP and icosahedral B12P2 are predicted to be stable. As for the binary As-P system, As1 -xPx disordered alloys are predicted at elevated temperature—for example, a disordered solid solution of up to ˜75 at.% As in black phosphorus as well as a small solubility of ˜1 at.% P in gray arsenic at T =750 K, together with the presence of miscibility gaps. The calculated large solubility of As in black phosphorus explains the experimental syntheses of black-phosphorus-type As1 -xPx alloys with tunable compositions, recently reported in the literature. We investigate the phase stabilities in the ternary B-As-P system and demonstrate a high tendency for a formation of alloys in the icosahedral B12(As1 -xPx )2 structure by intermixing of As and P atoms at the diatomic chain sites. The phase diagram displays noticeable mutual solubility of the icosahedral subpnictides in each other even at room temperature as well as a closure of a pseudobinary miscibility gap around 900 K. As for pseudobinary BAs1 -xPx alloys, only a tiny amount of BAs is predicted to be able to dissolve in BP to form the BAs1 -xPx disordered alloys at elevated temperature. For example, less than 5% of BAs can dissolve in BP at T =1000 K. The small solubility limit of BAs in BP is attributed to the thermodynamic instability of BAs with respect to B12As2 and As.

Quasicrystals at extreme conditions: The role of pressure in stabilizing icosahedral Al 63Cu 24Fe 13 at high temperature

DOE PAGES

Stagno, Vincenzo; Bindi, Luca; Park, Changyong; ...

2015-11-20

Icosahedrite, the first natural quasicrystal with composition Al 63Cu 24Fe 13, was discovered in several grains of the Khatyrka meteorite, a unique CV3 carbonaceous chondrite. The presence in the meteorite fragments of icosahedrite strictly associated with high-pressure phases like ahrensite and stishovite indicates a formation conditions at high pressures and temperatures, likely during an impact-induced shock occurred in contact with the reducing solar nebula gas. In contrast, previous experimental studies on the stability of synthetic icosahedral AlCuFe, which were limited to ambient pressure, indicated incongruent melting at ~1123 K, while high-pressure experiments carried out at room temperature showed structural stabilitymore » up to about 35 GPa. These data are insufficient to experimentally constrain the formation and stability of icosahedrite under extreme conditions. Here we present the results of in situ high pressure experiments using diamond anvil cells of the compressional behavior of synthetic icosahedrite up to ~50 GPa at room temperature. Simultaneous high P-T experiments have been also carried out using both laser-heated diamond anvil cells combined with in situ synchrotron X-ray diffraction (at ~42 GPa) and multi-anvil apparatus (at 21 GPa) to investigate the structural evolution of icosahedral Al 63Cu 24Fe 13 and crystallization of possible coexisting phases. The results demonstrate that the quasiperiodic symmetry of icosahedrite is retained over the entire experimental pressure range explored. In addition, we show that pressure acts to stabilize the icosahedral symmetry at temperatures much higher than previously reported. Based on our experimental study, direct crystallization of Al-Cu-Fe quasicrystals from an unusual Al-Cu-rich melt would be possible but limited to a narrow temperature range beyond which crystalline phases would form, like those observed in the Khatyrka meteorite. Here, an alternative mechanism would consist in late formation of the quasicrystal after crystallization and solid-solid reaction of Al-rich phases. In both cases, linking our results with observations in nature, quasicrystals are expected to preserve their structure even after hypervelocity impacts that involve simultaneous high pressures and temperatures, thus proving their cosmic stability.« less

T helper cell-mediated interferon-gamma expression after human parvovirus B19 infection: persisting VP2-specific and transient VP1u-specific activity

PubMed Central

Franssila, R; Auramo, J; Modrow, S; Möbs, M; Oker-Blom, C; Käpylä, P; Söderlund-Venermo, M; Hedman, K

2005-01-01

Human parvovirus B19 is a small non-enveloped DNA virus with an icosahedral capsid consisting of proteins of only two species, the major protein VP2 and the minor protein VP1. VP2 is contained within VP1, which has an additional unique portion (VP1u) of 227 amino acids. We determined the ability of eukaryotically expressed parvovirus B19 virus-like particles consisting of VP1 and VP2 in the ratio recommended for vaccine use, or of VP2 alone, to stimulate, in an HLA class II restricted manner, peripheral blood mononuclear cells (PBMC) to proliferate and to secrete interferon gamma (IFN-γ) and interleukin (IL)-10 cytokines among recently and remotely B19 infected subjects. PBMC reactivity with VP1u was determined specifically with a prokaryotically expressed VP1u antigen. In general, B19-specific IFN-γ responses were stronger than IL-10 responses in both recent and remote infection; however, IL-10 responses were readily detectable among both groups, with the exception of patients with relapsed or persisting symptoms who showed strikingly low IL-10 responses. Whereas VP1u-specific IFN-γ responses were very strong among the recently infected subjects, the VP1u-specific IFN-γ and IL-10 responses were virtually absent among the remotely infected subjects. The disappearance of VP1u-specific IFN-γ expression is surprising, as B-cell immunity against VP1u is well maintained. PMID:16178856

Ab initio molecular dynamics simulation of binary Cu64Zr36 bulk metallic glass: Validation of the cluster-plus-glue-atom model

NASA Astrophysics Data System (ADS)

Tian, Hua; Zhang, Chong; Wang, Lu; Zhao, JiJun; Dong, Chuang; Wen, Bin; Wang, Qing

2011-06-01

We have performed ab initio molecular dynamics simulation of Cu64Zr36 alloy at descending temperatures (from 2000 K to 400 K) and discussed the evolution of short-range order with temperature. The pair-correlation functions, coordination numbers, and chemical compositions of the most abundant local clusters have been analyzed. We found that icosahedral short-range order exists in the liquid, undercooled, and glass states, and it becomes dominant in the glass states. Moreover, we demonstrated the existence of Cu-centered Cu8Zr5 icosahedral clusters as the major local structural unit in the Cu64Zr36 amorphous alloy. This finding agrees well with our previous cluster model of Cu-Zr-based BMG as well as experimental evidences from synchrotron x ray and neutron diffraction measurements.

Characterization of Bacillus phage-K2 isolated from chungkookjang, a fermented soybean foodstuff.

PubMed

Kim, Eun Ju; Hong, Jeong Won; Yun, Na-Rae; Lee, Young Nam

2011-01-01

An investigation of a virulent Bacillus phage-K2 (named Bp-K2) isolated from chungkookjang (a fermented soybean foodstuff) was made. Bp-K2 differed in infectivity against a number of Bacillus subtilis strains including starter strains of chungkookjang and natto, being more infectious to Bacillus strains isolated from the chungkookjang, but much less active against a natto strain. Bp-K2 is a small DNA phage whose genome size is about 21 kb. Bp-K2 is a tailed bacteriophage with an isometric icosahedral head (50 nm long on the lateral side, 80 nm wide), a long contractile sheath (85-90 nm × 28 nm), a thin tail fiber (80-85 nm long, 10 nm wide), and a basal plate (29 nm long, 47 nm wide) with a number of spikes, but no collar. The details of the structures of Bp-K2 differ from natto phage ϕBN100 as well as other known Bacillus phages such as SPO1-like or ϕ 29-like viruses. These data suggest that Bp-K2 would be a new member of the Myoviridae family of Bacillus bacteriophages.

Role of Surface Charge Density in Nanoparticle-templated Assembly of Bromovirus Protein Cages

PubMed Central

Daniel, Marie-Christine; Tsvetkova, Irina B.; Quinkert, Zachary T.; Murali, Ayaluru; De, Mrinmoy; Rotello, Vincent M.; Kao, C. Cheng; Dragnea, Bogdan

2010-01-01

Self-assembling icosahedral protein cages have potencially useful physical and chemical characteristics for a variety of nanotechnology applications, ranging from therapeutic or diagnostic vectors to building blocks for hierarchical materials. For application-specific functional control of protein cage assemblies, a deeper understanding of the interaction between the protein cage and its payload is necessary. Protein-cage encapsulated nanoparticles, with their well-defined surface chemistry, allow for systematic control over key parameters of encapsulation such as the surface charge, hydrophobicity, and size. Independent control over these variables allows experimental testing of different assembly mechanism models. Previous studies done with Brome mosaic virus capsids and negatively-charged gold nanoparticles indicated that the result of the self-assembly process depends on the diameter of the particle. However, in these experiments, the surface-ligand density was maintained at saturation levels, while the total charge and the radius of curvature remained coupled variables, making the interpretation of the observed dependence on the core size difficult. The current work furnishes evidence of a critical surface charge density for assembly through an analysis aimed at decoupling the surface charge the core size. PMID:20575505

Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids.

PubMed

Nguyen, Hung D; Reddy, Vijay S; Brooks, Charles L

2007-02-01

Self-assembly of viral proteins into icosahedral capsids is an interesting yet poorly understood phenomenon of which elucidation may aid the exploration of beneficial applications of capsids in materials science and medicine. Using molecular dynamics simulations of coarse-grained models for capsid proteins, we show that the competition between the formation of full capsids and nonidealized structures is strongly dependent upon the protein concentration and temperature, occurring kinetically as a cascade of elementary reactions in which free monomers are added to the growing oligomers on a downhill free-energy landscape. However, the insertion of the final subunits is the rate-limiting, energetically unfavorable step in viral capsid assembly. A phase diagram has been constructed to show the regions where capsids or nonidealized structures are stable at each concentration and temperature. We anticipate that our findings will provide guidance in identifying suitable conditions required for in vitro viral capsid assembly experiments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Unal, B.; Jenks, C.J.; Thiel, P.A.

From other work, two preferred sites have been suggested for metals and semimetals adsorbed on the fivefold surfaces of icosahedral, Al-based quasicrystals. Because of their appearance in scanning tunneling microscopy (STM) images, these sites are known as dark stars and white flowers. In this paper, we analyze four bulk structural models in physical space to determine the types, chemical decorations, and densities of the dark star - and, to a lesser extent, the white flower - adsorption sites for the fivefold planes of icosahedral Al-Pd-Mn. We find that the chemical decorations of these sites are heterogeneous, even within a singlemore » model. Both features are also structurally heterogeneous, according to STM measurements, and the structural variation is consistent with the bulk structure models. Finally, from the models, the density of dark stars in the planes correlates with the step height. This may explain previous experimental observations of different properties for different terraces.« less

Present knowledge of electronic properties and charge transport of icosahedral boron-rich solids

NASA Astrophysics Data System (ADS)

Werheit, Helmut

2009-06-01

B12 icosahedra or related structure elements determine the different modifications of elementary boron and numerous boron-rich compounds from α-rhombohedral boron with 12 to YB66 type with about 1584 atoms per unit cell. Typical are well-defined high density intrinsic defects: Jahn-Teller distorted icosahedra, vacancies, incomplete occupancies, statistical occupancies and antisite defects. The correlation between intrinsic point defects and electron deficiencies solves the discrepancy between theoretically predicted metal and experimentally proved semiconducting character. The electron deficiencies generate split-off valence states, which are decisive for the electronic transport, a superposition of band-type and hopping-type conduction. Their share depends on actual conditions like temperature or pre-excitation. The theoretical model of bipolaron hopping is incompatible with numerous experiments. Technical application of the typically p-type icosahedral boron-rich solids requires suitable n-type counterparts; doping and other possibilities are discussed.

Structural properties of medium-range order in CuNiZr alloy

NASA Astrophysics Data System (ADS)

Gao, Tinghong; Hu, Xuechen; Xie, Quan; Li, Yidan; Ren, Lei

2017-10-01

The evolution characteristics of icosahedral clusters during the rapid solidification of Cu50Ni10Zr40 alloy at cooling rate of 1011 K s-1 are investigated based on molecular dynamics simulations. The structural properties of the short-range order and medium-range order of Cu50Ni10Zr40 alloy are analyzed by several structural characterization methods. The results reveal that the icosahedral clusters are the dominant short-range order structure, and that they assemble themselves into medium-range order by interpenetrating connections. The different morphologies of medium-range order are found in the system and include chain, triangle, tetrahedral, and their combination structures. The tetrahedral morphologies of medium-range order have excellent structural stability with decreasing temperature. The Zr atoms are favorable to form longer chains, while the Cu atoms are favorable to form shorter chains in the system. Those chains interlocked with each other to improve the structural stability.

New ligand platforms featuring boron-rich clusters as organomimetic substituents*,**

PubMed Central

Spokoyny, Alexander M.

2013-01-01

200 years of research with carbon-rich molecules have shaped the development of modern chemistry. Research pertaining to the chemistry of boron-rich species has historically trailed behind its more distinguished neighbor (carbon) in the periodic table. Notably, a potentially rich and, in many cases, unmatched field of coordination chemistry using boronrich clusters remains fundamentally underdeveloped. Our work has been devoted to examining several basic concepts related to the functionalization of icosahedral boron-rich clusters and their use as ligands, aimed at designing fundamentally new hybrid molecular motifs and materials. Particularly interesting are icosahedral carboranes, which can be regarded as 3D analogs of benzene. These species comprise a class of boron-rich clusters that were discovered in the 1950s during the “space race” while researchers were developing energetic materials for rocket fuels. Ultimately, the unique chemical and physical properties of carborane species, such as rigidity, indefinite stability to air and moisture, and 3D aromaticity, may allow one to access a set of properties not normally available in carbon-based chemistry. While technically these species are considered as inorganic clusters, the chemical properties they possess make these boron-rich species suitable for replacing and/or altering structural and functional features of the organic and organometallic molecules—a phenomenon best described as “organomimetic”. Aside from purely fundamental features associated with the organomimetic chemistry of icosahedral carboranes, their use can also provide new avenues in the development of systems relevant to solving current problems associated with energy production, storage, and conversion. PMID:24311823

How faceted liquid droplets grow tails: from surface topology to active motion

NASA Astrophysics Data System (ADS)

Sloutskin, Eli

Among all possible shapes of a volume V, a sphere has the smallest surface area A. Therefore, liquid droplets are spherical, minimizing their interfacial energy γA for a given interfacial tension γ > 0 . This talk will demonstrate that liquid oil (alkane) droplets in water, stabilized by a common surfactant can be temperature-tuned to adopt icosahedral and other faceted shapes, above the bulk melting temperature of the oil. Although emulsions have been studied for centuries no faceted liquid droplets have ever been reported. The formation of an icosahedral shape is attributed to the interplay between γ and the elastic properties of the interfacial monomolecular layer, which crystallizes here 10-15K above bulk melting, leaving the droplet's bulk liquid. The icosahedral symmetry is dictated by twelve five-fold topological defects, forming within the hexagonally-packed interfacial crystalline monolayer. Moreover, we demonstrate that upon further cooling this `interfacial freezing' effect makes γ transiently switch its sign, leading to a spontaneous splitting of droplets and an active growth of their surface area, reminiscent of the classical spontaneous emulsification, yet driven by completely different physics. The observed phenomena allow deeper insights to be gained into the fundamentals of molecular elasticity and open new vitas for a wide range of novel nanotechnological applications, from self-assembly of complex shapes to new delivery strategies in bio-medicine. Acknowledgment is made to the Donors of the American Chemical Society Petroleum Research Fund for support of this research and to the Kahn Foundation for the purchase of equipment.

Changes in the stability and biomechanics of P22 bacteriophage capsid during maturation.

PubMed

Kant, Ravi; Llauró, Aida; Rayaprolu, Vamseedhar; Qazi, Shefah; de Pablo, Pedro J; Douglas, Trevor; Bothner, Brian

2018-03-15

The capsid of P22 bacteriophage undergoes a series of structural transitions during maturation that guide it from spherical to icosahedral morphology. The transitions include the release of scaffold proteins and capsid expansion. Although P22 maturation has been investigated for decades, a unified model that incorporates thermodynamic and biophysical analyses is not available. A general and specific model of icosahedral capsid maturation is of significant interest to theoreticians searching for fundamental principles as well as virologists and material scientists seeking to alter maturation to their advantage. To address this challenge, we have combined the results from orthogonal biophysical techniques including differential scanning fluorimetry, atomic force microscopy, circular dichroism, and hydrogen-deuterium exchange mass spectrometry. By integrating these results from single particle and population measurements, an energy landscape of P22 maturation from procapsid through expanded shell to wiffle ball emerged, highlighting the role of metastable structures and the thermodynamics guiding maturation. The propagation of weak quaternary interactions across symmetric elements of the capsid is a key component for stability in P22. A surprising finding is that the progression to wiffle ball, which lacks pentamers, shows that chemical and thermal stability can be uncoupled from mechanical rigidity, elegantly demonstrating the complexity inherent in capsid protein interactions and the emergent properties that can arise from icosahedral symmetry. On a broader scale, this work demonstrates the power of applying orthogonal biophysical techniques to elucidate assembly mechanisms for supramolecular complexes and provides a framework within which other viral systems can be compared. Copyright © 2018 Elsevier B.V. All rights reserved.

Nanometer scale atomic structure of zirconium based bulk metallic glass

NASA Astrophysics Data System (ADS)

Hwang, Jinwoo

We have studied the nanometer scale structure of bulk metallic glass (BMG) using fluctuation electron microscopy (FEM). The nanometer scale medium range order (MRO) in BMG is of significant interest because of its possible relationship to the properties, but the experimental study of the MRO is difficult because conventional diffraction techniques are not sensitive to the MRO scale. FEM is a quantitative transmission electron microscopy technique which measures the nanoscale structural fluctuation associated with MRO in amorphous materials, and provides information about the size, distribution, and internal structure of MRO. In this work, we developed an improved method for FEM using energy-filtered STEM nanodiffraction with highly coherent probes with size up to 11nm in a state-of-the-art Cs- corrected STEM. We also developed an effective way to eliminate the effect of sample thickness variation to the FEM data by using Z-contrast images as references. To study the detailed structure of MRO, we developed a hybrid reverse Monte Carlo (H-RMC) simulation which combines an empirical atomic potential and the FEM data. H-RMC generated model structures that match the experimental data at short and medium range. In addition, the subtle rotational symmetries in the FEM nanodiffraction patterns were analyzed by angular correlation function to reveal more details of the internal structure of MRO. Our experiments and simulations show that Zr-based BMG contains pseudo-planar, crystal-like MRO as well as icosahedral clusters in its nanoscale structure. We found that some icosahedral clusters may be connected, and that structural relaxation by annealing increases the population of icosahedral clusters.

Next generation of the self-consistent and environment-dependent Hamiltonian: Applications to various boron allotropes from zero- to three-dimensional structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tandy, P.; Yu, Ming; Leahy, C.

2015-03-28

An upgrade of the previous self-consistent and environment-dependent linear combination of atomic orbitals Hamiltonian (referred as SCED-LCAO) has been developed. This improved version of the semi-empirical SCED-LCAO Hamiltonian, in addition to the inclusion of self-consistent determination of charge redistribution, multi-center interactions, and modeling of electron-electron correlation, has taken into account the effect excited on the orbitals due to the atomic aggregation. This important upgrade has been subjected to a stringent test, the construction of the SCED-LCAO Hamiltonian for boron. It was shown that the Hamiltonian for boron has successfully characterized the electron deficiency of boron and captured the complex chemicalmore » bonding in various boron allotropes, including the planar and quasi-planar, the convex, the ring, the icosahedral, and the fullerene-like clusters, the two-dimensional monolayer sheets, and the bulk alpha boron, demonstrating its transferability, robustness, reliability, and predictive power. The molecular dynamics simulation scheme based on the Hamiltonian has been applied to explore the existence and the energetics of ∼230 compact boron clusters B{sub N} with N in the range from ∼100 to 768, including the random, the rhombohedral, and the spherical icosahedral structures. It was found that, energetically, clusters containing whole icosahedral B{sub 12} units are more stable for boron clusters of larger size (N > 200). The ease with which the simulations both at 0 K and finite temperatures were completed is a demonstration of the efficiency of the SCED-LCAO Hamiltonian.« less

Next generation of the self-consistent and environment-dependent Hamiltonian: Applications to various boron allotropes from zero- to three-dimensional structures

NASA Astrophysics Data System (ADS)

Tandy, P.; Yu, Ming; Leahy, C.; Jayanthi, C. S.; Wu, S. Y.

2015-03-01

An upgrade of the previous self-consistent and environment-dependent linear combination of atomic orbitals Hamiltonian (referred as SCED-LCAO) has been developed. This improved version of the semi-empirical SCED-LCAO Hamiltonian, in addition to the inclusion of self-consistent determination of charge redistribution, multi-center interactions, and modeling of electron-electron correlation, has taken into account the effect excited on the orbitals due to the atomic aggregation. This important upgrade has been subjected to a stringent test, the construction of the SCED-LCAO Hamiltonian for boron. It was shown that the Hamiltonian for boron has successfully characterized the electron deficiency of boron and captured the complex chemical bonding in various boron allotropes, including the planar and quasi-planar, the convex, the ring, the icosahedral, and the fullerene-like clusters, the two-dimensional monolayer sheets, and the bulk alpha boron, demonstrating its transferability, robustness, reliability, and predictive power. The molecular dynamics simulation scheme based on the Hamiltonian has been applied to explore the existence and the energetics of ˜230 compact boron clusters BN with N in the range from ˜100 to 768, including the random, the rhombohedral, and the spherical icosahedral structures. It was found that, energetically, clusters containing whole icosahedral B12 units are more stable for boron clusters of larger size (N > 200). The ease with which the simulations both at 0 K and finite temperatures were completed is a demonstration of the efficiency of the SCED-LCAO Hamiltonian.

Structured populations of Sulfolobus acidocaldarius with susceptibility to mobile genetic elements

USGS Publications Warehouse

Anderson, Rika E.; Kouris, Angela; Seward, Christopher H.; Campbell, Kate M.; Whitaker, Rachel J.

2017-01-01

The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S. acidocaldarius apart from its sister Sulfolobus species. To test this hypothesis, we conducted a comparative analysis of 47 genomes of S. acidocaldarius from spatial and temporal sampling of two hot springs in Yellowstone National Park. While we confirm the low diversity in the core genome, we observe differentiation among S. acidocaldarius populations, likely resulting from low migration among hot spring “islands” in Yellowstone National Park. Patterns of genomic variation indicate that differing geological contexts result in the elimination or preservation of diversity among differentiated populations. We observe multiple deletions associated with a large genomic island rich in glycosyltransferases, differential integrations of the Sulfolobus turreted icosahedral virus, as well as two different plasmid elements. These data demonstrate that neither rapid dispersal nor lack of mobile genetic elements result in low diversity in the S. acidocaldariusgenomes. We suggest instead that significant differences in the recent evolutionary history, or the intrinsic evolutionary rates, of sister Sulfolobusspecies result in the relatively low diversity of the S. acidocaldarius genome.

