Fivefold Axis Research Articles

Infectious parvovirus B19 circulates in the blood coated with active host protease inhibitors

The lack of a permissive cell culture system has limited high-resolution structures of parvovirus B19 (B19V) to virus-like particles (VLPs). In this study, we present the atomic resolution structure (2.2 Å) of authentic B19V purified from a patient blood sample. There are significant differences compared to non-infectious VLPs. Most strikingly, two host protease inhibitors (PIs), inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4) and serpinA3, were identified in complex with the capsids in all patient samples tested. The ITIH4 binds specifically to the icosahedral fivefold axis and serpinA3 occupies the twofold axis. The protein-coated virions remain infectious, and the capsid-associated PIs retain activity; however, upon virion interaction with target cells, the PIs dissociate from the capsid prior to viral entry. Our finding of an infectious virion shielded by bound host serum proteins suggests an evolutionarily favored phenomenon to evade immune surveillance and escape host protease activity.

Flat-bands in translated and twisted bilayer Penrose quasicrystals

Correlated phases in Moiré materials together with the flat-bands in twisted systems play a central role to explain superconductivity in the new twisted bilayer graphene. In this paper, flat-bands are shown to exist in both translated and twisted bilayer of quasicrystals. Such flat-bands arise for different displacements and twisting angles of two-coupled Penrose lattices where Moiré patterns are also shown. Moiré patterns analyzed in this work have at least two inverted worms showing an interference pattern going along the five-fold axes of the pentagon. In order to analyze the behavior of the flat band, our study has been done for fixed interference worm directions but increasing the worm interference density, and for fixed worm interference density but increasing the number of worm directions. In case of rotations, the Moiré patterns that occurs for special angles such as π/5, 2π/5, 3π/5, 4π/5 and π are discussed in detail because they clearly show flat-bands along with quasicrystalline electronic states at the Fermi level.

Identification of four neutralizing antigenic sites on the enterovirus D68 capsid.

Enterovirus D68 (EV-D68) is an emerging respiratory pathogen associated with acute flaccid myelitis. Currently, no approved vaccines or antiviral drugs are available. Here, we report four functionally independent neutralizing antigenic sites (I to IV) by analyses of neutralizing monoclonal antibody (MAb)-resistant mutants. Site I is located in the VP1 BC loop near the fivefold axis. Site II resides in the VP2 EF loop, and site III is situated in VP1 C-terminus; both sites are located at the south rim of the canyon. Site IV is composed of residue in VP2 βB strand and residues in the VP3 BC loop and resides around the threefold axis. The developed MAbs targeting the antigenic sites can inhibit viral binding to cells. These findings advance the understanding of the recognition of EV-D68 by neutralizing antibodies and viral evolution and immune escape and also have important implications for the development of novel EV-D68 vaccines.

Structural Characterization of Canine Minute Virus, Rat and Porcine Bocavirus.

Bocaparvovirus is an expansive genus of the Parvovirinae, with a wide range of vertebrate hosts. This study investigates Canine minute virus (CnMV), Rat bocavirus (RBoV), and Porcine bocavirus 1 (PBoV1). Both CnMV and PBoV1 have been found in gastrointestinal infections in their respective hosts, with CnMV responsible for spontaneous abortions in dogs, while PBoV has been associated with encephalomyelitis in piglets. The pathogenicity of the recently identified RBoV is currently unknown. To initiate the characterization of these viruses, their capsids structures were determined by cryo-electron microscopy at resolutions ranging from 2.3 to 2.7 Å. Compared to other parvoviruses, the CnMV, PBoV1, and RBoV capsids showed conserved features, such as the channel at the fivefold symmetry axis. However, major differences were observed at the two- and threefold axes. While CnMV displays prominent threefold protrusions, the same region is more recessed in PBoV1 and RBoV. Furthermore, the typical twofold axis depression of parvoviral capsids is absent in CnMV or very small in PBoV and RBoV. These capsid structures extend the structural portfolio for the Bocaparvovirus genus and will allow future characterization of these pathogens on a molecular level. This is important, as no antivirals or vaccines exist for these viruses.

Formation mechanism of the quasicrystal in Al-Cu-Mg-Zn aluminum alloy resistance spot weld

In this study, the formation mechanism of the quaternary quasicrystal phase (59.59Al-8.85Cu-16.85Mg-14.71Zn, at. %) in the Al-Cu-Mg-Zn alloy resistance spot welding nugget was revealed. Transmission electron microscopy shows the quasicrystal phase was located at the inner-dendrite zone of which selected area electron diffraction spot exhibits a typical pattern of an icosahedral quasicrystal (fivefold axes). During the cooling process, Cu-Mg-Zn solute enriched within the remnant liquid at the inter-dendrite zone with short-range-ordered clusters structure. Instead transforming to typical crystalline phases, this undercooled remnant liquid forms the icosahedral quasicrystal phase due to the rapid cooling rate of resistance spot welding. This study shows the feasibility of acquiring massive quasicrystal phase in commercially-used aluminum alloy under common processing condition.

