2-fold Axis Research Articles

Keeping It Together: Structures, Functions, and Applications of Viral Decoration Proteins.

Decoration proteins are viral accessory gene products that adorn the surfaces of some phages and viral capsids, particularly tailed dsDNA phages. These proteins often play a “cementing” role, reinforcing capsids against accumulating internal pressure due to genome packaging, or environmental insults such as extremes of temperature or pH. Many decoration proteins serve alternative functions, including target cell recognition, participation in viral assembly, capsid size determination, or modulation of host gene expression. Examples that currently have structures characterized to high-resolution fall into five main folding motifs: β-tulip, β-tadpole, OB-fold, Ig-like, and a rare knotted α-helical fold. Most of these folding motifs have structure homologs in virus and target cell proteins, suggesting horizontal gene transfer was important in their evolution. Oligomerization states of decoration proteins range from monomers to trimers, with the latter most typical. Decoration proteins bind to a variety of loci on capsids that include icosahedral 2-, 3-, and 5-fold symmetry axes, as well as pseudo-symmetry sites. These binding sites often correspond to “weak points” on the capsid lattice. Because of their unique abilities to bind virus surfaces noncovalently, decoration proteins are increasingly exploited for technology, with uses including phage display, viral functionalization, vaccination, and improved nanoparticle design for imaging and drug delivery. These applications will undoubtedly benefit from further advances in our understanding of these versatile augmenters of viral functions.

Symmetrical arrangement of positively charged residues around the 5-fold axes of SAT type foot-and-mouth disease virus enhances cell culture of field viruses.

Field isolates of foot-and-mouth disease viruses (FMDVs) utilize integrin-mediated cell entry but many, including Southern African Territories (SAT) viruses, are difficult to adapt to BHK-21 cells, thus hampering large-scale propagation of vaccine antigen. However, FMDVs acquire the ability to bind to cell surface heparan sulphate proteoglycans, following serial cytolytic infections in cell culture, likely by the selection of rapidly replicating FMDV variants. In this study, fourteen SAT1 and SAT2 viruses, serially passaged in BHK-21 cells, were virulent in CHO-K1 cells and displayed enhanced affinity for heparan, as opposed to their low-passage counterparts. Comparative sequence analysis revealed the fixation of positively charged residues clustered close to the icosahedral 5-fold axes of the virus, at amino acid positions 83-85 in the βD-βE loop and 110-112 in the βF-βG loop of VP1 upon adaptation to cultured cells. Molecular docking simulations confirmed enhanced binding of heparan sulphate to a model of the adapted SAT1 virus, with the region around VP1 arginine 112 contributing the most to binding. Using this information, eight chimeric field strain mutant viruses were constructed with additional positive charges in repeated clusters on the virion surface. Five of these bound heparan sulphate with expanded cell tropism, which should facilitate large-scale propagation. However, only positively charged residues at position 110-112 of VP1 enhanced infectivity of BHK-21 cells. The symmetrical arrangement of even a single amino acid residue in the FMD virion is a powerful strategy enabling the virus to generate novel receptor binding and alternative host-cell interactions.

Oriented Se6 ring clusters in zeolite single crystals: Polarized Raman microscopy, optical absorption spectra and photo-induced effects

Polarized Raman and optical absorption spectra of oriented Se 6 ring clusters incorporated into free spaces of CHA, MOR and AFI zeolite single crystals are studied. The ring orientation was determined via polarization dependence of the bond-bending mode Raman activities which are high in the configuration with both incident and scattered lights polarized parallel to the ring plane. Se 6 rings seem to be compressed in CHA cavities, their original D 3d symmetry remaining preserved with the ring 3-fold axis orientation along the 3-fold axis of CHA. No symmetry distortion and less compression were found for the Se 6 rings in the AFI channels, with their 3-fold axes being oriented along the 3-fold axis of AFI. A noticeable structural distortion is found for Se 6 rings in MOR channels which are oriented by their 3-fold axes along the b -axis of MOR. Two broad peaks at 3.1–3.2 eV and 3.5–3.65 eV with rather clear polarization dependence were found in the optical absorption spectra of Se 6 rings. Photo-induced Se 6 ring fragmentation is demonstrated at illumination with the photon energies of ~1.96 eV and ~2.41 eV at the temperature of ~77 K, formation of Se 2 − (Se 3 ) and Se 8 molecules being observed in CHA and AFI, respectively. • Polarized Raman spectra of inner modes and librations of oriented Se 6 ring clusters in zeolites CHA, MOR and AFI are obtained. • The ring orientation was univocally determined via polarization dependencies of the bond-bending mode Raman activities. • The original D 3d symmetry of the Se 6 ring is preserved in CHA and AFI. While its strong structural distortion is observed in MOR.. • Two polarization-dependent peaks at 3.1–3.2 eV and 3.5–3.65 eV were found in the optical absorption spectra of the Se 6 rings. • Photo-induced Se 6 ring fragmentation at the temperature of ~77 K with the formation of Se 2 − or Se 3 in CHA-Se and formation of Se 8 in AFI-Se is demonstrated..