Capsid expansion mechanism of bacteriophage T7 revealed by multistate atomic models derived from cryo-EM reconstructions

PubMed Central

Guo, Fei; Liu, Zheng; Fang, Ping-An; Zhang, Qinfen; Wright, Elena T.; Wu, Weimin; Zhang, Ci; Vago, Frank; Ren, Yue; Jakana, Joanita; Chiu, Wah; Serwer, Philip; Jiang, Wen

2014-01-01

Many dsDNA viruses first assemble a DNA-free procapsid, using a scaffolding protein-dependent process. The procapsid, then, undergoes dramatic conformational maturation while packaging DNA. For bacteriophage T7 we report the following four single-particle cryo-EM 3D reconstructions and the derived atomic models: procapsid (4.6-Å resolution), an early-stage DNA packaging intermediate (3.5 Å), a later-stage packaging intermediate (6.6 Å), and the final infectious phage (3.6 Å). In the procapsid, the N terminus of the major capsid protein, gp10, has a six-turn helix at the inner surface of the shell, where each skewed hexamer of gp10 interacts with two scaffolding proteins. With the exit of scaffolding proteins during maturation the gp10 N-terminal helix unfolds and swings through the capsid shell to the outer surface. The refolded N-terminal region has a hairpin that forms a novel noncovalent, joint-like, intercapsomeric interaction with a pocket formed during shell expansion. These large conformational changes also result in a new noncovalent, intracapsomeric topological linking. Both interactions further stabilize the capsids by interlocking all pentameric and hexameric capsomeres in both DNA packaging intermediate and phage. Although the final phage shell has nearly identical structure to the shell of the DNA-free intermediate, surprisingly we found that the icosahedral faces of the phage are slightly (∼4 Å) contracted relative to the faces of the intermediate, despite the internal pressure from the densely packaged DNA genome. These structures provide a basis for understanding the capsid maturation process during DNA packaging that is essential for large numbers of dsDNA viruses. PMID:25313071

Flexible Connectors between Capsomer Subunits that Regulate Capsid Assembly.

PubMed

Hasek, Mary L; Maurer, Joshua B; Hendrix, Roger W; Duda, Robert L

2017-08-04

Viruses build icosahedral capsids of specific size and shape by regulating the spatial arrangement of the hexameric and pentameric protein capsomers in the growing shell during assembly. In the T=7 capsids of Escherichia coli bacteriophage HK97 and other phages, 60 capsomers are hexons, while the rest are pentons that are correctly positioned during assembly. Assembly of the HK97 capsid to the correct size and shape has been shown to depend on specific ionic contacts between capsomers. We now describe additional ionic interactions within capsomers that also regulate assembly. Each is between the long hairpin, the "E-loop," that extends from one subunit to the adjacent subunit within the same capsomer. Glutamate E153 on the E-loop and arginine R210 on the adjacent subunit's backbone alpha-helix form salt bridges in hexamers and pentamers. Mutations that disrupt these salt bridges were lethal for virus production, because the mutant proteins assembled into tubes or sheets instead of capsids. X-ray structures show that the E153-R210 links are flexible and maintained during maturation despite radical changes in capsomer shape. The E153-R210 links appear to form early in assembly to enable capsomers to make programmed changes in their shape during assembly. The links also prevent flattening of capsomers and premature maturation. Mutant phenotypes and modeling support an assembly model in which flexible E153-R210 links mediate capsomer shape changes that control where pentons are placed to create normal-sized capsids. The E-loop may be conserved in other systems in order to play similar roles in regulating assembly. Copyright © 2017 Elsevier Ltd. All rights reserved.

Building polyhedra by self-assembly: theory and experiment.

PubMed

Kaplan, Ryan; Klobušický, Joseph; Pandey, Shivendra; Gracias, David H; Menon, Govind

2014-01-01

We investigate the utility of a mathematical framework based on discrete geometry to model biological and synthetic self-assembly. Our primary biological example is the self-assembly of icosahedral viruses; our synthetic example is surface-tension-driven self-folding polyhedra. In both instances, the process of self-assembly is modeled by decomposing the polyhedron into a set of partially formed intermediate states. The set of all intermediates is called the configuration space, pathways of assembly are modeled as paths in the configuration space, and the kinetics and yield of assembly are modeled by rate equations, Markov chains, or cost functions on the configuration space. We review an interesting interplay between biological function and mathematical structure in viruses in light of this framework. We discuss in particular: (i) tiling theory as a coarse-grained description of all-atom models; (ii) the building game-a growth model for the formation of polyhedra; and (iii) the application of these models to the self-assembly of the bacteriophage MS2. We then use a similar framework to model self-folding polyhedra. We use a discrete folding algorithm to compute a configuration space that idealizes surface-tension-driven self-folding and analyze pathways of assembly and dominant intermediates. These computations are then compared with experimental observations of a self-folding dodecahedron with side 300 μm. In both models, despite a combinatorial explosion in the size of the configuration space, a few pathways and intermediates dominate self-assembly. For self-folding polyhedra, the dominant intermediates have fewer degrees of freedom than comparable intermediates, and are thus more rigid. The concentration of assembly pathways on a few intermediates with distinguished geometric properties is biologically and physically important, and suggests deeper mathematical structure.

Single-Particle Detection of Transcription following Rotavirus Entry

PubMed Central

Salgado, Eric N.; Upadhyayula, Srigokul

2017-01-01

ABSTRACT Infectious rotavirus particles are triple-layered, icosahedral assemblies. The outer layer proteins, VP4 (cleaved to VP8* and VP5*) and VP7, surround a transcriptionally competent, double-layer particle (DLP), which they deliver into the cytosol. During entry of rhesus rotavirus, VP8* interacts with cell surface gangliosides, allowing engulfment into a membrane vesicle by a clathrin-independent process. Escape into the cytosol and outer-layer shedding depend on interaction of a hydrophobic surface on VP5* with the membrane bilayer and on a large-scale conformational change. We report here experiments that detect the fate of released DLPs and their efficiency in initiating RNA synthesis. By replacing the outer layer with fluorescently tagged, recombinant proteins and also tagging the DLP, we distinguished particles that have lost their outer layer and entered the cytosol (uncoated) from those still within membrane vesicles. We used fluorescent in situ hybridization with probes for nascent transcripts to determine how soon after uncoating transcription began and what fraction of the uncoated particles were active in initiating RNA synthesis. We detected RNA synthesis by uncoated particles as early as 15 min after adding virus. The uncoating efficiency was 20 to 50%; of the uncoated particles, about 10 to 15% synthesized detectable RNA. In the format of our experiments, about 10% of the added particles attached to the cell surface, giving an overall ratio of added particles to RNA-synthesizing particles of between 250:1 and 500:1, in good agreement with the ratio of particles to focus-forming units determined by infectivity assays. Thus, RNA synthesis by even a single, uncoated particle can initiate infection in a cell. IMPORTANCE The pathways by which a virus enters a cell transform its packaged genome into an active one. Contemporary fluorescence microscopy can detect individual virus particles as they enter cells, allowing us to map their multistep entry pathways. Rotaviruses, like most viruses that lack membranes of their own, disrupt or perforate the intracellular, membrane-enclosed compartment into which they become engulfed following attachment to a cell surface, in order to gain access to the cell interior. The properties of rotavirus particles make it possible to determine molecular mechanisms for these entry steps. In the work described here, we have asked the following question: what fraction of the rotavirus particles that penetrate into the cell make new viral RNA? We find that of the cell-attached particles, between 20 and 50% ultimately penetrate, and of these, about 10% make RNA. RNA synthesis by even a single virus particle can initiate a productive infection. PMID:28701394

Structures of Adenovirus Incomplete Particles Clarify Capsid Architecture and Show Maturation Changes of Packaging Protein L1 52/55k

PubMed Central

Condezo, Gabriela N.; Marabini, Roberto; Ayora, Silvia; Carazo, José M.; Alba, Raúl; Chillón, Miguel

2015-01-01

ABSTRACT Adenovirus is one of the most complex icosahedral, nonenveloped viruses. Even after its structure was solved at near-atomic resolution by both cryo-electron microscopy and X-ray crystallography, the location of minor coat proteins is still a subject of debate. The elaborated capsid architecture is the product of a correspondingly complex assembly process, about which many aspects remain unknown. Genome encapsidation involves the concerted action of five virus proteins, and proteolytic processing by the virus protease is needed to prime the virion for sequential uncoating. Protein L1 52/55k is required for packaging, and multiple cleavages by the maturation protease facilitate its release from the nascent virion. Light-density particles are routinely produced in adenovirus infections and are thought to represent assembly intermediates. Here, we present the molecular and structural characterization of two different types of human adenovirus light particles produced by a mutant with delayed packaging. We show that these particles lack core polypeptide V but do not lack the density corresponding to this protein in the X-ray structure, thereby adding support to the adenovirus cryo-electron microscopy model. The two types of light particles present different degrees of proteolytic processing. Their structures provide the first glimpse of the organization of L1 52/55k protein inside the capsid shell and of how this organization changes upon partial maturation. Immature, full-length L1 52/55k is poised beneath the vertices to engage the virus genome. Upon proteolytic processing, L1 52/55k disengages from the capsid shell, facilitating genome release during uncoating. IMPORTANCE Adenoviruses have been extensively characterized as experimental systems in molecular biology, as human pathogens, and as therapeutic vectors. However, a clear picture of many aspects of their basic biology is still lacking. Two of these aspects are the location of minor coat proteins in the capsid and the molecular details of capsid assembly. Here, we provide evidence supporting one of the two current models for capsid architecture. We also show for the first time the location of the packaging protein L1 52/55k in particles lacking the virus genome and how this location changes during maturation. Our results contribute to clarifying standing questions in adenovirus capsid architecture and provide new details on the role of L1 52/55k protein in assembly. PMID:26178997

Histopathological investigation in porcine infected with torque teno sus virus type 2 by inoculation

PubMed Central

2011-01-01

Background Porcine torque teno sus virus (TTSuV) is a small icosahedral and non-enveloped virus which contains a single-stranded (ssDNA), circular and negative DNA genome and infects mainly vertebrates and is currently classified into the 'floating' genus Anellovirus of Circoviridae with two species. Viral DNA of both porcine TTSuV species has a high prevalence in both healthy and diseased pigs worldwide and multiple infections of TTSuV with distinct genotypes or subtypes of the same species has been documented in the United States, Europe and Asia. However, there exists no information about histopathological lesions caused by infection with porcine TTSuV2. Methods Porcine liver tissue homogenate with 1 ml of 6.91 × 107genomic copies viral loads of porcine TTSuV2 that had positive result for torque teno sus virus type 2 and negative result for torque teno sus virus type 1 and porcine pseudorabies virus type 2 were used to inoculate specific pathogen-free piglets by intramuscular route and humanely killed at 3,7,10,14,17,21 and 24 days post inoculation (dpi), the control pigs were injected intramuscularly with 1 ml of sterile DMEM and humanely killed the end of the study for histopathological examination routinely processed, respectively. Results All porcine TTSuV2 inoculated piglets were clinic asymptomatic but developed myocardial fibroklasts and endocardium, interstitial pneumonia, membranous glomerular nephropathy, and modest inflammatory cells infiltration in portal areas in the liver, foci of hemorrhage in some pancreas islet, a tiny amount red blood cells in venule of muscularis mucosae and outer longitudinal muscle, rarely red blood cells in the microvasculation and infiltration of inflammatory cells (lymphocytes and eosinophils) of tonsil and hilar lymph nodes, infiltration of inflammatory lymphocytes and necrosis or degeneration and focal gliosis of lymphocytes in the paracortical zone after inoculation with porcine TTSuV2-containing tissue homogenate. Conclusions Analysis of these presentations revealed that porcine TTSuV2 was readily transmitted to TTSuV-negative swine and that infection was associated with characteristic pathologic changes in specific pathogen-free piglets inoculated with porcine TTSuV2. Those results indicated no markedly histopathological changes happened in those parenchymatous organs, especially the digestive system and immune system when the specific pathogen-free pigs were infected with porcine TTSuV2, hence, to some extent, it was not remarkable pathological agent for domestic pigs at least. So, porcine TTSuV2 could be an unrecognized pathogenic viral infectious etiology of swine. This study indicated a directly related description of lesions responsible for TTSuV2 infection in swine. PMID:22171963

The FIM-iHYCOM Model in SubX: Evaluation of Subseasonal Errors and Variability

NASA Astrophysics Data System (ADS)

Green, B.; Sun, S.; Benjamin, S.; Grell, G. A.; Bleck, R.

2017-12-01

NOAA/ESRL/GSD has produced both real-time and retrospective forecasts for the Subseasonal Experiment (SubX) using the FIM-iHYCOM model. FIM-iHYCOM couples the atmospheric Flow-following finite volume Icosahedral Model (FIM) to an icosahedral-grid version of the Hybrid Coordinate Ocean Model (HYCOM). This coupled model is unique in terms of its grid structure: in the horizontal, the icosahedral meshes are perfectly matched for FIM and iHYCOM, eliminating the need for a flux interpolator; in the vertical, both models use adaptive arbitrary Lagrangian-Eulerian hybrid coordinates. For SubX, FIM-iHYCOM initializes four time-lagged ensemble members around each Wednesday, which are integrated forward to provide 32-day forecasts. While it has already been shown that this model has similar predictive skill as NOAA's operational CFSv2 in terms of the RMM index, FIM-iHYCOM is still fairly new and thus its overall performance needs to be thoroughly evaluated. To that end, this study examines model errors as a function of forecast lead week (1-4) - i.e., model drift - for key variables including 2-m temperature, precipitation, and SST. Errors are evaluated against two reanalysis products: CFSR, from which FIM-iHYCOM initial conditions are derived, and the quasi-independent ERA-Interim. The week 4 error magnitudes are similar between FIM-iHYCOM and CFSv2, albeit with different spatial distributions. Also, intraseasonal variability as simulated in these two models will be compared with reanalyses. The impact of hindcast frequency (4 times per week, once per week, or once per day) on the model climatology is also examined to determine the implications for systematic error correction in FIM-iHYCOM.

Diffuse Scattering in the Icosahedral AL-Li-Cu Quasicrystal

NASA Astrophysics Data System (ADS)

Proult, A.; Donnadieu, P.; Wang, K.; Garoche, P.

1995-12-01

Electron diffraction patterns of icosahedral quasicrystals frequently exhibit diffuse scattering features. We report a detailed analysis of diffuse scattering in Al{6}Li{3}Cu (T2) quasicrystalline samples. The samples have been specifically heat-treated which allows to observe pronounced diffuse effects. Diffuse streaks are observed along the 5-fold and 2-fold symmetry axes and are elongated perpendicularly to these directions. These streaks are due to discs in the 3-dimensional reciprocal space. The diffuse disc positions are only indexable in the 6-dimensional hyperspace but the disc intensities do not agree with the ones predicted by the Cut-and-Project method. The diffuse discs we observed seem to be related to an original quasicrystalline phenomenon overlapping with the icosahedral phase. Les diagrammes de diffraction électronique des quasicristaux icosaédriques présentent fréquemment des diffusions diffuses. Nous les analysons ici en détails sur des échantillons de phase quasicristalline Al{6}Li{3}Cu (T2) traités thermiquement dans lesquels les diffusions diffuses sont trés prononcées. Les intensités diffuses forment des batônnets centrés sur des positions appartenant aux rangées réciproques d'ordre 5 et d'ordre 2 et allongés perpendiculairement à ces directions. On montre qu'il s'agit en fait de disques diffus. dans le réseau réciproque à 3 dimensions, dont les positions ne peuvent s'indexer que sur le réseau à 6 dimensions. Toutefois, les intensités ne correspondent pas à celle prédites par l'algorithme de Coupe-et-Projection. Les disques de diffusion diffuse semblent relever d'une organisation quasicristalline originale se superposant à la phase icosaédrique.

The deviations of the Al6Li3Cu quasicrystal from icosahedral symmetry : a reminiscence of a cubic crystal

NASA Astrophysics Data System (ADS)

Donnadieu, Patricia

1994-05-01

The (Al6Li3Cu) (T2) quasicrystals are known to exhibit large deviations from the icosahedral symmetry. Series of electron diffraction patterns are used to investigate these imperfections in as-cast T, samples. A detailed analysis of the 5-fold and 3-fold symmetry diffraction patterns shows that they are compatible with the m3 point group instead of the m35 icosahedral group. This symmetry reduction is interprétéd as reminiscent of the cubic approximant phase (R-Al5Li3Cu) rather than of higher order approximant phases. This interpretation is supported by previous observations on crystal/quasicrystal phase transformation in the AlLiCu system. Les quasicristaux de phase T2(Al6Li3Cu) montrent d'importantes déviations à la symétrie icosaédrique. Ces imperfections sont mises en évidence par diffraction électronique dans des échantillons de phase T2 brut de coulée. Un examen détaillé des diagrammes de diffraction de symétrie d'ordre 3 et 5 révèle qu'ils sont compatibles avec le groupe ponctuel m3 au lieu du groupe de l'icosaèdre (m35). Cette réduction de symétrie est interprétée comme une réminiscence de la phase cubique approximante (R-Al5Li3Cu) et non l'apparition d'approximant d'ordre plus élevé. Cette interprétation est suggérée par des observations antérieures sur la transformation cristal/quasicristal dans le système AlLiCu.

Vertical Wave Coupling associated with Stratospheric Sudden Warming Events analyzed in an Isentropic-Coordinate NWP Model.

NASA Astrophysics Data System (ADS)

Bleck, R.; Sun, S.; Benjamin, S.; Brown, J. M.

2017-12-01

Two- to four-week predictions of stratospheric sudden warming events during the winter seasons of 1999-2014, carried out with a high-resolution icosahedral NWP model using potential temperature as vertical coordinate, are inspected for commonalities in the evolution of both minor and major warmings. Emphasis is on the evolution of the potential vorticity field at different levels in the stratosphere, as well as on the sign and magnitude of the vertical component of the Eliassen-Palm flux vector suggestive of wave forcing in either direction. Material is presented shedding light on the skill of the model (FIM, developed at NOAA/ESRL) in predicting stratospheric warmings generally 2 weeks in advance. With an icosahedral grid ideally suited for studying polar processes, and a vertical coordinate faithfully reproducing details in the evolution of the potential vorticity and EP flux vector fields, FIM is found to be a good tool for investigating the SSW mechanism.

Tropical cyclones over the North Indian Ocean: experiments with the high-resolution global icosahedral grid point model GME

NASA Astrophysics Data System (ADS)

Kumkar, Yogesh V.; Sen, P. N.; Chaudhari, Hemankumar S.; Oh, Jai-Ho

2018-02-01

In this paper, an attempt has been made to conduct a numerical experiment with the high-resolution global model GME to predict the tropical storms in the North Indian Ocean during the year 2007. Numerical integrations using the icosahedral hexagonal grid point global model GME were performed to study the evolution of tropical cyclones, viz., Akash, Gonu, Yemyin and Sidr over North Indian Ocean during 2007. It has been seen that the GME model forecast underestimates cyclone's intensity, but the model can capture the evolution of cyclone's intensity especially its weakening during landfall, which is primarily due to the cutoff of the water vapor supply in the boundary layer as cyclones approach the coastal region. A series of numerical simulation of tropical cyclones have been performed with GME to examine model capability in prediction of intensity and track of the cyclones. The model performance is evaluated by calculating the root mean square errors as cyclone track errors.

Multiple diffraction in an icosahedral Al-Cu-Fe quasicrystal

NASA Astrophysics Data System (ADS)

Fan, C. Z.; Weber, Th.; Deloudi, S.; Steurer, W.

2011-07-01

In order to reveal its influence on quasicrystal structure analysis, multiple diffraction (MD) effects in an icosahedral Al-Cu-Fe quasicrystal have been investigated in-house on an Oxford Diffraction four-circle diffractometer equipped with an Onyx™ CCD area detector and MoKα radiation. For that purpose, an automated approach for Renninger scans (ψ-scans) has been developed. Two weak reflections were chosen as the main reflections (called P) in the present measurements. As is well known for periodic crystals, it is also observed for this quasicrystal that the intensity of the main reflection may significantly increase if the simultaneous (H) and the coupling (P-H) reflections are both strong, while there is no obvious MD effect if one of them is weak. The occurrence of MD events during ψ-scans has been studied based on an ideal structure model and the kinematical MD theory. The reliability of the approach is revealed by the good agreement between simulation and experiment. It shows that the multiple diffraction effect is quite significant.

Medium-range structure and glass forming ability in Zr–Cu–Al bulk metallic glasses

DOE PAGES

Zhang, Pei; Maldonis, Jason J.; Besser, M. F.; ...

2016-03-05

Fluctuation electron microscopy experiments combined with hybrid reverse Monte Carlo modeling show a correlation between medium-range structure at the nanometer scale and glass forming ability in two Zr–Cu–Al bulk metallic glass (BMG) alloys. Both Zr 50Cu 35Al 15 and Zr 50Cu 45Al 5 exhibit two nanoscale structure types, one icosahedral and the other more crystal-like. In Zr 50Cu 35Al 15, the poorer glass former, the crystal-like structure is more stable under annealing below the glass transition temperature, T g, than in Zr 50Cu 45Al 5. Variable resolution fluctuation microscopy of the MRO clusters show that in Zr 50Cu 35Al 15more » on sub-Tg annealing, the crystal-like clusters shrink even as they grow more ordered, while icosahedral-like clusters grow. Furthermore, the results suggest that achieving better glass forming ability in this alloy system may depend more on destabilizing crystal-like structures than enhancing non-crystalline structures.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Pei; Maldonis, Jason J.; Besser, M. F.

Fluctuation electron microscopy experiments combined with hybrid reverse Monte Carlo modeling show a correlation between medium-range structure at the nanometer scale and glass forming ability in two Zr–Cu–Al bulk metallic glass (BMG) alloys. Both Zr 50Cu 35Al 15 and Zr 50Cu 45Al 5 exhibit two nanoscale structure types, one icosahedral and the other more crystal-like. In Zr 50Cu 35Al 15, the poorer glass former, the crystal-like structure is more stable under annealing below the glass transition temperature, T g, than in Zr 50Cu 45Al 5. Variable resolution fluctuation microscopy of the MRO clusters show that in Zr 50Cu 35Al 15more » on sub-Tg annealing, the crystal-like clusters shrink even as they grow more ordered, while icosahedral-like clusters grow. Furthermore, the results suggest that achieving better glass forming ability in this alloy system may depend more on destabilizing crystal-like structures than enhancing non-crystalline structures.« less

Improvement of aerosol optical properties modeling over Eastern Asia with MODIS AOD assimilation in a global non-hydrostatic icosahedral aerosol transport model.

