Twofold Symmetry Axis Research Articles

Mapping specific functions in the capsid structure of canine parvovirus and feline panleukopenia virus using infectious plasmid clones

DNA sequences between 0 and 98.8 genome map units (m.u.) from canine parvovirus (CPV) and feline panleukopenia virus (FPV) were cloned into plasmid vectors to form infectious molecular clones. Those plasmids were transfected into permissive cells and viruses recovered were shown to contain intact genomes, having regenerated the complete viral 5′ ends up to 100 m.u. The viruses derived from the plasmids were compared to the original viruses, and shown to be indistinguishable in antigenic type, hemagglutination (HA) type and host range. The plasmid origin of the viruses was shown by preparing recombinant clones between CPV and FPV, and demonstrating the recombinant nature of the resulting viruses by restriction mapping and by sequencing viral DNA across the recombination sites. The sequences of our wild-type isolates CPV-d and FPV-b were completed, revealing 50 nucleotide sequence differences, of which 16 determined coding changes—5 in NS-1, 2 in NS-2, and 9 in VP-2 protein. The sequences of the 5′ ends (95.3–100 m.u.) of both viruses were also determined. Analysis of recombinant viruses mapped both CPV- and FPV-specific antigenic epitopes, the pH dependence of HA, and sequences affecting canine host range of the viruses within the VP-1 and VP-2 structural protein genes. Most of the specific changes were shown to be either on, or within one amino acid of, the surface of the virus capsid, indicating that the exposed surface of the parvovirus capsid plays an important role in determining a number of virus functions. The specific epitopes were affected by differences in a raised area on the capsid (“threefold spike”), while the pH dependence of HA difference was adjacent to a depression in the surface of the capsid at the twofold axis of symmetry.

Transmission-electron-microscopy studies of small dislocation loops in Al76Si4Mn20 icosahedral phase.

Small dislocation loops with characteristic diffraction contrast of black-white lobes have been observed experimentally in annealed ${\mathrm{Al}}_{76}$${\mathrm{Si}}_{4}$${\mathrm{Mn}}_{20}$ quasicrystalline icosahedral phase by using transmission electron microscopy. The variation of the features of the diffraction-contrast images of the small dislocation loops with experimental conditions has been observed and computer simulated systematically. By taking the Burgers vector b and the normal n of the loops to be along the [100100] direction, i.e., parallel to one of the twofold symmetry axes, we have arrived at good agreement between the observed and computer-simulated features of the diffraction-contrast images.

Structure of a five-coordinate copper(II) hexaaza macrotricyclic complex: chloro(1,3,6,9,11,14-hexaazatricyclo[12.2.1.16,9]octadecane)copper(II) perchlorate

CuCl(C12H26N6)) CIO4, Mr = 4527, ortho- rhombic, P212~2, a = 14.124 (11), b = 9.837 (4), c = 6.570 (4) A, V= 912.8 (2)/~3, Z = 2, Ox = 1.647 g cm -3, a(Mo Ka) = 0.71069 A, /z = 14-9 cm- ~, F(000) = 470, T= 291 K, R = 0.059 for 649 reflections with I ___ 3~r(/). The Cu ion is coordi- nated to four N atoms of the macrocycle and a C1- ion to form a distorted square-pyramidal geometry. The cation possesses crystallographic twofold sym- metry through the Cu--CI bond. The Cu ion lies 0.316 (1)A above the basal coordination plane. The Cu--N (2.043(8) and 2.022 (8) /~) and Cu--C1 (2.483 (4) ~) coordination bond distances are normal. Two 1,3-diazacyclopentane ring moieties of the ligand are in the same direction as the C1- ligand and are almost perpendicular to the ruffled 14- membered macrocycle. The perchlorate anion which is on the twofold symmetry axis is statistically dis- ordered in two positions. Introduction. Macrocyclic complexes show enhanced thermodynamic and kinetic stabilities and the

Correlations between nuclear magnetic resonance spectra and crystal structure. III. A13C nuclear magnetic resonance study in the solid state of bis(xanthato) complexes of mercury(II); The crystal and molecular structure of bis(n-propyl-dithiocarbonato)mercury(II)

