Twofold Symmetry Axis Research Articles

Crystal structure of {2-[({2-[(2-amino-ethyl)amino]-ethyl}imino)-meth-yl]-6-hy-droxy-phenolato-κ(4) N,N',N'',O (1)}(nitrato-κO)copper(II) ethanol 0.25-solvate.

In the crystal structure of the title mononuclear CuII complex, [Cu(C11H16N3O2)(NO3)]·0.25C2H5OH, the complex molecules are linked by N—H⋯O and O—H⋯O hydrogen bonds, forming a dimer with an approximate non-crystallographic twofold rotation axis of symmetry. In the monomeric unit, the Cu2+ ion exhibits a distorted square-pyramidal configuration, whereby the anionic [HL]− Schiff base ligand binds in a tetradentate fashion via the O and the three N atoms which all are approximately coplanar. The O atom of a nitrate anion occupies the fifth coordination site, causing the CuII atom to move slightly out of the approximate basal plane toward the bound nitrate group. The structure exhibits disorder of the ethanol solvent mol­ecule.

Preparation and structures of two mixed-ligand 4-methylpyridine indium bromide complexes

We describe the structures of two indium complexes obtained during the attempted syntheses of solid-state materials precursors. The geometries of mer-InBr3(pic)31 and [In(μ-OH)Br2(pic)2·2pic]22 (pic = 4-methylpyridine) are distorted octahedra about the metal atoms. Two molecules which differ mainly with respect to the relative orientation of the γ-picoline planes are present in the asymmetric unit of 1, and a trans influence is observed for the ligands. Two indium atoms and two hydroxyl groups form a four atom ring in 2, with the four bromine atoms not coplanar. A two-fold rotational symmetry axis is present with the two indium atoms occupying special positions. A trans influence is also observed. Two nonequivalent γ-picolines not coordinated to the metals are present, one of which forms a hydrogen bond to the hydroxyl group while the other exhibits no strong intermolecular associations.

Entropy-Driven Chiral Order in a System of Achiral Bent Particles.

Why should achiral particles organize into a helical structure? Here, using theory and molecular dynamics simulations we show that at high concentration crescent-shaped particles interacting through a purely repulsive potential form the twist-bend nematic phase, which features helical order of the twofold symmetry axes of particles, with doubly degenerate handedness. Spontaneous breaking of the chiral symmetry is driven by the entropic gain that derives from the decrease in excluded volume in the helical arrangement. Crucial to this purpose is the concave shape of particles. This study is based on a general formulation of the Onsager theory, which includes biaxiality and polarity of phase and particles, in addition to the space modulation of order. Molecular dynamics simulations corroborate the theoretical predictions and provide further insights into the structure of the helical phase.

Crystal structure of tetra-ethyl-ammonium chloride 3,4,5,6-tetra-fluoro-1,2-di-iodo-benzene.

Equimolar qu­anti­ties of tetra­ethyl­ammonium chloride (Et4NCl) and 3,4,5,6-tetra­fluoro-1,2-di­iodo­benzene (o-DITFB or o-C6F4I2) have been co-crystallized in a solution of di­chloro­methane yielding a pure halogen-bonded compound, 3,4,5,6-tetra­fluoro-1,2-di­iodo­benzene–tetra­ethyl ammonium chloride (2/1), Et4N+·Cl−·2C6F4I2, in the form of translucent needles. [(Et4NCl)(o-C6F4I2)2] packs in the C2/c space group. The asymmetric unit includes one mol­ecule of DITFB, one Et4N+ cation located on a twofold rotation axis, and one chloride anion also located on a twofold rotation symmetry axis. This compound has an inter­esting halogen-bonding environment surrounding the halide. Here, the chloride anion acts as a tetra­dentate halogen bond acceptor and forms a distorted square-pyramidal geometry, with I⋯Cl−⋯I angles of 80.891 (6) and 78.811 (11)°, where two crystallographically distinct iodine atoms form halogen bonds with the chloride anion. Resulting from that square-pyramidal geometry are short contacts between some of the adjacent F atoms. Along the b axis, the halogen-bonding inter­action results in a polymeric network, producing a sheet in which the two closest chloride ions are 7.8931 (6) Å apart. The Et4N+ cation alternates in columns with the halide ion. The expected short contacts (shorter than the sum of their van der Waals radii) are observed for the halogen bonds [3.2191 (2) and 3.2968 (2) Å], as well as almost linear angles [170.953 (6) and 173.529 (6)°].