PubMed

Dai, Tie; Schutgens, Nick A J; Goto, Daisuke; Shi, Guangyu; Nakajima, Teruyuki

2014-12-01

A new global aerosol assimilation system adopting a more complex icosahedral grid configuration is developed. Sensitivity tests for the assimilation system are performed utilizing satellite retrieved aerosol optical depth (AOD) from the Moderate Resolution Imaging Spectroradiometer (MODIS), and the results over Eastern Asia are analyzed. The assimilated results are validated through independent Aerosol Robotic Network (AERONET) observations. Our results reveal that the ensemble and local patch sizes have little effect on the assimilation performance, whereas the ensemble perturbation method has the largest effect. Assimilation leads to significantly positive effect on the simulated AOD field, improving agreement with all of the 12 AERONET sites over the Eastern Asia based on both the correlation coefficient and the root mean square difference (assimilation efficiency). Meanwhile, better agreement of the Ångström Exponent (AE) field is achieved for 8 of the 12 sites due to the assimilation of AOD only. Copyright © 2014 Elsevier Ltd. All rights reserved.

Chain-like structure elements in Ni40Ta60 metallic glasses observed by scanning tunneling microscopy

PubMed Central

Pawlak, Rémy; Marot, Laurent; Sadeghi, Ali; Kawai, Shigeki; Glatzel, Thilo; Reimann, Peter; Goedecker, Stefan; Güntherodt, Hans-Joachim; Meyer, Ernst

2015-01-01

The structure of metallic glasses is a long-standing question because the lack of long-range order makes diffraction based techniques difficult to be applied. Here, we used scanning tunneling microscopy with large tunneling resistance of 6 GΩ at low temperature in order to minimize forces between probe and sample and reduce thermal fluctuations of metastable structures. Under these extremely gentle conditions, atomic structures of Ni40Ta60 metallic glasses are revealed with unprecedented lateral resolution. In agreement with previous models and experiments, icosahedral-like clusters are observed. The clusters show a high degree of mobility, which explains the need of low temperatures for stable imaging. In addition to icosahedrons, chain-like structures are resolved and comparative density functional theory (DFT) calculations confirm that these structures are meta-stable. The co-existence of icosahedral and chain-like structures might be an key ingredient for the understanding of the mechanical properties of metallic glasses. PMID:26268430

Quantum transport through single and multilayer icosahedral fullerenes

NASA Astrophysics Data System (ADS)

Lovey, Daniel A.; Romero, Rodolfo H.

2013-10-01

We use a tight-binding Hamiltonian and Green functions methods to calculate the quantum transmission through single-wall fullerenes and bilayered and trilayered onions of icosahedral symmetry attached to metallic leads. The electronic structure of the onion-like fullerenes takes into account the curvature and finite size of the fullerenes layers as well as the strength of the intershell interactions depending on to the number of interacting atom pairs belonging to adjacent shells. Misalignment of the symmetry axes of the concentric iscosahedral shells produces breaking of the level degeneracies of the individual shells, giving rise some narrow quasi-continuum bands instead of the localized discrete peaks of the individual fullerenes. As a result, the transmission function for non symmetrical onions is rapidly varying functions of the Fermi energy. Furthermore, we found that most of the features of the transmission through the onions are due to the electronic structure of the outer shell with additional Fano-like antiresonances arising from coupling with or between the inner shells.

A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress.

PubMed

McHugh, Colleen A; Fontana, Juan; Nemecek, Daniel; Cheng, Naiqian; Aksyuk, Anastasia A; Heymann, J Bernard; Winkler, Dennis C; Lam, Alan S; Wall, Joseph S; Steven, Alasdair C; Hoiczyk, Egbert

2014-09-01

Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound nanocompartments. Encapsulins constitute a class of nanocompartments widespread in bacteria and archaea whose functions have hitherto been unclear. Here, we characterize the encapsulin nanocompartment from Myxococcus xanthus, which consists of a shell protein (EncA, 32.5 kDa) and three internal proteins (EncB, 17 kDa; EncC, 13 kDa; EncD, 11 kDa). Using cryo-electron microscopy, we determined that EncA self-assembles into an icosahedral shell 32 nm in diameter (26 nm internal diameter), built from 180 subunits with the fold first observed in bacteriophage HK97 capsid. The internal proteins, of which EncB and EncC have ferritin-like domains, attach to its inner surface. Native nanocompartments have dense iron-rich cores. Functionally, they resemble ferritins, cage-like iron storage proteins, but with a massively greater capacity (~30,000 iron atoms versus ~3,000 in ferritin). Physiological data reveal that few nanocompartments are assembled during vegetative growth, but they increase fivefold upon starvation, protecting cells from oxidative stress through iron sequestration. © 2014 The Authors.

Cryo-Electron Microscopy Reconstruction Shows Poliovirus 135S Particles Poised for Membrane Interaction and RNA Release

PubMed Central

Butan, Carmen; Filman, David J.

2014-01-01

During infection, binding of mature poliovirus to cell surface receptors induces an irreversible expansion of the capsid, to form an infectious cell-entry intermediate particle that sediments at 135S. In these expanded virions, the major capsid proteins (VP1 to VP3) adopt an altered icosahedral arrangement to open holes in the capsid at 2-fold and quasi-3-fold axes, and internal polypeptides VP4 and the N terminus of VP1, which can bind membranes, become externalized. Cryo-electron microscopy images for 117,330 particles were collected using Leginon and reconstructed using FREALIGN. Improved rigid-body positioning of major capsid proteins established reliably which polypeptide segments become disordered or rearranged. The virus-to-135S transition includes expansion of 4%, rearrangements of the GH loops of VP3 and VP1, and disordering of C-terminal extensions of VP1 and VP2. The N terminus of VP1 rearranges to become externalized near its quasi-3-fold exit, binds to rearranged GH loops of VP3 and VP1, and attaches to the top surface of VP2. These details improve our understanding of subsequent stages of infection, including endocytosis and RNA transfer into the cytoplasm. PMID:24257617

The Rhinovirus Subviral A-Particle Exposes 3′-Terminal Sequences of Its Genomic RNA

PubMed Central

Harutyunyan, Shushan; Kowalski, Heinrich

2014-01-01

ABSTRACT Enteroviruses, which represent a large genus within the family Picornaviridae, undergo important conformational modifications during infection of the host cell. Once internalized by receptor-mediated endocytosis, receptor binding and/or the acidic endosomal environment triggers the native virion to expand and convert into the subviral (altered) A-particle. The A-particle is lacking the internal capsid protein VP4 and exposes N-terminal amphipathic sequences of VP1, allowing for its direct interaction with a lipid bilayer. The genomic single-stranded (+)RNA then exits through a hole close to a 2-fold axis of icosahedral symmetry and passes through a pore in the endosomal membrane into the cytosol, leaving behind the empty shell. We demonstrate that in vitro acidification of a prototype of the minor receptor group of common cold viruses, human rhinovirus A2 (HRV-A2), also results in egress of the poly(A) tail of the RNA from the A-particle, along with adjacent nucleotides totaling ∼700 bases. However, even after hours of incubation at pH 5.2, 5′-proximal sequences remain inside the capsid. In contrast, the entire RNA genome is released within minutes of exposure to the acidic endosomal environment in vivo. This finding suggests that the exposed 3′-poly(A) tail facilitates the positioning of the RNA exit site onto the putative channel in the lipid bilayer, thereby preventing the egress of viral RNA into the endosomal lumen, where it may be degraded. IMPORTANCE For host cell infection, a virus transfers its genome from within the protective capsid into the cytosol; this requires modifications of the viral shell. In common cold viruses, exit of the RNA genome is prepared by the acidic environment in endosomes converting the native virion into the subviral A-particle. We demonstrate that acidification in vitro results in RNA exit starting from the 3′-terminal poly(A). However, the process halts as soon as about 700 bases have left the viral shell. Conversely, inside the cell, RNA egress completes in about 2 min. This suggests the existence of cellular uncoating facilitators. PMID:24672023

Dissecting the herpesvirus architecture by targeted proteolysis.

PubMed

Daniel, Gina R; Pegg, Caitlin E; Smith, Gregory A

2018-06-13

Herpesvirus particles have a complex architecture consisting of an icosahedral capsid that is surrounded by a lipid envelope. Connecting these two components is a layer of tegument that consists of varying amounts of twenty or more proteins. The arrangement of proteins within the tegument cannot easily be assessed and instead is inferred from tegument interactions identified in reductionist models. To better understand the tegument architecture, we have developed an approach to probe capsid-tegument interactions of extracellular viral particles by encoding tobacco etch virus (TEV) protease sites in viral structural proteins, along with distinct fluorescent tags in capsid and tegument components. In this study, TEV sites were engineered within the pUL36 large tegument protein: a critical structural element that is anchored directly on the capsid surface. Purified pseudorabies virus extracellular particles were permeabilized and TEV protease was added to selectively cleave the exposed pUL36 backbone. Interactions with the capsid were assessed in situ by monitoring the fate of the fluorescent signals following cleavage. Although several regions of pUL36 are proposed to bind capsids, pUL36 was found stably anchored to the capsid exclusively at its carboxyl terminus. Two additional tegument proteins, pUL37 and pUS3, were tethered to the capsid via pUL36 whereas the pUL16, pUL47, pUL48, and pUL49 tegument proteins were not stably bound to the capsid. IMPORTANCE: Neuroinvasive alphaherpesviruses produce diseases of clinical and economic significance in humans and veterinary animals, but are predominantly associated with less serious recurrent disease. Like all viruses, herpesviruses assemble a metastable particle that selectively dismantles during initial infection. This process is made more complex by the presence of a tegument layer that resides between the capsid surface and envelope. Components of the tegument are essential for particle assembly and also serve as critical effectors that promote infection upon entry into cells. How this dynamic network of protein interactions is arranged within virions is largely unknown. We present a molecular approach to dissect the tegument and with it, begin to tease apart the protein interactions that underlie this complex layer of the virion architecture. Copyright © 2018 American Society for Microbiology.

Correlation of Mechanical Properties in Bulk Metallic Glasses with 27Al NMR Characteristics

DTIC Science & Technology

2011-12-01

recycle delay of 300 ms. Magnetization measurements were conducted at room temperature using a Quantum Design SQUID magne- tometer. The magnetization of...Gangopadhyay A K, et al. First X-ray scattering studies on electrostatically levitated metallic liquids: Demonstrated influence of local icosahedral

Shear localization and size-dependent strength of YCd 6 quasicrystal approximant at the micrometer length scale

DOE PAGES

Song, Gyuho; Kong, Tai; Dusoe, Keith J.; ...

2018-01-24

Mechanical properties of materials are strongly dependent of their atomic arrangement as well as the sample dimension, particularly at the micrometer length scale. Here in this study, we investigated the small-scale mechanical properties of single-crystalline YCd 6, which is a rational approximant of the icosahedral Y-Cd quasicrystal. In situ microcompression tests revealed that shear localization always occurs on {101} planes, but the shear direction is not constrained to any particular crystallographic directions. Furthermore, the yield strengths show the size dependence with a power law exponent of 0.4. Shear localization on {101} planes and size-dependent yield strength are explained in termsmore » of a large interplanar spacing between {101} planes and the energetics of shear localization process, respectively. The mechanical behavior of the icosahedral Y-Cd quasicrystal is also compared to understand the influence of translational symmetry on the shear localization process in both YCd 6 and Y-Cd quasicrystal micropillars. Finally, the results of this study will provide an important insight in a fundamental understanding of shear localization process in novel complex intermetallic compounds.« less

Shear localization and size-dependent strength of YCd 6 quasicrystal approximant at the micrometer length scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Gyuho; Kong, Tai; Dusoe, Keith J.

Mechanical properties of materials are strongly dependent of their atomic arrangement as well as the sample dimension, particularly at the micrometer length scale. Here in this study, we investigated the small-scale mechanical properties of single-crystalline YCd 6, which is a rational approximant of the icosahedral Y-Cd quasicrystal. In situ microcompression tests revealed that shear localization always occurs on {101} planes, but the shear direction is not constrained to any particular crystallographic directions. Furthermore, the yield strengths show the size dependence with a power law exponent of 0.4. Shear localization on {101} planes and size-dependent yield strength are explained in termsmore » of a large interplanar spacing between {101} planes and the energetics of shear localization process, respectively. The mechanical behavior of the icosahedral Y-Cd quasicrystal is also compared to understand the influence of translational symmetry on the shear localization process in both YCd 6 and Y-Cd quasicrystal micropillars. Finally, the results of this study will provide an important insight in a fundamental understanding of shear localization process in novel complex intermetallic compounds.« less

Local order and crystallization of dense polydisperse hard spheres

NASA Astrophysics Data System (ADS)

Coslovich, Daniele; Ozawa, Misaki; Berthier, Ludovic

2018-04-01

Computer simulations give precious insight into the microscopic behavior of supercooled liquids and glasses, but their typical time scales are orders of magnitude shorter than the experimentally relevant ones. We recently closed this gap for a class of models of size polydisperse fluids, which we successfully equilibrate beyond laboratory time scales by means of the swap Monte Carlo algorithm. In this contribution, we study the interplay between compositional and geometric local orders in a model of polydisperse hard spheres equilibrated with this algorithm. Local compositional order has a weak state dependence, while local geometric order associated to icosahedral arrangements grows more markedly but only at very high density. We quantify the correlation lengths and the degree of sphericity associated to icosahedral structures and compare these results to those for the Wahnström Lennard-Jones mixture. Finally, we analyze the structure of very dense samples that partially crystallized following a pattern incompatible with conventional fractionation scenarios. The crystal structure has the symmetry of aluminum diboride and involves a subset of small and large particles with size ratio approximately equal to 0.5.

Dynamics of Transformation from Platinum Icosahedral Nanoparticles to Larger FCC Crystal at Millisecond Time Resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Wenpei; Wu, Jianbo; Yoon, Aram

Atomic motion at grain boundaries is essential to microstructure development, growth and stability of catalysts and other nanostructured materials. However, boundary atomic motion is often too fast to observe in a conventional transmission electron microscope (TEM) and too slow for ultrafast electron microscopy. We report on the entire transformation process of strained Pt icosahedral nanoparticles (ICNPs) into larger FCC crystals, captured at 2.5 ms time resolution using a fast electron camera. Results show slow diffusive dislocation motion at nm/s inside ICNPs and fast surface transformation at μm/s. By characterizing nanoparticle strain, we show that the fast transformation is driven bymore » inhomogeneous surface stress. And interaction with pre-existing defects led to the slowdown of the transformation front inside the nanoparticles. Particle coalescence, assisted by oxygen-induced surface migration at T ≥ 300°C, also played a critical role. Thus by studying transformation in the Pt ICNPs at high time and spatial resolution, we obtain critical insights into the transformation mechanisms in strained Pt nanoparticles.« less

Magnetic Resonance Characterization of Defects in Icosahedral and Cubic Boron Arsenide Bulk Crystals

NASA Astrophysics Data System (ADS)

Glaser, E. R.; Freitas, J. A., Jr.; Cress, C. D.; Perkins, F. K.; Prokes, S. M.; Ruppalt, L. B.; Culbertson, J. C.; Whiteley, C.; Edgar, J. H.; Tian, F.; Ren, Z.; Kim, J.; Shi, L.; Naval Research Lab Team; Kansas State U. Team; U. Houston Team; U. Texas Team

Low-temperature electron spin resonance (ESR) at 9.5 GHz and optically-detected magnetic resonance (ODMR) at 24 GHz were employed to investigate point defects in icosahedral and cubic Boron Arsenide bulk crystals. These semiconductors are of interest for use in high radiation and/or high temperature environments. ESR of the (001) B12As2 (Eg = 3.47 eV) mm-size platelets revealed two distinct features of unknown origin. The first signal is characterized by Zeeman splitting g-values of g|| = 2.017, g⊥ = 2.0183 while the second with g|| = 2.0182, g⊥ = 1.9997. Most notably, the second signal was also observed from ODMR on the broad 2.4 eV ``yellow/green'' photoluminescence band previously reported for these crystals and suggests its direct involvement in this likely defect-related radiative recombination process. Preliminary ESR obtained for the 100-300 micron-size cubic BAs crystals revealed a signal with g-value of 2.018 (very similar to that found for the B12As2 crystals) and broad FWHM value of 182 G. Possible origins of these defects will be discussed.

Melting phenomena: effect of composition for 55-atom Ag-Pd bimetallic clusters.

PubMed

Cheng, Daojian; Wang, Wenchuan; Huang, Shiping

2008-05-14

Understanding the composition effect on the melting processes of bimetallic clusters is important for their applications. Here, we report the relationship between the melting point and the metal composition for the 55-atom icosahedral Ag-Pd bimetallic clusters by canonical Monte Carlo simulations, using the second-moment approximation of the tight-binding potentials (TB-SMA) for the metal-metal interactions. Abnormal melting phenomena for the systems of interest are found. Our simulation results reveal that the dependence of the melting point on the composition is not a monotonic change, but experiences three different stages. The melting temperatures of the Ag-Pd bimetallic clusters increase monotonically with the concentration of the Ag atoms first. Then, they reach a plateau presenting almost a constant value. Finally, they decrease sharply at a specific composition. The main reason for this change can be explained in terms of the relative stability of the Ag-Pd bimetallic clusters at different compositions. The results suggest that the more stable the cluster, the higher the melting point for the 55-atom icosahedral Ag-Pd bimetallic clusters at different compositions.

Shock synthesis of quasicrystals with implications for their origin in asteroid collisions.

PubMed

Asimow, Paul D; Lin, Chaney; Bindi, Luca; Ma, Chi; Tschauner, Oliver; Hollister, Lincoln S; Steinhardt, Paul J

2016-06-28

We designed a plate impact shock recovery experiment to simulate the starting materials and shock conditions associated with the only known natural quasicrystals, in the Khatyrka meteorite. At the boundaries among CuAl5, (Mg0.75Fe(2+) 0.25)2SiO4 olivine, and the stainless steel chamber walls, the recovered specimen contains numerous micron-scale grains of a quasicrystalline phase displaying face-centered icosahedral symmetry and low phason strain. The compositional range of the icosahedral phase is Al68-73Fe11-16Cu10-12Cr1-4Ni1-2 and extends toward higher Al/(Cu+Fe) and Fe/Cu ratios than those reported for natural icosahedrite or for any previously known synthetic quasicrystal in the Al-Cu-Fe system. The shock-induced synthesis demonstrated in this experiment reinforces the evidence that natural quasicrystals formed during a shock event but leaves open the question of whether this synthesis pathway is attributable to the expanded thermodynamic stability range of the quasicrystalline phase at high pressure, to a favorable kinetic pathway that exists under shock conditions, or to both thermodynamic and kinetic factors.

Shock synthesis of quasicrystals with implications for their origin in asteroid collisions

NASA Astrophysics Data System (ADS)

Asimow, Paul D.; Lin, Chaney; Bindi, Luca; Ma, Chi; Tschauner, Oliver; Hollister, Lincoln S.; Steinhardt, Paul J.

2016-06-01

We designed a plate impact shock recovery experiment to simulate the starting materials and shock conditions associated with the only known natural quasicrystals, in the Khatyrka meteorite. At the boundaries among CuAl5, (Mg0.75Fe2+0.25)2SiO4 olivine, and the stainless steel chamber walls, the recovered specimen contains numerous micron-scale grains of a quasicrystalline phase displaying face-centered icosahedral symmetry and low phason strain. The compositional range of the icosahedral phase is Al68-73Fe11-16Cu10-12Cr1-4Ni1-2 and extends toward higher Al/(Cu+Fe) and Fe/Cu ratios than those reported for natural icosahedrite or for any previously known synthetic quasicrystal in the Al-Cu-Fe system. The shock-induced synthesis demonstrated in this experiment reinforces the evidence that natural quasicrystals formed during a shock event but leaves open the question of whether this synthesis pathway is attributable to the expanded thermodynamic stability range of the quasicrystalline phase at high pressure, to a favorable kinetic pathway that exists under shock conditions, or to both thermodynamic and kinetic factors.

Shape-dependent surface magnetism of Co-Pt and Fe-Pt nanoparticles from first principles

NASA Astrophysics Data System (ADS)

Liu, Zhenyu; Wang, Guofeng

2017-12-01

In this paper, we have performed the first-principles density functional theory calculations to predict the magnetic properties of the CoPt and FePt nanoparticles in cuboctahedral, decahedral, and icosahedral shapes. The modeled alloy nanoparticles have a diameter of 1.1 nm and consist of 31 5 d Pt atoms and 24 3 d Co (or Fe) atoms. For both CoPt and FePt, we found that the decahedral nanoparticles had appreciably lower surface magnetic moments than the cuboctahedral and icosahedral nanoparticles. Our analysis indicated that this reduction in the surface magnetism was related to a large contraction of atomic spacing and high local Co (or Fe) concentration in the surface of the decahedral nanoparticles. More interestingly, we predicted that the CoPt and FePt cuboctahedral nanoparticles exhibited dramatically different surface spin structures when noncollinear magnetism was taken into account. Our calculation results revealed that surface anisotropy energy decided the fashion of surface spin canting in the CoPt and FePt nanoparticles, confirming previous predictions from atomistic Monte Carlo simulations.

The quantum structure of anionic hydrogen clusters

NASA Astrophysics Data System (ADS)

Calvo, F.; Yurtsever, E.

2018-03-01

A flexible and polarizable interatomic potential has been developed to model hydrogen clusters interacting with one hydrogen anion, (H2)nH-, in a broad range of sizes n = 1-54 and parametrized against coupled cluster quantum chemical calculations. Using path-integral molecular dynamics simulations at 1 K initiated from the putative classical global minima, the equilibrium structures are found to generally rely on icosahedral shells with the hydrogen molecules pointing toward the anion, producing geometric magic numbers at sizes n = 12, 32, and 44 that are in agreement with recent mass spectrometry measurements. The energetic stability of the clusters is also connected with the extent of vibrational delocalization, measured here by the fluctuations among inherent structures hidden in the vibrational wave function. As the clusters grow, the outer molecules become increasingly free to rotate, and strong finite size effects are also found between magic numbers, associated with more prominent vibrational delocalization. The effective icosahedral structure of the 44-molecule cluster is found to originate from quantum nuclear effects as well, the classical structure showing no particular symmetry.

Human Adenovirus Core Protein V Is Targeted by the Host SUMOylation Machinery To Limit Essential Viral Functions.

