Twofold Symmetry Axis Research Articles

Computational design of non-porous pH-responsive antibody nanoparticles

Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and is important for targeted delivery of biologics. Here we describe the design of octahedral non-porous nanoparticles with a targeting antibody on the two-fold symmetry axis, a designed trimer programmed to disassemble below a tunable pH transition point on the three-fold axis, and a designed tetramer on the four-fold symmetry axis. Designed non-covalent interfaces guide cooperative nanoparticle assembly from independently purified components, and a cryo-EM density map closely matches the computational design model. The designed nanoparticles can package protein and nucleic acid payloads, are endocytosed following antibody-mediated targeting of cell surface receptors, and undergo tunable pH-dependent disassembly at pH values ranging between 5.9 and 6.7. The ability to incorporate almost any antibody into a non-porous pH-dependent nanoparticle opens up new routes to antibody-directed targeted delivery.

Bipartite genome and structural organization of the parvovirus Acheta domesticus segmented densovirus

Parvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression cassettes within their genome. We report the discovery of a parvovirus with a bipartite genome, Acheta domesticus segmented densovirus (AdSDV), isolated from house crickets (Acheta domesticus), in which it is pathogenic. We found that the AdSDV harbors its NS and VP cassettes on two separate genome segments. Its vp segment acquired a phospholipase A2-encoding gene, vpORF3, via inter-subfamily recombination, coding for a non-structural protein. We showed that the AdSDV evolved a highly complex transcription profile in response to its multipartite replication strategy compared to its monopartite ancestors. Our structural and molecular examinations revealed that the AdSDV packages one genome segment per particle. The cryo-EM structures of two empty- and one full-capsid population (3.3, 3.1 and 2.3 Å resolution) reveal a genome packaging mechanism, which involves an elongated C-terminal tail of the VP, “pinning” the ssDNA genome to the capsid interior at the twofold symmetry axis. This mechanism fundamentally differs from the capsid-DNA interactions previously seen in parvoviruses. This study provides new insights on the mechanism behind ssDNA genome segmentation and on the plasticity of parvovirus biology.

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

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

Chiral phonons in binary compounds [formula omitted]Bi ([formula omitted] = K, Rb, Cs) with P2[formula omitted]/c structure

Binary compounds ABi (A = K, Rb, Cs) crystallize in P21/c structure containing both clockwise and anticlockwise chiral chains of Bi atoms. Electronic band structure exhibits the insulating nature of these systems, with the band gap about 0.25eV. The presented study of dynamical properties confirm a stability of the system with P21/c symmetry. The crystal structure contains the quasi-one-dimensional Bi chains, exhibiting four-fold-like rotational “local” symmetry. Nevertheless, the system formally possesses two-fold rotational symmetry. Independently of the absence of the three-fold (or higher) rotational symmetry axes for the whole crystal, the chiral modes propagate along the Bi atom chains in these systems. We discuss basic properties of these modes in monoatomic chiral chains. We show that the two-fold rotational symmetry axis affects the main properties of the chiral phonons, which are not realized at the high-symmetry points, but along some paths between them in the reciprocal space. In addition, in the doped system, the chiral phonons possess non-zero total angular momentum.

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

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

Analysis of Acousto-Optic Figure of Merit in KGW and KYW Crystals.

Monoclinic potassium rare-earth crystals are known as efficient materials for solid-state lasers and acousto-optic modulators. A number of specific configurations for acousto-optic devices based on those crystals have recently been proposed, but the acousto-optic effect of those crystals has only been analyzed fragmentarily for some interaction directions. In this work, we numerically searched for the global maxima of an acousto-optic figure of merit for isotropic diffraction in KGd(WO4)2 and KY(WO4)2 crystals. It was demonstrated that the global maxima of the acousto-optic figure of merit in those crystals occur in the slow optical mode propagating along the crystal's twofold symmetry axis and in the acoustic wave propagating orthogonally, both for quasi-longitudinal and quasi-shear acoustic modes. The proposed calculation method can be readily used for the optimization of the acousto-optic interaction geometry in crystals with arbitrary symmetry.

Nematic pinning of the superconducting state in the doped topological insulator SrxBi2Se3

The discovery of a rotational symmetry breaking, or nematic, state in the superconducting doped topological insulator MxBi2Se3 (M = Cu, Sr, Nb) indicates a multicomponent superconducting order parameter which is topological. Many questions remain in this family of materials. In particular, the nematic axis of twofold symmetry is always pinned along one of three rotationally equivalent directions in the threefold symmetric basal plane in the rhombohedral crystal. Crystallographic strain has been proposed as the origin of the choice of pinning axis. Here, we discuss nematic pinning of the superconducting state, summarizing our magnetotransport, magnetization, penetration depth, and calorimetry measurements, which support the theoretical picture of topological superconductivity. We discuss the impact of controlled disorder via proton irradiation on the nematic superconducting state and discuss results of our multimodal technique for searching for crystallographic strain below 1 K via simultaneous diffraction and magnetotransport measurements.

