2-fold Axis Research Articles

Explicit description of viral capsid subunit shapes by unfolding dihedrons.

Viral capsid assembly and the design of capsid-based nanocontainers critically depend on understanding the shapes and interfaces of constituent protein subunits. However, a comprehensive framework for characterizing these features is still lacking. Here, we introduce a novel approach based on spherical tiling theory that explicitly describes the 2D shapes and interfaces of subunits in icosahedral capsids. Our method unfolds spherical dihedrons defined by icosahedral symmetry axes, enabling systematic characterization of all possible subunit geometries. Applying this framework to real T = 1 capsid structures reveals distinct interface groups within this single classification, with variations in interaction patterns around 3-fold and 5-fold symmetry axes. We validate our classification through molecular docking simulations, demonstrating its consistency with physical subunit interactions. This analysis suggests different assembly pathways for capsid nucleation. Our general framework is applicable to other triangular numbers, paving the way for broader studies in structural virology and nanomaterial design.

Atomic Structure and 3D Shape of a Multibranched Plasmonic Nanostar from a Single Spatially Resolved Electron Diffraction Map.

Despite the interest in improving the sensitivity of optical sensors using plasmonic nanoparticles (NPs) (rods, wires, and stars), the full structural characterization of complex shape nanostructures is challenging. Here, we derive from a single scanning transmission electron microscope diffraction map (4D-STEM) a detailed determination of both the 3D shape and atomic arrangement of an individual 6-branched AuAg nanostar (NS) with high-aspect-ratio legs. The NS core displays an icosahedral structure, and legs are decahedral rods attached along the 5-fold axes at the core apexes. The NS legs show an anomalous anisotropic spatial distribution (all close to a plane) due to an interplay between the icosahedral symmetry and the unzipping of the surfactant layer on the core. The results significantly improve our understanding of the star growth mechanism. This low dose diffraction mapping is promising for the atomic structure study of individual multidomain, multibranched, or multiphase NPs, even when constituted of beam-sensitive materials.

Pentagonal Symmetry in Aperiodic Cyclic Multiply Twinned Nano- and Mesodiamonds.

This Review provides the first comprehensive overview of the structure and properties of exotic sp3-crystalline aperiodic cyclic multiply twinned nano- (10-100 nm) and meso- (up to 1 mm) diamond particles (MTPs) exhibiting pentagonal symmetry. It spans their independent experimental discoveries (1963, 1964, 1972, and 1983) and theoretical structural insights (1993) to recent advancements. The Review focuses on high-symmetry MTPs formed by the fusion of multiple cubic diamond fragments through [111] facets. The sp3 diamond lattice of individual fragments offers a vast range of MTP varieties. These particles are shown to be a special case of aperiodic crystalline solids with limited dimensions and rotational symmetry, leading to a breakdown of translational invariance. Detailed mathematical analysis of the MTPs' lattices highlights the crucial role of central cores in determining the symmetry and effective dimensions of these structures. Both structural and kinetic aspects of the formation mechanisms of pentagonal diamond particles are considered, revealing the main role of embryo seeds (low fullerenes, polyhexacyclo[5.5.1.12,6.18,12.03,11.05,9]pentadecane (C15), and polyheptacyclo[5.5.1.12,7.19,14.03,13.06,11]octadecane (C18)) in determining the MTPs' symmetry and structure. The effective dimensions of multiply twinned diamonds are shown to be limited by structural stress caused by the mismatch of perfect pentagonal and tetrahedral dihedral angles. The extraordinary mechanical and electronic properties of multiply twinned diamonds are discussed, highlighting that hexagonal interfaces between cubic diamond fragments may determine exceptional ultrahard and quantum characteristics. The MTP X-ray diffraction spectra reveal clear pentagonal patterns with single (diamond decahedrons or dodecahedrons) or ten (diamond icosahedra) central 5-fold axes. A comparative analysis of experimental structural data and simulations at different theoretical levels demonstrates a perfect correspondence of theoretical models with crystalline lattices.