Symmetry breaking in the solid state of 9,10-anthracene amino acid conjugates as seen by X-ray diffraction and NMR spectroscopy

Three novel structures of 9,10-anthracene amino acid conjugates have been determined by combination of single crystal and powder X-ray diffraction measurements, pseudopotential plane wave DFT optimizations and 13C solid state NMR spectroscopy, including GIPAW calculation of the NMR parameters. All three structures show anti-conformation of amino acid side chains attached to the anthracene unit. For compounds Ant–(CO–Phe-OMe)2, (1) and Ant–(CO–Gly-Phe-OMe)2 (2), anti-conformation is in accordance with nearly centrosymmetric crystallographic structures, while for Ant–(CO–Val-OMe)2 (3), anti-conformation is in accordance with approximate 2-fold molecular axis passing through the plane of anthracene unit. Centres of inversion in 1 and 2 are approximate due to the usage of optically pure amino acids. Rotation axis in 3 is approximate due to the displacement of molecules from crystallographic 2-fold axes present in tetragonal P41212 space group, resulting in a structure more accurate described in space group P212121.

Synthesis, Structures, and Photoluminescence of Elongated Face-Centered-Cubic Ag14 Clusters Containing Lipoic Acid and Its Amide Analogue.

Three face-centered-cubic (fcc) silver clusters-namely, [Ag14(LA)2(HLA)4(PPh3)8]2- (1), [Ag14(HLA)6(PPh3)8] (2), and [Ag14(NLA)6(PPh3)8] (3)-that are coprotected by lipoic acid (or its amide derivative) and phosphine ligands have been synthesized and structurally characterized (HLA = (±)-α-lipoic acid, LA = (±)-α-lipoate, and NLA = d,l-6,8-thioctamide). These clusters possess two superatomic electrons (the Jellium model), in harmony with a bonding octahedral Ag6 core capped with 8 Ag atoms. Alternatively, the metal framework of 1-3 can be described as adopting a face-centered cubic (fcc) structure elongated along one of the 3-fold axes. The 12 S atoms from the six bioligands bridge the 12 edges of the (fcc) cube, forming a distorted icosahedron. The counterions, solvent or guest molecules play an important role in dictating the crystal lattices of the products. This is the first report of atom-precise structures of Ag-lipoic acid (or its derivatives) clusters, paving the way for further study of structure-property relationships of these bioligand protected metal nanoclusters. Photoluminescence was observed for cluster 3 with complex temperature-dependent emission patterns and efficiencies.

Structural Characterization of Cuta- and Tusavirus: Insight into Protoparvoviruses Capsid Morphology

Several members of the Protoparvovirus genus, capable of infecting humans, have been recently discovered, including cutavirus (CuV) and tusavirus (TuV). To begin the characterization of these viruses, we have used cryo-electron microscopy and image reconstruction to determine their capsid structures to ~2.9 Å resolution, and glycan array and cell-based assays to identify glycans utilized for cellular entry. Structural comparisons show that the CuV and TuV capsids share common features with other parvoviruses, including an eight-stranded anti-parallel β-barrel, depressions at the icosahedral 2-fold and surrounding the 5-fold axes, and a channel at the 5-fold axes. However, the viruses exhibit significant topological differences in their viral protein surface loops. These result in three separated 3-fold protrusions, similar to the bufaviruses also infecting humans, suggesting a host-driven structure evolution. The surface loops contain residues involved in receptor binding, cellular trafficking, and antigenic reactivity in other parvoviruses. In addition, terminal sialic acid was identified as the glycan potentially utilized by both CuV and TuV for cellular entry, with TuV showing additional recognition of poly-sialic acid and sialylated Lewis X (sLeXLeXLeX) motifs reported to be upregulated in neurotropic and cancer cells, respectively. These structures provide a platform for annotating the cellular interactions of these human pathogens.