Two-Sided Simultaneous Block of a F- Channel (FLUC)

The recently discovered family of F- channels, the Flucs, are highly selective for F- and function to rescue microorganisms from F- toxicity in acidic environments. Structurally, Fluc is a four pass transmembrane protein that assembles as a dual-topology homodimer. This architecture, where two Fluc subunits orient antiparallel with respect to each other, is unique among ion channels and requires a two-fold symmetry axis parallel to the membrane plane. The symmetry axis further suggests that Fluc may present identical interfaces on both sides of a membrane.In fact, using fibronectin III domain “monobody” blockers specifically selected from a phage display library for nano-molar binding affinity, it was shown that a single Fluc channel is blocked on both sides of a planar lipid bilayer [Stockbridge et. al. Nature Comm., in press]. This leaves open the question of whether the sites of block on either side of the channel can be occupied simultaneously. We approach this question by experimentally testing a two site block model O B1 B2 by analysis of monobody dependent block times in single channel electrophysiology recordings. In the case of symmetric block, this scheme postulates that the dwell times of the B1 and B2 composite blocked state should exhibit monobody concentration dependence. In addition, information about cooperativity, whether negative or positive, between the two blocking sites can be quantitatively determined.

One- and two-dimensional Cd(II) coordination polymers constructed from 2-(2-methyl-1H-benzimidazol-1-yl)acetate ligands.

The one- and two-dimensional polymorphic cadmium polycarboxylate coordination polymers, catena-poly[bis[μ2-2-(2-methyl-1H-benzimidazol-1-yl)acetato-κ(3)N(3):O,O']cadmium(II)], [Cd(C10H9N2O2)2]n, and poly[bis[μ2-2-(2-methyl-1H-benzimidazol-1-yl)acetato-κ(3)N(3):O,O']cadmium(II)], also [Cd(C10H9N2O2)2]n, were prepared under solvothermal conditions. In each structure, each Cd(II) atom is coordinated by four O atoms and two N atoms from four different ligands. In the former structure, two crystallographically independent Cd(II) atoms are located on twofold symmetry axes and doubly bridged in a μ2-N:O,O'-mode by the ligands into correspondingly independent chains that run in the [100] and [010] directions. Chains containing crystallographically related Cd(II) atoms are linked into sheets via π-π stacking interactions. Sheets containing one of the distinct types of Cd(II) atom are stacked perpendicular to [001] and alternate with sheets containing the other type of Cd(II) atom. The second complex is a two-dimensional homometallic Cd(II) (4,4) net structure in which each Cd(II) atom is singly bridged to four neighbouring Cd(II) atoms by four ligands also acting in a μ2-N:O,O'-mode. A square-grid network results and the three-dimensional supramolecular framework is completed by π-π stacking interactions between the aromatic ring systems.

Structure and properties of 9,10,11,12,13,14-hexahydro-9,10[1′,4′]-benzenoanthracene and 9,10,11,12,13,14,15,16-octahydro-9,10[1′,4′]-benzenoanthracene

The title compounds were prepared by 4πs+4πs photochemical cycloaddition between anthracene and 1,3-cyclohexadiene, followed by catalytic hydrogenation. The results confirm the structure of the initial cycloadduct, 9,10,11,12,13,14-hexahydro-9,10[1′,4′]-benzenoanthracene (1), which in the crystal exhibits positional disorder about the cyclohexadiene-derived fragment that is only partially resolved. The origin of the disorder is considered in light of the crystallographic packing interactions and compared with intermolecular contacts in the hydrogenated derivative, 9,10,11,12,13,14,15,16-octahydro-9,10[1′,4′]-benzenoanthracene (2), which is not disordered. The asymmetric unit of 2 contains one-half of a molecule situated about a two-fold symmetry axis. Both structures contain relatively long interannular bonds between the bridgehead carbons of the anthracene- and cyclohexadiene-derived fragments, in agreement with ab initio calculations and considered in terms of bond strain in the carbon framework of these compounds.