Synthesis, crystal structure, DFT studies, and Hirshfeld surface analysis of 2,2'-(((methylene-bis(4,1-phenylene))bis(azanylylidene))bis(methanylylidene))diphenol

The synthesis, characterization, and theoretical studies of the title compound has been reported in this study. The molecular structure has been characterized by room-temperature single-crystal X-ray diffraction study which reveals that it has an angular shape with intramolecular and intermolecular hydrogen bonding. Crystal data for the title compound, C27H22N2O2 (M =406.46 g/mol): monoclinic, space group C2/c (no. 15), a = 36.371(10) Å, b = 4.6031(12) Å, c = 12.192(3) Å, β = 94.972(6)°, V = 2033.5(9) Å3, Z = 4, T = 100 K, μ(MoKα) = 0.084 mm-1, Dcalc = 1.328 g/cm3, 8812 reflections measured (2.248° ≤ 2Θ ≤ 49.734°), 1773 unique (Rint = 0.0323, Rsigma = 0.0239) which were used in all calculations. The final R1 was 0.0411 (I > 2σ(I)) and wR2 was 0.1165 (all data). In crystal structure, the molecule exits in the enol form and is located on a two-fold axis of symmetry; where the central methylene carbon atom of the diphenylmethane moiety is displaced from the aromatic ring planes. The Hirshfeld surface analysis of the title compound shows that H···H, C···H, and O···H interactions of 53.3, 13.2, and 5.4%; respectively, which exposed that the main intermolecular interactions were H···H intermolecular interactions. The HOMO-LUMO energy gap in the title compound is 2.9639 eV. Molecular electrostatic potential of the investigated compound has also been studied.

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.

Catena-Poly[[(2,2'-bi-pyridine-κ2 N,N')manganese(II)]-di-μ-bromido

In the polymeric title complex, [MnBr2(C10H8N2)] n , the MnII ion, situated on a twofold axis of symmetry, is six-coordinated in a distorted octa-hedral coordination geometry defined by two N atoms from the chelating 2,2'-bi-pyridine ligand and four bridging Br- anions. The crystal reveals a one-dimensional Br-bridged chain along the c-axis direction with a zigzag topology. In the crystals, contacts between chains include π-π inter-actions between pyridyl rings [inter-centroid separation = 4.082 (1) Å].

From ambient- to high-pressure dielectric response of perovskite formamidinium manganese formate

In this work, we discuss the ambient- and high-pressure dynamic behaviour and dielectric properties of perovskite-like formamidinium-templated inorganic–organic hybrid [NH2CHNH2][Mn(HCOO)3] (FAMn).

Crystal structure of the catalytic subunit of bovine pyruvate dehydrogenase phosphatase.

Mammalian pyruvate dehydrogenase (PDH) activity is tightly regulated by phosphorylation and dephosphorylation, which is catalyzed by PDH kinase isomers and PDH phosphatase isomers, respectively. PDH phosphatase isomer 1 (PDP1) is a heterodimer consisting of a catalytic subunit (PDP1c) and a regulatory subunit (PDP1r). Here, the crystal structure of bovine PDP1c determined at 2.1 Å resolution is reported. The crystals belonged to space group P3221, with unit-cell parameters a = b = 75.3, c = 173.2 Å. The structure was solved by molecular-replacement methods and refined to a final R factor of 21.9% (Rfree = 24.7%). The final model consists of 402 of a possible 467 amino-acid residues of the PDP1c monomer, two Mn2+ ions in the active site, an additional Mn2+ ion coordinated by His410 and His414, two MnSO4 ion pairs at special positions near the crystallographic twofold symmetry axis and 226 water molecules. Several new features of the PDP1c structure are revealed. The requirements are described and plausible bases are deduced for the interaction of PDP1c with PDP1r and other components of the pyruvate dehydrogenase complex.