Phage G Structure at 6.1 Å Resolution, Condensed DNA, and Host Identity Revision to a Lysinibacillus

Phage G has the largest capsid and genome of any known propagated phage. Many aspects of its structure, assembly, and replication have not been elucidated. Herein, we present the dsDNA-packed and empty phage G capsid at 6.1 and 9 Å resolution, respectively, using cryo-EM for structure determination and mass spectrometry for protein identification. The major capsid protein, gp27, is identified and found to share the HK97-fold universally conserved in all previously solved dsDNA phages. Trimers of the decoration protein, gp26, sit on the 3-fold axes and are thought to enhance the interactions of the hexameric capsomeres of gp27, for other phages encoding decoration proteins. Phage G's decoration protein is longer than what has been reported in other phages, and we suspect the extra interaction surface area helps stabilize the capsid. We identified several additional capsid proteins, including a candidate for the prohead protease responsible for processing gp27. Furthermore, cryo-EM reveals a range of partially full, condensed DNA densities that appear to have no contact with capsid shell. Three analyses confirm that the phage G host is a Lysinibacillus, and not Bacillus megaterium: identity of host proteins in our mass spectrometry analyses, genome sequence of the phage G host, and host range of phage G.

Acquired Functional Capsid Structures in Metazoan Totivirus-like dsRNA Virus

Non-enveloped icosahedral double-stranded RNA (dsRNA) viruses possess multifunctional capsids required for their proliferation. Whereas protozoan/fungal dsRNA viruses have a relatively simple capsid structure, which suffices for the intracellular phase in their life cycle, metazoan dsRNA viruses have acquired additional structural features as an adaptation for extracellular cell-to-cell transmission in multicellular hosts. Here, we present the first atomic model of a metazoan dsRNA totivirus-like virus and the structure reveals three unique structural traits: a C-terminal interlocking arm, surface projecting loops, and an obstruction at the pore on the 5-fold symmetry axis. These traits are keys to understanding the capsid functions of metazoan dsRNA viruses, such as particle stability and formation, cell entry, and endogenous intraparticle transcription of mRNA. On the basis of molecular dynamics simulations of the obstructed pore, we propose a possible mechanism of intraparticle transcription in totivirus-like viruses, which dynamically switches between open and closed states of the pore(s).

Features of structure of copper microparticles in form of truncate icosahedrons

In the present work for the first time copper icosahedral microparticles in form of truncated icosahedrons were grown. They have 5-fold axis and appearance are similar with fullerene C60. Their shape, faceting, surface morphology and unique structure were investigated. The main idea of the work was to describe transformation during the process of growth of fullerene-like copper microparticles, which have non-equilibrium heterogeneous structure, to perfect icosahedron. The perfect icosahedrons have 5-fold axis; however, they have more equilibrium crystal state. Results of electron microscopic studies of icosahedral particles are described. The obtained copper microparticles can be used as effective and low-cost low temperature catalysts.