PubMed

Freudenberger, Nora; Meyer, Tina; Groitl, Peter; Dobner, Thomas; Schreiner, Sabrina

2018-02-15

Human adenoviruses (HAdV) are nonenveloped viruses containing a linear, double-stranded DNA genome surrounded by an icosahedral capsid. To allow proper viral replication, the genome is imported through the nuclear pore complex associated with viral core proteins. Until now, the role of these incoming virion proteins during the early phase of infection was poorly understood. The core protein V is speculated to bridge the core and the surrounding capsid. It binds the genome in a sequence-independent manner and localizes in the nucleus of infected cells, accumulating at nucleoli. Here, we show that protein V contains conserved SUMO conjugation motifs (SCMs). Mutation of these consensus motifs resulted in reduced SUMOylation of the protein; thus, protein V represents a novel target of the host SUMOylation machinery. To understand the role of protein V SUMO posttranslational modification during productive HAdV infection, we generated a replication-competent HAdV with SCM mutations within the protein V coding sequence. Phenotypic analyses revealed that these SCM mutations are beneficial for adenoviral replication. Blocking protein V SUMOylation at specific sites shifts the onset of viral DNA replication to earlier time points during infection and promotes viral gene expression. Simultaneously, the altered kinetics within the viral life cycle are accompanied by more efficient proteasomal degradation of host determinants and increased virus progeny production than that observed during wild-type infection. Taken together, our studies show that protein V SUMOylation reduces virus growth; hence, protein V SUMOylation represents an important novel aspect of the host antiviral strategy to limit virus replication and thereby points to potential intervention strategies. IMPORTANCE Many decades of research have revealed that HAdV structural proteins promote viral entry and mainly physical stability of the viral genome in the capsid. Our work over the last years showed that this concept needs expansion as the functions are more diverse. We showed that capsid protein VI regulates the antiviral response by modulation of the transcription factor Daxx during infection. Moreover, core protein VII interacts with SPOC1 restriction factor, which is beneficial for efficient viral gene expression. Here, we were able to show that core protein V also represents a novel substrate of the host SUMOylation machinery and contains several conserved SCMs; mutation of these consensus motifs reduced SUMOylation of the protein. Unexpectedly, we observed that introducing these mutations into HAdV promotes adenoviral replication. In conclusion, we offer novel insights into adenovirus core proteins and provide evidence that SUMOylation of HAdV factors regulates replication efficiency. Copyright © 2018 American Society for Microbiology.

An Externalized Polypeptide Partitions between Two Distinct Sites on Genome-Released Poliovirus Particles ▿

PubMed Central

Lin, Jun; Cheng, Naiqian; Chow, Marie; Filman, David J.; Steven, Alasdair C.; Hogle, James M.; Belnap, David M.

2011-01-01

During cell entry, native poliovirus (160S) converts to a cell-entry intermediate (135S) particle, resulting in the externalization of capsid proteins VP4 and the amino terminus of VP1 (residues 1 to 53). Externalization of these entities is followed by release of the RNA genome (uncoating), leaving an empty (80S) particle. The antigen-binding fragment (Fab) of a monospecific peptide 1 (P1) antibody, which was raised against a peptide corresponding to amino-terminal residues 24 to 40 of VP1, was utilized to track the location of the amino terminus of VP1 in the 135S and 80S states of poliovirus particles via cryogenic electron microscopy (cryo-EM) and three-dimensional image reconstruction. On 135S, P1 Fabs bind to a prominent feature on the external surface known as the “propeller tip.” In contrast, our initial 80S-P1 reconstruction showed P1 Fabs also binding to a second site, at least 50 Å distant, at the icosahedral 2-fold axes. Further analysis showed that the overall population of 80S-P1 particles consisted of three kinds of capsids: those with P1 Fabs bound only at the propeller tips, P1 Fabs bound only at the 2-fold axes, or P1 Fabs simultaneously bound at both positions. Our results indicate that, in 80S particles, a significant fraction of VP1 can deviate from icosahedral symmetry. Hence, this portion of VP1 does not change conformation synchronously when switching from the 135S state. These conclusions are compatible with previous observations of multiple conformations of the 80S state and suggest that movement of the amino terminus of VP1 has a role in uncoating. Similar deviations from icosahedral symmetry may be biologically significant during other viral transitions. PMID:21775460

A Molecular Dynamics Study of the Structure-Dynamics Relationships of Supercooled Liquids and Glasses

NASA Astrophysics Data System (ADS)

Soklaski, Ryan

Central to the field of condensed matter physics is a decades old outstanding problem in the study of glasses -- namely explaining the extreme slowing of dynamics in a liquid as it is supercooled towards the so-called glass transition. Efforts to universally describe the stretched relaxation processes and heterogeneous dynamics that characteristically develop in supercooled liquids remain divided in both their approaches and successes. Towards this end, a consensus on the role that atomic and molecular structures play in the liquid is even more tenuous. However, mounting material science research efforts have culminated to reveal that the vast diversity of metallic glass species and their properties are rooted in an equally-broad set of structural archetypes. Herein lies the motivation of this dissertation: the detailed information available regarding the structure-property relationships of metallic glasses provides a new context in which one can study the evolution of a supercooled liquid by utilizing a structural motif that is known to dominate the glass. Cu64Zr36 is a binary alloy whose good glass-forming ability and simple composition makes it a canonical material to both empirical and numerical studies. Here, we perform classical molecular dynamics simulations and conduct a comprehensive analysis of the dynamical regimes of liquid Cu64Zr36, while focusing on the roles played by atomic icosahedral ordering -- a structural motif which ultimately percolates the glass' structure. Large data analysis techniques are leveraged to obtain uniquely detailed structural and dynamical information in this context. In doing so, we develop the first account of the origin of icosahedral order in this alloy, revealing deep connections between this incipient structural ordering, frustration-limited domain theory, and recent important empirical findings that are relevant to the nature of metallic liquids at large. Furthermore, important dynamical landmarks such as the breakdown of the Stokes-Einstein relationship, the decoupling of particle diffusivities, and the development of general "glassy" relaxation features are found to coincide with successive manifestation of icosahedral ordering that arise as the liquid is supercooled. Remarkably, we detect critical-like features in the growth of the icosahedron network, with signatures that suggest that a liquid-liquid phase transition may occur in the deeply supercooled regime to precede glass formation. Such a transition is predicted to occur in many supercooled liquids, although explicit evidence of this phenomenon in realistic systems is scarce. Ultimately this work concludes that icosahedral order characterizes all dynamical regimes of Cu64Zr 36, demonstrating the importance and utility of studying supercooled liquids in the context of locally-preferred structure. More broadly, it serves to confirm and inform recent theoretical and empirical findings that are central to understanding the physics underlying the glass transition.

Surface decorated platinum carbonyl clusters

NASA Astrophysics Data System (ADS)

Ciabatti, Iacopo; Femoni, Cristina; Iapalucci, Maria Carmela; Longoni, Giuliano; Zacchini, Stefano; Zarra, Salvatore

2012-06-01

Four molecular Pt-carbonyl clusters decorated by Cd-Br fragments, i.e., [Pt13(CO)12{Cd5(μ-Br)5Br2(dmf)3}2]2- (1), [Pt19(CO)17{Cd5(μ-Br)5Br3(Me2CO)2}{Cd5(μ-Br)5Br(Me2CO)4}]2- (2), [H2Pt26(CO)20(CdBr)12]8- (3) and [H4Pt26(CO)20(CdBr)12(PtBr)x]6- (4) (x = 0-2), have been obtained from the reactions between [Pt3n(CO)6n]2- (n = 2-6) and CdBr2.H2O in dmf at 120 °C. The structures of these molecular clusters with diameters of 1.5-2 nm have been determined by X-ray crystallography. Both 1 and 2 are composed of icosahedral or bis-icosahedral Pt-CO cores decorated on the surface by Cd-Br motifs, whereas 3 and 4 display a cubic close packed Pt26Cd12 metal frame decorated by CO and Br ligands. An oversimplified and unifying approach to interpret the electron count of these surface decorated platinum carbonyl clusters is suggested, and extended to other low-valent organometallic clusters and Au-thiolate nanoclusters.Four molecular Pt-carbonyl clusters decorated by Cd-Br fragments, i.e., [Pt13(CO)12{Cd5(μ-Br)5Br2(dmf)3}2]2- (1), [Pt19(CO)17{Cd5(μ-Br)5Br3(Me2CO)2}{Cd5(μ-Br)5Br(Me2CO)4}]2- (2), [H2Pt26(CO)20(CdBr)12]8- (3) and [H4Pt26(CO)20(CdBr)12(PtBr)x]6- (4) (x = 0-2), have been obtained from the reactions between [Pt3n(CO)6n]2- (n = 2-6) and CdBr2.H2O in dmf at 120 °C. The structures of these molecular clusters with diameters of 1.5-2 nm have been determined by X-ray crystallography. Both 1 and 2 are composed of icosahedral or bis-icosahedral Pt-CO cores decorated on the surface by Cd-Br motifs, whereas 3 and 4 display a cubic close packed Pt26Cd12 metal frame decorated by CO and Br ligands. An oversimplified and unifying approach to interpret the electron count of these surface decorated platinum carbonyl clusters is suggested, and extended to other low-valent organometallic clusters and Au-thiolate nanoclusters. CCDC 867747 and 867748. For crystallographic data in CIF or other electronic format see DOI: 10.1039/c2nr30400g

Comparative genomic and morphological analyses of Listeria phages isolated from farm environments.

PubMed

Denes, Thomas; Vongkamjan, Kitiya; Ackermann, Hans-Wolfgang; Moreno Switt, Andrea I; Wiedmann, Martin; den Bakker, Henk C

2014-08-01

The genus Listeria is ubiquitous in the environment and includes the globally important food-borne pathogen Listeria monocytogenes. While the genomic diversity of Listeria has been well studied, considerably less is known about the genomic and morphological diversity of Listeria bacteriophages. In this study, we sequenced and analyzed the genomes of 14 Listeria phages isolated mostly from New York dairy farm environments as well as one related Enterococcus faecalis phage to obtain information on genome characteristics and diversity. We also examined 12 of the phages by electron microscopy to characterize their morphology. These Listeria phages, based on gene orthology and morphology, together with previously sequenced Listeria phages could be classified into five orthoclusters, including one novel orthocluster. One orthocluster (orthocluster I) consists of large genome (~135-kb) myoviruses belonging to the genus “Twort-like viruses,” three orthoclusters (orthoclusters II to IV) contain small-genome (36- to 43-kb) siphoviruses with icosahedral heads, and the novel orthocluster V contains medium-sized-genome (~66-kb) siphoviruses with elongated heads. A novel orthocluster (orthocluster VI) of E. faecalis phages, with medium-sized genomes (~56 kb), was identified, which grouped together and shares morphological features with the novel Listeria phage orthocluster V. This new group of phages (i.e., orthoclusters V and VI) is composed of putative lytic phages that may prove to be useful in phage-based applications for biocontrol, detection, and therapeutic purposes.

L2, the minor capsid protein of papillomavirus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Joshua W.; Roden, Richard B.S., E-mail: roden@jhmi.edu; Department of Oncology, The Johns Hopkins University, Baltimore, MD 21287

2013-10-15

The capsid protein L2 plays major roles in both papillomavirus assembly and the infectious process. While L1 forms the majority of the capsid and can self-assemble into empty virus-like particles (VLPs), L2 is a minor capsid component and lacks the capacity to form VLPs. However, L2 co-assembles with L1 into VLPs, enhancing their assembly. L2 also facilitates encapsidation of the ∼8 kbp circular and nucleosome-bound viral genome during assembly of the non-enveloped T=7d virions in the nucleus of terminally differentiated epithelial cells, although, like L1, L2 is not detectably expressed in infected basal cells. With respect to infection, L2 ismore » not required for particles to bind to and enter cells. However L2 must be cleaved by furin for endosome escape. L2 then travels with the viral genome to the nucleus, wherein it accumulates at ND-10 domains. Here, we provide an overview of the biology of L2. - Highlights: • L2 is the minor antigen of the non-enveloped T=7d icosahedral Papillomavirus capsid. • L2 is a nuclear protein that can traffic to ND-10 and facilitate genome encapsidation. • L2 is critical for infection and must be cleaved by furin. • L2 is a broadly protective vaccine antigen recognized by neutralizing antibodies.« less

Dissection of Antibody Specificities Induced by Yellow Fever Vaccination

PubMed Central

Vratskikh, Oksana; Stiasny, Karin; Zlatkovic, Jürgen; Tsouchnikas, Georgios; Jarmer, Johanna; Karrer, Urs; Roggendorf, Michael; Roggendorf, Hedwig; Allwinn, Regina; Heinz, Franz X.

2013-01-01

The live attenuated yellow fever (YF) vaccine has an excellent record of efficacy and one dose provides long-lasting immunity, which in many cases may last a lifetime. Vaccination stimulates strong innate and adaptive immune responses, and neutralizing antibodies are considered to be the major effectors that correlate with protection from disease. Similar to other flaviviruses, such antibodies are primarily induced by the viral envelope protein E, which consists of three distinct domains (DI, II, and III) and is presented at the surface of mature flavivirions in an icosahedral arrangement. In general, the dominance and individual variation of antibodies to different domains of viral surface proteins and their impact on neutralizing activity are aspects of humoral immunity that are not well understood. To gain insight into these phenomena, we established a platform of immunoassays using recombinant proteins and protein domains that allowed us to dissect and quantify fine specificities of the polyclonal antibody response after YF vaccination in a panel of 51 vaccinees as well as determine their contribution to virus neutralization by serum depletion analyses. Our data revealed a high degree of individual variation in antibody specificities present in post-vaccination sera and differences in the contribution of different antibody subsets to virus neutralization. Irrespective of individual variation, a substantial proportion of neutralizing activity appeared to be due to antibodies directed to complex quaternary epitopes displayed on the virion surface only but not on monomeric E. On the other hand, DIII-specific antibodies (presumed to have the highest neutralizing activity) as well as broadly flavivirus cross-reactive antibodies were absent or present at very low titers. These data provide new information on the fine specificity as well as variability of antibody responses after YF vaccination that are consistent with a strong influence of individual-specific factors on immunodominance in humoral immune responses. PMID:23818856

Assembly of the Herpes Simplex Virus Capsid: Preformed Triplexes Bind to the Nascent Capsid

PubMed Central

Spencer, Juliet V.; Newcomb, William W.; Thomsen, Darrell R.; Homa, Fred L.; Brown, Jay C.

1998-01-01

The herpes simplex virus type 1 (HSV-1) capsid is a T=16 icosahedral shell that forms in the nuclei of infected cells. Capsid assembly also occurs in vitro in reaction mixtures created from insect cell extracts containing recombinant baculovirus-expressed HSV-1 capsid proteins. During capsid formation, the major capsid protein, VP5, and the scaffolding protein, pre-VP22a, condense to form structures that are extended into procapsids by addition of the triplex proteins, VP19C and VP23. We investigated whether triplex proteins bind to the major capsid-scaffold protein complexes as separate polypeptides or as preformed triplexes. Assembly products from reactions lacking one triplex protein were immunoprecipitated and examined for the presence of the other. The results showed that neither triplex protein bound unless both were present, suggesting that interaction between VP19C and VP23 is required before either protein can participate in the assembly process. Sucrose density gradient analysis was employed to determine the sedimentation coefficients of VP19C, VP23, and VP19C-VP23 complexes. The results showed that the two proteins formed a complex with a sedimentation coefficient of 7.2S, a value that is consistent with formation of a VP19C-VP232 heterotrimer. Furthermore, VP23 was observed to have a sedimentation coefficient of 4.9S, suggesting that this protein exists as a dimer in solution. Deletion analysis of VP19C revealed two domains that may be required for attachment of the triplex to major capsid-scaffold protein complexes; none of the deletions disrupted interaction of VP19C with VP23. We propose that preformed triplexes (VP19C-VP232 heterotrimers) interact with major capsid-scaffold protein complexes during assembly of the HSV-1 capsid. PMID:9557680

Dissection of antibody specificities induced by yellow fever vaccination.

PubMed

Vratskikh, Oksana; Stiasny, Karin; Zlatkovic, Jürgen; Tsouchnikas, Georgios; Jarmer, Johanna; Karrer, Urs; Roggendorf, Michael; Roggendorf, Hedwig; Allwinn, Regina; Heinz, Franz X

2013-01-01

The live attenuated yellow fever (YF) vaccine has an excellent record of efficacy and one dose provides long-lasting immunity, which in many cases may last a lifetime. Vaccination stimulates strong innate and adaptive immune responses, and neutralizing antibodies are considered to be the major effectors that correlate with protection from disease. Similar to other flaviviruses, such antibodies are primarily induced by the viral envelope protein E, which consists of three distinct domains (DI, II, and III) and is presented at the surface of mature flavivirions in an icosahedral arrangement. In general, the dominance and individual variation of antibodies to different domains of viral surface proteins and their impact on neutralizing activity are aspects of humoral immunity that are not well understood. To gain insight into these phenomena, we established a platform of immunoassays using recombinant proteins and protein domains that allowed us to dissect and quantify fine specificities of the polyclonal antibody response after YF vaccination in a panel of 51 vaccinees as well as determine their contribution to virus neutralization by serum depletion analyses. Our data revealed a high degree of individual variation in antibody specificities present in post-vaccination sera and differences in the contribution of different antibody subsets to virus neutralization. Irrespective of individual variation, a substantial proportion of neutralizing activity appeared to be due to antibodies directed to complex quaternary epitopes displayed on the virion surface only but not on monomeric E. On the other hand, DIII-specific antibodies (presumed to have the highest neutralizing activity) as well as broadly flavivirus cross-reactive antibodies were absent or present at very low titers. These data provide new information on the fine specificity as well as variability of antibody responses after YF vaccination that are consistent with a strong influence of individual-specific factors on immunodominance in humoral immune responses.

Three-dimensional structure of the human immunodeficiency virus type 1 matrix protein.

PubMed

Massiah, M A; Starich, M R; Paschall, C; Summers, M F; Christensen, A M; Sundquist, W I

1994-11-25

The HIV-1 matrix protein forms an icosahedral shell associated with the inner membrane of the mature virus. Genetic analyses have indicated that the protein performs important functions throughout the viral life-cycle, including anchoring the transmembrane envelope protein on the surface of the virus, assisting in viral penetration, transporting the proviral integration complex across the nuclear envelope, and localizing the assembling virion to the cell membrane. We now report the three-dimensional structure of recombinant HIV-1 matrix protein, determined at high resolution by nuclear magnetic resonance (NMR) methods. The HIV-1 matrix protein is the first retroviral matrix protein to be characterized structurally and only the fourth HIV-1 protein of known structure. NMR signal assignments required recently developed triple-resonance (1H, 13C, 15N) NMR methodologies because signals for 91% of 132 assigned H alpha protons and 74% of the 129 assignable backbone amide protons resonate within chemical shift ranges of 0.8 p.p.m. and 1 p.p.m., respectively. A total of 636 nuclear Overhauser effect-derived distance restraints were employed for distance geometry-based structure calculations, affording an average of 13.0 NMR-derived distance restraints per residue for the experimentally constrained amino acids. An ensemble of 25 refined distance geometry structures with penalties (sum of the squares of the distance violations) of 0.32 A2 or less and individual distance violations under 0.06 A was generated; best-fit superposition of ordered backbone heavy atoms relative to mean atom positions afforded root-mean-square deviations of 0.50 (+/- 0.08) A. The folded HIV-1 matrix protein structure is composed of five alpha-helices, a short 3(10) helical stretch, and a three-strand mixed beta-sheet. Helices I to III and the 3(10) helix pack about a central helix (IV) to form a compact globular domain that is capped by the beta-sheet. The C-terminal helix (helix V) projects away from the beta-sheet to expose carboxyl-terminal residues essential for early steps in the HIV-1 infectious cycle. Basic residues implicated in membrane binding and nuclear localization functions cluster about an extruded cationic loop that connects beta-strands 1 and 2. The structure suggests that both membrane binding and nuclear localization may be mediated by complex tertiary structures rather than simple linear determinants.

Semiconducting icosahedral boron arsenide crystal growth for neutron detection

NASA Astrophysics Data System (ADS)

Whiteley, C. E.; Zhang, Y.; Gong, Y.; Bakalova, S.; Mayo, A.; Edgar, J. H.; Kuball, M.

2011-03-01

Semiconducting icosahedral boron arsenide, B12As2, is an excellent candidate for neutron detectors, thermoelectric converters, and radioisotope batteries, for which high quality single crystals are required. Thus, the present study was undertaken to grow B12As2 crystals by precipitation from metal solutions (nickel) saturated with elemental boron (or B12As2 powder) and arsenic in a sealed quartz ampoule. B12As2 crystals of 10-15 mm were produced when a homogeneous mixture of the three elements was held at 1150 °C for 48-72 h and slowly cooled (3.5 °C/h). The crystals varied in color and transparency from black and opaque to clear and transparent. X-ray topography (XRT), and elemental analysis by energy dispersive X-ray spectroscopy (EDS) confirmed that the crystals had the expected rhombohedral structure and chemical stoichiometry. The concentrations of residual impurities (nickel, carbon, etc.) were low, as measured by Raman spectroscopy and secondary ion mass spectrometry (SIMS). Additionally, low etch-pit densities (4.4×107 cm-2) were observed after etching in molten KOH at 500 °C. Thus, the flux growth method is viable for growing large, high-quality B12As2 crystals.

The characterisation of atomic structure and glass-forming ability of the Zr-Cu-Co metallic glasses studied by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Celtek, M.; Sengul, S.

2018-03-01

In the present work, the glass formation process and structural properties of Zr50Cu50-xCox (0 ≤ x ≤ 50) bulk metallic glasses were investigated by a molecular dynamics simulation with the many body tight-binding potentials. The evolution of structure and glass formation process with temperature were discussed using the coordination number, the radial distribution functions, the volume-temperature curve, icosahedral short-range order, glass transition temperature, Voronoi analysis, Honeycutt-Andersen pair analysis technique and the distribution of bond-angles. Results indicate that adding Co causes similar responses on the nature of the Zr50Cu50-xCox (0 ≤ x ≤ 50) alloys except for higher glass transition temperature and ideal icosahedral type ordered local atomic environment. Also, the differences of the atomic radii play the key role in influencing the atomic structure of these alloys. Both Cu and Co atoms play a significant role in deciding the chemical and topological short-range orders of the Zr50Cu50-xCox ternary liquids and amorphous alloys. The glass-forming ability of these alloys is supported by the experimental observations reported in the literature up to now.

Cooperative Jahn-Teller phase transition of icosahedral molecular units

NASA Astrophysics Data System (ADS)

Nasrollahi, Seyed H.; Vvedensky, Dimitri D.

