Icosahedral Symmetry Research Articles

Atomic structure of the predominant GII.4 human norovirus capsid reveals novel stability and plasticity

Human noroviruses (HuNoVs) cause sporadic and epidemic viral gastroenteritis worldwide. The GII.4 variants are responsible for most HuNoV infections, and GII.4 virus-like particles (VLPs) are being used in vaccine development. The atomic structure of the GII.4 capsid in the native T = 3 state has not been determined. Here we present the GII.4 VLP structure with T = 3 symmetry determined using X-ray crystallography and cryo-EM at 3.0 Å and 3.8 Å resolution, respectively, which reveals unanticipated novel features. A novel aspect in the crystal structure determined without imposing icosahedral symmetry is the remarkable adaptability of the capsid protein VP1 driven by the flexible hinge between the shell and the protruding domains. In both crystal and cryo-EM structures, VP1 adopts a stable conformation with the protruding domain resting on the shell domain, in contrast to the ‘rising’ conformation observed in recent cryo-EM structures of other GII.4 VLPs. Our studies further revealed that the resting state of VP1 dimer is stabilized by a divalent ion, and chelation using EDTA increases capsid diameter, exposing new hydrophobic and antigenic sites and suggesting a transition to the rising conformation. These novel insights into GII.4 capsid structure, stability, and antigen presentation may be useful for ongoing vaccine development.

Cryo-EM Structure of a Kinetically Trapped Dodecameric Portal Protein from the Pseudomonas-phage PaP3

Portal proteins are dodecameric assemblies that occupy a unique 5-fold vertex of the icosahedral capsid of tailed bacteriophages and herpesviruses. The portal vertex interrupts the icosahedral symmetry, and in vivo, its assembly and incorporation in procapsid are controlled by the scaffolding protein. Ectopically expressed portal oligomers are polymorphic in solution, and portal rings built by a different number of subunits have been documented in the literature. In this paper, we describe the cryo-EM structure of the portal protein from the Pseudomonas-phage PaP3, which we determined at 3.4 Å resolution. Structural analysis revealed a dodecamer with helical rather than rotational symmetry, which we hypothesize is kinetically trapped. The helical assembly was stabilized by local mispairing of portal subunits caused by the slippage of crown and barrel helices that move like a lever with respect to the portal body. Removing the C-terminal barrel promoted assembly of undecameric and dodecameric rings with quasi-rotational symmetry, suggesting that the barrel contributes to subunits mispairing. However, ΔC-portal rings were intrinsically asymmetric, with most particles having one open portal subunit interface. Together, these data expand the structural repertoire of viral portal proteins to Pseudomonas-phages and shed light on the unexpected plasticity of the portal protein quaternary structure.

The interaction of dengue virus capsid protein with negatively charged interfaces drives the in vitro assembly of nucleocapsid-like particles.

Dengue virus (DENV) causes a major arthropod-borne viral disease, with 2.5 billion people living in risk areas. DENV consists in a 50 nm-diameter enveloped particle in which the surface proteins are arranged with icosahedral symmetry, while information about nucleocapsid (NC) structural organization is lacking. DENV NC is composed of the viral genome, a positive-sense single-stranded RNA, packaged by the capsid (C) protein. Here, we established the conditions for a reproducible in vitro assembly of DENV nucleocapsid-like particles (NCLPs) using recombinant DENVC. We analyzed NCLP formation in the absence or presence of oligonucleotides in solution using small angle X-ray scattering, Rayleigh light scattering as well as fluorescence anisotropy, and characterized particle structural properties using atomic force and transmission electron microscopy imaging. The experiments in solution comparing 2-, 5- and 25-mer oligonucleotides established that 2-mer is too small and 5-mer is sufficient for the formation of NCLPs. The assembly process was concentration-dependent and showed a saturation profile, with a stoichiometry of 1:1 (DENVC:oligonucleotide) molar ratio, suggesting an equilibrium involving DENVC dimer and an organized structure compatible with NCLPs. Imaging methods proved that the decrease in concentration to sub-nanomolar concentrations of DENVC allows the formation of regular spherical NCLPs after protein deposition on mica or carbon surfaces, in the presence as well as in the absence of oligonucleotides, in this latter case being surface driven. Altogether, the results suggest that in vitro assembly of DENV NCLPs depends on DENVC charge neutralization, which must be a very coordinated process to avoid unspecific aggregation. Our hypothesis is that a specific highly positive spot in DENVC α4-α4’ is the main DENVC-RNA binding site, which is required to be firstly neutralized to allow NC formation.