Free energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation

Abstract Entecavir, triphosphorylated in liver cells, is an antiviral reagent against Hepatitis B virus (HBV). The reagent inhibits reverse transcription of RNA inside the virus capsid. In the present study, free energy profile of an Entecavir triphosphate (ETVTP) molecule has been calculated when it passes through pores of the capsid along two- and three-fold rotational symmetry axes in order to investigate permeation pathway of the reagent to the inside of the capsid. The calculations have been done based on thermodynamic integration (TI) method combined with all-atomistic molecular dynamic (MD) calculations. A free energy minimum of −19 kJ/mol was found at the entrance of the pore from the outside along the three-fold symmetry axis. This stabilization is from the interaction of negatively charged ETVTP with positively charged capsid methionine residues. This excess free energy concentrates of the reagent at the entrance of the pore by a factor of about 2000. A free energy barrier of approximately 13 kJ/mol was also found near the exit of the pore to the inside of the capsid due to narrow space of the pore surrounded by hydrophobic wall made by proline residues and negatively charged wall by aspartic acid residues. There, ETVTP is partially dehydrated in order to pass through the narrow space, which causes the great free energy loss. Further, the negatively charged residues produce repulsive forces on the ETVTP molecule. In contrast, in the case of the pore along the two-fold symmetry axis, the calculated free energy profile showed shallower free energy minimum, −4 kJ/mol at the entrance in spite of the similarly high barrier, 7 kJ/mol, near the exit of the pore.

Magnetic order and single-ion anisotropy inTb3Ga5O12

Terbium gallium garnet (TGG), Tb$_3$Ga$_5$O$_{12}$, is well known for its applications in laser optics, but also exhibits complex low-temperature magnetism that is not yet fully understood. Its low-temperature magnetic order is determined by means of time-of-flight neutron powder diffraction. It is found to be a multiaxial antiferromagnet with magnetic Tb$^{3+}$ ions forming six sublattices of magnetic moments aligned parallel and anti-parallel to the $\langle100\rangle$ crystallographic directions of the cubic unit cell. The structure displays strong easy-axis anisotropy with respect to a two-fold axis of symmetry in the local orthorhombic environment of the Tb$^{3+}$ sites. The crystal-field splitting within the single-ion ground-state manifold is investigated by inelastic neutron scattering on powder samples. A strong temperature dependence of the quasidoublet ground-state is observed and revised parameters of the crystal-field Hamiltonian are given. The results of bulk magnetic susceptibility and magnetisation measurements are in good agreement with values based on the crystal-field model down to 20~K, where the onset of magnetic correlations is observed.

Distinguishing Between Monomeric scFv and Diabody in Solution Using Light and Small Angle X-ray Scattering.

Depending on the linker length between the V and the V domain, single-chain Fv (scFv) antibody fragments form monomers, dimers (diabodies) or higher oligomers. We aimed at generating a diabody of the anti-MET antibody 3H3 to use it as crystallization chaperone to promote crystallization of the MET ectodomain through the introduction of a pre-formed twofold axis of symmetry. Size exclusion chromatography, however, suggested the protein to be monomeric. Hence, we used scattering techniques applied to solutions to further investigate its oligomerization state. The small angle X-ray scattering (SAXS) curve measured for our protein nicely fits to the scattering curve calculated from the known crystal structure of a diabody. In addition, concentration-dependent photon correlation spectroscopy (PCS) measurements revealed a hydrodynamic radius of 3.4 nm at infinite dilution and a negative interaction parameter , indicating attractive interactions that are beneficial for crystallization. Both SAXS and PCS measurements clearly suggest our antibody fragment to be a diabody in solution. Chemical cross-linking with glutaraldehyde and cell motility assays confirmed this conclusion.

The third structural switch in the archaeal translation initiation factor 2 (aIF2) molecule and its possible role in the initiation of GTP hydrolysis and the removal of aIF2 from the ribosome.

The structure of the γ subunit of archaeal translation initiation factor 2 (aIF2) from Sulfolobus solfataricus (SsoIF2γ) was determined in complex with GDPCP (a GTP analog). Crystals were obtained in the absence of magnesium ions in the crystallization solution. They belonged to space group P1, with five molecules in the unit cell. Four of these molecules are related in pairs by a common noncrystallographic twofold symmetry axis, while the fifth has no symmetry equivalent. Analysis of the structure and its comparison with other known aIF2 γ-subunit structures in the GTP-bound state show that (i) the magnesium ion is necessary for the formation and the maintenance of the active form of SsoIF2γ and (ii) in addition to the two previously known structural switches 1 and 2, eukaryotic translation initiation factor 2 (eIF2) and aIF2 molecules have another flexible region (switch 3), the function of which may consist of initiation of the hydrolysis of GTP and the removal of e/aIF2 from the ribosome after codon-anticodon recognition.

The structure of an iron-containing alcohol dehydrogenase from a hyperthermophilic archaeon in two chemical states.