2017-02-01

Non-linear molecules undergo distortions when the orbital degeneracy of the highest occupied level is lifted by the Jahn-Teller effect. If such molecules or clusters of atoms are coupled to one another, the system may experience a cooperative Jahn-Teller effect (CJTE). In this paper, we describe a model of how the CJTE leads to the crystallization of the disordered phase. The model Hamiltonian is based on a normal mode decomposition of the clusters in order to maintain the symmetry labels. We take account of the electron-strain and the electron-phonon couplings and, by displacing the coordinates of the oscillators, obtain a term that explicitly couples the Jahn-Teller centers, enabling us to perform a mean-field analysis. The calculation of the free energy then becomes straightforward, and obtaining phase diagrams in various regimes follows from the minimization of this free energy. The results show that the character of the phase transition may change from strong to weak first order and even to second-order, depending on the coupling to the vibrational modes. Taken together, these results may serve as a paradigm for crystallization near the transition temperature, where the atoms tend to form clusters of icosahedral symmetry.

Pd surface and Pt subsurface segregation in Pt1-c Pd c nanoalloys

NASA Astrophysics Data System (ADS)

De Clercq, A.; Giorgio, S.; Mottet, C.

2016-02-01

The structure and chemical arrangement of Pt1-c Pd c nanoalloys with the icosahedral and face centered cubic symmetry are studied using Monte Carlo simulations with a tight binding interatomic potential fitted to density-functional theory calculations. Pd surface segregation from the lowest to the highest coordinated sites is predicted by the theory together with a Pt enrichment at the subsurface, whatever the structure and the size of the nanoparticles, and which subsists when increasing the temperature. The onion-shell chemical configuration is found for both symmetries and is initiated from the Pd surface segregation. It is amplified in the icosahedral symmetry and small sizes but when considering larger sizes, the oscillating segregation profile occurs near the surface on about three to four shells whatever the structure. Pd segregation results from the significant lower cohesive energy of Pd as compared to Pt and the weak ordering tendency leads to the Pt subsurface segregation. The very weak size mismatch does not prevent the bigger atoms (Pt) from occupying subsurface sites which are in compression whereas the smaller ones (Pd) occupy the central site of the icosahedra where the compression is an order of magnitude higher.

Shock synthesis of quasicrystals with implications for their origin in asteroid collisions

DOE PAGES

Asimow, Paul D.; Lin, Chaney; Bindi, Luca; ...

2016-06-28

Here, we designed a plate impact shock recovery experiment to simulate the starting materials and shock conditions associated with the only known natural quasicrystals, in the Khatyrka meteorite. At the boundaries among CuAl5, (Mg 0.75Fe 0.25 2+) 2SiO 4 olivine, and the stainless steel chamber walls, the recovered specimen contains numerous micron-scale grains of a quasicrystalline phase displaying face-centered icosahedral symmetry and low phason strain. The compositional range of the icosahedral phase is Al 68-73Fe 11-16Cu 10-12Cr 1-4Ni 1-2 and extends toward higher Al/(Cu+Fe) and Fe/Cu ratios than those reported for natural icosahedrite or for any previously known synthetic quasicrystalmore » in the Al-Cu-Fe system. The shock-induced synthesis demonstrated in this experiment reinforces the evidence that natural quasicrystals formed during a shock event but leaves open the question of whether this synthesis pathway is attributable to the expanded thermodynamic stability range of the quasicrystalline phase at high pressure, to a favorable kinetic pathway that exists under shock conditions, or to both thermodynamic and kinetic factors.« less

Shock synthesis of quasicrystals with implications for their origin in asteroid collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Asimow, Paul D.; Lin, Chaney; Bindi, Luca

Here, we designed a plate impact shock recovery experiment to simulate the starting materials and shock conditions associated with the only known natural quasicrystals, in the Khatyrka meteorite. At the boundaries among CuAl5, (Mg 0.75Fe 0.25 2+) 2SiO 4 olivine, and the stainless steel chamber walls, the recovered specimen contains numerous micron-scale grains of a quasicrystalline phase displaying face-centered icosahedral symmetry and low phason strain. The compositional range of the icosahedral phase is Al 68-73Fe 11-16Cu 10-12Cr 1-4Ni 1-2 and extends toward higher Al/(Cu+Fe) and Fe/Cu ratios than those reported for natural icosahedrite or for any previously known synthetic quasicrystalmore » in the Al-Cu-Fe system. The shock-induced synthesis demonstrated in this experiment reinforces the evidence that natural quasicrystals formed during a shock event but leaves open the question of whether this synthesis pathway is attributable to the expanded thermodynamic stability range of the quasicrystalline phase at high pressure, to a favorable kinetic pathway that exists under shock conditions, or to both thermodynamic and kinetic factors.« less

High-resolution electron microscopy observation of a new crystalline approximant W' of Mg-Zn-Y icosahedral quasicrystal

PubMed

Luo; Hashimoto

2000-10-01

A new ordered structure W' with a lattice parameter (a = 2.05 nm) about three times as large as that of the fundamental face-centered cubic W phase (a = 0.6848 nm) has been found in the Mg-Zn-Y system by means of transmission electron microscopy. The W' and W phases have the cube-to-cube orientation relationship. Moreover, the strong electron diffraction spots of the W' phase showed pseudoicosahedral symmetry, implying that it is a crystalline approximant of the Mg-Zn-Y icosahedral quasicrystal. In the high-resolution electron microscopic images of the W' phase, Penrose tiles of pentagons and boats with an edge length of a(p) = 0.481 nm can be identified. A binary tile of crown subunit has also been deduced from such a tiling. Translation domains of the W' phase have also been observed and the translation vectors at the domain boundary are: a(p), tau x a(p) and (1 + tau) x a(p), respectively, where (1 + tau) x a(p) equals to the edge length a(r) of the big obtuse rhombus of the W' phase and tau = (1 + square root of 5)/2, is the golden ratio.

Unparalleled lithium and sodium superionic conduction in solid electrolytes with large monovalent cage-like anions

DOE PAGES

Tang, Wan Si; Unemoto, Atsushi; Zhou, Wei; ...

2015-10-08

Solid electrolytes with sufficiently high conductivities and stabilities are the elusive answer to the inherent shortcomings of organic liquid electrolytes prevalent in today's rechargeable batteries. We recently revealed a novel fast-ion-conducting sodium salt, Na 2B 12H 12, which contains large, icosahedral, divalent B 12H 12 2– anions that enable impressive superionic conductivity, albeit only above its 529 K phase transition. Its lithium congener, Li 2B 12H 12, possesses an even more technologically prohibitive transition temperature above 600 K. Here we show that the chemically related LiCB 11H 12 and NaCB 11H 12 salts, which contain icosahedral, monovalent CB 11H 12–more » anions, both exhibit much lower transition temperatures near 400 K and 380 K, respectively, and truly stellar ionic conductivities (>0.1 S cm –1) unmatched by any other known polycrystalline materials at these temperatures. Furthermore with proper modifications, we are confident that room-temperature-stabilized superionic salts incorporating such large polyhedral anion building blocks are attainable, thus enhancing their future prospects as practical electrolyte materials in next-generation, all-solid-state batteries.« less

Dynamical, structural and chemical heterogeneities in a binary metallic glass-forming liquid

NASA Astrophysics Data System (ADS)

Puosi, F.; Jakse, N.; Pasturel, A.

2018-04-01

As it approaches the glass transition, particle motion in liquids becomes highly heterogeneous and regions with virtually no mobility coexist with liquid-like domains. This complex dynamic is believed to be responsible for different phenomena including non-exponential relaxation and the breakdown of the Stokes-Einstein relation. Understanding the relationships between dynamical heterogeneities and local structure in metallic liquids and glasses is a major scientific challenge. Here we use classical molecular dynamics simulations to study the atomic dynamics and microscopic structure of Cu50Zr50 alloy in the supercooling regime. Dynamical heterogeneities are identified via an isoconfigurational analysis. We demonstrate the transition from isolated to clustering low mobility with decreasing temperature. These slow clusters, whose sizes grow upon cooling, are also associated with concentration fluctuations, characterized by a Zr-enriched phase, with a composition CuZr2 . In addition, a structural analysis of slow clusters based on Voronoi tessellation evidences an increase with respect of the bulk system of the fraction of Cu atoms having a local icosahedral order. These results are in agreement with the consolidated scenario of the relevant role played by icosahedral order in the dynamic slowing-down in supercooled metal alloys.

Nanosized (mu12-Pt)Pd164-xPtx(CO)72(PPh3)20 (x approximately 7) containing Pt-centered four-shell 165-atom Pd-Pt core with unprecedented intershell bridging carbonyl ligands: comparative analysis of icosahedral shell-growth patterns with geometrically related Pd145(CO)x(PEt3)30 (x approximately 60) containing capped three-shell Pd145 core.

PubMed

Mednikov, Evgueni G; Jewell, Matthew C; Dahl, Lawrence F

2007-09-19

Presented herein are the preparation and crystallographic/microanalytical/magnetic/spectroscopic characterization of the Pt-centered four-shell 165-atom Pd-Pt cluster, (mu(12)-Pt)Pd(164-x)Pt(x)(CO)(72)(PPh(3))(20) (x approximately 7), 1, that replaces the geometrically related capped three-shell icosahedral Pd(145) cluster, Pd(145)(CO)(x)(PEt(3))(30) (x approximately 60), 2, as the largest crystallographically determined discrete transition metal cluster with direct metal-metal bonding. A detailed comparison of their shell-growth patterns gives rise to important stereochemical implications concerning completely unexpected structural dissimilarities as well as similarities and provides new insight concerning possible synthetic approaches for generation of multi-shell metal clusters. 1 was reproducibly prepared in small yields (<10%) from the reaction of Pd(10)(CO)(12)(PPh(3))(6) with Pt(CO)(2)(PPh(3))(2). Its 165-atom metal-core geometry and 20 PPh(3) and 72 CO ligands were established from a low-temperature (100 K) CCD X-ray diffraction study. The well-determined crystal structure is attributed largely to 1 possessing cubic T(h) (2/m3) site symmetry, which is the highest crystallographic subgroup of the noncrystallographic pseudo-icosahedral I(h) (2/m35) symmetry. The "full" four-shell Pd-Pt anatomy of 1 consists of: (a) shell 1 with the centered (mu(12)-Pt) atom encapsulated by the 12-atom icosahedral Pt(x)Pd(12-x) cage, x = 1.2(3); (b) shell 2 with the 42-atom nu(2) icosahedral Pt(x)Pd(42-x) cage, x = 3.5(5); (c) shell 3 with the anti-Mackay 60-atom semi-regular rhombicosidodecahedral Pt(x)Pd(60-x) cage, x = 2.2(6); (d) shell 4 with the 50-atom nu(2) pentagonal dodecahedral Pd(50) cage. The total number of crystallographically estimated Pt atoms, 8 +/- 3, which was obtained from least-squares (Pt(x)/Pd(1-x))-occupancy analysis of the X-ray data that conclusively revealed the central atom to be pure Pt (occupancy factor, x = 1.00(3)), is fortuitously in agreement with that of 7.6(7) found from an X-ray Pt/Pd microanalysis (WDS spectrometer) on three crystals of 1. Our utilization of this site-occupancy (Pt(x)Pd(1-x))-analysis for shells 1-3 originated from the microanalytical results; otherwise, the presumed metal-core composition would have been (mu(12)-Pt)Pd(164). [Alternatively, the (mu(12)-Pt)M(164) core-geometry of 1 may be viewed as a pseudo-Ih Pt-centered six-shell successive nu(1) polyhedral system, each with radially equivalent vertex atoms: Pt@M(12)(icosahedron)@M(30)(icosidodecahedron)@M(12)(icosahedron)@M(60)(rhombicosidodecahedron)@M(30)(icosidodecahedron)@M(20)(pentagonal dodecahedron)]. Completely surprising structural dissimilarities between 1 and 2 are: (1) to date 1 is only reproducibly isolated as a heterometallic Pd-Pt cluster with a central Pt instead of Pd atom; (2) the 50 atoms comprising the outer fourth nu(2) pentagonal dodecahedral shell in 1 are less than the 60 atoms of the inner third shell in 1, in contradistinction to shell-by-shell growth processes in all other known shell-based structures; (3) the 10 fewer PR3 ligands in 1 necessitate larger bulky PPh(3) ligands to protect the Pd-Pt core-geometry; (4) the 72 CO ligands consist of six bridging COs within each of the 12 pentagons in shell 4 that are coordinated to intershell metal atoms. SQUID magnetometry measurements showed a single-crystal sample of 1 to be diamagnetic over the entire temperature range of 10-300 K.

From Quasicrystals to Crystals with Interpenetrating Icosahedra in Ca–Au–Al: In Situ Variable-Temperature Transformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pham, Joyce; Meng, Fanqiang; Lynn, Matthew J.

The irreversible transformation from an icosahedral quasicrystal (i-QC) CaAu 4.39Al 1.61 to its cubic 2/1 crystalline approximant (CA) Ca 13Au 56.31(3)Al 21.69 (CaAu 4.33(1)Al1.67, Pamore » $$\\bar{3}$$ (No. 205); Pearson symbol: cP728; a = 23.8934(4)), starting at ~570 °C and complete by ~650 °C, is discovered from in situ, high-energy, variable-temperature powder X-ray diffraction (PXRD), thereby providing direct experimental evidence for the relationship between QCs and their associated CAs. The new cubic phase crystallizes in a Tsai-type approximant structure under the broader classification of polar intermetallic compounds, in which atoms of different electronegativities, viz., electronegative Au + Al vs electropositive Ca, are arranged in concentric shells. From a structural chemical perspective, the outermost shell of this cubic approximant may be described as interpenetrating and edge-sharing icosahedra, a perspective that is obtained by splitting the traditional structural description of this shell as a 92-atom rhombic triacontahedron into an 80-vertex cage of primarily Au [Au 59.86(2)Al 17.14⟂ 3.00] and an icosahedral shell of only Al [Al 10.5⟂ 1.5]. Following the proposal that the cubic 2/1 CA approximates the structure of the i-QC and on the basis of the observed transformation, an atomic site analysis of the 2/1 CA, which shows a preference to maximize the number of heteroatomic Au–Al nearest neighbor contacts over homoatomic Al–Al contacts, implies a similar outcome for the i-QC structure. Analysis of the most intense reflections in the diffraction pattern of the cubic 2/1 CA that changed during the phase transformation shows correlations with icosahedral symmetry, and the stability of this cubic phase is assessed using valence electron counts. Finally, according to electronic structure calculations, a cubic 1/1 CA, “Ca 24Au 88Al 64” (CaAu 3.67Al 2.67) is proposed.« less

Molecular Structure of a 9-MDa Icosahedral Pyruvate Dehydrogenase Subcomplex Containing the E2 and E3 Enzymes Using Cryoelectron Microscopy*

PubMed Central

Milne, Jacqueline L. S.; Wu, Xiongwu; Borgnia, Mario J.; Lengyel, Jeffrey S.; Brooks, Bernard R.; Shi, Dan; Perham, Richard N.; Subramaniam, Sriram

2006-01-01

The pyruvate dehydrogenase multienzyme complexes are among the largest multifunctional catalytic machines in cells, catalyzing the production of acetyl CoA from pyruvate. We have previously reported the molecular architecture of an 11-MDa subcomplex comprising the 60-mer icosahedral dihydrolipoyl acetyltransferase (E2) decorated with 60 copies of the heterotetrameric (α2β2) 153-kDa pyruvate decarboxylase (E1) from Bacillus stearothermophilus (Milne, J. L. S., Shi, D., Rosenthal, P. B., Sunshine, J. S., Domingo, G. J., Wu, X., Brooks, B. R., Perham, R. N., Henderson, R., and Subramaniam, S. (2002) EMBO J. 21, 5587–5598). An annular gap of ~90 Å separates the acetyltransferase catalytic domains of the E2 from an outer shell formed of E1 tetramers. Using cryoelectron microscopy, we present here a three-dimensional reconstruction of the E2 core decorated with 60 copies of the homodimeric 100-kDa dihydrolipoyl dehydrogenase (E3). The E2E3 complex has a similar annular gap of ~75 Å between the inner icosahedral assembly of acetyltransferase domains and the outer shell of E3 homodimers. Automated fitting of the E3 coordinates into the map suggests excellent correspondence between the density of the outer shell map and the positions of the two best fitting orientations of E3. As in the case of E1 in the E1E2 complex, the central 2-fold axis of the E3 homodimer is roughly oriented along the periphery of the shell, making the active sites of the enzyme accessible from the annular gap between the E2 core and the outer shell. The similarities in architecture of the E1E2 and E2E3 complexes indicate fundamental similarities in the mechanism of active site coupling involved in the two key stages requiring motion of the swinging lipoyl domain across the annular gap, namely the synthesis of acetyl CoA and regeneration of the dithiolane ring of the lipoyl domain. PMID:16308322

From Quasicrystals to Crystals with Interpenetrating Icosahedra in Ca–Au–Al: In Situ Variable-Temperature Transformation

DOE PAGES

Pham, Joyce; Meng, Fanqiang; Lynn, Matthew J.; ...

2017-12-29

The irreversible transformation from an icosahedral quasicrystal (i-QC) CaAu 4.39Al 1.61 to its cubic 2/1 crystalline approximant (CA) Ca 13Au 56.31(3)Al 21.69 (CaAu 4.33(1)Al1.67, Pamore » $$\\bar{3}$$ (No. 205); Pearson symbol: cP728; a = 23.8934(4)), starting at ~570 °C and complete by ~650 °C, is discovered from in situ, high-energy, variable-temperature powder X-ray diffraction (PXRD), thereby providing direct experimental evidence for the relationship between QCs and their associated CAs. The new cubic phase crystallizes in a Tsai-type approximant structure under the broader classification of polar intermetallic compounds, in which atoms of different electronegativities, viz., electronegative Au + Al vs electropositive Ca, are arranged in concentric shells. From a structural chemical perspective, the outermost shell of this cubic approximant may be described as interpenetrating and edge-sharing icosahedra, a perspective that is obtained by splitting the traditional structural description of this shell as a 92-atom rhombic triacontahedron into an 80-vertex cage of primarily Au [Au 59.86(2)Al 17.14⟂ 3.00] and an icosahedral shell of only Al [Al 10.5⟂ 1.5]. Following the proposal that the cubic 2/1 CA approximates the structure of the i-QC and on the basis of the observed transformation, an atomic site analysis of the 2/1 CA, which shows a preference to maximize the number of heteroatomic Au–Al nearest neighbor contacts over homoatomic Al–Al contacts, implies a similar outcome for the i-QC structure. Analysis of the most intense reflections in the diffraction pattern of the cubic 2/1 CA that changed during the phase transformation shows correlations with icosahedral symmetry, and the stability of this cubic phase is assessed using valence electron counts. Finally, according to electronic structure calculations, a cubic 1/1 CA, “Ca 24Au 88Al 64” (CaAu 3.67Al 2.67) is proposed.« less

The allosteric switching mechanism in bacteriophage MS2

NASA Astrophysics Data System (ADS)

Perkett, Matthew R.; Mirijanian, Dina T.; Hagan, Michael F.

2016-07-01

We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.

In Vitro Evolution and Affinity-Maturation with Coliphage Qβ Display

PubMed Central

Skamel, Claudia; Aller, Stephen G.; Bopda Waffo, Alain

2014-01-01

The Escherichia coli bacteriophage, Qβ (Coliphage Qβ), offers a favorable alternative to M13 for in vitro evolution of displayed peptides and proteins due to high mutagenesis rates in Qβ RNA replication that better simulate the affinity maturation processes of the immune response. We describe a benchtop in vitro evolution system using Qβ display of the VP1 G-H loop peptide of foot-and-mouth disease virus (FMDV). DNA encoding the G-H loop was fused to the A1 minor coat protein of Qβ resulting in a replication-competent hybrid phage that efficiently displayed the FMDV peptide. The surface-localized FMDV VP1 G-H loop cross-reacted with the anti-FMDV monoclonal antibody (mAb) SD6 and was found to decorate the corners of the Qβ icosahedral shell by electron microscopy. Evolution of Qβ-displayed peptides, starting from fully degenerate coding sequences corresponding to the immunodominant region of VP1, allowed rapid in vitro affinity maturation to SD6 mAb. Qβ selected under evolutionary pressure revealed a non-canonical, but essential epitope for mAb SD6 recognition consisting of an Arg-Gly tandem pair. Finally, the selected hybrid phages induced polyclonal antibodies in guinea pigs with good affinity to both FMDV and hybrid Qβ-G-H loop, validating the requirement of the tandem pair epitope. Qβ-display emerges as a novel framework for rapid in vitro evolution with affinity-maturation to molecular targets. PMID:25393763

The allosteric switching mechanism in bacteriophage MS2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perkett, Matthew R.; Mirijanian, Dina T.; Hagan, Michael F., E-mail: hagan@brandeis.edu

2016-07-21

We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we usemore » all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.« less

Comparative Genomic and Morphological Analyses of Listeria Phages Isolated from Farm Environments

PubMed Central

Denes, Thomas; Ackermann, Hans-Wolfgang; Moreno Switt, Andrea I.; Wiedmann, Martin; den Bakker, Henk C.

2014-01-01

The genus Listeria is ubiquitous in the environment and includes the globally important food-borne pathogen Listeria monocytogenes. While the genomic diversity of Listeria has been well studied, considerably less is known about the genomic and morphological diversity of Listeria bacteriophages. In this study, we sequenced and analyzed the genomes of 14 Listeria phages isolated mostly from New York dairy farm environments as well as one related Enterococcus faecalis phage to obtain information on genome characteristics and diversity. We also examined 12 of the phages by electron microscopy to characterize their morphology. These Listeria phages, based on gene orthology and morphology, together with previously sequenced Listeria phages could be classified into five orthoclusters, including one novel orthocluster. One orthocluster (orthocluster I) consists of large-genome (∼135-kb) myoviruses belonging to the genus “Twort-like viruses,” three orthoclusters (orthoclusters II to IV) contain small-genome (36- to 43-kb) siphoviruses with icosahedral heads, and the novel orthocluster V contains medium-sized-genome (∼66-kb) siphoviruses with elongated heads. A novel orthocluster (orthocluster VI) of E. faecalis phages, with medium-sized genomes (∼56 kb), was identified, which grouped together and shares morphological features with the novel Listeria phage orthocluster V. This new group of phages (i.e., orthoclusters V and VI) is composed of putative lytic phages that may prove to be useful in phage-based applications for biocontrol, detection, and therapeutic purposes. PMID:24837381

Differential depuration of poliovirus, Escherichia coli, and a coliphage by the common mussel, Mytilus edulis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Power, U.F.; Collins, J.K.