The cross-polarization magic angle carbon-13 nmr spectra of a series of bis(xanthato) complexes of mercury(II) are reported; [Hg(S2COR)2] n R=Me, Et, n Pr and i Pr. The spectra correlate well with the known crystal structures of theR=Me, Et, and i Pr compounds and with that of theR= n Pr derivative for which a single-crystal X-ray diffraction study is also reported. The X-ray analysis of [Hg(S2CO n Pr)2] n shows that this compound adopts a two-dimensional structure comprised of connected 16-membered rings which arise as a result of bridgingn-propylxanthate ligands. The mercury atom lies on a crystallographic twofold axis of symmetry and exists in a distorted tetrahedral geometry with two unique Hg-S bond distances of 2.418(3) and 2.835(4) A. Unit-cell dimensions for [Hg(S2CO n Pr)2] n are:a=7.371(3),b=8.534(4),c=11.618(4) A andZ=2 for the orthorhombic space groupP21212. The structure was refined by a full-matrix least-squares procedure to finalR=0.047 andR w =0.044 for 899 reflections withI≥2.5σ(I). While the solid state nmr spectra provide information on molecular (and crystallographic) symmetry they do not provide sufficient detail to enable structure determination for the [Hg(S2COR)2] compounds.

Synthesis, nuclear magnetic resonance, and X-ray investigations of 1,10-diazacyclooctadeca-2,9-dione

The structure of the title compound has been investigated in the solid state and in solution by X-ray and NMR methods, respectively. The crystals are triclinic, space groupP¯1, with cell dimensions:a=9.616(5),b=9.923(9),c=10.21(1)A,α=118.42(4)°,β=96.10(5)°, γ=94.77(5)°. The structure was solved by direct methods, and refined against 3051 unique reflections by a full-matrix, least-squares procedure, givingR=0.049. A twofold symmetry element in the molecule, found from1H-NMR investigations, has been established by X-ray investigations to be an approximate twofold symmetry axis, bisecting the C(5)-C(6) and C(14)-C(15) bonds.

Single-crystal EPR and ENDOR study of nitrogenase from clostridium pasteurianum

The molybdenum-iron (MoFe) protein of nitrogenase from Clostridium pasteurianum forms monoclinic crystals in space group P2 1. The unit cell comprises two molecules, each of which possesses a molecular twofold symmetry axis and binds two chemically identical molybdenum-iron cofactors (M centers). Thus, there are four magnetically distinct M centers within the unit cell related by two different symmetry operations: a molecular twofold axis of symmetry in the bc ∗ plane relates the two EPR centers within a molecule; a crystallographic twofold screw axis of symmetry along the b axis of the unit cell relates the two different molecules in a unit cell. Single-crystal EPR studies at X-band (9.5 GHz) and Q-band (35 GHz) microwave frequencies have been employed to determine g tensors in the crystallographic frame for the four magnetically distinct M centers. Determination of these tensors has been achieved by a novel procedure that relies heavily on the symmetry relations between sites; it rests primarily on measurements that only involve rotation of the magnetic field parallel to a single plane of the crystal and uses g values from frozen-solution samples instead of additional rotations. Single-crystal 1H ENDOR spectra of the M centers are presented.

The crystal and molecular structure of [(C 5HMe 4)TiBr(μ-O)] 4 and [(C 5Me 5)TiBr(μ-O)] 3, by-products from the preparation of titanocene dibromides

The compounds [(C 5HMe 4)TiBr(μ-O] 4 (I) and [(C 5Me 5)TiBr(μ-O)] 3 (II) result from hydrolysis of (C 5HMe 4)TiBr 3 and (C 5Me 5)TiBr 3, respectively, in THF with aqueous HBr. They appear as byproducts if during the preparation of the corresponding titanocene dibromides air is accidentally introduced, or if substoichiometric amounts of reducing agents are present prior to addition of aqueous HBr. Such conditions cause formation of the cyclopentadienyltitanium dibromides or tribromides. The molecule of I forms a planar eight-membered titanoxane cycle with a two-fold symmetry axis perpendicular to the plane of the cycle. The TiOTi angles are alternately 149 and 176° whereas the OTiO angles are nearly constant at 103–106°. The six-membered titanoxane cycle in II is planar except for the oxygen atom which connects the titanium atoms bearing those C 5Me 5 ligands orientated on the same side with respect to the plane; displacement of the oxygen atom is 0.4 Å.