Synthesis, crystal structure and topological features of microporous “anti-zeolite” Yb3(BO3)(OH)6∙2.1H2O, a new cubic borate with isolated BO3 groups

Abstract A new cubic borate, Yb3[BO3](OH)6⋅2.1H2O was synthesized in a multi-component hydrothermal system Yb2(CO3)3: B2O3: P2O5 = 5 : 2: 1 (T = 280 °C; P = 90–100 atm; pH = 3). The crystal structure was studied using single crystal X-ray analysis. The structure has been refined in the space group I432, possesses the unit cell parameter a = 12.2808(15) A. A microporous positively charged framework is formed by predominant Yb cations coordinated by O2−, OH− as a tetragonal antiprism, which are linked together via common edges and vertices. The extra framework BO3 triangles center narrow channels, directed along 3-fold axis, are perpendicular to them and clamped between large Yb polyhedra. The large cavities with the effective cavity width 7.7 A are filled by disordered water molecules. The crystal chemical formula could be written as (Z = 8): |(BO3)(H2O)2.1|[Yb3(OH)6]. A topological analysis was performed using the ToposPro software. The framework is characterized by the following tile sequence: [34]6[324.46.68]; the calculated structural complexity parameters are: v = 48 atoms, IG = 1.500 bits/atom, and IG,total = 72.000 bits/unit cell; the framework density is 12.96 Yb/1000 A3. The Yb-borate is similar to the tetragonal compounds with the general formula ABa12(BO3)7F4 (A = Li, Na) and LixNa1-xBa12(BO3)7F4, which are characterized by co-called “anti-zeolite” frameworks, formed by Ba2+ cations. The excess of water in the structure of the new borate compound Yb3[BO3](OH)6⋅2.1H2O is determined by its zeolitic nature and by hydrothermal growth conditions.

Synthesis, Crystal Structure, and Nonlinear Optical Properties of Zn(II) Complex with 4,4',4''-Tri-tert-Butyl-2,2':6',2''-Terpyridine: A Dual Exploration

The metal complexes are getting immense importance as hi-tech functional materials. In the present investigation, a new Zn(II) complex [Zn(C27H35N3)Cl2] (1) has been synthesized by using 4,4′,4″-tri-tert-butyl-2,2′:6′,2″-terpyridine ligand. The synthesized compound 1 is characterized by X-ray crystallography, IR spectroscopy as well as elemental analysis. The X-rays structure revealed that compound 1 crystallizes in trigonal space group P3221 in which Zn(II) atom is penta coordinated having highly distorted trigonal bipyramidal geometry. The compound 1 has a 2-fold rotational axis parallel to the b axis, which is passing through two opposite N and C atoms in the central pyridine ring, and the Zn atom. Moreover, quantum computational study has been performed to get insights into the optical and nonlinear optical response properties of compound 1. The geometrical structure of compound 1 has been optimized with M06-2X functional and LANL2DZ/6-311G** basis set and it shows good resemblance with the experimental coordinates. The linear polarizabilities including isotropic (αiso) and anisotropic (αaniso) polarizability amplitudes are found to be 69.44 × 10−24 and 34.99 × 10−24 esu, respectively. Similarly, the NLO polarizability (❬γ❭) amplitude for compound 1 is found to be 104.19 × 10–36 esu at M06-2X method, which is ~5 times greater than the p-NA (a model NLO molecule). Additionally, frontier molecular orbitals, molecular electrostatic potentials and Hirshfeld analysis are used to explore the structure-property relationship of compound 1. Thus, the indigenously synthesized compound 1 might be a reasonable candidate for its possible applications as optical and NLO material.

Use of a Glycan Library Reveals a New Model for Enteric Virus Oligosaccharide Binding and Virion Stabilization.