Structure of anellovirus-like particles reveal a mechanism for immune evasion

Anelloviruses are nonpathogenic viruses that comprise a major portion of the human virome. Despite being ubiquitous in the human population, anelloviruses (ANVs) remain poorly understood. Basic features of the virus, such as the identity of its capsid protein and the structure of the viral particle, have been unclear until now. Here, we use cryogenic electron microscopy to describe the first structure of an ANV-like particle. The particle, formed by 60 jelly roll domain-containing ANV capsid proteins, forms an icosahedral particle core from which spike domains extend to form a salient part of the particle surface. The spike domains come together around the 5-fold symmetry axis to form crown-like features. The base of the spike domain, the P1 subdomain, shares some sequence conservation between ANV strains while a hypervariable region, forming the P2 subdomain, is at the spike domain apex. We propose that this structure renders the particle less susceptible to antibody neutralization by hiding vulnerable conserved domains while exposing highly diverse epitopes as immunological decoys, thereby contributing to the immune evasion properties of anelloviruses. These results shed light on the structure of anelloviruses and provide a framework to understand their interactions with the immune system.

Exploring Canine Picornavirus Diversity in the USA Using Wastewater Surveillance: From High-Throughput Genomic Sequencing to Immuno-Informatics and Capsid Structure Modeling.

The SARS-CoV-2 pandemic resulted in a scale-up of viral genomic surveillance globally. However, the wet lab constraints (economic, infrastructural, and personnel) of translating novel virus variant sequence information to meaningful immunological and structural insights that are valuable for the development of broadly acting countermeasures (especially for emerging and re-emerging viruses) remain a challenge in many resource-limited settings. Here, we describe a workflow that couples wastewater surveillance, high-throughput sequencing, phylogenetics, immuno-informatics, and virus capsid structure modeling for the genotype-to-serotype characterization of uncultivated picornavirus sequences identified in wastewater. Specifically, we analyzed canine picornaviruses (CanPVs), which are uncultivated and yet-to-be-assigned members of the family Picornaviridae that cause systemic infections in canines. We analyzed 118 archived (stored at -20 °C) wastewater (WW) samples representing a population of ~700,000 persons in southwest USA between October 2019 to March 2020 and October 2020 to March 2021. Samples were pooled into 12 two-liter volumes by month, partitioned (into filter-trapped solids [FTSs] and filtrates) using 450 nm membrane filters, and subsequently concentrated to 2 mL (1000×) using 10,000 Da MW cutoff centrifugal filters. The 24 concentrates were subjected to RNA extraction, CanPV complete capsid single-contig RT-PCR, Illumina sequencing, phylogenetics, immuno-informatics, and structure prediction. We detected CanPVs in 58.3% (14/24) of the samples generated 13,824,046 trimmed Illumina reads and 27 CanPV contigs. Phylogenetic and pairwise identity analyses showed eight CanPV genotypes (intragenotype divergence <14%) belonging to four clusters, with intracluster divergence of <20%. Similarity analysis, immuno-informatics, and virus protomer and capsid structure prediction suggested that the four clusters were likely distinct serological types, with predicted cluster-distinguishing B-cell epitopes clustered in the northern and southern rims of the canyon surrounding the 5-fold axis of symmetry. Our approach allows forgenotype-to-serotype characterization of uncultivated picornavirus sequences by coupling phylogenetics, immuno-informatics, and virus capsid structure prediction. This consequently bypasses a major wet lab-associated bottleneck, thereby allowing resource-limited settings to leapfrog from wastewater-sourced genomic data to valuable immunological insights necessary for the development of prophylaxis and other mitigation measures.

The Structure of Spiroplasma Virus 4: Exploring the Capsid Diversity of the Microviridae.