Four-Stranded DNA Helices: Conformational Analysis of Regular Poly(dT) · Poly(dA) · Poly(dA) · Poly(dT) Helices with Various Types of Base Binding

The paper presents results obtained in conformational analysis of homopolymeric four-stranded poly(dT).poly(dA).poly(dA).poly(dT) DNA helices in which the pairs of strands with identical bases are parallel and have a two-fold symmetry axis. All possible models of base binding to yield a symmetric complex have been considered. The dihedral angles of sugar-phosphate backbones and helix parameters, which are consistent with the minima of conformational energy for four-stranded DNAs, have been determined using the results of optimization of conformational energy calculated at atom-atom approximation. Potential energy is shown to depend on the structure of base complexes and on the mutual orientation of unlike strands. Possible biological functions of four-stranded helices are discussed.

Wide-line 2H n.m.r. study of perdeuterated pyridine imbibed in a premium coal

The motion of perdeuterated pyridine imbibed in Argonne premium high-volatile coal (no. 601) has been studied by wide-line 2H n.m.r. spectroscopy. The coal sample had been saturated with perdeuterated pyridine for several days, then evacuated until the pyridine reached a concentration of 3.5%. The entrapped pyridine molecules undergo two tyes of rotation about the twofold symmetry axis: rapid diffusional rotation with a correlation time of 1 × 10 −7 s; and 180 ° jumps with a residence time of 6 × 10 −6 s. It is estimated that roughly half of the pyridine molecules execute each kind of motion. There is no evidence for a pyridine fraction that executes rapid isotropic rotation. The anisotropic nature of the rotation indicates that the interaction between pyridine and the coal structure is strong enough to prevent isotropic rotation.

Gd 3+ EPR study of phase transitions in A NH 4Nd(SO 4) 2·4H 2O single crystal and superposition-model calculation of the zero-field splitting parameters

The phase transitions undergone by a NH 4Nd(SO 4) 2·4H 2O (ANST) single crystal have been studied via the EPR of the Gd 3+ ion between 3.8 and 304 K. Three first-order phase transitions, at 280±0.5 K, at 176±0.5 K and at 19±1 K have been found to occur, as indicated by the behaviour of the overall splittings of EPR lines and that of the EPR linewidths. The spin-Hamiltonian parameters for Gd 3+ at room temperature have been evaluated from the positions of the allowed EPR lines by the use of a least-squares fitting procedure. The local symmetry of the Gd 3+ ion in an ANST host lattice has been deduced to be monoclinic, with the two-fold symmetry axis parallel to the magnetic z axis. The absolute sign of the zero-field splitting parameter b 0 2 for the Gd 3+ ion in ANST has been determined to be positive by using the superposition model of Newman; the intrinsic parameters, b 2 and b 4, for Gd 3+ in the ANST crystal have been calculated to be -5.263 and 0.021 GHz, respectively, with t 2 = 8.5, t 4 = 14.0, associated with an angular distortion of Δθ = 1.5° of the ligand ion positions.

Molecular structure of leucine aminopeptidase at 2.7-A resolution.

The three-dimensional structure of bovine lens leucine aminopeptidase (EC 3.4.11.1) complexed with bestatin, a slow-binding inhibitor, has been solved to 3.0-A resolution by the multiple isomorphous replacement method with phase combination and density modification. In addition, the structure of the isomorphous native enzyme has been refined at 2.7-A resolution, and the current crystallographic R factor is 0.169 for a model that includes the two zinc ions and all 487 amino acid residues comprising the asymmetric unit. The enzyme is physiologically active as a hexamer, which has 32 symmetry and is triangular in shape with a triangle edge length of 115 A and maximal thickness of 90 A. The monomers are crystallographically equivalent and each is folded into two unequal alpha/beta domains connected by an alpha-helix to give a comma-like shape with approximate maximal dimensions of 90 x 55 x 55 A3. The secondary structural composition is 40% alpha-helix and 19% beta-strand. The N-terminal domain (160 amino acids) mediates trimer-trimer interactions and does not appear to participate directly in catalysis. The C-terminal domain (327 amino acids) is responsible for catalysis and binds the two zinc ions, which are 2.88 A apart. The pair of metal ions is located near the edge of an eight-stranded, saddle-shaped beta-sheet. One zinc ion is coordinated by carboxylate oxygen atoms of Asp-255, Asp-332, and Glu-334 and the carbonyl oxygen of Asp-332. The other zinc ion is coordinated by the carboxylate oxygen atoms of Asp-255, Asp-273, and Glu-334. The active site also contains two positively charged residues, Lys-250 and Arg-336. The six active sites are themselves located in the interior of the hexamer, where they line a disk-shaped cavity of radius 15 A and thickness 10 A. Access to this cavity is provided by solvent channels that run along the twofold symmetry axes.