Microstructure of die-cast alloys Mg–Zn–Al(–Ca): a study by electron microscopy and small-angle neutron scattering

AbstractThe microstructure of a magnesium die-cast alloy with 8 wt.% Zn and 5 wt.% Al (ZA85) and of two alloy modifications with 0.3 and 0.9 wt.% Ca (ZACa8503 and ZACa8509) are compared. Optical, scanning electron and transmission electron microscopy (TEM) were used to study the microstructure in as-cast and annealed conditions. Small-angle neutron scattering (SANS) measurements were carried out to characterize the early stages of the precipitation process. The die-cast microstructure of ZA85, ZACa8503 and ZACa8509 consists of dendritic α-Mg grains and coarse intermetallic grain-boundary phases. In the Ca-free ZA85 alloy, grain boundaries are decorated with a quasi-crystalline phase with icosahedral point-group symmetry (I phase), a metastable modification of the equilibriumτphase (Mg32(Al, Zn)49). At the grain boundaries of the Ca-containing ZA85 alloys, small amounts of the stable cubicτphase Mg32(Al, Zn, Ca)49as well as Al2(Ca, Zn) phase, were detected in addition to the I phase. In the as-cast condition, regions supersaturated with Al and Zn were found to surround the α-Mg grains and to becomeτphase precipitation sites during high-temperature annealing in all alloys investigated. TEM and SANS measurements revealed no influence of Ca on the size distribution and the coarsening rate of the precipitates, which are formed by a continuous precipitation process.

Monitoring the hepatitis B viral (HBV) capsid assembly by charge transfer spectroscopy

HBV virions are double-shelled particles, 40–42 nm in diameter containing a viral nucleocapsid, or the HBV core which is an ordered assembly of stable homo-dimeric HBV Core protein (Cp). Both the full-length Cp containing 183 residues as well as the first-149 residues fragment, Cp149 can assemble spontaneously in vitro into capsids triggered by high ionic strength (0.2-0.5M NaCl) into 120 Cp dimers in an icosahedral symmetry (T=4) or into 90 Cp dimers with (T=3) icosahedral symmetry. Both the Cp149/Cp183 capsids and their assembly-disassembly is generally studied by Size Exclusion Chromatography, Light Scattering, Electron microscopy, Atomic Force Microscopy and other high-end labour-intensive techniques.

​Isolation and Identification of Novel Staphylococcus Phage as a Novel Therapeutic Agent from Sewage of Livestock Farms

Background: Bacteriophages are viruses that infect bacteria. They are obligate intracellular infective agents requiring specific bacterial organism as a host cell for their replication. They are most widely distributed and diverse entities in the biosphere and ubiquitously present in all reservoirs populated by bacterial hosts, such as soil and the intestine of animals. Bacteriophages are very specific in nature selectively replicate in particular bacteria. Methods: In present study we have isolated the bacteriophages from sewage of various livestock farms. Sewage samples (n=150) were collected from different depths of the sewage collection tank from different species viz. cow, buffalo, goat and pig. All the samples were subjected primarily to isolation bacteriophage against S. aureus. Recovered bacteriophages were identified with transmission electron microscopy (TM). Result: Total of twenty seven sewage samples were showing plaque formation by producing lytic activity against S. aureus in double agar overlay method. The recovery percentage of bacteriophages was maximum from cattle farm sewage (30%), followed by buffalo farm sewage (20%) and pig farm sewage (17.50%). The result indicated that recovered Bacteriophage had icosahedral symmetry and head size 52.20 nm with 109 nm tail. Bacteriophage selectively infected S. aureus with a narrow host range. Results indicated that the recovered isolates of bacteriophage remained viable at 50°C for one and two min and no viable survivors were seen at the 5 min exposure. They remained viable at 60°C for 1 min only and did not show viability for 2 and 5 min exposure at 60°C. None of the bacteriophages survived at 70°C for 1, 2 and 5 min. Bacteriophage isolates were completely inactivated below pH 3 and above 11; they remained viable only in pH range of 5 to 9.