Enteric viruses infect the gastrointestinal tract, and bacteria can promote replication and transmission of several enteric viruses. Viruses can be inactivated by exposure to heat or bleach, but poliovirus, coxsackievirus B3, and reovirus can be stabilized by bacteria or bacterial polysaccharides, limiting inactivation and aiding transmission. We previously demonstrated that certain N-acetylglucosamine (GlcNAc)-containing polysaccharides can stabilize poliovirus. However, the detailed virus-glycan binding specificity and glycan chain length requirements, and thus the mechanism of virion stabilization, have been unclear. A previous limitation was our lack of defined-length glycans to probe mechanisms and consequences of virus-glycan interactions. Here, we generated a panel of polysaccharides and oligosaccharides to determine the properties required for binding and stabilization of poliovirus. Poliovirus virions are nonenveloped icosahedral 30-nm particles with 60 copies of each of four capsid proteins, VP1 to VP4. VP1 surrounds the 5-fold axis, and our past work indicates that this region likely contains the glycan binding site. We found that relatively short GlcNAc oligosaccharides, such as a six-unit GlcNAc oligomer, can bind poliovirus but fail to enhance virion stability. Virion stabilization required binding of long GlcNAc polymers of greater than 20 units. Our data suggest a model where GlcNAc polymers of greater than 20 units bind and bridge adjacent 5-fold axes, thus aiding capsid rigidity and stability. This study provides a deeper understanding of enteric virus-bacterial glycan interactions, which are important for virion environmental stability and transmission.IMPORTANCE Enteric viruses are transmitted through the fecal-oral route, but how enteric viruses survive in the environment is unclear. Previously, we found that bacterial polysaccharides enhance poliovirus stability against heat or bleach inactivation, but the specific molecular requirements have been unknown. Here, we showed that certain short-chain oligosaccharides can bind to poliovirus but do not increase virion stability. Long-chain polysaccharides bind and may bridge adjacent sites on the viral surface, thus increasing capsid rigidity and stability. This work defines the unique interactions of poliovirus and glycans, which provides insight into virion environmental stability and transmission.

Neutralization Mechanism of a Monoclonal Antibody Targeting a Porcine Circovirus Type 2 Cap Protein Conformational Epitope.

Porcine circovirus type 2 (PCV2) is an important pathogen in swine herds, and its infection of pigs has caused severe economic losses to the pig industry worldwide. The capsid protein of PCV2 is the only structural protein that is associated with PCV2 infection and immunity. Here, we report a neutralizing monoclonal antibody (MAb), MAb 3A5, that binds to intact PCV2 virions of the PCV2a, PCV2b, and PCV2d genotypes. MAb 3A5 neutralized PCV2 by blocking viral attachment to PK15 cells. To further explore the neutralization mechanism, we resolved the structure of the PCV2 virion in complex with MAb 3A5 Fab fragments by using cryo-electron microscopy single-particle analysis. The binding sites were located at the topmost edges around 5-fold icosahedral symmetry axes, with each footprint covering amino acids from two adjacent capsid proteins. Most of the epitope residues (15/18 residues) were conserved among 2,273 PCV2 strains. Mutations of some amino acids within the epitope had significant effects on the neutralizing activity of MAb 3A5. This study reveals the molecular and structural bases of this PCV2-neutralizing antibody and provides new and important information for vaccine design and therapeutic antibody development against PCV2 infections.IMPORTANCE PCV2 is associated with several clinical manifestations collectively known as PCV2-associated diseases (PCVADs). Neutralizing antibodies play a crucial role in the prevention of PCVADs. We demonstrated previously that a MAb, MAb 3A5, neutralizes the PCV2a, PCV2b, and PCV2d genotypes with different degrees of efficiency, but the underlying mechanism remains elusive. Here, we report the neutralization mechanism of this MAb and the structure of the PCV2 virion in complex with MAb 3A5 Fabs, showing a binding mode in which one Fab interacted with more than two loops from two adjacent capsid proteins. This binding mode has not been observed previously for PCV2-neutralizing antibodies. Our work provides new and important information for vaccine design and therapeutic antibody development against PCV2 infections.

Structural Insight into African Swine Fever Virus dUTPase Reveals a Novel Folding Pattern in the dUTPase Family.