Spiroplasma virus 4 (SpV4) is a bacteriophage of the Microviridae, which packages circular ssDNA within non-enveloped T = 1 icosahedral capsids. It infects spiroplasmas, which are known pathogens of honeybees. Here, the structure of the SpV4 virion is determined using cryo-electron microscopy to a resolution of 2.5 Å. A striking feature of the SpV4 capsid is the mushroom-like protrusions at the 3-fold axes, which is common among all members of the subfamily Gokushovirinae. While the function of the protrusion is currently unknown, this feature varies widely in this subfamily and is therefore possibly an adaptation for host recognition. Furthermore, on the interior of the SpV4 capsid, the location of DNA-binding protein VP8 was identified and shown to have low structural conservation to the capsids of other viruses in the family. The structural characterization of SpV4 will aid future studies analyzing the virus-host interaction, to understand disease mechanisms at a molecular level. Furthermore, the structural comparisons in this study, including a low-resolution structure of the chlamydia phage 2, provide an overview of the structural repertoire of the viruses in this family that infect various bacterial hosts, which in turn infect a wide range of animals and plants.

A stargate mechanism of Microviridae genome delivery unveiled by cryogenic electron tomography.

Single-stranded DNA bacteriophages of the Microviridae family are major components of the global virosphere. Microviruses are highly abundant in aquatic ecosystems and are prominent members of the mammalian gut microbiome, where their diversity has been linked to various chronic health disorders. Despite the clear importance of microviruses, little is known about the molecular mechanism of host infection. Here, we have characterized an exceptionally large microvirus, Ebor, and provide crucial insights into long-standing mechanistic questions. Cryogenic electron microscopy of Ebor revealed a capsid with trimeric protrusions that recognise lipopolysaccharides on the host surface. Cryogenic electron tomography of the host cell colonized with virus particles demonstrated that the virus initially attaches to the cell via five such protrusions, located at the corners of a single pentamer. This interaction triggers a stargate mechanism of capsid opening along the 5-fold symmetry axis, enabling delivery of the virus genome. Despite variations in specific virus-host interactions among different Microviridae family viruses, structural data indicate that the stargate mechanism of infection is universally employed by all members of the family. Startlingly, our data reveal a mechanistic link for the opening of relatively small capsids made out of a single jelly-roll fold with the structurally unrelated giant viruses.

Higher-Order Structure of Adeno-Associated Virus Serotype 8 by Hydrogen/Deuterium Exchange Mass Spectrometry.

The higher-order structure (HOS) is a critical quality attribute of recombinant adeno-associated viruses (rAAVs). Evaluating the HOS of the entire rAAV capsid is challenging because of the flexibility and/or less folded nature of the VP1 unique (VP1u) and VP1/VP2 common regions, which are structural features essential for these regions to exert their functions following viral infection. In this study, hydrogen/deuterium exchange mass spectrometry (HDX-MS) was used for the structural analysis of full and empty rAAV8 capsids. We obtained 486 peptides representing 85% sequence coverage. Surprisingly, the VP1u region showed rapid deuterium uptake even though this region contains the phospholipase A2 domain composed primarily of α-helices. The comparison of deuterium uptake between full and empty capsids showed significant protection from hydrogen/deuterium exchange in the full capsid at the channel structure of the 5-fold symmetry axis. This corresponds to cryo-electron microscopy studies in which the extended densities were observed only in the full capsid. In addition, deuterium uptake was reduced in the VP1u region of the full capsid, suggesting the folding and/or interaction of this region with the encapsidated genome. This study demonstrated HDX-MS as a powerful method for probing the structure of the entire rAAV capsid.

3-O-β-chacotriosyl glycyrrhetinic acid derivatives as potential small-molecule SARS-CoV-2 fusion inhibitors against SARS-CoV-2 entry into host cells