Optical Characterization of Large Icosahedral Colloidal Clusters

AbstractColloidal particles form a face‐centered‐cubic (FCC) lattice on crystallization; however, recent studies have indicated that the cluster with the icosahedral symmetry can be formed under spherical confinement. The icosahedral cluster appears only when the number of constituent particles is small because the FCC lattice is favored thermodynamically for a bulk colloidal crystal. This paper reports the observation of a large icosahedral colloidal cluster comprising ≈4.9 × 105 colloidal particles, which is considerably larger than the previously reported number. This large icosahedral cluster clearly exhibits the triangular reflection pattern that corresponds to one face of the icosahedron. Further, an oblique illumination with sample rotation is found to be an effective method to characterize the icosahedral cluster optically. In this study, larger colloidal particles are used than those in previous studies. It is hypothesized that slow reconfiguration during the evaporation process can result in the formation of a large icosahedral cluster due to the large particle size.

Terahertz spectroscopy of the helium endofullerene He@C60.

We studied the quantized translational motion of single He atoms encapsulated in molecular cages by terahertz absorption. The temperature dependence of the THz absorption spectra of 3He@C60 and 4He@C60 crystal powder samples was measured between 5 and 220 K. At 5 K there is an absorption line at 96.8 cm-1 (2.90 THz) in 3He@C60 and at 81.4 cm (2.44 THz) in 4He@C60, while additional absorption lines appear at higher temperature. An anharmonic spherical oscillator model with a displacement-induced dipole moment was used to model the absorption spectra. Potential energy terms with powers of two, four and six and induced dipole moment terms with powers one and three in the helium atom displacement from the fullerene cage center were sufficient to describe the experimental results. Excellent agreement is found between potential energy functions derived from measurements on the 3He and 4He isotopes. One absorption line corresponds to a three-quantum transition in 4He@C60, allowed by the anharmonicity of the potential function and by the non-linearity of the dipole moment in He atom displacement. The potential energy function of icosahedral symmetry does not explain the fine structure observed in the low temperature spectra.

How One can Repair Non-integrable Kahan Discretizations. II. A Planar System with Invariant Curves of Degree 6

We find a novel one-parameter family of integrable quadratic Cremona maps of the plane preserving a pencil of curves of degree 6 and of genus 1. They turn out to serve as Kahan-type discretizations of a novel family of quadratic vector fields possessing a polynomial integral of degree 6 whose level curves are of genus 1, as well. These vector fields are non-homogeneous generalizations of reduced Nahm systems for magnetic monopoles with icosahedral symmetry, introduced by Hitchin, Manton and Murray. The straightforward Kahan discretization of these novel non-homogeneous systems is non-integrable. However, this drawback is repaired by introducing adjustments of order O(epsilon ^2) in the coefficients of the discretization, where epsilon is the stepsize.

Crystal structure of the potato leafroll virus coat protein and implications for viral assembly

Luteoviruses, poleroviruses, and enamoviruses are insect-transmitted, agricultural pathogens that infect a wide array of plants, including staple food crops. Previous cryo-electron microscopy studies of virus-like particles show that luteovirid viral capsids are built from a structural coat protein that organizes with T = 3 icosahedral symmetry. Here, we present the crystal structure of a truncated version of the coat protein monomer from potato leafroll virus at 1.80-Å resolution. In the crystal lattice, monomers pack into flat sheets that preserve the two-fold and three-fold axes of icosahedral symmetry and show minimal structural deviations when compared to the full-length subunits of the assembled virus-like particle. These observations have important implications in viral assembly and maturation and suggest that the CP N-terminus and its interactions with RNA play an important role in generating capsid curvature.

Experimental Observation of Long-Range Magnetic Order in Icosahedral Quasicrystals.