The African swine fever virus (ASFV) is the deadly pathogen of African swine fever (ASF) that induces high mortality, approaching 100% in domestic pigs, causes enormous losses to the global pig industry, and threatens food security. Currently, there is no effective treatment or preventive countermeasure. dUTPases (deoxyuridine 5'-triphosphate pyrophosphatases) are ubiquitous enzymes that are essential for the hydrolysis of dUTP and prevent the misincorporation of dUTP into newly synthesized DNA. Here, we present the crystal structures of the ASFV dUTPase in complex with the product dUMP and cofactor Mg2+ at a resolution of 2.2 Å. We observed that a unique "turning point" at G125 plays an unexpected critical role in the swapping region of the C-terminal segment, which is further stabilized by the interactions of the last C-terminal β strand with the β1 and β2 strands, thereby positioning the catalytic motif 5 into the active site of its own subunit instead of into a third subunit. Therefore, the ASFV dUTPase employs a novel two-subunit active site that is different than the classic trimeric dUTPase active site, which is composed of all three subunits. Meanwhile, further results confirmed that the configuration of motifs 1 to 5 has high structural homology with and a catalytic mechanism similar to that of the known trimeric dUTPases. In general, our study expands the information not only on the structural diversity of the conserved dUTPase family but also on the details needed to utilize this dUTPase as a novel target in the treatment of ASF.IMPORTANCE African swine fever virus (AFSV), a large enveloped double-stranded DNA virus, causes a deadly infection in domestic pigs. In addition to Africa, Europe, and South America, countries in Asia, such as China, Vietnam, and Mongolia, have suffered the hazards posed by ASFV outbreaks in recent years. Until now, there has been no vaccine for protection from ASFV infection or effective treatments to cure ASF. Here, we solved the crystal structure of the ASFV dUTPase-dUMP-Mg2+ complex. The ASFV dUTPase displays a noncanonical folding pattern that differs from that of the classic homotrimeric dUTPase, in which the active site is composed of two subunits. In addition, several nonconserved residues within the 3-fold axis channel play a vital role in ASFV dUTPase homotrimer stability. Our finding on these unique structural features of the ASFV dUTPase could be explored for the design of potential specific inhibitors that target this unique enzyme.

Near-Atomic-Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus: Evolutionary Divergence at the Icosahedral Three-Fold Axes.

Members of the Tombusviridae family have highly similar structures, and yet there are important differences among them in host, transmission, and capsid stabilities. Viruses in the Tombusviridae family have single-stranded RNA (ssRNA) genomes with T=3 icosahedral protein shells with a maximum diameter of ∼340 Å. Each capsid protein is comprised of three domains: R (RNA binding), S (shell), and P (protruding). Between the R domain and S domain is the "arm" region that studies have shown to play a critical role in assembly. To better understand how the details of structural differences and similarities influence the Tombusviridae viral life cycles, the structures of cucumber leaf spot virus (CLSV; genus Aureusvirus) and red clover necrotic mosaic virus (RCNMV; genus Dianthovirus) were determined to resolutions of 3.2 Å and 2.9 Å, respectively, with cryo-electron microscopy and image reconstruction methods. While the shell domains had homologous structures, the stabilizing interactions at the icosahedral 3-fold axes and the R domains differed greatly. The heterogeneity in the R domains among the members of the Tombusviridae family is likely correlated with differences in the sizes and characteristics of the corresponding genomes. We propose that the changes in the R domain/RNA interactions evolved different arm domain interactions at the β-annuli. For example, RCNMV has the largest genome and it appears to have created the necessary space in the capsid by evolving the shortest R domain. The resulting loss in RNA/R domain interactions may have been compensated for by increased intersubunit β-strand interactions at the icosahedral 3-fold axes. Therefore, the R and arm domains may have coevolved to package different genomes within the conserved and rigid shell.IMPORTANCE Members of the Tombusviridae family have nearly identical shells, and yet they package genomes that range from 4.6 kb (monopartite) to 5.3 kb (bipartite) in size. To understand how this genome flexibility occurs within a rigidly conserved shell, we determined the high-resolution cryo-electron microscopy (cryo-EM) structures of cucumber leaf spot virus and red clover necrotic mosaic virus. In response to genomic size differences, it appears that the ssRNA binding (R) domain of the capsid diverged evolutionarily in order to recognize the different genomes. The next region, the "arm," seems to have also coevolved with the R domain to allow particle assembly via interactions at the icosahedral 3-fold axes. In addition, there are differences at the icosahedral 3-fold axes with regard to metal binding that are likely important for transmission and the viral life cycle.