Anin situelectron microscope investigation of the icosahedral-to-decagonal quasicrystalline transformation in Al-20 at.% Mn

Abstract The solid-state transformation behaviour of the icosahedral phase in rapidly solidified Al-20 at.% Mn has been investigated by in situ heating experiments in the transmission electron microscope. As-rapidly-solidified Al-20 at.% Mn consists mainly of a dendritic icosahedral phase, with a small amount of interdendritic f.c.c. α-Al. During subsequent heat treatment at temperatures below about 500°C, the dendritic icosahedral phase grows and consumes the interdendritic α-Al. At about 500°C the decagonal phase nucleates near icosahedral dendrite and grain boundaries and then grows into the icosahedral matrix by lateral motion of ledges 10–20 nm high across facet planes normal to the twofold symmetry axes. At about 600°C the decagonal phase transforms into a crystalline phase. The present study suggests that solid-state decomposition of the icosahedral phase is the mechanism of decagonal phase formation in as-rapidly-solidified Al-Mn alloys.

Spectroscopic studies on monomers and dimers of thiaporphyrins

Synthesis and spectroscopic properties of porphyrin macrocycles with sulphur as the heteroatom in the porphyrin core have been studied. Electronic absorption spectra of these macrocycles show porphyrin-like behaviour with a strong Soret band and weakQ-bands. Substitution of the -NH groups of tetraphenylporphyrin (TPPH2) by sulphur causes a red shift of all the absorption bands and the magnitude of the red shift depends on the number of sulphur atoms substituted. Both the mono and dications of dithiaporphyrins (S2TPP) show larger bathochromic shifts ofQ-bands relative to TPPH2 indicating a stronger resonance interaction with the phenyl groups. A positive shift for both oxidation and reduction potentials is observed upon substitution of sulphur atoms.1H NMR spectra of symmetrically substituted dithiaporphyrins show two sharp singlets for pyrrole protons and thiophene protons confirming the presence of a two-fold axis of symmetry. Only monothia derivatives (STPPH) form metal complexes [Ni(II), Cu(II)] and these metal complexes are five-coordinate with an apical chloride ligand.

Diisopropylammonium chloride

C6H16N+.Cl-,Mr = 137.65, orthorhombic, P2(1)2(1)2(1), a = 7.825 (4), b = 8.257 (1), c = 13.268 (2) A, V = 857.3 (5) A3, Z = 4, Dx = 1.066 g cm-3, lambda(Mo K alpha) = 0.71073 A, mu = 3.6 cm-1, F(000) = 304, T = 295 K, R = 0.030 for 556 observations (of 901 unique data). Each H on the N atom is hydrogen bonded to a Cl atom. N--H...Cl bond lengths (N--Cl distance) are 3.180 (3) and 3.163 (3) A with N--H...Cl angles 176 (2) and 175 (2) degrees respectively. Each Cl atom is involved in two hydrogen bonds. The cation has an approximate twofold axis of symmetry.

Direct observations of enzymes and their complexes by scanning tunneling microscopy

Scanning tunneling microscopy (STM) has been used as a method of studying the relationships between the enzymes of muscle glycogenolysis. In skeletal muscles the activation of phosphorylase b is catalyzed by phosphorylase kinase. This interaction is believed to occur in vivo as part of a multienzyme complex. The molecular structures of phosphorylase b and phosphorylase kinase have been visualized by STM.1 Phosphorylase b can be seen in dimeric and tetrameric forms as well as linear and circular aggregates. Individual molecules of phosphorylase kinase image as planar, bilobate structures with a twofold axis of symmetry and a central depression. STM has also been used to visualize complexes between phosphorylase kinase and its substrate, phosphorylase b.