Quasicrystals (QCs), first discovered in 1984, generally do not exhibit long-range magnetic order. Here, we report on long-range magnetic order in the real icosahedral quasicrystals (i QCs) Au–Ga–Gd and Au–Ga–Tb. The Au65Ga20Gd15i QC exhibits a ferromagnetic transition at TC = 23 K, manifested as a sharp anomaly in both magnetic susceptibility and specific heat measurements, along with an appearance of magnetic Bragg peak below TC. This is the first observation of long-range magnetic order in a real quasicrystal, in contrast to the spin-glass-like behaviors observed for the other magnetic quasicrystals found to date. Moreover, when Gd is replaced by Tb, i.e., for the Au65Ga20Tb15i QC, a ferromagnetic behavior is still retained with TC = 16 K. Although the sharp anomaly in the specific heat observed for the Au65Ga20Gd15i QC becomes broadened upon Tb substitution, neutron diffraction experiments clearly show marked development of magnetic Bragg peaks just below TC, indicating long-range magnetic order for the Au65Ga20Tb15i QC also. Our findings can contribute to the further investigation of exotic magnetic orders formed on real quasiperiodic lattices with unprecedented highest global symmetry, i.e., icosahedral symmetry.

Atomic structure of liquid refractory Nb5Si3 intermetallic compound alloy based upon deep neural network potential

The knowledge of atomic structure for liquids, especially for liquid alloys with complex crystal structure and high liquidus temperatures, remains poorly understood. In this work, we have extended the development of deep neural network (DNN) potential for liquid Nb5Si3. The DNN potential captures the structural features of liquid alloys compared with ab initio results. The chemical short-range order parameter suggests that there exists strong affinity between Nb and Si atoms. The dynamic property was investigated, and the diffusion coefficient obeys the Arrhenius relationship. The atomic structure has been subsequently explored for normal and undercooled liquid Nb5Si3. Large amounts of fivefold symmetry Honeycutt–Andersen pairs have been identified in liquid Nb5Si3. However, due to the violent thermal motion in a high-temperature Nb5Si3 melt, icosahedral symmetry and distorted icosahedrons (ICOs) account for little proportion according to Voronoi polyhedron (VP) analysis. The effect of thermal motion on VPs has been discussed. Except from the well documented ⟨0,2,8,2⟩ and ⟨0,1,10,2⟩ distorted ICOs, six more quasi-ICOs (⟨0,1,9,3⟩, ⟨0,2,8,1⟩, ⟨0,2,8,4⟩, ⟨0,2,8,5⟩, ⟨0,1,10,3⟩, and ⟨0,1,10,4⟩) have been proven to deform from ICOs at high temperatures. The local environment motif obtained by the atomic cluster alignment method demonstrates the existence of dominant distorted ICOs. At last, the atomic structure during melting process is discussed by VP analysis. It is found that ⟨0,2,8,1⟩, ⟨0,2,8,2⟩, ⟨0,2,8,5⟩, and ⟨0,1,10,4⟩ prefer to form at the beginning of the melting but rapidly reduce when it is fully melted.

Canine parvovirus: A review

Canine parvovirus (CPV) is a non-enveloped and single-stranded DNA virus. This virus is belonging to parvoviridae family that necessitates quickly dividing cells to replicate. On the other hand, it is extremely hardy, withstanding many common disinfectants and staying alive for months to years in ground surface or on fomites. This virion is an icosahedral symmetry. It has rough surface and form a triangular units. The parvoviruses have two sizes of viral proteins: small (VP2–5) and large (VP1). This virus is classified into three strains that widely recognized: CPV2a, CPV2b and CPV2c. It is extremely contagious and therefore is distributed from canine to canine via fecal oral contact. It has been reported worldwide. Sources of stress includes early weaning, overcrowding, and parasite load. On the other hand, lacking of the active or passive immunity, geographic area, and the incidence of other pathogens are all related to the development of clinical parvovirus disease. Puppies have been identified to have a more severe case of the disease than older dogs. There are two clinical forms: gastro-enteritis and myocarditis. The gastroenteritis form is general in dogs, while the myocarditis form is public in puppies. The symptoms of the disease include fever, leucopenia, anorexia, vomiting, diarrhea, dehydration. This disease was primarily controlled through hygienic measures and vaccination. The interference of maternal antibodies is thought to be a main reason of CPV immunization failures in puppies. The viral diagnosis is confirmed using different laboratory methods such as direct and indirect examination. The direct methods include viral isolation, detection of viral morphology, detection of viral antigen and detection of viral genome. As well as the indirect methods include detection the specific antibodies against virus.