1989-06-01

The elimination of sewage effluent-associated poliovirus, Escherichia coli, and a 22-nm icosahedral coliphage by the common mussel, Mytilus edulis, was studied. Both laboratory-and commercial-scale recirculating, UV depuration systems were used in this study. In the laboratory system, the logarithms of the poliovirus, E. coli, and coliphage levels were reduced by 1.86, 2.9, and 2.16, respectively, within 52 h of depuration. The relative patterns and rates of elimination of the three organisms suggest that they are eliminated from mussels by different mechanisms during depuration under suitable conditions. Poliovirus was not included in experiments undertaken in the commercial-scale depuration system. The differencesmore » in the relative rates and patterns of elimination were maintained for E. coli and coliphage in this system, with the logarithm of the E. coli levels being reduced by 3.18 and the logarithm of the coliphage levels being reduced by 0.87. The results from both depuration systems suggest that E. coli is an inappropriate indicator of the efficiency of virus elimination during depuration. The coliphage used appears to be a more representative indicator. Depuration under stressful conditions appeared to have a negligible affect on poliovirus and coliphage elimination rates from mussels. However, the rate and pattern of E. coli elimination were dramatically affected by these conditions. Therefore, monitoring E. coli counts might prove useful in ensuring that mussels are functioning well during depuration.« less

MS2 bacteriophage as a delivery vessel of porphyrins for photodynamic therapy

NASA Astrophysics Data System (ADS)

Cohen, Brian A.; Kaloyeros, Alain E.; Bergkvist, Magnus

2011-02-01

Challenges associated with photodynamic therapy (PDT) include the packaging and site-specific delivery of therapeutic agents to the tissue of interest. Nanoscale encapsulation of PDT agents inside targeted virus capsids is a novel concept for packaging and site-specific targeting. The icosahedral MS2 bacteriophage is one potential candidate for such a packaging-system. MS2 has a porous capsid with an exterior diameter of ~28 nm where the pores allow small molecules access to the capsid interior. Furthermore, MS2 presents suitable residues on the exterior capsid for conjugation of targeting ligands. Initial work by the present investigators has successfully demonstrated RNA-based self-packaging of a heterocyclic PDT agent (meso-tetrakis(para-N-trimethylanilinium)porphine, TMAP) into the MS2 capsid. Packaging photoactive compounds in confined spaces could result in energy transfer between the molecules upon photoactivation, which could in turn reduce the production of radical oxygen species (ROS). ROS are key components in photodynamic therapy, and a reduced production could negatively impact the efficacy of PDT treatment. Here, findings are presented from an investigation of ROS generation of TMAP encapsulated within the MS2 capsid compared to free TMAP in solution. Monitoring of ROS production upon photoactivation via a specific singlet oxygen assay revealed the impact on ROS generation between packaged porphyrins as compared to free porphyrin in an aqueous solution. Follow on work will study the ability of MS2-packaged porphyrins to generate ROS in vitro and subsequent cytotoxic effects on cells in culture.

The allosteric switching mechanism in bacteriophage MS2

PubMed Central

Perkett, Matthew R.; Mirijanian, Dina T.

2016-01-01

We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates. PMID:27448905

Necrotizing hepatitis in a domestic pigeon (Columba livia).

PubMed

Himmel, L; O'Connor, M; Premanandan, C

2014-11-01

An adult male domestic pigeon (Columba livia) was presented for necropsy following natural death after a period of chronic weight loss and severe intestinal ascariasis. Histopathologic examination of the liver found moderate to marked, multifocal necrotizing hepatitis with large, basophilic intranuclear inclusion bodies. Transmission electron microscopy of affected hepatocytes demonstrated numerous intra- and perinuclear icosahedral virions arranged in a lattice structure, consistent with adenoviral infection. © The Author(s) 2014.

Thermodynamic consideration and ground-state search of icosahedral boron subselenide B12(B1-xSex) 2 from a first-principles cluster expansion

NASA Astrophysics Data System (ADS)

Ektarawong, A.

2018-05-01

The phase stability of icosahedral boron subselenide B12(B1-xSex) 2 , where 0.5 ≤x ≤1 , is explored using a first-principles cluster expansion. The results shows that, instead of a continuous solid solution, B12(B1-xSex) 2 is thermodynamically stable as an individual line compound at the composition of B9.5Se . The ground-state configuration of B9.5Se is represented by a mixture of B12(Se-Se), B12(B-Se), and B12(Se-B) with a ratio of 1:1:1, where they form a periodic A B C A B C ⋯ stacking sequence of B12(Se-Se), B12(B-Se), and B12(Se-B) layers along the c axis of the hexagonal conventional unit cell. The structural and electronic properties of the ground-state B9.5Se are also derived and discussed. By comparing the derived ground-state properties of B9.5Se to the existing experimental data of boron subselenide B˜13Se , I proposed that the as-synthesized boron subselenide B˜13Se , as reported in the literature, has the actual composition of B9.5Se .

Electrical Characterization of Irradiated Semiconducting Amorphous Hydrogenated Boron Carbide

NASA Astrophysics Data System (ADS)

Peterson, George Glenn

Semiconducting amorphous partially dehydrogenated boron carbide has been explored as a neutron voltaic for operation in radiation harsh environments, such as on deep space satellites/probes. A neutron voltaic device could also be used as a solid state neutron radiation detector to provide immediate alerts for radiation workers/students, as opposed to the passive dosimetry badges utilized today. Understanding how the irradiation environment effects the electrical properties of semiconducting amorphous partially dehydrogenated boron carbide is important to predicting the stability of these devices in operation. p-n heterojunction diodes were formed from the synthesis of semiconducting amorphous partially dehydrogenated boron carbide on silicon substrates through the use of plasma enhanced chemical vapor deposition (PECVD). Many forms of structural and electrical measurements and analysis have been performed on the p-n heterojunction devices as a function of both He+ ion and neutron irradiation including: transmission electron microscopy (TEM), selected area electron diffraction (SAED), current versus voltage I(V), capacitance versus voltage C(V), conductance versus frequency G(f), and charge carrier lifetime (tau). In stark contrast to nearly all other electronic devices, the electrical performance of these p-n heterojunction diodes improved with irradiation. This is most likely the result of bond defect passivation and resolution of degraded icosahedral based carborane structures (icosahedral molecules missing a B, C, or H atom(s)).

Formation mechanism of atomic cluster structures in Al-Mg alloy during rapid solidification processes

NASA Astrophysics Data System (ADS)

Liu, Feng-xiang; Liu, Rang-su; Hou, Zhao-yang; Liu, Hai-Rong; Tian, Ze-an; Zhou, Li-li

2009-02-01

The rapid solidification processes of Al 50Mg 50 liquid alloy consisting of 50,000 atoms have been simulated by using molecular dynamics method based on the effective pair potential derived from the pseudopotential theory. The formation mechanisms of atomic clusters during the rapid solidification processes have been investigated adopting a new cluster description method—cluster-type index method (CTIM). The simulated partial structure factors are in good agreement with the experimental results. And Al-Mg amorphous structure characterized with Al-centered icosahedral topological short-range order (SRO) is found to form during the rapid solidification processes. The icosahedral cluster plays a key role in the microstructure transition. Besides, it is also found that the size distribution of various clusters in the system presents a magic number sequence of 13, 19, 23, 25, 29, 31, 33, 37, …. The magic clusters are more stable and mainly correspond to the incompact arrangements of linked icosahedra in the form of rings, chains or dendrites. And each magic number point stands correspondingly for one certain combining form of icosahedra. This magic number sequence is different from that generated in the solidification structure of liquid Al and those obtained by methods of gaseous deposition and ionic spray, etc.

Use of ion-mobility mass spectrometry (IMS-MS) to map polyoxometalate Keplerate clusters and their supramolecular assemblies.

PubMed

Robbins, Philip J; Surman, Andrew J; Thiel, Johannes; Long, De-Liang; Cronin, Leroy

2013-03-07

We present the high-resolution (HRES-MS) and ion-mobility (IMS-MS) mass spectrometry studies of icosahedral nanoscale polyoxometalate-based {L(30)}{(Mo)Mo(5)} Keplerate clusters, and demonstrate the use of IMS-MS to resolve and map intact nanoclusters, and its potential for the discovery of new structures, in this case the first gas phase observation of 'proto-clustering' of higher order Keplerate supramolecular aggregates.

Structural, Mechanistic, and Antigenic Characterization of the Human Astrovirus Capsid

PubMed Central

York, Royce L.; Yousefi, Payam A.; Bogdanoff, Walter; Haile, Sara; Tripathi, Sarvind

2015-01-01

ABSTRACT Human astroviruses (HAstVs) are nonenveloped, positive-sense, single-stranded RNA viruses that are a leading cause of viral gastroenteritis. HAstV particles display T=3 icosahedral symmetry formed by 180 copies of the capsid protein (CP), which undergoes proteolytic maturation to generate infectious HAstV particles. Little is known about the molecular features that govern HAstV particle assembly, maturation, infectivity, and immunogenicity. Here we report the crystal structures of the two main structural domains of the HAstV CP: the core domain at 2.60-Å resolution and the spike domain at 0.95-Å resolution. Fitting of these structures into the previously determined 25-Å-resolution electron cryomicroscopy density maps of HAstV allowed us to characterize the molecular features on the surfaces of immature and mature T=3 HAstV particles. The highly electropositive inner surface of HAstV supports a model in which interaction of the HAstV CP core with viral RNA is a driving force in T=3 HAstV particle formation. Additionally, mapping of conserved residues onto the HAstV CP core and spike domains in the context of the immature and mature HAstV particles revealed dramatic changes to the exposure of conserved residues during virus maturation. Indeed, we show that antibodies raised against mature HAstV have reactivity to both the HAstV CP core and spike domains, revealing for the first time that the CP core domain is antigenic. Together, these data provide new molecular insights into HAstV that have practical applications for the development of vaccines and antiviral therapies. IMPORTANCE Astroviruses are a leading cause of viral diarrhea in young children, immunocompromised individuals, and the elderly. Despite the prevalence of astroviruses, little is known at the molecular level about how the astrovirus particle assembles and is converted into an infectious, mature virus. In this paper, we describe the high-resolution structures of the two main astrovirus capsid proteins. Fitting these structures into previously determined low-resolution maps of astrovirus allowed us to characterize the molecular surfaces of immature and mature astroviruses. Our studies provide the first evidence that astroviruses undergo viral RNA-dependent assembly. We also provide new insight into the molecular mechanisms that lead to astrovirus maturation and infectivity. Finally, we show that both capsid proteins contribute to the adaptive immune response against astrovirus. Together, these studies will help to guide the development of vaccines and antiviral drugs targeting astrovirus. PMID:26656707

Bam35 tectivirus intraviral interaction map unveils new function and localization of phage ORFan proteins.

PubMed

Berjón-Otero, Mónica; Lechuga, Ana; Mehla, Jitender; Uetz, Peter; Salas, Margarita; Redrejo-Rodríguez, Modesto

2017-07-26

Tectiviridae comprises a group of tail-less, icosahedral, membrane-containing bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria.In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology. With the aim of increasing the knowledge of the viral proteome, we carried out a comprehensive yeast two-hybrid analysis among all the putative proteins encoded by the Bam35 genome. The resulting protein interactome comprises 76 unique interactions among 24 proteins, of which 12 have an unknown function. These results suggested that the P17 protein is the minor capsid protein of Bam35 and P24 is the penton protein, being the latter also supported by iterative threading protein modeling. Moreover, the inner membrane transglycosylase protein P26 could have an additional structural role. We also detected interactions involving non-structural proteins, such as the DNA binding protein P1 and the genome terminal protein (P4), which was confirmed by co-immunoprecipitation of recombinant proteins. Altogether, our results provide a functional view of the Bam35 viral proteome, with a focus on the composition and organization of the viral particle. IMPORTANCE Tail-less viruses of the family Tectiviridae can infect commensal and pathogenic Gram-positive and Gram-negative bacteria. Moreover, they have been proposed to be at the evolutionary origin of several groups of large eukaryotic DNA viruses and self-replicating plasmids. However, due to their ancient origin and complex diversity, many tectiviral proteins are ORFans of unknown function.Comprehensive protein-protein interaction (PPI) analysis among viral proteins can eventually disclose biological mechanisms and thus provide new insights into protein function unattainable by studying proteins one by one. Here we comprehensively describe intraviral PPIs among tectivirus Bam35 proteins using multi-vector yeast two-hybrid screening that was further supported by co-immunoprecipitation assays and protein structural models. This approach allowed us to propose new functions for known proteins and hypothesize on the biological role localization within the viral particle of some viral ORFan proteins that will be helpful for understanding the biology of Gram-positive tectivirus. Copyright © 2017 American Society for Microbiology.

Bam35 Tectivirus Intraviral Interaction Map Unveils New Function and Localization of Phage ORFan Proteins

PubMed Central

Berjón-Otero, Mónica; Lechuga, Ana; Mehla, Jitender; Uetz, Peter

2017-01-01

ABSTRACT The family Tectiviridae comprises a group of tailless, icosahedral, membrane-containing bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well-characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria. In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology. With the aim of increasing knowledge about the viral proteome, we carried out a comprehensive yeast two-hybrid analysis of all the putative proteins encoded by the Bam35 genome. The resulting protein interactome comprised 76 unique interactions among 24 proteins, of which 12 have an unknown function. These results suggest that the P17 protein is the minor capsid protein of Bam35 and P24 is the penton protein, with the latter finding also being supported by iterative threading protein modeling. Moreover, the inner membrane transglycosylase protein P26 could have an additional structural role. We also detected interactions involving nonstructural proteins, such as the DNA-binding protein P1 and the genome terminal protein (P4), which was confirmed by coimmunoprecipitation of recombinant proteins. Altogether, our results provide a functional view of the Bam35 viral proteome, with a focus on the composition and organization of the viral particle. IMPORTANCE Tailless viruses of the family Tectiviridae can infect commensal and pathogenic Gram-positive and Gram-negative bacteria. Moreover, they have been proposed to be at the evolutionary origin of several groups of large eukaryotic DNA viruses and self-replicating plasmids. However, due to their ancient origin and complex diversity, many tectiviral proteins are ORFans of unknown function. Comprehensive protein-protein interaction (PPI) analysis of viral proteins can eventually disclose biological mechanisms and thus provide new insights into protein function unattainable by studying proteins one by one. Here we comprehensively describe intraviral PPIs among tectivirus Bam35 proteins determined using multivector yeast two-hybrid screening, and these PPIs were further supported by the results of coimmunoprecipitation assays and protein structural models. This approach allowed us to propose new functions for known proteins and hypothesize about the biological role of the localization of some viral ORFan proteins within the viral particle that will be helpful for understanding the biology of tectiviruses infecting Gram-positive bacteria. PMID:28747494

The Efficiency of Delone Coverings of the Canonical Tilings T^*(A4) and T^*(D6)

NASA Astrophysics Data System (ADS)

Papadopolos, Zorka; Kasner, Gerald

This chapter is devoted to the coverings of the two quasiperiodic canonical tilings T^*(A4) and T^*(D6) T^*(2F), obtained by projection from the root lattices A4 and D6, respectively. In the first major part of this chapter, in Sect. 5.2, we shall introduce a Delone covering C^sT^*(A4) of the 2-dimensional decagonal tiling T^*(A4). In the second major part of this chapter, Sect. 5.3, we summarize the results related to the Delone covering of the icosahedral tiling T^*(D6), CT^*(D6) and determine the zero-, single-, and double- deckings and the resulting thickness of the covering. In the conclusions section, we give some suggestions as to how the definition of the Delone covering might be changed in order to reach some real (full) covering of the icosahedral tiling T^*(D6). In Section 5.2 the definition of the Delone covering is also changed in order to avoid an unnecessary large thickness of the covering.

Model Parameter Estimation Using Ensemble Data Assimilation: A Case with the Nonhydrostatic Icosahedral Atmospheric Model NICAM and the Global Satellite Mapping of Precipitation Data

NASA Astrophysics Data System (ADS)

Kotsuki, Shunji; Terasaki, Koji; Yashiro, Hasashi; Tomita, Hirofumi; Satoh, Masaki; Miyoshi, Takemasa

2017-04-01

This study aims to improve precipitation forecasts from numerical weather prediction (NWP) models through effective use of satellite-derived precipitation data. Kotsuki et al. (2016, JGR-A) successfully improved the precipitation forecasts by assimilating the Japan Aerospace eXploration Agency (JAXA)'s Global Satellite Mapping of Precipitation (GSMaP) data into the Nonhydrostatic Icosahedral Atmospheric Model (NICAM) at 112-km horizontal resolution. Kotsuki et al. mitigated the non-Gaussianity of the precipitation variables by the Gaussian transform method for observed and forecasted precipitation using the previous 30-day precipitation data. This study extends the previous study by Kotsuki et al. and explores an online estimation of model parameters using ensemble data assimilation. We choose two globally-uniform parameters, one is the cloud-to-rain auto-conversion parameter of the Berry's scheme for large scale condensation and the other is the relative humidity threshold of the Arakawa-Schubert cumulus parameterization scheme. We perform the online-estimation of the two model parameters with an ensemble transform Kalman filter by assimilating the GSMaP precipitation data. The estimated parameters improve the analyzed and forecasted mixing ratio in the lower troposphere. Therefore, the parameter estimation would be a useful technique to improve the NWP models and their forecasts. This presentation will include the most recent progress up to the time of the symposium.

Electronic shell structure in Ga12 icosahedra and the relation to the bulk forms of gallium.

PubMed

Schebarchov, D; Gaston, N

2012-07-28

The electronic structure of known cluster compounds with a cage-like icosahedral Ga(12) centre is studied by first-principles theoretical methods, based on density functional theory. We consider these hollow metalloid nanostructures in the context of the polymorphism of the bulk, and identify a close relation to the α phase of gallium. This previously unrecognised connection is established using the electron localisation function, which reveals the ubiquitous presence of radially-pointing covalent bonds around the Ga(12) centre--analogous to the covalent bonds between buckled deltahedral planes in α-Ga. Furthermore, we find prominent superatom shell structure in these clusters, despite their hollow icosahedral motif and the presence of covalent bonds. The exact nature of the electronic shell structure is contrasted with simple electron shell models based on jellium, and we demonstrate how the interplay between gallium dimerisation, ligand- and crystal-field effects can alter the splitting of the partially filled 1F shell. Finally, in the unique compound where the Ga(12) centre is bridged by six phosphorus ligands, the electronic structure most closely resembles that of δ-Ga and there are no well-defined superatom orbitals. The results of this comprehensive study bring new insights into the nature of chemical bonding in metalloid gallium compounds and the relation to bulk gallium metal, and they may also guide the development of more general models for ligand-protected clusters.

Fine Structure of Diffuse Scattering Rings in Al-Li-Cu Quasicrystal: A Comparative X-ray and Electron Diffraction Study

NASA Astrophysics Data System (ADS)

Donnadieu, P.; Dénoyer, F.

1996-11-01

A comparative X-ray and electron diffraction study has been performed on Al-Li-Cu icosahedral quasicrystal in order to investigate the diffuse scattering rings revealed by a previous work. Electron diffraction confirms the existence of rings but shows that the rings have a fine structure. The diffuse aspect on the X-ray diffraction patterns is then due to an averaging effect. Recent simulations based on the model of canonical cells related to the icosahedral packing give diffractions patterns in agreement with this fine structure effect. Nous comparons les diagrammes de diffraction des rayon-X et des électrons obtenus sur les mêmes échantillons du quasicristal icosaèdrique Al-Li-Cu. Notre but est d'étudier les anneaux de diffusion diffuse mis en évidence par un travail précédent. Les diagrammes de diffraction électronique confirment la présence des anneaux mais ils montrent aussi que ces anneaux possèdent une structure fine. L'aspect diffus des anneaux révélés par la diffraction des rayons X est dû à un effet de moyenne. Des simulations récentes basées sur la décomposition en cellules canoniques de l'empilement icosaédrique produisent des diagrammes de diffraction en accord avec ces effects de structure fine.

A mimetic, semi-implicit, forward-in-time, finite volume shallow water model: comparison of hexagonal-icosahedral and cubed sphere grids

NASA Astrophysics Data System (ADS)

Thuburn, J.; Cotter, C. J.; Dubos, T.

2013-12-01

A new algorithm is presented for the solution of the shallow water equations on quasi-uniform spherical grids. It combines a mimetic finite volume spatial discretization with a Crank-Nicolson time discretization of fast waves and an accurate and conservative forward-in-time advection scheme for mass and potential vorticity (PV). The algorithm is implemented and tested on two families of grids: hexagonal-icosahedral Voronoi grids, and modified equiangular cubed-sphere grids. Results of a variety of tests are presented, including convergence of the discrete scalar Laplacian and Coriolis operators, advection, solid body rotation, flow over an isolated mountain, and a barotropically unstable jet. The results confirm a number of desirable properties for which the scheme was designed: exact mass conservation, very good available energy and potential enstrophy conservation, consistent mass, PV and tracer transport, and good preservation of balance including vanishing ∇ × ∇, steady geostrophic modes, and accurate PV advection. The scheme is stable for large wave Courant numbers and advective Courant numbers up to about 1. In the most idealized tests the overall accuracy of the scheme appears to be limited by the accuracy of the Coriolis and other mimetic spatial operators, particularly on the cubed sphere grid. On the hexagonal grid there is no evidence for damaging effects of computational Rossby modes, despite attempts to force them explicitly.

A mimetic, semi-implicit, forward-in-time, finite volume shallow water model: comparison of hexagonal-icosahedral and cubed-sphere grids

NASA Astrophysics Data System (ADS)

Thuburn, J.; Cotter, C. J.; Dubos, T.

2014-05-01

A new algorithm is presented for the solution of the shallow water equations on quasi-uniform spherical grids. It combines a mimetic finite volume spatial discretization with a Crank-Nicolson time discretization of fast waves and an accurate and conservative forward-in-time advection scheme for mass and potential vorticity (PV). The algorithm is implemented and tested on two families of grids: hexagonal-icosahedral Voronoi grids, and modified equiangular cubed-sphere grids. Results of a variety of tests are presented, including convergence of the discrete scalar Laplacian and Coriolis operators, advection, solid body rotation, flow over an isolated mountain, and a barotropically unstable jet. The results confirm a number of desirable properties for which the scheme was designed: exact mass conservation, very good available energy and potential enstrophy conservation, consistent mass, PV and tracer transport, and good preservation of balance including vanishing ∇ × ∇, steady geostrophic modes, and accurate PV advection. The scheme is stable for large wave Courant numbers and advective Courant numbers up to about 1. In the most idealized tests the overall accuracy of the scheme appears to be limited by the accuracy of the Coriolis and other mimetic spatial operators, particularly on the cubed-sphere grid. On the hexagonal grid there is no evidence for damaging effects of computational Rossby modes, despite attempts to force them explicitly.