Electron Paramagnetic Resonance Spectra of Pentagonal Bipyramidal Gadolinium Complexes

Gadolinium is a special case in spectroscopy because of the near isotropic nature of the 4f7 configuration of the +3 oxidation state. Gd3+ complexes have been studied in several symmetries to understand the underlying mechanisms of the ground state splitting. The abundance of information in Gd3+ spectra can be used as a probe for properties of the other rare earth ions in the same complexes. In this work, the zero-field splitting (ZFS) of a series of Gd3+ pentagonal bipyramidal complexes of the form [GdX1X2(Leq)5]n+ [n = 1, X = axial ligands: Cl-, -OtBu, -OArF5 or n = 3, X = tBuPO(NHiPr)2, Leq = equatorial ligand: Py, THF or H2O] with near fivefold symmetry axes along X1-Gd-X2 was investigated. The ZFS parameters were determined by fitting of room-temperature continuous wave electron paramagnetic resonance (EPR) spectra (at X-, K-, and Q-band) to a spin Hamiltonian incorporating extended Stevens operators compatible with C5 symmetry. Examination of the acquired parameters led to the conclusion that the ZFS is dominated by the B20 term and that the magnitude of B20 is almost entirely dependent on, and inversely proportional to, the donor strength of the axial ligands. Surveying the continuous shape measure and the X1-Gd-X2 angle of the complexes showed that there is some correlation between the proximity of each complex to D5h symmetry and the magnitude of the B65 parameter, but that the deformation of the X1-Gd-X2 angle is more significant than other distortions. Finally, the magnitude of B20 was found to be inversely proportional to the thermal barrier for the reversal of the magnetic moment (Ueff) of the corresponding isostructural Dy3+ complexes.

Non-equilibrium virus particle dynamics: Microsecond MD simulations of the complete Flock House virus capsid under different conditions

Flock House virus (FHV) is an animal virus and considered a model system for non-enveloped viruses. It has a small, icosahedral capsid (T=3) and a bipartite positive-sense RNA genome. We present an extensive study of the FHV capsid dynamics from all-atom molecular dynamics simulations of the complete capsid. The simulations explore different biologically relevant conditions (neutral/low pH, with/without RNA in the capsid) using the CHARMM force field. The results show that low pH destabilizes the capsid, causing radial expansion, and RNA stabilizes the capsid. The finding of low pH destabilization is biologically relevant because the capsid is exposed to low pH in the endosome, where conformational changes occur leading to genome release. We also observe structural changes at the fivefold and twofold symmetry axes that likely relate to the externalization of membrane active γ peptides through the fivefold vertex and extrusion of RNA at the twofold axis. Simulations using the Amber force field at neutral pH are also performed and display similar characteristics to the CHARMM simulations.

Peak Wavelength Mapping of Triangular Reflection in Spherical Colloidal Cluster with Icosahedral Symmetry

Spherical colloidal clusters have various types of particle arrangements. Interestingly, one type has an icosahedron symmetry, characterized by the existence of five-fold axes. When the colloidal particle size is comparable to the wavelength of light, icosahedral colloidal clusters exhibit a unique triangular reflection with a specific wavelength, owing to optical interference. In this paper, we report the results of a detailed optical study on the position-dependent peak wavelength within the triangular region. Based on the map of the peak wavelength and spectral shape, we propose a structural model of the icosahedral colloidal cluster and discuss its formation process.

First-principles study of the initial stage of Pentacene adsorption on the twofold surface of the Ag-In-Yb quasicrystal

The adsorption of the pentacene (Pn) molecule on the twofold surface of icosahedral (i)-Ag-In-Yb Quasicrystal (QC) have been studied by means of density functional theory (DFT) calculations. We calculate the adsorption energy of Pn at various positions with the molecular axis parallel to the surface and aligned along the fivefold or twofold symmetry axes directions. Pn is stabilised on a Yb trapezoid site from the acute rhombohedron units located between the rhombic triacontahedral clusters. The calculated adsorption energies for different molecular orientations can explain a recent experimental observation.

Structural characterization of a full-length heteromeric glycine receptor in multiple functional states.