A Unique Protein Self-Assembling Nanoparticle with Significant Advantages in Vaccine Development and Production

Nanoparticles are playing an increasingly powerful role in vaccine development. Here, we report the repurposing of nonstructural proteins 10 and 11 (hereafter NSP10) from the replicase polyprotein 1a (pp1a) of the human SARS coronavirus (severe acute respiratory syndrome) as a novel self-assembling platform for bioengineered nanoparticles for a variety of applications including vaccines. NSP10 represents a 152 amino acid, 17 kD zinc finger transcription/regulatory protein which self-assembles to form a spherical 84 Å diameter nanoparticle with dodecahedral trigonal 32 point symmetry. As a self-assembling nanoparticle, NSP10 possesses numerous advantages in vaccine development and antigen display, including the unusual particle surface disposition of both the N- and C-termini. Each set of N- or C-termini is spatially disposed in a tetrahedral arrangement and positioned at optimal distances from the 3-fold axes (8-10 Å) to nucleate and stabilize the correct folding of complex helical or fibrous trimeric receptors, such as those responsible for viral tropism and cell infection. An application example in the exploratory development of a therapeutic vaccine for idiopathic pulmonary fibrosis (IPF), including preliminary analysis and immunogenic properties, is presented. The use of this system could accelerate the discovery and development of vaccines for a number of human, livestock, and veterinary applications.

A complex between the Zika virion and the Fab of a broadly cross-reactive neutralizing monoclonal antibody revealed by cryo-EM and single particle analysis at 4.1 Å resolution

Zika virus (ZIKV) recently emerged as a major public health concern because it can cause fetal microcephaly and neurological disease such as the Guillain-Barré syndrome. A particularly potent class of broadly neutralizing antibodies (nAbs) targets a quaternary epitope located at the interface of two envelope proteins monomers, exposed at the surface of the mature virion. This “E-dimer-dependent epitope” (EDE), comprises the fusion loop of one monomer at the tip of domain II of E and a portion of the domains I and III of the adjacent monomer. Since this epitope largely overlaps with the binding site of the precursor membrane protein (prM) during Zika virion maturation, its molecular surface is evolutionary conserved in flaviviruses such as Dengue and Zika viruses, and can elicit antibodies that broadly neutralize various ZIKV strains. Here, we present a cryo-EM reconstruction at 4.1 Å resolution of the virion bound to the antigen binding fragment (Fab) of an antibody that targets this mutationally-constrained quaternary epitope. The Fab incompletely covers the surface of the virion as it does not bind next to its 5-fold icosahedral axes. The structure reveals details of the binding mode of this potent neutralizing class of antibodies and can inform the design of immunogens and vaccines targeting this conserved epitope.

Icosahedral quasicrystals and their cubic approximants in the Cd-Mg-RE (RE = Y, Sm, Gd, Tb, Dy, Ho, Er, Tm) systems

The formation and stability of icosahedral quasicrystals and their cubic approximants in the Cd-Mg-RE (RE = Y, Sm, Gd, Tb, Dy, Ho, Er, Tm) systems are studied in detail, with a focus on the effects of Mg substitution as well as the dependence on temperature and RE species. The results show that the compositional region of the icosahedral phase in the ternary phase diagram shrinks gradually as the RE element becomes smaller in atomic size. This phenomenon is correlated with the geometric ‘stability’ of a so-called Tsai-type cluster described as a packing of spheres that represent the atomic radii of the constituent elements. Moreover, the icosahedral quasicrystals are found to be stabilized at lower RE concentrations (12–13.5 at.%) and temperatures (T < 773 K) compared to their cubic approximants, contrary to earlier findings for the Cd-Mg-Yb system. Single grains of the icosahedral, 2/1 and 1/1 cubic approximant phases with, respectively, rhombic triacontahedron, octahedron and rhombic dodecahedron morphologies ranging ≈1.5–2.5 mm in diameter are further synthesized using a self-flux method. It is confirmed that the bounding facets of the single grains are {111} and {110} for the 2/1 and 1/1 cubic approximants, respectively, through orientation analysis using electron backscatter diffraction. Finally, microstructures involving the Cd-Mg-RE icosahedral quasicrystal and Cd-Mg hexagonal solid solution are analysed to show parallel alignment of 2-fold rotational axes of the former with the 6-fold and 2-fold rotational axes of the latter. This orientation relationship is further discussed in terms of the coincidence of interplanar spacings between the two phases.