To study the inhibitory activities of 3-O-β-chacotriosyl glycyrrhetinic acid derivatives against the entry of SARS-CoV-2 into host cells. With pentacyclic triterpene saponin glycyrrhizic acid (a natural SARS-CoV-2 entry inhibitor) as the lead compound, a series of 3-O-β-chacotriosyl glycyrrhetinic acid derivatives were designed and synthesized based on hypridization principle, and their inhibitory activities against virus entry were tested in SARS-CoV-2 pseudovirusinfected cells. The antiviral targets of the lead compound 1b was identified by pseudotyped SARS-CoV-2 infection assay and surface plasmon resonance (SPR) assay, and the S protein-mediated cell-cell fusion assay was used to evaluate the effect of 1b on virus-cell membrane fusion. Molecular docking and single amino acid mutagenesis were carried out to analyze the effect of 1b on binding activitiy of S protein. The lead compound 1b showed significant inhibitory effect against Omicron pseudovirus with an EC50 value of 3.28 μmol/L (P < 0.05), and had broad-spectrum antiviral activity against other SARS-CoV-2 pseudovirus. Spike-dependent cell-cell fusion assay demonstrated an inhibitory effect of 1b against SARS-CoV-2 S proteinmediated cell-cell fusion. Molecular docking analysis predicted that the lead compound 1b could be well fitted into a cavity between the attachment (S1) and fusion (S2) subunits at the 3-fold axis, where it formed multiple hydrophobic interactions with Glu309, Ser305, Arg765 and Lys964 residues with a KD value of -8.6 kcal/mol. The compound 1b at 10, 5, 2.5 and 1.25 μmol/L showed a significantly reduced inhibitory activity against the pseudovirus with mutated Arg765, Lys964, Glu309 and Leu303 (P < 0.01). 3-O-β-chacotriosyl glycyrrhetinic acid derivatives are capable of stabilizing spike protein in the pre-fusion step to interfere with the fusion of SARS-CoV-2 with host cell membrane, and can thus serve as potential novel small-molecule SARS-CoV-2 fusion inhibitors.

Sequence of Structural and Magnetic Phase Transitions in (NO)Mn6(NO3)13.

New nitrosonium manganese(II) nitrate, (NO)Mn6(NO3)13, has been synthesized and structurally characterized. In the temperature range of 45-298 K, the crystal is hexagonal (centrosymmetric sp. gr. P63/m). Mn2+ ions are assembled into tubes along axis c with both NO3- filling and coating. The nitrosonium cation is located in the framework cavity and is disordered by a 3-fold axis. At the temperature TS1 = 190 K, a structural phase transition related to the libration of the intertube NO3 group and a small variation of Mn polyhedron is observed. Moreover, the anomalies in physical properties of (NO)Mn6(NO3)13 allow suggesting that ordering of NO+ units occurs at low temperatures. The antiferromagnetic ordering in this compound is preceded by the formation of a short-range correlation regime at about 25 K and takes place in two steps at TN1 = 12.0 K and TN2 = 8.4 K.

Single crystal polarization-orientation Raman spectroscopy of zeolite LTA with confined S3− anions - High dielectric constant nanoporous material

We apply polarization-orientation Raman spectroscopy, as an alternative to X-ray diffraction, to LTA single crystals containing S3− in sodalite cages additionally to S8 rings in large cavities. The sample was obtained via sulfur vapor adsorption at ∼550 °C (LTA-S-550). We show that S3− is located in the (110) plane with its 2-fold axis along the LTA 4-fold axis. The anion position suggests strong interaction of its terminal atoms with Na+ localized in LTA 6-membered rings. The anions display optical absorption band at ∼590 nm (2.1 eV) and resonant Raman enhancement. We observe a record-high S3− bond-bending mode frequency ∼274 cm−1 due to a strong bond-angle contraction. This leads to the Fermi resonance of its overtone with the symmetric bond-stretching mode in the frequency range of 544–552 cm−1. An anomalous Raman downshift of the S3− bond-stretching modes with a decrease of temperature is observed and attributed to partial compressive stress relaxation. Luminescence band at ∼845 nm is observed suggesting considering LTA-S-550 as an interesting light-emitting material. We discuss a role of S3− in the high dielectric constant up to ∼160 and a possible contribution of the anion to the ion-exchange selectivity to Sr2+/Cs+ enhancements of LTA with sulfur.

Structural basis of the recognition of adeno-associated virus by the neurological system-related receptor carbonic anhydrase IV.