Glycine receptors (GlyR) are chloride-conducting ligand-gated ion channels that provide inhibitory neuronal input, particularly in the spinal cord. Synaptic GlyR is a heteromeric protein complex composed of five homologous subunits arranged pseudo-symmetrically about the channel pore. Individual subunits come in two varieties, α and β. Here, we present the structures of full-length zebrafish α1/β GlyR solved without any fiducial marker that may alter the functional state of the protein. This was done in the presence of an antagonist (strychnine), agonist (glycine) and agonist with an allosteric modulator (glycine and ivermectin). These structures confirm other recent findings regarding the stoichiometry of heteromeric GlyR (4α:1β) and also reveal previously uncharacterized subunit-specific features in the extracellular and intracellular domain. The functional state of each structure was assessed by molecular dynamics simulations. The strychnine-bound pore is in a closed state that is mostly symmetric about the five-fold axis. The glycine structures with and without ivermectin both adopted desensitized conformations, but the ivermectin structure has significant asymmetry at the intracellular entrance to the channel pore. Consistent with this observation, ligand density near the ivermectin binding pocket was only observed at the sole α/β interface, and not at α/α interfaces as observed in past homomeric GlyR structures. Simulations show a small number of permeation events for the ivermectin-bound state, suggestive of an asymmetric mechanism for channel opening. Together, these results highlight distinct structural features of heteromeric GlyR and demonstrate the functional range of this physiologically important protein channel.

A 3D characterization of equiaxed grains induced by mediated nucleation in additively manufactured Inconel 718

In additive manufacturing of Ni-based alloy IN718, what causes Icosahedral Short-Range Order (ISRO) or iQC mediated nucleation of equiaxed grains is still not understood. In order to have a better comprehension of the microstructure formation, a more comprehensive characterization both on grain structure and chemical heterogeneities must be achieved. In this work, a scanning electron microscope equipped with a focused ion beam (FIB) allowed to perform a 3D EDS chemical analysis and EBSD orientation mapping of the volume in an equiaxed grain zone. After the 3D reconstruction of the equiaxed grains has been performed, grain-to-grain orientation analysis allowed to analyze multiple twin boundaries orientation relationships in a volume containing hundreds of grains. Chemical mapping using EDS allowed to identify TiC inclusions from which a five-fold symmetry axis seem to emerge, indicating a potential nucleation site. Such areas were analyzed in transmission electron microscopy (TEM) to investigate the different present phases. The nucleation sequence and potential origin of mediated nucleation are further discussed, opening new prospects for grain refinement in additively manufactured nickel-based alloys.

Viral Capsid Change upon Encapsulation of Double-Stranded DNA into an Infectious Hypodermal and Hematopoietic Necrosis Virus-like Particle.

In this study, we aimed to encapsulate the sizable double-stranded DNA (dsDNA, 3.9 kbp) into a small-sized infectious hypodermal and hematopoietic necrosis virus-like particle (IHHNV-VLP; T = 1) and compared the changes in capsid structure between dsDNA-filled VLP and empty VLP. Based on our encapsulation protocol, IHHNV-VLP was able to load dsDNA at an efficiency of 30-40% (w/w) into its cavity. Structural analysis revealed two subclasses of IHHNV-VLP, so-called empty and dsDNA-filled VLPs. The three-dimensional (3D) structure of the empty VLP produced in E. coli was similar to that of the empty IHHNV-VLP produced in Sf9 insect cells. The size of the dsDNA-filled VLP was slightly bigger (50 Å) than its empty VLP counterpart; however, the capsid structure was drastically altered. The capsid was about 1.5-fold thicker due to the thickening of the capsid interior, presumably from DNA-capsid interaction evident from capsid protrusions or nodules on the interior surface. In addition, the morphological changes of the capsid exterior were particularly observed in the vicinity of the five-fold axes, where the counter-clockwise twisting of the "tripod" structure at the vertex of the five-fold channel was evident, resulting in a widening of the channel's opening. Whether these capsid changes are similar to virion capsid maturation in the host cells remains to be investigated. Nevertheless, the ability of IHHNV-VLP to encapsulate the sizable dsDNA has opened up the opportunity to package a dsDNA vector that can insert exogenous genes and target susceptible shrimp cells in order to halt viral infection.

Discovery of core-shell quasicrystalline particles

Submicron-sized quasicrystalline particles were obtained in an Al-Zn-Mg-Cu alloy produced by traditional melting. These particles consist of an Al-Fe-Ni core and a Mg-Cu-Zn shell and were found to be stable and embedded randomly in the Al matrix. The diffraction patterns of these core-shell particles reveal a decagonal core and an icosahedral shell with, respectively, ten- and five-fold axes aligned. High resolution scanning transmission electron microscopy of the Mg-Cu-Zn shell confirms the five-fold symmetry atomic arrangement and the icosahedral structure. It can therefore be concluded that Fe and Ni impurities play an important role in mediating the formation of such an unusual ternary core-shell quasicrystalline particle. These findings provide some novel insights in the formation of quasicrystals in traditional industrial Al alloys.