Isovalent and aliovalent cation substitutions in the anion sublattice of whitlockite-type ferroelectrics Ca9RE(VO4)7 with RE =Y and Yb

A solid state route was used for the preparation of whitlockite-type solid solutions Ca9Y(NbO4)x(VO4)7–x and Ca9+0.5xYb (GeO4)x(VO4)7–х in both powder and ceramic forms. The complex of methods, including synchrotron powder diffraction, were applied for the characterization of the first-time obtained compounds. The limits of the anionic substitution were found up to х = 0.28 (Nb) and 0.35 (Ge). The synthesized solid solutions show ferroelectric properties. The Curie temperatures Tc were determined and gradually rise with x. The increase of Tc correlates with the enlargement of tetrahedral units upon Nb5+ or Ge4+ substitutions for V5+ cations. The intensity of optical second harmonic generation (SHG) induced by a Nd:YAG laser depends non-monotonically on the grain size in powder Ca9Y(NbO4)x(VO4)7–x samples, marking the length of the phase matching lc = 15 μm for x = 0.28 in comparison with lc = 9.14 μm in Ca9Y(VO4)7. Manifold increase in the SHG intensity in both solid solutions is partly related to the appearance of more polarizable Nb5+ and Ge4+ cations in the E1O4 tetrahedra on the 3-fold axis, resulting in an enlarged birefringence of the materials. The photoluminescence study of the Ca9+0.5xYb(GeO4)x(VO4)7–х reveals the same environment of the Yb3+ ions all alone the solid solution. The intensity of the luminescence rises with germanium substitution for vanadium about 2 times.

Antiangiogenic Vascular Endothelial Growth Factor-Blocking Peptides Displayed on the Capsid of an Infectious Oncolytic Parvovirus: Assembly and Immune Interactions.

As many tumor cells synthetize vascular endothelial growth factors (VEGF) that promote neo-vascularization and metastasis, frontline cancer therapies often administer anti-VEGF (α-VEGF) antibodies. To target the oncolytic parvovirus minute virus of mice (MVM) to the tumor vasculature, we studied the functional tolerance, evasion of neutralization, and induction of α-VEGF antibodies of chimeric viruses in which the footprint of a neutralizing monoclonal antibody within the 3-fold capsid spike was replaced by VEGF-blocking peptides: P6L (PQPRPL) and A7R (ATWLPPR). Both peptides allowed viral genome replication and nuclear translocation of chimeric capsid subunits. MVM-P6L efficiently propagated in culture, exposing the heterologous peptide on the capsid surface, and evaded neutralization by the anti-spike monoclonal antibody. In contrast, MVM-A7R yielded low infectious titers and was poorly recognized by an α-A7R monoclonal antibody. MVM-A7R showed a deficient assembly pattern, suggesting that A7R impaired a transitional configuration that the subunits must undergo in the 3-fold axis to close up the capsid shell. The MVM-A7R chimeric virus consistently evolved in culture into a mutant carrying the P6Q amino acid substitution within the A7R sequence, which restored normal capsid assembly and infectivity. Consistent with this finding, anti-native VEGF antibodies were induced in mice by a single injection of MVM-A7R empty capsids, but not by MVM-A7R virions. This fundamental study provides insights to endow an infectious parvovirus with immune antineovascularization and evasion capacities by replacing an antibody footprint in the capsid 3-fold axis with VEGF-blocking peptides, and it also illustrates the evolutionary capacity of single-stranded DNA (ssDNA) viruses to overcome engineered capsid structural restrictions.IMPORTANCE Targeting the VEGF signaling required for neovascularization by vaccination with chimeric capsids of oncolytic viruses may boost therapy for solid tumors. VEGF-blocking peptides (VEbp) engineered in the capsid 3-fold axis endowed the infectious parvovirus MVM with the ability to induce α-VEGF antibodies without adjuvant and to evade neutralization by MVM-specific antibodies. However, these properties may be compromised by structural restraints that the capsid imposes on the peptide configuration and by misassembly caused by the heterologous peptides. Significantly, chimeric MVM-VEbp resolved the structural restrictions by selecting mutations within the engineered peptides that restored efficient capsid assembly. These data show the promise of antineovascularization vaccines using chimeric VEbp-icosahedral capsids of oncolytic viruses but also raise safety concerns regarding the genetic stability of manipulated infectious parvoviruses in cancer and gene therapies.