Carbonic anhydrase IV (Car4) is a newly identified receptor that allows adeno-associated virus (AAV) 9P31 to cross the blood-brain barrier and achieve efficient infection in the central nervous system (CNS) in mouse models. However, the molecular mechanism by which engineered AAV capsids with 7-mer insertion in the variable region (VR) VIII recognize these novel cellular receptors is unknown. Here we report the cryo-EM structures of AAV9P31 and its complex with Mus musculus Car4 at atomic resolution by utilizing the block-based reconstruction (BBR) method. The structures demonstrated that Car4 binds to the protrusions at 3-fold axes of the capsid. The inserted 7-mer extends into a hydrophobic region near the catalytic center of Car4 to form stable interactions. Mutagenesis studies also identified the key residues in Car4 responsible for the AAV9P31 interaction. These findings provide new insights into the novel receptor recognition mechanism of AAV generated by directed evolution and highlight the application of the BBR method to studying the virus-receptor molecular mechanism.

Uneven Strain Distribution Induces Consecutive Dislocation Slipping, Plane Gliding, and Subsequent Detwinning of Penta-Twinned Nanoparticles.

Twin structures possess distinct physical and chemical properties by virtue of their specific twin configuration. However, twinning and detwinning processes are not fully understood on the atomic scale. Integrating in situ high resolution transmission electron microscopy and molecular dynamic simulations, we find tensile strain in the asymmetrical 5-fold twins of Au nanoparticles leads to twin boundary migration through dislocation sliding (slipping of an atomic layer) along twin boundaries and dislocation reactions at the 5-fold axis under an electron beam. Migration of one or two layers of twin planes is governed by energy barriers, but overall, the total energy, including surface, lattice strain, and twin boundary energy, is relaxed after consecutive twin boundary migration, leading to a detwinning process. In addition, surface rearrangement of 5-fold twinned nanoparticles can aid in the detwinning process.

Magnetic structure of a multiferroic compound: Cu2OCl2.

The Cu2OCl2 compound has been shown to be a high-temperature spin-driven multiferroic system, with a linear magneto-electric coupling. In this paper we propose a complete study of its magnetic structure. We derive the low energy magnetic Hamiltonian using ab initio multi-reference configuration interaction and the spin structure using Monte-Carlo simulations. Among the three magnetic structures proposed in the literature from different experimental results, our calculations support the incommensurate cycloid magnetic structure with a q⃑ = (qa,0,0) propagation vector. Using symmetry analysis, we show that all experimental results (polarization, magnetic order, magneto-electric coupling) can be accounted for in the Fd'd'2 magnetic space group (2-fold axis along c⃑).

Hierarchical self-assembly of Au-nanoparticles into filaments: evolution and break.

We compare the assembly of individual Au nanoparticles in a vacuum and between two Au(111) surfaces via classical molecular dynamics on a timescale of 100 ns. In a vacuum, the assembly of three nanoparticles used as seeds, initially showing decahedral, truncated octahedral and icosahedral shapes with a diameter of 1.5-1.7 nm, evolves into a spherical object with about 10-12 layers and a gyration radius ∼2.5-2.8 nm. In a vacuum, 42% show just one 5-fold symmetry axis, 33% adopt a defected icosahedral arrangement, and 25% lose all 5-fold symmetry and display a face-centred-cubic shape with several parallel stacking faults. We model a constrained version of the same assembly that takes place between two Au(111) surfaces. During the dynamics, the two Au(111) surfaces are kept fixed at distances of 55 Å, 55.5 Å, 56 Å, and 56.5 Å. The latter distance accommodates 24 Au layers with no strain, while the others correspond to nominal strains of 1.5%, 2.4%, and 3.3%, respectively. In the constrained assembly, each individual seed tends to reorganize into a layered configuration, but the filament may break. The probability of breaking the assembled nanofilament depends on the individual morphology of the seeds. It is more likely to break at the decahedron/icosahedron interface, whilst it is more likely to layer with respect to the (111) orientation when a truncated octahedron sits between the decahedron and the icosahedron. We further observe that nanofilaments between surfaces at 56 Å have a >90% probability of breaking, which decreases to 8% when the surfaces are 55 Å apart. We attribute the dramatic change in probability of breaking to the peculiar decahedron/icosahedron interface and the higher average atomic strain in the nanofilaments. This in silico experiment can shed light on the understanding and control of the formation of metallic nanowires and nanoparticle-assembled networks, which find applications in next-generation electronic devices, such as resistive random access memories and neuromorphic devices.