An iron-containing alcohol dehydrogenase (FeADH) from the hyperthermophilic archaeon Thermococcus thioreducens was crystallized in unit cells belonging to space groups P21, P212121 and P43212, and the crystal structures were solved at 2.4, 2.1 and 1.9 Å resolution, respectively, by molecular replacement using the FeADH from Thermotoga maritima (Schwarzenbacher et al., 2004) as a model. In the monoclinic and orthorhombic crystals the dehydrogenase (molecular mass 41.5 kDa) existed as a dimer containing a twofold noncrystallographic symmetry axis, which was crystallographic in the tetragonal crystals. In the monoclinic and orthorhombic asymmetric units one molecule contained iron and an NADP molecule, while the other did not. The tetragonal crystals lacked both iron and NADP. The structure is very similar to that of the FeADH from T. maritima (average r.m.s. difference for Cα atoms of 1.8 Å for 341 aligned atoms). The iron, which is internally sequestered, is bound entirely by amino acids from one domain: three histidines and one aspartic acid. The coenzyme is in an extended conformation, a feature that is common to the large superfamily of NADH-dependent dehydrogenases that share a classical nucleotide-binding domain. A long broad tunnel passes entirely through the enzyme between the two domains, completely encapsulating the coenzyme.

Easy Synthesis and Crystal Structure of a Novel Ortho Hydroxyl Schiff Base Compound CH2-{CYCLO-C6H10)-NCH-C6H4-OH-2}2

A one-pot and neat reaction procedure is used for the synthesis of CH2-{cyclo-C6H10)-NCH-C6H4-OH-2}2. 1H NMR shows a mixture of ZE and EE isomers in a ratio of 2:0.9. The EE isomer is easily isolated as crystals suitable for the X-ray analysis. 1H,13C NMR and UV-visible spectra of the title compound are studied in different solvents. The crystal structure shows intramolecular H bonds as an EE isomer. The molecule lies about a twofold symmetry axis, passing through the C1 atom. The cyclo-hexyl ring C2-7 shows a chair conformation, with both C2-C1 and C5-N1 bonds in equatorial orientations. The phenolic hydrogen atom H1a forms a good hydrogen bond with the imino nitrogen atom N1 and the N1-C8 bond is short, as expected for a double bond (1.265(4) A).

A 1:2 co-crystal of 2,2'-di-thiodi-benzoic acid and benzoic acid: crystal structure, Hirshfeld surface analysis and computational study.

The asymmetric unit of the title 1:2 co-crystal, C14H10O4S2·2C7H6O2, comprises half a mol-ecule of di-thiodi-benzoic acid [systematic name: 2-[(2-carb-oxy-phen-yl)disulfan-yl]benzoic acid, DTBA], as the mol-ecule is located about a twofold axis of symmetry, and a mol-ecule of benzoic acid (BA). The DTBA mol-ecule is twisted about the di-sulfide bond [the C-S-S-C torsion angle is -83.19 (8)°] resulting in a near perpendicular relationship between the benzene rings [dihedral angle = 71.19 (4)°]. The carb-oxy-lic acid group is almost co-planar with the benzene ring to which it is bonded [dihedral angle = 4.82 (12)°]. A similar near co-planar relationship pertains for the BA mol-ecule [dihedral angle = 3.65 (15)°]. Three-mol-ecule aggregates are formed in the crystal whereby two BA mol-ecules are connected to a DTBA mol-ecule via hy-droxy-O-H⋯O(hydroxy) hydrogen bonds and eight-membered {⋯HOC=O}2 synthons. These are connected into a supra-molecular layer in the ab plane through C-H⋯O inter-actions. The inter-actions between layers to consolidate the three-dimensional architecture are π-π stacking inter-actions between DTBA and BA rings [inter-centroid separation = 3.8093 (10) Å] and parallel DTBA-hy-droxy-O⋯π(BA) contacts [O⋯ring centroid separation = 3.9049 (14) Å]. The importance of the specified inter-actions as well as other weaker contacts, e.g. π-π and C-H⋯S, are indicated in the analysis of the calculated Hirshfeld surface and inter-action energies.

Easy synthesis and crystal structure of a novel ortho hydroxyl Schiff base compound CH2—{cyclo-C6H10)—NCH—C6H4—OH-2}2

A one-pot and neat reaction procedure is used for the synthesis of CH2—{cyclo-C6H10)—NCH—C6H4—OH-2}2. 1H NMR shows a mixture of ZE and EE isomers in a ratio of 2:0.9. The EE isomer is easily isolated as crystals suitable for the X-ray analysis. 1H,13C NMR and UV-visible spectra of the title compound are studied in different solvents. The crystal structure shows intramolecular H bonds as an EE isomer. The molecule lies about a twofold symmetry axis, passing through the C1 atom. The cyclo-hexyl ring C2—7 shows a chair conformation, with both C2—C1 and C5—N1 bonds in equatorial orientations. The phenolic hydrogen atom H1a forms a good hydrogen bond with the imino nitrogen atom N1 and the N1—C8 bond is short, as expected for a double bond (1.265(4) Å).