High-resolution crystal structures of alternate forms of the human CD44 hyaluronan-binding domain reveal a site for protein interaction.

Two new crystal structures of the extracellular hyaluronan-binding domain of human CD44 are described at high resolution. A hexagonal crystal form at 1.60 Å resolution and a monoclinic form at 1.08 Å resolution both have two molecules in the asymmetric unit arranged about a similar noncrystallographic twofold axis of symmetry. These structures are compared with those previously reported at 2.20 Å resolution to show that the fold is quite resistant to structural deformation in different crystal environments. Unexpectedly, a short peptide is found in the monoclinic crystals at a site remote from the known hyaluronan-binding groove. The peptide with a valine at the carboxy-terminus must have co-purified from the bacterial expression host and binds on the opposite side of the domain from the known hyaluronan-binding groove. This opportunistic binding may identify a site of interaction used as CD44 assembles with other proteins to accomplish effective signaling regarding changes to the extracellular environment.

Crystal structure of 8-hy-droxy-quinoline: a new monoclinic polymorph.

In an attempt to grow 8-hy­droxy­quinoline–acetamino­phen co-crystals from equimolar amounts of conformers in a chloro­form–ethanol solvent mixture at room temperature, the title compound, C9H7NO, was obtained. The mol­ecule is planar, with the hy­droxy H atom forming an intra­molecular O—H⋯N hydrogen bond. In the crystal, mol­ecules form centrosymmetric dimers via two O—H⋯N hydrogen bonds. Thus, the hy­droxy H atoms are involved in bifurcated O—H⋯N hydrogen bonds, leading to the formation of a central planar four-membered N2H2 ring. The dimers are bound by inter­molecular π–π stacking [the shortest C⋯C distance is 3.2997 (17) Å] and C—H⋯π inter­actions into a three-dimensional framework. The crystal grown represents a new monoclinic polymorph in the space group P21/n. The mol­ecular structure of the present monoclinic polymorph is very similar to that of the ortho­rhom­bic polymorph (space group Fdd2) studied previously [Roychowdhury et al. (1978 ▶). Acta Cryst. B34, 1047–1048; Banerjee & Saha (1986 ▶). Acta Cryst. C42, 1408–1411]. The structures of the two polymorphs are distinguished by the different geometries of the hydrogen-bonded dimers, which in the crystal of the ortho­rhom­bic polymorph possess twofold axis symmetry, with the central N2H2 ring adopting a butterfly conformation.

Structural differences among subfamilies of EF-hand proteins-A view from the pseudo two-fold symmetry axis

We have analyzed the conformations of EF-lobes, adjacent pairs of EF-hand domains, in a coordinate system based on the approximate two-fold (z) axis that relates the two EF-hands. Two parameters - dE(ø), the azimuthal angle between the y-axis and the projection of the offset vector to helix E onto the yz-plane, and δdF(ø), the difference angle between the two helices (F1 and F2) of odd and even domains--characterize the openness of a single EF-hand domain and of an EF-lobe, respectively. We describe and compare values of dE(ø) and of δdF(ø) for EF-hand proteins of five subfamilies--CTER, CPV, S100, PARV, CALP--in calci- and apo- forms, with and without bound target proteins. Each subfamily has characteristic changes associated with binding calcium and/or target proteins.