Optical study of Te8 ring clusters: comparison with density functional theory and a step towards materials design using nanoporous zeolite space.

The Te8 ring molecule (cluster) is poorly investigated due to the lack of experimental data. Here, we report an experimental and theoretical study of a regular array of oriented Te8 rings formed in the ∼1.14 nm diameter cavities of zeolite LTA, which are arranged in a cubic lattice with a spacing of ∼1.2 nm. Single crystals of LTA with encapsulated tellurium (LTA-Te) were studied using Raman spectroscopy (RS) and optical absorption spectroscopy (OAS). The experimental LTA-Te spectra were found to be in agreement with those calculated using density functional theory (PBE0 hybrid functional and def2-TZVP basis sets) for the crown-shaped Te8 ring molecule with D4d symmetry. Using polarization-orientation RS, we show that the Te8 rings are oriented by their major axes along the 4-fold axes of cubic LTA. We also show that the site symmetry of Te8 in LTA-Te is lower than D4d. Te8 bond-bending modes are well described in the harmonic approximation, while bond-stretching modes are mixed due to the reduced ring symmetry and, probably, anharmonicity. Importantly, OAS data of LTA-Te display dependence on the Te8 concentration, implying the interaction of the rings from neighbouring LTA cavities with the generation of the valence and conduction electron bands of such a cluster crystal.

Mallestigite, Pb3Sb(SO4)(AsO4)(OH)6·3H2O, from the type locality – new data, crystal structure, and structural relationships

A report of the supergene mineral mallestigite, Pb3Sb5+(SO4)(AsO4)(OH)6·3H2O, from the type locality Neufinkenstein-Grabanz district, Mallestiger Mittagskogel, Carinthia, Austria, is given in order to close gaps that have been left open since its first description. At the type locality, the dump of an abandoned small copper-lead-zinc mine, the mineral occurs frequently in up to ⁓2 mm long clear colourless idiomorphic hexagonal prisms {100} terminated by the bipyramid {101}. Details of the occurrence, paragenesis, physical properties, a FTIR spectrum and X-ray powder diffraction data are reported. Chemical analysis in a scanning electron microscope in conjunction with a crystal structure analysis gave the empirical formula Pb3.02Sb1.06(SO4)0.96(AsO4)0.97(OH)6·3H2O. An ab-initio crystal structure determination with CCD diffractometer data, MoKα radiation, and a nearly untwinned crystal proved that mallestigite is hexagonal, space group P63, a = 8.9326(4), c = 11.1044(5) Å, V = 767.33(8) Å3, Z = 2, and gave a final R1 = 0.0184 for 1632 independent reflections with I > 2σ(I). Mallestigite belongs to the fleischerite group. The structure is built up from [Sb5+(OH)6]1– octahedra which are linked by triplets of edge-sharing Pb2+ into chains [Pb3Sb(OH)6]5+ extending along a 63 axis. Each three of such chains are bridged by triplets of H2O and by rows of SO42– and AsO43– tetrahedra alternating along a 3-fold axis and showing very different links to the Pb atom. Pb2+ is in a strongly distorted one-sided [9]-coordination by O atoms that makes the structure clearly hemimorphic. Structural relationships to the fleischerite group minerals schaurteite, genplesite, despujolsite and fleischerite as well as to synthetic Ba3Sn4+(SeO4)2(OH)6·3H2O are outlined and changes in the space group symmetry of despujolsite (P6¯\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\overline6$$\\end{document}2c → P63/mmc) and fleischerite (P6¯\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\overline6$$\\end{document}2c → P63) are proposed.

Multiple LDLR class A repeats on very-low-density lipoprotein receptor promote the cross-species transmission of Semliki Forest virus.