Structures of L-BC virus and its open particle provide insight into Totivirus capsid assembly

L-BC virus persists in the budding yeast Saccharomyces cerevisiae, whereas other viruses from the family Totiviridae infect a diverse group of organisms including protists, fungi, arthropods, and vertebrates. The presence of totiviruses alters the fitness of the host organisms, for example, by maintaining the killer system in yeast or increasing the virulence of Leishmania guyanensis. Despite the importance of totiviruses for their host survival, there is limited information about Totivirus structure and assembly. Here we used cryo-electron microscopy to determine the structure of L-BC virus to a resolution of 2.9 Å. The L-BC capsid is organized with icosahedral symmetry, with each asymmetric unit composed of two copies of the capsid protein. Decamers of capsid proteins are stabilized by domain swapping of the C-termini of subunits located around icosahedral fivefold axes. We show that capsids of 9% of particles in a purified L-BC sample were open and lacked one decamer of capsid proteins. The existence of the open particles together with domain swapping within a decamer provides evidence that Totiviridae capsids assemble from the decamers of capsid proteins. Furthermore, the open particles may be assembly intermediates that are prepared for the incorporation of the virus (+) strand RNA.

Erratum for Hsieh et al., “3,4-Dicaffeoylquinic Acid from the Medicinal Plant Ilex kaushue Disrupts the Interaction between the Five-Fold Axis of Enterovirus A-71 and the Heparan Sulfate Receptor”

Erratum for Hsieh et al., “3,4-Dicaffeoylquinic Acid from the Medicinal Plant <i>Ilex kaushue</i> Disrupts the Interaction between the Five-Fold Axis of Enterovirus A-71 and the Heparan Sulfate Receptor”

3,4-Dicaffeoylquinic Acid from the Medicinal Plant Ilex kaushue Disrupts the Interaction Between the Five-Fold Axis of Enterovirus A-71 and the Heparan Sulfate Receptor

While infections by enterovirus A71 (EV-A71) are generally self-limiting, they can occasionally lead to serious neurological complications and death. No licensed therapies against EV-A71 currently exist. Using anti-virus-induced cytopathic effect assays, 3,4-dicaffeoylquinic acid (3,4-DCQA) from Ilex kaushue extracts was found to exert significant anti-EV-A71 activity, with a broad inhibitory spectrum against different EV-A71 genotypes. Time-of-drug-addition assays revealed that 3,4-DCQA affects the initial phase (entry step) of EV-A71 infection by directly targeting viral particles and disrupting viral attachment to host cells. Using resistant virus selection experiments, we found that 3,4-DCQA targets the glutamic acid residue at position 98 (E98) and the proline residue at position 246 (P246) in the 5-fold axis located within the VP1 structural protein. Recombinant viruses harboring the two mutations were resistant to 3,4-DCQA-elicited inhibition of virus attachment and penetration into human rhabdomyosarcoma (RD) cells. Finally, we showed that 3,4-DCQA specifically inhibited the attachment of EV-A71 to the host receptor heparan sulfate (HS), but not to the scavenger receptor class B member 2 (SCARB2) and P-selectin glycoprotein ligand-1 (PSGL1). Molecular docking analysis confirmed that 3,4-DCQA targets the 5-fold axis to form a stable structure with the E98 and P246 residues through noncovalent and van der Waals interactions. The targeting of E98 and P246 by 3,4-DCQA was found to be specific; accordingly, HS binding of viruses carrying the K242A or K244A mutations in the 5-fold axis was successfully inhibited by 3,4-DCQA.The clinical utility of 3,4-DCQA in the prevention or treatment of EV-A71 infections warrants further scrutiny. IMPORTANCE The canyon region and the 5-fold axis of the EV-A71 viral particle located within the VP1 protein mediate the interaction of the virus with host surface receptors. The three most extensively investigated cellular receptors for EV-A71 include SCARB2, PSGL1, and cell surface heparan sulfate. In the current study, a RD cell-based anti-cytopathic effect assay was used to investigate the potential broad spectrum inhibitory activity of 3,4-DCQA against different EV-A71 strains. Mechanistically, we demonstrate that 3,4-DCQA disrupts the interaction between the 5-fold axis of EV-A71 and its heparan sulfate receptor; however, no effect was seen on the SCARB2 or PSGL1 receptors. Taken together, our findings show that this natural product may pave the way to novel anti-EV-A71 therapeutic strategies.