Crystal Structure Explains Crystal Habit for the Antiviral Drug Rimantadine Hydrochloride

The crystal structure of the antiviral drug rimantadine hydrochloride, C12H22N+ Cl−, has been elucidated by a single-crystal X-ray structure analysis. The structure consists of 1-(1- adamantyl)ethanamine (rimantadinium) cations and chloride anions. The Cl− anions link the rimantadinium cations via N-H...Cl hydrogen bonds into infinite rectangular chord-like structural units with charged groups in the inner channel and aliphatic groups on the surface, and oriented along the unit cell c axis. In contrast to strong electrostatic and hydrogen bonding inner interactions the chords in the crystal are held together by weak van der Waals forces only. A two-fold symmetry axis passes through the center of the chord. By indexing of the crystal faces it has been shown that the maximal dimension of the needle-like crystals coincides with the direction of the unit cell c axis. These structural features explain the crystal habit and the anisotropy of the mechanical properties of rimantadine hydrochloride crystals observed upon slicing and cleavage.

Crystal structure of a heterotetrameric NMDA receptor ion channel.

N-Methyl-D-aspartate (NMDA) receptors belong to the family of ionotropic glutamate receptors, which mediate most excitatory synaptic transmission in mammalian brains. Calcium permeation triggered by activation of NMDA receptors is the pivotal event for initiation of neuronal plasticity. Here, we show the crystal structure of the intact heterotetrameric GluN1-GluN2B NMDA receptor ion channel at 4 angstroms. The NMDA receptors are arranged as a dimer of GluN1-GluN2B heterodimers with the twofold symmetry axis running through the entire molecule composed of an amino terminal domain (ATD), a ligand-binding domain (LBD), and a transmembrane domain (TMD). The ATD and LBD are much more highly packed in the NMDA receptors than non-NMDA receptors, which may explain why ATD regulates ion channel activity in NMDA receptors but not in non-NMDA receptors.

AAV8 capsid variable regions at the two-fold symmetry axis contribute to high liver transduction by mediating nuclear entry and capsid uncoating

Adeno-associated virus serotype 8 (AAV8) is a promising vector for liver-directed gene therapy. Although efficient uncoating of viral capsids has been implicated in AAV8׳s robust liver transduction, much about the biology of AAV8 hepatotropism remains unclear. Our study investigated the structural basis of AAV8 liver transduction efficiency by constructing chimeric vector capsids containing sequences derived from AAV8 and AAV2 – a highly homologous yet poorly hepatotropic serotype. Engineered vectors containing capsid variable regions (VR) VII & IX from AAV8 in an AAV2 backbone mediated near AAV8-like transduction in mouse liver, with higher numbers of chimeric genomes detected in whole liver cells and isolated nuclei. Interestingly, chimeric capsids within liver nuclei also uncoated similarly to AAV8 by 6 weeks after administration, in contrast with AAV2, of which a significantly smaller proportion were uncoated. This study links specific AAV capsid regions to the transduction ability of a clinically relevant AAV serotype.

Structural reinvestigation of the photoluminescent complex [NdCl2(H2O)6]Cl

The structure of the photoluminescent compound hexaaquadichloridoneodymium(III) chloride has been redetermined from single-crystal X-ray diffraction data at 100 K, with the aim of providing an accurate structural model for the bulk crystalline material. The crystal structure may be described as a network of [NdCl2(H2O)6](+) cations with distorted square-antiprism geometry around the Nd(III) centre. The Nd(III) cation and the nonbonded Cl(-) anion are both located on twofold symmetry axes. The crystal packing consists of three different neodymium pairs linked by a three-dimensional network of O-H···Cl intermolecular interactions. The pair distribution function (PDF) calculated from the experimentally determined structure is used for the discussion of the local structure.

Human Rhinovirus Subviral A Particle Binds to Lipid Membranes over a Twofold Axis of Icosahedral Symmetry

Minor group human rhinoviruses bind low-density lipoprotein (LDL) receptors for endocytosis. Once they are inside endosomes, the acidic pH triggers their dissociation from the receptors and conversion into hydrophobic subviral A particles; these attach to the membrane and transfer their single-strand, positive-sense RNA genome into the cytosol. Here, we allowed human rhinovirus 2 (HRV2) A particles, produced in vitro by incubation at pH 5.4, to attach to liposomes; cryo-electron microscopy 3-dimensional single-particle image reconstruction revealed that they bind to the membrane around a 2-fold icosahedral symmetry axis.