Multiple LDLR class A (LA) repeats around LA3 promote synergistic binding to Semliki Forest virus (SFV) E1-DIII near the 2-fold and 5-fold symmetry axes. Meanwhile, the multiple consecutive LAs concatemer shows approximately 1000 times higher binding affinity than that of LA3s, which can help to effectively and synergistically bind with E1-DIII of viral envelope protein.

Structural and Biophysical Analysis of Adeno-Associated Virus Serotype 2 Capsid Assembly Variants.

Adeno-associated virus (AAV) is a nonenveloped single-stranded DNA (ssDNA) icosahedral T=1 virus being developed as a vector for clinical gene delivery systems. Currently, there are approximately 160 AAV clinical trials, with AAV2 being the most widely studied serotype. To further understand the AAV gene delivery system, this study investigates the role of viral protein (VP) symmetry interactions on capsid assembly, genome packaging, stability, and infectivity. A total of 25 (seven 2-fold, nine 3-fold, and nine 5-fold symmetry interface) AAV2 VP variants were studied. Six 2-fold and two 5-fold variants did not assemble capsids based on native immunoblots and anti-AAV2 enzyme-linked immunosorbent assays (ELISAs). Seven of the 3-fold and seven of the 5-fold variants that assembled capsids were less stable, while the only 2-fold variant that assembled had ~2°C higher thermal stability (Tm) than recombinant wild-type AAV2 (wtAAV2). Three of the 3-fold variants (AAV2-R432A, AAV2-L510A, and N511R) had an approximately 3-log defect in genome packaging. Consistent with previous reports of the 5-fold axes, the region of the capsid is important for VP1u externalization and genome ejection, and one 5-fold variant (R404A) had a significant defect in viral infectivity. The structures of wtAAV2 packaged with a transgene (AAV2-full) and without a transgene (AAV2-empty) and one 5-fold variant (AAV2-R404A) were determined by cryo-electron microscopy and three dimensional (3D)-image reconstruction to 2.8, 2.9, and 3.6 Å resolution, respectively. These structures revealed the role of stabilizing interactions on the assembly, stability, packaging, and infectivity of the virus capsid. This study provides insight into the structural characterization and functional implications of the rational design of AAV vectors. IMPORTANCE Adeno-associated viruses (AAVs) have been shown to be useful vectors for gene therapy applications. Consequently, AAV has been approved as a biologic for the treatment of several monogenic disorders, and many additional clinical trials are ongoing. These successes have generated significant interest in all aspects of the basic biology of AAV. However, to date, there are limited data available on the importance of the capsid viral protein (VP) symmetry-related interactions required to assemble and maintain the stability of the AAV capsids and the infectivity of the AAV capsids. Characterizing the residue type and interactions at these symmetry-driven assembly interfaces of AAV2 has provided the foundation for understanding their role in AAV vectors (serotypes and engineered chimeras) and has determined the residues or regions of the capsid that can or cannot tolerate alterations.

Search for Toroidal Ground State and Magnetoelectric Effects in Molecular Spin Triangles with Antiferromagnetic Exchange

Using first-principles methods and spin models, we investigate the magnetic properties of transition-metal trimers Cr3 and Cu3. We calculate exchange coupling constants and zero-field splitting parameters using density functional theory and, with these parameters, determine the ground spin state as well as thermodynamic properties via spin models. Results for Cr3 indicate uniaxial magnetic anisotropy with a magnetic easy axis aligned along the 3-fold rotational symmetry axis and a mostly isotropic exchange interaction. The Cu3 molecule lacks rotational symmetry and our results show strong antisymmetric interactions for three distinct exchange couplings within the molecule. We are able to reproduce experimental findings on magnetic susceptibility and magnetization of Cr3 with the first-principles spin-Hamiltonian parameters. Our results show no presence of a toroidal ordering of spins for Cr3 and a finite toroidal moment for Cu3 in the ground state. We apply an external electric field up to 0.08 V/Å to each system to reveal the field dependence of exchange coupling as magnetoelectric effects. Finally, we scan the parameter space of a spin Hamiltonian to gain insights into which parameters would lead to a sizable toroidal moment in such systems.