Nano-jewellery: C5Au12--a gold-plated diamond at molecular level.

PubMed

Naumkin, F

2006-06-07

A mixed carbon-metal cluster is designed by combining the tetrahedral C(5) radical (with a central atom-the skeleton of the C(5)H(12) molecule) and the spherical Au(12) layer (the external atomic shell of the Au(13) cluster). The C(5)Au(12) cluster and its negative and positive ionic derivatives, C(5)Au(12)(+/-), are investigated ab initio (DFT) in terms of optimized structures and relative energies of a few spin-states, for the icosahedral-like and octahedral-like isomers. The cluster is predicted to be generally more stable in its octahedral shape (similar to C(5)H(12)) which prevails for the negative ion and may compete with the icosahedral shape for the neutral system and positive ion. Adiabatic ionization energies (AIE) and electron affinities (AEA) of C(5)Au(12), vertical electron-detachment (VDE) energies of C(5)Au(12)(-), and vertical ionization and electron-attachment energies (VIE, VEA) of C(5)Au(12) are calculated as well, and compared with those for the corresponding isomers of the Au(13) cluster. The AIE and VIE values are found to be close for the two systems, while the AEA and VDE values are significantly reduced for the radical-based species. A simple fragment-based model is proposed for the decomposition of the total interaction into carbon-gold and gold-gold components.

Wavelet data compression for archiving high-resolution icosahedral model data

NASA Astrophysics Data System (ADS)

Wang, N.; Bao, J.; Lee, J.

2011-12-01

With the increase of the resolution of global circulation models, it becomes ever more important to develop highly effective solutions to archive the huge datasets produced by those models. While lossless data compression guarantees the accuracy of the restored data, it can only achieve limited reduction of data size. Wavelet transform based data compression offers significant potentials in data size reduction, and it has been shown very effective in transmitting data for remote visualizations. However, for data archive purposes, a detailed study has to be conducted to evaluate its impact to the datasets that will be used in further numerical computations. In this study, we carried out two sets of experiments for both summer and winter seasons. An icosahedral grid weather model and a highly efficient wavelet data compression software were used for this study. Initial conditions were compressed and input to the model to run to 10 days. The forecast results were then compared to those forecast results from the model run with the original uncompressed initial conditions. Several visual comparisons, as well as the statistics of numerical comparisons are presented. These results indicate that with specified minimum accuracy losses, wavelet data compression achieves significant data size reduction, and at the same time, it maintains minimum numerical impacts to the datasets. In addition, some issues are discussed to increase the archive efficiency while retaining a complete set of meta data for each archived file.

Average crystal structure(s) of the embedded meta stable η‧-phase in the Al-Mg-Zn system

NASA Astrophysics Data System (ADS)

Bøvik Larsen, Helge; Thorkildsen, Gunnar; Natland, Sølvi; Pattison, Philip

2014-05-01

Meta stable embedded nano-sized ?-particles within a single grain extracted from an alloy having the nominal composition ? have been examined with X-ray diffraction. By applying the orientational and metric relationships that exist between the hexagonal unit cell of the ?-particles and the cubic unit cell of the Al-matrix, it has been proven possible to directly collect diffracted intensity data from the ?-particle ensemble. This has been done using synchrotron radiation and a ?-diffractometer having a scintillator point detector setup. The approach has resulted in improved data quality compared to previous experiments. The interpretation of the data set, based on a combination of Patterson syntheses, direct methods and geometrical restraints, yielded two possible average structural representations: one Al-rich with the approximate stoichiometric composition ? and one Al-depleted with approximate stoichiometric composition ?. Both structures are realized in the same space group, ?, and are most probably superimposed in the crystalline system examined. The geometries are discussed within the atomic environment approach where icosahedral or near-icosahedral configurations are encountered. Comparison with previous published models and the equilibrium structure reveals a main difference related to the distribution of the Zn-sites in the unit cell. A possible transformation path is also suggested. Various aspects and challenges regarding data collection, data reduction and data quality are specifically addressed.

Twelve previously unknown phage genera are ubiquitous in global oceans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holmfeldt, Karin; Solonenko, Natalie; Shah, Manesh B

Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in unknowns dominating culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an underrepresented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four wellknown viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria.more » Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage host systems for experimental hypothesis testing.« less

Crystallization of the C-terminal head domain of the avian adenovirus CELO long fibre

PubMed Central

Guardado Calvo, Pablo; Llamas-Saiz, Antonio L.; Langlois, Patrick; van Raaij, Mark J.

2006-01-01

Avian adenovirus CELO contains two different fibres: fibre 1, the long fibre, and fibre 2, the short fibre. The short fibre is responsible for binding to an unknown avian receptor and is essential for infection of birds. The long fibre is not essential, but is known to bind the coxsackievirus and adenovirus receptor protein. Both trimeric fibres are attached to the same penton base, of which each icosahedral virus contains 12 copies. The short fibre extends straight outwards, while the long fibre emerges at an angle. The carboxy-terminal amino acids 579–793 of the avian adenovirus long fibre have been expressed with an amino-terminal hexahistidine tag and the expressed trimeric protein has been purified by nickel-affinity chromatography and crystallized. Crystals were grown at low pH using PEG 10 000 as precipitant and belonged to space group C2. The crystals diffracted rotating-anode Cu Kα radiation to at least 1.9 Å resolution and a complete data set was collected from a single crystal to 2.2 Å resolution. Unit-cell parameters were a = 216.5, b = 59.2, c = 57.5 Å, β = 101.3°, suggesting one trimer per asymmetric unit and a solvent content of 46%. The long fibre head does not have significant sequence homology to any other protein of known structure and molecular-replacement attempts with known fibre-head structures were unsuccessful. However, a map calculated using SIRAS phasing shows a clear trimer with a shape similar to known adenovirus fibre-head structures. Structure solution is in progress. PMID:16682773

Atomic force microscopy investigation of the giant mimivirus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuznetsov, Yuri G.; Xiao Chuan; Sun Siyang

2010-08-15

Mimivirus was investigated by atomic force microscopy in its native state following serial degradation by lysozyme and bromelain. The 750-nm diameter virus is coated with a forest of glycosylated protein fibers of lengths about 140 nm with diameters 1.4 nm. Fibers are capped with distinctive ellipsoidal protein heads of estimated Mr = 25 kDa. The surface fibers are attached to the particle through a layer of protein covering the capsid, which is in turn composed of the major capsid protein (MCP). The latter is organized as an open network of hexagonal rings with central depressions separated by 14 nm. Themore » virion exhibits an elaborate apparatus at a unique vertex, visible as a star shaped depression on native particles, but on defibered virions as five arms of 50 nm width and 250 nm length rising above the capsid by 20 nm. The apparatus is integrated into the capsid and not applied atop the icosahedral lattice. Prior to DNA release, the arms of the star disengage from the virion and it opens by folding back five adjacent triangular faces. A membrane sac containing the DNA emerges from the capsid in preparation for fusion with a membrane of the host cell. Also observed from disrupted virions were masses of distinctive fibers of diameter about 1 nm, and having a 7-nm periodicity. These are probably contained within the capsid along with the DNA bearing sac. The fibers were occasionally observed associated with toroidal protein clusters interpreted as processive enzymes modifying the fibers.« less

Metabolic-morphologic characteristics of the integument of teleost fish with mature lymphocystis nodules.

PubMed

Spitzer, R H; Koch, E A; Reid, R B; Downing, S W

1982-01-01

Normal and virus-infected (lymphocystis disease) integument from five species of teleosts was examined by light and TEM autoradiography and SEM to establish metabolic-morphologic characteristics of integument with mature lymphocystis cells (LC's). LC's with numerous morphologic attributes of a late developmental stage showed highest incorporation of [3H]-thymidine in vivo (1-91 h) above the intracytoplasmic inclusion body (ci) with little radiolabel in nuclei, cytoplasmic icosahedral deoxyriboviruses (ICDV's) or capsule. Analysis by quantitative autoradiography revealed that the % total cell label in ci and cytoplasm did not vary appreciably from 1-91 h and was corroborative with morphologic criteria of maturity. A possibly phylogenetic difference was noted between teleosts, wherein normal integument showed uptake of [3H]-thymidine in vivo (1 h) by cells at all levels of the epidermis, and cyclostomes (Spitzer et al. 1979) wherein labeling was confined to the basal third of the epidermis. Among four infected teleost species, the mean diameters of the ICDV's measured under the same conditions, ranged from 259.5 nm to 290.0 nm with the mean for each species differing significantly (p less than 0.01) from each of the other means. Ruptured LC's were shown by TEM and SEM to have released ICDV's onto the lesions and integument. Various stages of LC degeneration, host response, and integumental repair processes were documented. An evaluation of labeling in vivo of the capsular matrix was compatible ([3H]-D-galactose greater than [3H]-L-lysine much greater than [3H]-L-fucose) with a glycosaminoglycan-protein structure.

Twelve previously unknown phage genera are ubiquitous in global oceans.

PubMed

Holmfeldt, Karin; Solonenko, Natalie; Shah, Manesh; Corrier, Kristen; Riemann, Lasse; Verberkmoes, Nathan C; Sullivan, Matthew B

2013-07-30

Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in "unknowns" dominating culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an underrepresented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four well-known viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria. Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage-host systems for experimental hypothesis testing.

Syntheses of super-hard boron-rich solids in the B-C-N-O system

NASA Astrophysics Data System (ADS)

Hubert, Herve Pierre

Alpha-rhombohedral (alpha-rh.) B-rich materials belonging to the B-C-N-O system were prepared using high-pressure, high-temperature techniques. The samples were synthesized using a multianvil device and characterized by powder X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and parallel electron energy-loss spectroscopy (PEELS). In the B-O system, the formation of BsbxO materials produced from mixtures of B and Bsb2Osb3 between 1 to 10 GPa and 1000 to 1800sp°C was investigated. Graphitic and diamond-like Bsb2O, reported in previous studies, were not detected. The refractory boron suboxide, nominally Bsb6O, which has the alpha-rh. B structure, is the dominant suboxide in the P and T range of our investigation. High-pressure techniques were used successfully to synthesize boron suboxide of improved purity and crystallinity, and less oxygen-deficient (i.e., closer to the nominal Bsb6O composition) in comparison to room-pressure syntheses. Quantitative analyses indicate compositions of Bsb6Osb{0.95} and Bsb6Osb{0.77} for high-pressure and room-pressure samples, respectively. The first preparation, between 4 to 5.5 GPa, of Bsb6O in which the preferred form of the material is as macroscopic near-perfect regular icosahedra (to 30 mum in diameter) is reported. The Bsb6O icosahedra are similar to the multiply-twinned particles observed in some cubic materials. However, a major difference is that Bsb6O has a rhombohedral structure that closely fits the geometrical requirements for obtaining icosahedral twins. The Bsb6O grains are neither 3D-periodic nor quasicrystalline. Their formation can be described as a Mackay packing of icosahedral Bsb{12} units and provides an alternative to crystal formation by propagation of translational symmetry. Icosahedral twins ranging from 20 nm to 30 mum in diameter, as well as micron-sized euhedral crystals (to 40 mum) were prepared. The structural similarity of compounds with the alpha-rh. B structure is thought to lead to solid solution. In the B-C-O system, intermediate phases were prepared showing evidence of solid solution between Bsb4C and Bsb6O. Boron carbide crystals containing a significant amount of O, typically Bsb6Csb{1.1}Osb{0.33} and Bsb6Csb{1.28}Osb{0.31}, were grown to 20 mum in diameter from mixtures in which B and C were reacted with excess Bsb2Osb3 at 7.5 GPa and 1700sp°C. Cyclic five-fold twins or twins that approximate Bsb6O icosahedra were observed, but the cell dimensions of the B-C-O materials preclude the formation of icosahedral twins. Nanorods with composition near Bsb6C with minor O were grown in a Bsb2Osb3 melt. The mechanism controlling the growth of the nanorods is similar to the solution-liquid-solid (SLS) process. The first conclusive bulk synthesis of a new boron nitride, Bsb6Nsb1-x, was obtained by reacting B and hexagonal BN at 7.5 GPa and 1700sp°C. XRD and PEELS substantiate that this material has a structure related to that of alpha-rh. B and chemical analysis of this compound showed an average composition of Bsb6Nsb{0.92}.

Photoluminescence Investigation of the Indirect Band Gap and Shallow Impurities in Icosahedral B12As2

DTIC Science & Technology

2012-07-05

semiconductor that exhibits unusual properties as the result of the bonding within the 12-atom boron icosahe- dron that is an integral part of its crystal...aware that notwithstanding any other provision of law, no person shall be subject to a penalty for failing to comply with a collection of information if...LIMITATION OF ABSTRACT Same as Report (SAR) 18. NUMBER OF PAGES 13 19a. NAME OF RESPONSIBLE PERSON a. REPORT unclassified b. ABSTRACT

Pairing Heterocyclic Cations with closo-Icosahedral Borane and Carborane Anions, II: Benchtop Alternative Synthetic Methodologies for Binary Triazolium and Tetrazolium Salts with Significant Water Solubility (POSTPRINT)

DTIC Science & Technology

2012-01-01

interesting property, eutectic melting-point depression. Recrystallization of ternary salts 12–14 was not attempted because of a concern that a cation... recrystallization solvent mixture for these powders, and while some individual successes resulted, a general efficient solvent system for all salt...product recrystallizations could not be found. So, rather than recrystallizing each individual adduct, spectroscopic examination of the amorphous solids was

Pairing Heterocyclic Cations with closo-Icosahedral Borane and Carborane Anions. II. Benchtop Alternative Synthetic Methodologies for Binary Triazolium and Tetrazolium Salts with Significant Water Solubility

DTIC Science & Technology

2010-04-01

produced from eutectic melts. Nat. Mater. 2008, 7, 626-630. 9. Any attempt at recrystallizing the 1:1 mixture of cations in (12) is likely to afford... recrystallizations . So, rather than recrystallizing each individual adduct, we concentrated on performing a careful spectroscopic examination of the...suggested. [1] While it is well-known that an admixture of two neutral compounds often affords eutectic behavior, we wondered whether or not the same

A first-principles core-level XPS study on the boron impurities in germanium crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamauchi, Jun; Yoshimoto, Yoshihide; Suwa, Yuji

2013-12-04

We systematically investigated the x-ray photoelectron spectroscopy (XPS) core-level shifts and formation energies of boron defects in germanium crystals and compared the results to those in silicon crystals. Both for XPS core-level shifts and formation energies, relationship between defects in Si and Ge is roughly linear. From the similarity in the formation energy, it is expected that the exotic clusters like icosahedral B12 exist in Ge as well as in Si.

Correlation of nonorthogonality of best hybrid bond orbitals with bond strength of orthogonal orbitals

PubMed Central

Pauling, Linus

1976-01-01

An expression is derived for the bond length of two spd orbitals with maximum values in two directions forming a given bond angle by consideration of the nonorthogonality integral of two best orbitals in these directions. This equation is equivalent to the expression derived by formulating the pair of orthogonal orbitals. Similar expressions are derived for spdf orbitals. Applications are made to icosahedral and cuboctahedral bonds and to the packing of nucleons in atomic nuclei. PMID:16578736

Correlation of nonorthogonality of best hybrid bond orbitals with bond strength of orthogonal orbitals.

PubMed

Pauling, L

1976-02-01

An expression is derived for the bond length of two spd orbitals with maximum values in two directions forming a given bond angle by consideration of the nonorthogonality integral of two best orbitals in these directions. This equation is equivalent to the expression derived by formulating the pair of orthogonal orbitals. Similar expressions are derived for spdf orbitals. Applications are made to icosahedral and cuboctahedral bonds and to the packing of nucleons in atomic nuclei.

Bridged Heterocyclium Di-Cationic closo-Icosahedral Perfluoroborane, Borane, and Carborane Salts via Aqueous, Open-Air Benchtop Synthesis (Preprint)

DTIC Science & Technology

2010-03-11

AFB CA 93524-7680 AFRL-RZ-ED-JA-2010-090 9. SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM(S) Air...Force Research Laboratory (AFMC) AFRL/RZS 11. SPONSOR/MONITOR’S 5 Pollux Drive NUMBER(S) Edwards AFB CA 93524-7048 AFRL-RZ-ED-JA-2010...Strauss § Air Force Research Laboratory, Propellants Branch (AFRL/RZSP), 10 East Saturn Blvd., Edwards AFB, CA 93524-7680, Department of Chemistry and

Al{sub 70}Pd{sub 21.5}Mn{sub 8.5}: A quasicrystal showing the de haas-van Alphen effect

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haanappel, E.G.; Kycia, S.W.; Harmon, B.N.

1995-07-01

We have measured the de Haas-van Alphen effect in the icosahedral quasicrystal Al{sub 70}Pd{sub 21.5}Mn{sub 8.5}. We have found two well-defined frequencies with the magnetic field parallel to a five-fold axis, and two different ones with the field parallel to a two-fold axis. On increasing the temperature, the amplitude of the oscillations substantially decreased, suggesting that the carriers have large masses.

Development of a High Throughput Assay for Indirectly Measuring Phage Growth Using the OmniLog (trademark) System

DTIC Science & Technology

2012-09-01

and phage Giraffe exhibits a similar morphology (Fig. 1A). Phage BA39 (Fig. 1E) appears to belong to the Myoviridae family (icosahedral head and...see later) but this assignment is tentative. Monitoring the kinetics of bacterial growth using OmniLogTM system upon infection with Giraffe phage...spores with and without infection by Giraffe phage are shown in Figure 2A and B respectively. The growth of 7702 without phage infection followed a

Smooth Scaling of Valence Electronic Properties in Fullerenes: From One Carbon Atom, to C60, to Graphene

DTIC Science & Technology

2012-09-18

Smooth scaling of valence electronic properties in fullerenes: from one carbon atom , to C60, to graphene Greyson R. Lewis,1 William E. Bunting,1...pacitance scaling lines of the fullerenes. Lastly, it is found that points representing the carbon atom and the graphene limit lie on scaling lines for...icosahedral fullerenes, so their quantum capacitances and their detachment energies scale smoothly from one C atom , through C60, to graphene. I

Red clover necrotic mosaic virus: Biophysics and Biotechnology

NASA Astrophysics Data System (ADS)

Lockney, Dustin M.

Red clover necrotic mosaic virus (RCNMV) is a highly robust (Tm=60 °C), 36 nm icosahedral plant virus. The capsid of RCNMV is assembled from 180 chemically equivalent coat proteins (CPs). The CPs arrange in a T=3 symmetry, in 1 of 3 conformations forming the asymmetric subunit (ASU). There are two Ca(II) binding sites per CP; the removal of divalent cations causes the CP subunits of the ASU to rotate away from each other forming a ˜13 A channel. These channels lead to the highly organized bipartite genome of RCNMV and can be closed by adding back Ca(II). Titrimetric analysis and tryptophan fluorescence was used to determine the affinity of RCNMV for Ca(II) to be ˜Kd < 300 nM. It has been shown that doxorubicin (Dox) can be infused into the capsid at a mole ratio of ˜1000:1, Dox-to-virus, and unlike other nanoparticles, there is no detectable leakage. The high loading of Dox is most likely due to intercalation into the genome and significant intercalation or exposure to denaturants was observed to cause loss of capsid stability. To better understand the limitations of cargo loading, Dox and other intercalating molecules (rhodamine 800, ethidium bromide, and propidium iodide) were assayed to determine optimum infusion conditions. Dox was observed to have a propensity to aggregate. In order to manage the Dox aggregation, the infusion buffer was changed from 50 mM Tris-HCl/50 mM NaOAc/50 mM EDTA or 200 mM EDTA at pH 8.0 to 5 mM HEPES/5 mM Na4EDTA/10 mM NaCl pH 7.8. The Dox:RCNMV infusion mole ratio was also lowered from 5000:1 to 500:1 and the incubation temperature was changed from 4 °C to 22 °C for <12 hours, opposed to 24 hours. To impart targeting functionality to RCNMV, biomimetic peptides were conjugated to either the surface capsid lysines or cysteines using standard bioconjugation methods. For all of the biomimetic peptides screened, sulfosuccinimidyl 4-(N-maleimidomethyl) cyclohexane-1-carboxylate (sulfo-SMCC) was used to orthogonally attach the cysteineterminated peptides to the surface lysines of RCNMV. The efficacy of a plant virus nanoparticle (PVN), loaded with a cargo (Dox or propidium iodide) and armed with a targeting peptide, was tested in vitro against several cell line using cell viability assays. ADH304, an N-cadherin targeting peptide, was synthesized to contain a lys[maleimide]. Dox infused RCNMV was armed with ADH304maleimide by conjugating the peptide to the endogenous C267 located in the P-domain. The use of a cysteine reactive peptide increased the PVN yield from ˜30% to ˜70% by eliminating several synthetic steps. The efficacy of this PVN formulation was tested on a human melanoma tumor in a xenograft mouse model. This results of this study showed that a) a PVN could suppress tumor growth at 4 x the MTD (maximum tolerated dose) without acute toxicity and b) Dox, otherwise not effective against melanoma, was able to suppress tumor growth when formulated in a PVN. This is most likely due to the PVN entering the tumor cells through an endocytic pathway versus the simple diffusion of Dox which is subject to cellular efflux pumps.