Multiple nanocages of a cyanophage small heat shock protein with icosahedral and octahedral symmetries

The structures of a cyanophage small heat shock protein (sHSP) were determined as octahedrons of 24-mers and 48-mers and as icosahedrons of 60-mers. An N-terminal deletion construct of an 18 kDa sHSP of Synechococcus sp. phage S-ShM2 crystallized as a 24-mer and its structure was determined at a resolution of 7 Å. The negative stain electron microscopy (EM) images showed that the full-length protein is a mixture of a major population of larger and a minor population of smaller cage-like particles. Their structures have been determined by electron cryomicroscopy 3D image reconstruction at a resolution of 8 Å. The larger particles are 60-mers with icosahedral symmetry and the smaller ones are 48-mers with octahedral symmetry. These structures are the first of the viral/phage origin and the 60-mer is the largest and the first icosahedral assembly to be reported for sHSPs.

High Resolution Structure of the Mature Capsid of Ralstonia solanacearum Bacteriophage ϕRSA1 by Cryo-Electron Microscopy.

The ϕRSA1 bacteriophage has been isolated from Ralstonia solanacearum, a gram negative bacteria having a significant economic impact on many important crops. We solved the three-dimensional structure of the ϕRSA1 mature capsid to 3.9 Å resolution by cryo-electron microscopy. The capsid shell, that contains the 39 kbp of dsDNA genome, has an icosahedral symmetry characterized by an unusual triangulation number of T = 7, dextro. The ϕRSA1 capsid is composed solely of the polymerization of the major capsid protein, gp8, which exhibits the typical “Johnson” fold first characterized in E. coli bacteriophage HK97. As opposed to the latter, the ϕRSA1 mature capsid is not stabilized by covalent crosslinking between its subunits, nor by the addition of a decoration protein. We further describe the molecular interactions occurring between the subunits of the ϕRSA1 capsid and their relationships with the other known bacteriophages.

Foot and mouth disease virus: A review

As seen by prior tragic outbreaks in many places throughout the world, the foot and mouth disease virus, or "FMDV," is one of the most critical challenges in animal health. In this review, the major features of FMDV, as well as aspects of its interactions with cells and hosts, were discussed. On the other hand, present and upcoming FMD treatment approaches. The first vertebrate virus found was the foot-and-mouth disease virus (FMDV). A capsid protein and the viral genome (+ve sense single strand RNA) make up FMDV. The icosahedral symmetry of the viral structure is made up of structural proteins (VP1, VP2, VP3, and VP4) as well as non-structural proteins (L, 1A, 1B, 1C, 1D, 2A, 2B, 2C, 3A, 3B, 3C, and 3D). The viral replication takes place in the cytoplasm of the cell. Because FMDV has a short incubation period, it spreads quickly. Direct contact is the most often used method of FMDV transmission. The occurrence of direct contact via aerosol and mechanical transmission (fomites, feed, and water). The immunological response is stimulated by the infection with FMD. However, due to virus antigenic diversity, the immune response does not always protect against FMD (antigenic shift). FMDV is divided into seven serotypes based on antigenic variation. O, A, C, SAT-1, SAT-2, SAT-3, and Asia-1 are the serotypes in question. O is the most frequent serotype.

Aqueous Corrosion of Aluminum-Transition Metal Alloys Composed of Structurally Complex Phases: A Review.