The three-dimensional structures of bacterial reaction centers

This review presents a broad overview of the research that enabled the structure determination of the bacterial reaction centers from Blastochloris viridis and Rhodobacter sphaeroides, with a focus on the contributions from Duysens, Clayton, and Feher. Early experiments performed in the laboratory of Duysens and others demonstrated the utility of spectroscopic techniques and the presence of photosynthetic complexes in both oxygenic and anoxygenic photosynthesis. The laboratories of Clayton and Feher led efforts to isolate and characterize the bacterial reaction centers. The availability of well-characterized preparations of pure and stable reaction centers allowed the crystallization and subsequent determination of the structures using X-ray diffraction. The three-dimensional structures of reaction centers revealed an overall arrangement of two symmetrical branches of cofactors surrounded by transmembrane helices from the L and M subunits, which also are related by the same twofold symmetry axis. The structure has served as a framework to address several issues concerning bacterial photosynthesis, including the directionality of electron transfer, the properties of the reaction center-cytochrome c 2 complex, and the coupling of proton and electron transfer. Together, these research efforts laid the foundation for ongoing efforts to address an outstanding question in oxygenic photosynthesis, namely the molecular mechanism of water oxidation.

The Enterovirus 71 A-particle Forms a Gateway to Allow Genome Release: A CryoEM Study of Picornavirus Uncoating

Since its discovery in 1969, enterovirus 71 (EV71) has emerged as a serious worldwide health threat. This human pathogen of the picornavirus family causes hand, foot, and mouth disease, and also has the capacity to invade the central nervous system to cause severe disease and death. Upon binding to a host receptor on the cell surface, the virus begins a two-step uncoating process, first forming an expanded, altered “A-particle”, which is primed for genome release. In a second step after endocytosis, an unknown trigger leads to RNA expulsion, generating an intact, empty capsid. Cryo-electron microscopy reconstructions of these two capsid states provide insight into the mechanics of genome release. The EV71 A-particle capsid interacts with the genome near the icosahedral two-fold axis of symmetry, which opens to the external environment via a channel ∼10 Å in diameter that is lined with patches of negatively charged residues. After the EV71 genome has been released, the two-fold channel shrinks, though the overall capsid dimensions are conserved. These structural characteristics identify the two-fold channel as the site where a gateway forms and regulates the process of genome release.

Bootstrap Elasticity II: Corrections and Extensions

The purpose of this paper is to correct misconceptions in a previous paper and to construct correspondingly correct minimal constitutive representations for trigonal 32, tetragonal, and hexagonal symmetries. These results emphasize the strong interplay between shearing and secondary twofold axes of symmetry.

Ion-selective and complexation properties, vibrational spectra, and crystal and molecular structure of 1,5-bis[2-(hydroxyethoxyphosphoryl)phenoxy]-3-oxapentane

The ion-selective properties of 1,5-bis[2-(hydroxyethoxyphosphoryl)phenoxy]-3-oxapentane H2R2 have been described. The molecular and crystal structure of H2R2 has been determined by powder X-ray crystallography and IR spectroscopy. The molecule has the twofold symmetry axis, orthorhombic crystal system, space group Pbcn, a = 16.830(2) A, b = 8.866(15) A, c = 15.7190(2) A, V = 2346.1(6) A3, Z = 4. A new CuR2 · 2H2O complex has been synthesized and characterized.

(±)-(rel-3R,3′R)-1,1′-Dimethyl-3,3′-bipyrrolidine-2,2′-dithione

The asymmetric unit of the racemic title compound, C10H16N2S2, a C 2-symmetric bis­(thiol­actam), contains one half-mol­ecule, the complete mol­ecule being generated by a twofold axis symmetry operation. The five-membered ring is nearly planar, with a maximum deviation of 0.025 (1) Å. In the crystal, the mol­ecules are linked via weak C—H⋯S inter­actions, forming infinite chains along the b-axis direction.