Cooling rate dependence of simulated Cu{sub 64.5}Zr{sub 35.5} metallic glass structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryltsev, R. E.; Ural Federal University, 19 Mira Str., 620002 Ekaterinburg; L.D. Landau Institute for Theoretical Physics, Russian Academy of Sciences, 2 Kosygina Str., 119334 Moscow

Using molecular dynamics simulations with embedded atom model potential, we study structural evolution of Cu{sub 64.5}Zr{sub 35.5} alloy during the cooling in a wide range of cooling rates γ ∈ (1.5 ⋅ 10{sup 9}, 10{sup 13}) K/s. Investigating short- and medium-range orders, we show that the structure of Cu{sub 64.5}Zr{sub 35.5} metallic glass essentially depends on cooling rate. In particular, a decrease of the cooling rate leads to an increase of abundances of both the icosahedral-like clusters and Frank-Kasper Z16 polyhedra. The amounts of these clusters in the glassy state drastically increase at the γ{sub min} = 1.5 ⋅ 10{supmore » 9} K/s. Analysing the structure of the glass at γ{sub min}, we observe the formation of nano-sized crystalline grain of Cu{sub 2}Zr intermetallic compound with the structure of Cu{sub 2}Mg Laves phase. The structure of this compound is isomorphous with that for Cu{sub 5}Zr intermetallic compound. Both crystal lattices consist of two types of clusters: Cu-centered 13-atom icosahedral-like cluster and Zr-centered 17-atom Frank-Kasper polyhedron Z16. That suggests the same structural motifs for the metallic glass and intermetallic compounds of Cu–Zr system and explains the drastic increase of the abundances of these clusters observed at γ{sub min}.« less

Ultrafast Relaxation Dynamics of Au 38 (SC 2 H 4 Ph) 24 Nanoclusters and Effects of Structural Isomerism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Meng; Tian, Shubo; Zeng, Chenjie

Structural isomerism in nanoparticles has recently emerged as a new topic and stimulated research interest because the atomic structures of ultrasmall nanoparticles may have great impact on their fundamental properties and applications. We report the correlation between ultrafast relaxation dynamics and atomic structures of two isomers of thiolate-protected Au 38(SC 2H 4Ph) 24. The bi-icosahedral Au 38 (denoted as Au 38Q) with a Au 23 inner core in its atomic structure shows rapid decay (1.5 ps) followed by nanosecond relaxation to the ground state, whereas its structural isomer (Au 38T) exhibits similar relaxation processes, but the rapid decay is acceleratedmore » by ~50% (1.0 ps). The picosecond relaxations in both cases can be assigned to core–shell charge transfer or electronic rearrangement within the metal core. The acceleration of the fast decay in Au38T is ascribed to its unique core structure, which is made up of a mono-icosahedral Au 13 capped by a Au 12 tri-tetrahedron by sharing two atoms. Interestingly, coherent phonon emissions (25 cm –1 for Au 38Q, 27 and 60 cm –1 for Au 38T) are observed in both isomers with pumping in the NIR region. These results illustrate for the first time the importance of atomic structures in the photophysics of same sized gold nanoclusters.« less

DYNAMICO, an atmospheric dynamical core for high-performance climate modeling

NASA Astrophysics Data System (ADS)

Dubos, Thomas; Meurdesoif, Yann; Spiga, Aymeric; Millour, Ehouarn; Fita, Lluis; Hourdin, Frédéric; Kageyama, Masa; Traore, Abdoul-Khadre; Guerlet, Sandrine; Polcher, Jan

2017-04-01

Institut Pierre Simon Laplace has developed a very scalable atmospheric dynamical core, DYNAMICO, based on energy-conserving finite-difference/finite volume numerics on a quasi-uniform icosahedral-hexagonal mesh. Scalability is achieved by combining hybrid MPI/OpenMP parallelism to asynchronous I/O. This dynamical core has been coupled to radiative transfer physics tailored to the atmosphere of Saturn, allowing unprecedented simulations of the climate of this giant planet. For terrestrial climate studies DYNAMICO is being integrated into the IPSL Earth System Model IPSL-CM. Preliminary aquaplanet and AMIP-style simulations yield reasonable results when compared to outputs from IPSL-CM5. The observed performance suggests that an order of magnitude may be gained with respect to IPSL-CM CMIP5 simulations either on the duration of simulations or on their resolution. Longer simulations would be of interest for the study of paleoclimate, while higher resolution could improve certain aspects of the modeled climate such as extreme events, as will be explored in the HighResMIP project. Following IPSL's strategic vision of building a unified global-regional modelling system, a fully-compressible, non-hydrostatic prototype of DYNAMICO has been developed, enabling future convection-resolving simulations. Work supported by ANR project "HEAT", grant number CE23_2014_HEAT Dubos, T., Dubey, S., Tort, M., Mittal, R., Meurdesoif, Y., and Hourdin, F.: DYNAMICO-1.0, an icosahedral hydrostatic dynamical core designed for consistency and versatility, Geosci. Model Dev., 8, 3131-3150, doi:10.5194/gmd-8-3131-2015, 2015.

Ab initio molecular dynamics simulations of short-range order in Zr 50Cu 45Al 5 and Cu 50Zr 45Al 5 metallic glasses

DOE PAGES

Huang, Yuxiang; Huang, Li; Wang, C. Z.; ...

2016-02-01

Comparative analysis between Zr-rich Zr 50Cu 45Al 5 and Cu-rich Cu 50Zr 45Al 5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr 50Cu 45Al 5 and Cu 50Zr 45Al 5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons < 0,0,12,0 > is dominant, and in the Cu-rich one the distorted icosahedral orders, especially < 0,2,8,2 > and , are prominent. And the < 0,2,8,2 > polyhedra in Cu 50Zr 45Al 5 MG mainly originate from Al-centered clusters, while the < 0,0,12,0 > in Zr 50Cu 45Al 5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. Lastly, the relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr 50Cu 45Al 5.« less

Ab initio molecular dynamics simulations of short-range order in Zr50Cu45Al5 and Cu50Zr45Al5 metallic glasses

NASA Astrophysics Data System (ADS)

Huang, Yuxiang; Huang, Li; Wang, C. Z.; Kramer, M. J.; Ho, K. M.

2016-03-01

Comparative analysis between Zr-rich Zr50Cu45Al5 and Cu-rich Cu50Zr45Al5 metallic glasses (MGs) is extensively performed to locate the key structural motifs accounting for their difference of glass forming ability. Here we adopt ab initio molecular dynamics simulations to investigate the local atomic structures of Zr50Cu45Al5 and Cu50Zr45Al5 MGs. A high content of icosahedral-related (full and distorted) orders was found in both samples, while in the Zr-rich MG full icosahedrons < 0,0,12,0> is dominant, and in the Cu-rich one the distorted icosahedral orders, especially < 0,2,8,2> and < 0,2,8,1> , are prominent. And the < 0,2,8,2> polyhedra in Cu50Zr45Al5 MG mainly originate from Al-centered clusters, while the < 0,0,12,0> in Zr50Cu45Al5 derives from both Cu-centered clusters and Al-centered clusters. These difference may be ascribed to the atomic size difference and chemical property between Cu and Zr atoms. The relatively large size of Zr and large negative heat of mixing between Zr and Al atoms, enhancing the packing density and stability of metallic glass system, may be responsible for the higher glass forming ability of Zr50Cu45Al5.

Ultrafast Relaxation Dynamics of Au 38 (SC 2 H 4 Ph) 24 Nanoclusters and Effects of Structural Isomerism

DOE PAGES

Zhou, Meng; Tian, Shubo; Zeng, Chenjie; ...

2016-12-22

Structural isomerism in nanoparticles has recently emerged as a new topic and stimulated research interest because the atomic structures of ultrasmall nanoparticles may have great impact on their fundamental properties and applications. We report the correlation between ultrafast relaxation dynamics and atomic structures of two isomers of thiolate-protected Au 38(SC 2H 4Ph) 24. The bi-icosahedral Au 38 (denoted as Au 38Q) with a Au 23 inner core in its atomic structure shows rapid decay (1.5 ps) followed by nanosecond relaxation to the ground state, whereas its structural isomer (Au 38T) exhibits similar relaxation processes, but the rapid decay is acceleratedmore » by ~50% (1.0 ps). The picosecond relaxations in both cases can be assigned to core–shell charge transfer or electronic rearrangement within the metal core. The acceleration of the fast decay in Au38T is ascribed to its unique core structure, which is made up of a mono-icosahedral Au 13 capped by a Au 12 tri-tetrahedron by sharing two atoms. Interestingly, coherent phonon emissions (25 cm –1 for Au 38Q, 27 and 60 cm –1 for Au 38T) are observed in both isomers with pumping in the NIR region. These results illustrate for the first time the importance of atomic structures in the photophysics of same sized gold nanoclusters.« less

[New, newer, newest human polyomaviruses: how far?].

PubMed

Us, Dürdal

2013-04-01

Polyomaviruses, classified in Polyomaviridae family, are non-enveloped small (40-45 nm) viruses with icosahedral symmetry and circular double-stranded DNA genome. Polyomaviruses can infect a variety of vertebrates including birds, rodents, cattle, monkeys and humans. The characteristics such as establishment of latent infections, reactivations during immunosuppression and oncogenic potencies render the human polyomaviruses (HPyVs) of considerable importance for public health. The first polyomavirus (Mouse polyomavirus) has been identified in 1953 as filterable tumor-causing agents in mice, followed by Simian vacuolating virus (SV40) isolated from rhesus monkey kidney cells that had been used for poliovirus vaccine preparation in 1960. Due to the known transforming capacity of SV40, it was initially thought that the incidence of cancer could increase following the administration of SV40-contaminated polio vaccines, however advanced studies yielded inconsistent results, without any evidence to conclude whether or not the contaminated polio vaccine caused cancer. Several studies have reported the detection of SV40 genome in some of the human tumors, as well as in the clinical samples of healthy subjects. In addition SV40 seropositivity was reported in human populations although in low rates (2-10%). These data have raised the possibility that SV40 infects humans and circulates in human populations unrelated to being exposed to the vaccine. The discovery of the first human polyomaviruses was in 1971 independently from each other, one was BK virus (BKPyV) isolated from the urine sample of a renal transplant patient, and the other was JC virus (JCPyV) isolated from the brain tissue of a patient with progressive multifocal leukoencephalopathy, and both were named after the patients' initials. BK and JC viruses were the only well-known human polyomaviruses throughout 36 years, however drammatical increase in number of newly identified human polyomaviruses was recorded in the last six years due to the use of sophisticated molecular methods and new-generation sequencing technologies. In 2007, two new HPyVs were identified independently from nasopharyngeal aspirates of children with acute respiratory tract infections; one was KI (Karolinska Institute) and the other was WU (Washington University) polyomaviruses, named after the initials of institutes which they were first described. In 2008, the fifth HPyV namely Merkel cell polyomavirus (MCPyV) was isolated from the skin tumor sample of a patient with Merkel cell carcinoma. In 2010, three other novel human polyomaviruses were discovered, two were from skin samples of healthy subjects (HPyV-6 and HPyV-7), and one (Trichodysplasia Spinulosa-associated virus; TSPyV) from keratotic spicule sample of a heart-transplanted patient. Another new HPyV was identified in 2011 named HPyV-9, from the blood and urine samples of an asymptomatic patient with kidney transplant. Most recently, three new HPyVs have been sequentially discovered during the last quarter of 2012. The 10th HPyV (HPyV10) was identified in condyloma samples of an immunocompromised patient with WHIM syndrome (Wart, Hypogammaglobulinemia, Infections, Myelokathexis), 11th virus was isolated from stool sample of a healthy child from Malawi (Malawi polyomavirus; MWPyV), and 12th was described from fecal sample of a diarrheal child from Mexico (Mexico polyomavirus; MXPyV). The whole genome sequence analysis of HPyV10, MWPyV and MXPyV pointed out that they are closely related viruses. The last novel polyomavirus, namely Saint Louis polyomavirus (STLPyV) has been reported in a study published on February 2013, identified from the stool sample of a healthy child. Seroepidemiological studies indicated that most of the novel HPyVs are highly prevalent (average rate: 40-80%) worldwide and likely acquired asymptomatically during childhood, similar to the old ones, BKPyV and JCPyV. However data about HPyV10, MWPyV, MXPyV and STLPyV are not enough as they have been discovered most recently. Similarly, little is known about the pathogenesis, route of infection and the relationship with clinical diseases of novel HPyVs except MCPyV and TSPyV which are known to be responsible for Merkel cell carcinoma and trichodysplasia spinulosa, respectively. The expanding repertoire of human polyomaviruses made us think that many others will be uncovered in the future thanking to the advances in molecular methods. In this review, recent developments subjecting new human polyomaviruses have been summarized.

A two-pronged structural analysis of retroviral maturation indicates that core formation proceeds by a disassembly-reassembly pathway rather than a displacive transition.

PubMed

Keller, Paul W; Huang, Rick K; England, Matthew R; Waki, Kayoko; Cheng, Naiqian; Heymann, J Bernard; Craven, Rebecca C; Freed, Eric O; Steven, Alasdair C

2013-12-01

Retrovirus maturation involves sequential cleavages of the Gag polyprotein, initially arrayed in a spherical shell, leading to formation of capsids with polyhedral or conical morphology. Evidence suggests that capsids assemble de novo inside maturing virions from dissociated capsid (CA) protein, but the possibility persists of a displacive pathway in which the CA shell remains assembled but is remodeled. Inhibition of the final cleavage between CA and spacer peptide SP1/SP blocks the production of mature capsids. We investigated whether retention of SP might render CA assembly incompetent by testing the ability of Rous sarcoma virus (RSV) CA-SP to assemble in vitro into icosahedral capsids. Capsids were indeed assembled and were indistinguishable from those formed by CA alone, indicating that SP was disordered. We also used cryo-electron tomography to characterize HIV-1 particles produced in the presence of maturation inhibitor PF-46396 or with the cleavage-blocking CA5 mutation. Inhibitor-treated virions have a shell that resembles the CA layer of the immature Gag shell but is less complete. Some CA protein is generated but usually not enough for a mature core to assemble. We propose that inhibitors like PF-46396 bind to the Gag lattice where they deny the protease access to the CA-SP1 cleavage site and prevent the release of CA. CA5 particles, which exhibit no cleavage at the CA-SP1 site, have spheroidal shells with relatively thin walls. It appears that this lattice progresses displacively toward a mature-like state but produces neither conical cores nor infectious virions. These observations support the disassembly-reassembly pathway for core formation.

Isolation and characterization of a virulent bacteriophage SPW specific for Staphylococcus aureus isolated from bovine mastitis of lactating dairy cattle.

PubMed

Li, Longping; Zhang, Zhiying

2014-09-01

Mastitis in dairy cattle continues to be an economically important disease. However, control is complicated by a high prevalence of resistance to antibiotics. Phage therapy, therefore, is considered as an alternative way of controlling bacterial infections and contaminations. In this study, we have described isolation and characterization of a highly virulent phage SPW from wastewater of dairy farm, which possesses a strong lytic capability against mastitis-associated Staphylococcus aureus, the most important pathogen in bovine clinical and subclinical mastitis. The phage SPW produced large, round and clear plaques on bacterial culture plates. TEM showed phage SPW has an icosahedral head 62.5 nm in diameter and long tail of 106 nm, head and tail were held together by a connector of 18 ± 1.5 nm long and can be classified as a member of the Myoviridae family. Restriction analysis indicated that phage SPW was a dsDNA virus with an approximate genome size of 65-69 kb. One-step growth kinetics showed a short latency period of about 10-15 min and a rise period of 50 min and a relatively small burst size was 44 ± 3 phages particles/infected cell. Moreover, adsorption rates were not influenced by calcium ions and phage SPW was relatively stable in a wide range of temperature and pH values, and resistant to chloroform and isopropanol. The optimal multiplicity of infection (MOI) was 0.01. When phage SPW was used to infect five other clinically isolated pathogenic isolates, it showed relatively wide spectrum host range. Phage SPW was capable of eliciting efficient lysis of S. aureus, revealing it potentially as an effective approach to prophylaxis or treatment of S. aureus-associated mastitis in dairy cows.

Assembly of silver Trigons into a buckyball-like Ag180 nanocage

PubMed Central

Wang, Zhi; Su, Hai-Feng; Tan, Yuan-Zhi; Schein, Stan; Lin, Shui-Chao; Liu, Wei; Wang, Shu-Ao; Wang, Wen-Guang; Tung, Chen-Ho; Zheng, Lan-Sun

2017-01-01

Buckminsterfullerene (C60) represents a perfect combination of geometry and molecular structural chemistry. It has inspired many creative ideas for building fullerene-like nanopolyhedra. These include other fullerenes, virus capsids, polyhedra based on DNA, and synthetic polynuclear metal clusters and cages. Indeed, the regular organization of large numbers of metal atoms into one highly complex structure remains one of the foremost challenges in supramolecular chemistry. Here we describe the design, synthesis, and characterization of a Ag180 nanocage with 180 Ag atoms as 4-valent vertices (V), 360 edges (E), and 182 faces (F)––sixty 3-gons, ninety 4-gons, twelve 5-gons, and twenty 6-gons––in agreement with Euler’s rule V − E + F = 2. If each 3-gon (or silver Trigon) were replaced with a carbon atom linked by edges along the 4-gons, the result would be like C60, topologically a truncated icosahedron, an Archimedean solid with icosahedral (Ih) point-group symmetry. If C60 can be described mathematically as a curling up of a 6.6.6 Platonic tiling, the Ag180 cage can be described as a curling up of a 3.4.6.4 Archimedean tiling. High-resolution electrospray ionization mass spectrometry reveals that {Ag3}n subunits coexist with the Ag180 species in the assembly system before the final crystallization of Ag180, suggesting that the silver Trigon is the smallest building block in assembly of the final cage. Thus, we assign the underlying growth mechanism of Ag180 to the Silver-Trigon Assembly Road (STAR), an assembly path that might be further employed to fabricate larger, elegant silver cages. PMID:29087328

Herpesvirus capsid assembly and DNA packaging

PubMed Central

Heming, Jason D.; Conway, James F.; Homa, Fred L.

2017-01-01

Herpes simplex virus type I (HSV-1) is the causative agent of several pathologies ranging in severity from the common cold sore to life-threatening encephalitic infection. During productive lytic infection, over 80 viral proteins are expressed in a highly regulated manner, resulting in the replication of viral genomes and assembly of progeny virions. The virion of all herpesviruses consists of an external membrane envelope, a proteinaceous layer called the tegument, and an icosahedral capsid containing the double-stranded linear DNA genome. The capsid shell of HSV-1 is built from four structural proteins: a major capsid protein, VP5, which forms the capsomers (hexons and pentons), the triplex consisting of VP19C and VP23 found between the capsomers, and VP26 which binds to VP5 on hexons but not pentons. In addition, the dodecameric pUL6 portal complex occupies one of the 12 capsid vertices, and the capsid vertex specific component (CVSC), a heterotrimer complex of pUL17, pUL25 and pUL36 binds specifically to the triplexes adjacent to each penton. The capsid is assembled in the nucleus where the viral genome is packaged into newly assembled closed capsid shells. Cleavage and packaging of replicated, concatemeric viral DNA requires the seven viral proteins encoded by the UL6, UL15, UL17, UL25, UL28, UL32, and UL33 genes. Considerable advances have been made in understanding the structure of the herpesvirus capsid and the function of several of the DNA packaging proteins by applying biochemical, genetic, and structural techniques. This review is a summary of recent advances with respect to the structure of the HSV-1 virion capsid and what is known about the function of the seven packaging proteins and their interactions with each other and with the capsid shell. PMID:28528442

Defining the Enterovirus Diversity Landscape of a Fecal Sample: A Methodological Challenge?

PubMed

Faleye, Temitope Oluwasegun Cephas; Adewumi, Moses Olubusuyi; Adeniji, Johnson Adekunle

2016-01-12

Enteroviruses are a group of over 250 naked icosahedral virus serotypes that have been associated with clinical conditions that range from intrauterine enterovirus transmission withfataloutcome through encephalitis and meningitis, to paralysis. Classically, enterovirus detection was done by assaying for the development of the classic enterovirus-specific cytopathic effect in cell culture. Subsequently, the isolates were historically identified by a neutralization assay. More recently, identification has been done by reverse transcriptase-polymerase chain reaction (RT-PCR). However, in recent times, there is a move towards direct detection and identification of enteroviruses from clinical samples using the cell culture-independent RT semi-nested PCR (RT-snPCR) assay. This RT-snPCR procedure amplifies the VP1 gene, which is then sequenced and used for identification. However, while cell culture-based strategies tend to show a preponderance of certain enterovirus species depending on the cell lines included in the isolation protocol, the RT-snPCR strategies tilt in a different direction. Consequently, it is becoming apparent that the diversity observed in certain enterovirus species, e.g., enterovirus species B(EV-B), might not be because they are the most evolutionarily successful. Rather, it might stem from cell line-specific bias accumulated over several years of use of the cell culture-dependent isolation protocols. Furthermore, it might also be a reflection of the impact of the relative genome concentration on the result of pan-enterovirus VP1 RT-snPCR screens used during the identification of cell culture isolates. This review highlights the impact of these two processes on the current diversity landscape of enteroviruses and the need to re-assess enterovirus detection and identification algorithms in a bid to better balance our understanding of the enterovirus diversity landscape.

Defining the Enterovirus Diversity Landscape of a Fecal Sample: A Methodological Challenge?

PubMed Central

Faleye, Temitope Oluwasegun Cephas; Adewumi, Moses Olubusuyi; Adeniji, Johnson Adekunle

2016-01-01

Enteroviruses are a group of over 250 naked icosahedral virus serotypes that have been associated with clinical conditions that range from intrauterine enterovirus transmission withfataloutcome through encephalitis and meningitis, to paralysis. Classically, enterovirus detection was done by assaying for the development of the classic enterovirus-specific cytopathic effect in cell culture. Subsequently, the isolates were historically identified by a neutralization assay. More recently, identification has been done by reverse transcriptase-polymerase chain reaction (RT-PCR). However, in recent times, there is a move towards direct detection and identification of enteroviruses from clinical samples using the cell culture-independent RT semi-nested PCR (RT-snPCR) assay. This RT-snPCR procedure amplifies the VP1 gene, which is then sequenced and used for identification. However, while cell culture-based strategies tend to show a preponderance of certain enterovirus species depending on the cell lines included in the isolation protocol, the RT-snPCR strategies tilt in a different direction. Consequently, it is becoming apparent that the diversity observed in certain enterovirus species, e.g., enterovirus species B(EV-B), might not be because they are the most evolutionarily successful. Rather, it might stem from cell line-specific bias accumulated over several years of use of the cell culture-dependent isolation protocols. Furthermore, it might also be a reflection of the impact of the relative genome concentration on the result of pan-enterovirus VP1 RT-snPCR screens used during the identification of cell culture isolates. This review highlights the impact of these two processes on the current diversity landscape of enteroviruses and the need to re-assess enterovirus detection and identification algorithms in a bid to better balance our understanding of the enterovirus diversity landscape. PMID:26771630

The Effects of Stoichiometry on the Mechanical Properties of Icosahedral Boron Carbide Under Loading

DTIC Science & Technology

2012-11-19

ranging from 10% to 20% C using glancing incidence x - ray diffraction and similar experimental studies of structure as a function of stoichiometry were...blue) positions. it has been suggested that x - ray diffraction analysis of a series of boron-rich materials indicates a distinct change in the c lattice...Angstroms, angles in degrees, volume in cubic Angstroms). Structure Formula % C a b c α β γ Volume Experiment37 B5.6C 15.2 5.19 5.19 5.19 65.18 65.18