Icosahedral quasicrystal enhanced nucleation in commercially pure Ni processed by selective laser melting

This work provides unambiguous evidence for the occurrence of icosahedral quasicrystal (iQC) enhanced nucleation during selective laser melting of gas atomized commercially-pure Ni powders. This solidification mechanism, which has only been recently reported in a few alloys and has to date never been observed in pure metals, consists on the solidification of grains of the primary phase on the facets of iQCs formed due to the presence of icosahedral short range order in the liquid. The occurrence of iQC enhanced nucleation has been inferred from the observation in the SLM processed pure Ni samples of an excess fraction of partially incoherent twin boundaries and of clusters of twinned grain pairs sharing common 〈110〉 five-fold symmetry axes. This work further evidences that additive manufacturing methods may constitute an invaluable tool for investigating the fundamentals of solidification and for the design of unprecedented grain boundary networks.

Recent advances in the structural biology of encapsulin bacterial nanocompartments

Large capsid-like nanocompartments called encapsulins are common in bacteria and archaea and contain cargo proteins with diverse functions. Advances in cryo-electron microscopy have enabled structure determination of many encapsulins in recent years. Here we summarize findings from recent encapsulin structures that have significant implications for their biological roles. We also compare important features such as the E-loop, cargo-peptide binding site, and the fivefold axis channel in different structures. In addition, we describe the discovery of a flavin-binding pocket within the encapsulin shell that may reveal a role for this nanocompartment in iron metabolism.

Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts.

The structures of new crystal forms of Satellite tobacco mosaic virus (STMV) are described. These belong to space groups I2, P21212 (a low-resolution form), R3 (H3) and P23. The R3 crystals are 50%/50% twinned, as are two instances of the P23 crystals. The I2 and P21212 crystals were grown from ammonium sulfate solutions, as was one crystal in space group P23, while the R3 and the other P23 crystals were grown from sodium chloride, sodium bromide and sodium nitrate. The monoclinic and orthorhombic crystals have half a virus particle as the asymmetric unit, while the rhombohedral and cubic crystals have one third of a virus particle. RNA segments organized about the icosahedral twofold axes were present in crystals grown from ammonium sulfate and sodium chloride, as in the canonical I222 crystals (PDB entry 4oq8), but were not observed in crystals grown from sodium bromide and sodium nitrate. Bromide and nitrate ions generally replaced the RNA phosphates present in the I222 crystals, including the phosphates seen on fivefold axes, and were also found at threefold vertices in both the rhombohedral and cubic forms. An additional anion was also found on the fivefold axis 5 Å from the first anion, and slightly outside the capsid in crystals grown from sodium chloride, sodium bromide and sodium nitrate, suggesting that the path along the symmetry axis might be an ion channel. The electron densities for RNA strands at individual icosahedral dyads, as well as at the amino-terminal peptides of protein subunits, exhibited a diversity of orientations, in particular the residues at the ends.

The role of conformational epitopes in the evolutionary divergence of enterovirus D68 clades: A bioinformatics-based study.

Enterovirus D68 (EV-D68), as one of the major pathogens of paediatric respiratory disease, has been widely spread in the population in recent years. As the basis of virus antigenicity, antigenic epitopes are essential to monitoring the transformation of virus antigenicity. However, there is a lack of systematic studies on the antigenic epitopes of EV-D68. In this study, a bioinformatics-based prediction algorithm for human enteroviruses was used to predict the conformational epitopes of EV-D68. The prediction results showed that the conformational epitopes of EV-D68 were clustered into three sites: site 1, site 2, and site 3. Site 1 was located in the "north rim" region of the canyon near the fivefold axis; site 2 was located in the "puff" region near the twofold axis; and site 3 consisted of two parts, one in the "knob" region on the south rim of the canyon and the other in the threefold axis region. The predicted epitopes overlapped highly with the binding regions of four reported monoclonal antibodies (mAbs), indicating that the predictions were highly reliable. Phylogenetic analysis showed that amino acid mutations in the epitopes of the VP1 BC loop, DE loop, C-terminus, and VP2 EF loop played a crucial role in the evolutionary divergence of EV-D68 clades/subclades and epidemics. This finding indicated that the VP1 BC loop, DE loop, C-terminus, and VP2 EF loop were the most important epitopes of EV-D68. Research on the epitopes of EV-D68 will contribute to outbreak surveillance and to the development of diagnostic reagents and recombinant vaccines.