Exchange and crystal-field interactions of Ho3+ in GdAl2: a single-crystal NMR study

The hyperfine splitting of holmium, as a dilute (1%) substituent in ferromagnetic GdAl2 has been studied by spin-echo NMR at liquid helium temperatures. The measurements were made on oriented single crystals, with fields up to 8 T applied along twofold, threefold and fourfold crystallographic symmetry axes. The field dependence of the hyperfine splitting is interpreted in terms of the standard three-parameter mean-field model for lanthanide ions at sites of cubic symmetry. The crystal-field coefficients are found to be 30% to 40% smaller than those for pure HoAl2; moreover, the molecular field seen by the holmium ion is more than 20% below the lower bound derived from a current model of exchange in RAl2 compounds. These unexpected results are strikingly confirmed by a recent analysis of FMR data on a dilute Ho:GdAl2 alloy. Possible explanations are considered.

Structural analysis of the S-Layer of Lampropedia hyalina

The two-dimensional (2D) structure of the regularly structured surface layer (S-layer) of the gram-negative eubacterium Lampropedia hyalina has been determined at the molecular level to a nominal resolution of 2.1 nm by transmission electron microscopy and digital image processing. The inner, or “perforate,” layer consists of dimeric block-shaped units located at two-fold symmetry axes. These morphological dimers associate around three-fold symmetry axes to form a continuous layer with p6 symmetry and a lattice constant of 14.6 ± 0.4 nm. Scanning transmission electron microscopy (STEM) yields a mass-per-area (MPA) value for the perforate layer of 3.5 kDa/nm 2. The outer, or “punctate,” layer is composed of long, roughly cylindrical units centered on six-fold symmetry axes, which are connected by six fine linking arms joining at the three-fold symmetry axes to create a hexagonal layer with a lattice constant of 25.6 ± 0.5 nm. The MPA of the “composite”-i.e., perforate plus punctate—layer is 10.2 kDa/nm 2.

Structural Differences between Al-Fe-Cu and Al-Li-Cu Quasicrystals Studied by High-Resolution Electron Microscopy

Stable icosahedral phases of Al-Fe-Cu and Al-Li-Cu, which are recognized as icosahedral quasicrystals corresponding to face-centered and simple 6D-hypercubic lattices, respectively, were examined by high-resolution electron microscopy with the incident beam parallel to the two-fold symmetry axis. Images observed were analyzed in detail with the aid of computerized image processing. In the image of Al-Li-Cu, a contrast modulation of about τ3 times distance of lattice spacing was observed on lattice fringes perpendicular to the 5-fold symmetry axes, whereas in Al-Fe-Cu, complex contrast modulations with various distances of 2, 3, and 5 lattice spacings were observed on the lattice fringes perpendicular to the same axes.

Dynamic interchange between

A temperature-dependent reversible change in local symmetry, as well as substantial line broadening, has been observed in the X-band electron-paramagnetic-resonance spectrum of the center [${\mathrm{FeO}}_{4}$/Na${]}^{0}$ in \ensuremath{\alpha}-quartz in the range 40--70 K. Models for this effect, involving sodium ion hopping across a twofold-symmetry axis of the crystal, are discussed qualitatively. Line-shape analysis yields an Arrhenius activation energy of 39(1) meV and preexponential factor of 1.3(1)\ifmmode\times\else\texttimes\fi{}${10}^{\mathrm{\ensuremath{-}}12}$ s, consistent with values in the literature obtained from Debye analysis of dielectric relaxation effects.

On the dynamics of ethene molecules sorbed in the zeolite NaY

The deuteron magnetic resonance spectra of ethene-d 4 sorbed in the zeolite NaY at one molecule/supercage loading level were measured at temperatures between 290 and 78 K. From the solid-state patterns at low and the isotropically averaged singlet spectra at high temperatures, the correlation times of the anisotropic rotation around the twofold symmetry axis normal to the molecular plane as well as of the isotropic site-exchange motion are deduced. The intracrystalline diffusion coefficient is derived as D/ m 2 s −1 = 3.4 · 10 −7 exp( −2000 T K −1 ).