Complex metallic alloys (CMAs) are materials composed of structurally complex intermetallic phases (SCIPs). The SCIPs consist of large unit cells containing hundreds or even thousands of atoms. Well-defined atomic clusters are found in their structure, typically of icosahedral point group symmetry. In SCIPs, a long-range order is observed. Aluminum-based CMAs contain approximately 70 at.% Al. In this paper, the corrosion behavior of bulk Al-based CMAs is reviewed. The Al–TM alloys (TM = transition metal) have been sorted according to their chemical composition. The alloys tend to passivate because of high Al concentration. The Al–Cr alloys, for example, can form protective passive layers of considerable thickness in different electrolytes. In halide-containing solutions, however, the alloys are prone to pitting corrosion. The electrochemical activity of aluminum-transition metal SCIPs is primarily determined by electrode potential of the alloying element(s). Galvanic microcells form between different SCIPs which may further accelerate the localized corrosion attack. The electrochemical nobility of individual SCIPs increases with increasing concentration of noble elements. The SCIPs with electrochemically active elements tend to dissolve in contact with nobler particles. The SCIPs with noble metals are prone to selective de-alloying (de–aluminification) and their electrochemical activity may change over time as a result of de-alloying. The metal composition of the SCIPs has a primary influence on their corrosion properties. The structural complexity is secondary and becomes important when phases with similar chemical composition, but different crystal structure, come into close physical contact.

Self-assembly of polyhedral bilayer vesicles from Piezo ion channels.

Piezo ion channels underlie many forms of mechanosensation in vertebrates and have been found to bend the membrane into strongly curved dome shapes. We develop a methodology describing the self-assembly of lipids and Piezo proteins into polyhedral bilayer vesicles. We validate this methodology for bilayer vesicles formed from bacterial mechanosensitive channels of small conductance, for which experiments found a polyhedral arrangement of proteins with snub cube symmetry and a well-defined characteristic vesicle size. On this basis, we calculate the self-assembly diagram for polyhedral bilayer vesicles formed from Piezo proteins. We find that the radius of curvature of the Piezo dome provides a critical control parameter for the self-assembly of Piezo vesicles, with high abundances of Piezo vesicles with octahedral, icosahedral, and snub cube symmetry with increasing Piezo dome radius of curvature.

Minimal Design Principles for Icosahedral Virus Capsids

The geometrical structures of single- and multiple-shell icosahedral virus capsids are reproduced as the targets that minimize the cost corresponding to relatively simple design functions. Capsid subunits are first identified as building blocks at a given coarse-grained scale and then represented in these functions as point particles located on an appropriate number of concentric spherical surfaces. Minimal design cost is assigned to optimal spherical packings of the particles. The cost functions are inspired by the packings favored for the Thomson problem, which minimize the electrostatic potential energy between identical charged particles. In some cases, icosahedral symmetry constraints are incorporated as external fields acting on the particles. The simplest cost functions can be obtained by separating particles in disjoint nonequivalent sets with distinct interactions, or by introducing interacting holes (the absence of particles). These functions can be adapted to reproduce any capsid structure found in real viruses. Structures absent in Nature require significantly more complex designs. Measures of information content and complexity are assigned to both the cost functions and the capsid geometries. In terms of these measures, icosahedral structures and the corresponding cost functions are the simplest solutions.

IPVP-MCV: A Multi-Classifier Voting Model for the Accurate Identification of Phage Virion Proteins

The classic structure of a bacteriophage is commonly characterized by complex symmetry. The head of the structure features icosahedral symmetry, whereas the tail features helical symmetry. The phage virion protein (PVP), a type of bacteriophage structural protein, is an essential material of the infectious viral particles and is responsible for multiple biological functions. Accurate identification of PVPs is of great significance for comprehending the interaction between phages and host bacteria and developing new antimicrobial drugs or antibiotics. However, traditional experimental approaches for identifying PVPs are often time-consuming and laborious. Therefore, the development of computational methods that can efficiently and accurately identify PVPs is desired. In this study, we proposed a multi-classifier voting model called iPVP-MCV to enhance the predictive performance of PVPs based on their amino acid sequences. First, three types of evolutionary features were extracted from the position-specific scoring matrix (PSSM) profiles to represent PVPs and non-PVPs. Then, a set of baseline models were trained based on the support vector machine (SVM) algorithm combined with each type of feature descriptors. Finally, the outputs of these baseline models were integrated to construct the proposed method iPVP-MCV by using the majority voting strategy. Our results demonstrated that the proposed iPVP-MCV model was superior to existing methods when performing the rigorous independent dataset test.