Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein

Conserved among all coronaviruses are four structural proteins: the matrix (M), small envelope (E), and spike (S) proteins that are embedded in the viral membrane and the nucleocapsid phosphoprotein (N), which exists in a ribonucleoprotein complex in the lumen. The N-terminal domain of coronaviral N proteins (N-NTD) provides a scaffold for RNA binding, while the C-terminal domain (N-CTD) mainly acts as oligomerization modules during assembly. The C terminus of the N protein anchors it to the viral membrane by associating with M protein. We characterized the structures of N-NTD from severe acute respiratory syndrome coronavirus (SARS-CoV) in two crystal forms, at 1.17 A (monoclinic) and at 1.85 A (cubic), respectively, resolved by molecular replacement using the homologous avian infectious bronchitis virus (IBV) structure. Flexible loops in the solution structure of SARS-CoV N-NTD are now shown to be well ordered around the beta-sheet core. The functionally important positively charged beta-hairpin protrudes out of the core, is oriented similarly to that in the IBV N-NTD, and is involved in crystal packing in the monoclinic form. In the cubic form, the monomers form trimeric units that stack in a helical array. Comparison of crystal packing of SARS-CoV and IBV N-NTDs suggests a common mode of RNA recognition, but they probably associate differently in vivo during the formation of the ribonucleoprotein complex. Electrostatic potential distribution on the surface of homology models of related coronaviral N-NTDs suggests that they use different modes of both RNA recognition and oligomeric assembly, perhaps explaining why their nucleocapsids have different morphologies.

Analysis of void volumes in proteins and application to stability of the p53 tumour suppressor protein

We have developed a new method for the analysis of voids in proteins (defined as empty cavities not accessible to solvent). This method combines analysis of individual discrete voids with analysis of packing quality. While these are different aspects of the same effect, they have traditionally been analysed using different approaches. The method has been applied to the calculation of total void volume and maximum void size in a non-redundant set of protein domains and has been used to examine correlations between thermal stability and void size. The tumour-suppressor protein p53 has then been compared with the non-redundant data set to determine whether its low thermal stability results from poor packing. We found that p53 has average packing, but the detrimental effects of some previously unexplained mutations to p53 observed in cancer can be explained by the creation of unusually large voids. (C) 2004 Elsevier Ltd. All rights reserved.

Low-temperature determination of theophylline dimethyl sulfoxide solvate

The title solvate, C7H8N4O2 center dot C2H6OS, was obtained unintentionally from a cocrystal screen involving theophylline and isophthalic acid. One molecule each of theophylline and dimethyl sulfoxide is present in the asymmetric unit. The packing consists of molecular sheets lying parallel to the ( 040) series of lattice planes, in which each theophylline molecule is hydrogen bonded to one dimethyl sulfoxide molecule through an N-H center dot center dot center dot O [2.7658 (15) angstrom] hydrogen bond. This particular hydrogen-bond donor was found to be used in this type of interaction in a variety of other crystal structures of theophylline.

21-Deoxycortisone (17 alpha-hydroxy4-pregnene-3,11,20-trione)

The title compound, C21H28O4, a synthetic glucocorticoid, crystallizes with a single molecule in the asymmetric unit. Ring A is almost in a half-chair conformation, rings B and C are almost in chair conformations, and ring D is between a twist and a 13 beta-envelope conformation. The A/B ring junction is quasi-trans, whereas the B/C and C/D ring junctions both approach trans characteristics. The molecule as a whole is slightly convex towards the beta side, with an angle of 9.60 (2)degrees between the C10-C19 and C13-C18 vectors. Molecular-packing and hydrogen-bonding (both intra- and inter-molecular) interactions play a major role in the structural association of the compound.

Polymorphism in [Co(SCN)(4)(ppz-H)(2)] (ppz, piperazine)

A one-pot reaction of [Co(NO3)(2)center dot 6H(2)O and piperazine] with NH4SCN/NaSCN in water-methanol (1:1) solvent leads to two polymorphs of [Co(SCN)(4)(ppz-H)(2)] (ppz, piperazine) (I and II). X-ray crystal structure reveals both have same space group but the differences in the alignment of pendant SCN- leads to two polymorphs. In I, trifurcated N-H...S hydrogen bonding plays a prominent role in crystal packing leading to S...S interactions between SCN fragments but in II, no such trifurcation arises and thereby the crystal packing occurs through hydrogen bonding interactions only leading to a distinctly different network topology. TG/DSC and FT-IR study reveal they are enantiotropically related. (c) 2007 Elsevier Ltd. All rights reserved.

Geometrical isomers of [TEAH][Co(L-Se)(2)]center dot xH(2)O: synthesis, structural, spectroscopic and computational studies

Trans-1, [HNEt3][Co-III(L-Se)(2)]center dot H2O and cis-1, [HNEt3][Co-III(L-Se)(2)]center dot 3H(2)O have been synthesized and characterized by single-crystal X-ray studies. The counter ion Et3NH+ plays a crucial role in the crystal packing leading to the formation of two distinctly different supramolecular assemblies in the two complexes. In trans-1, Co-bisphenolate units and triethylamine molecules are arranged in a linear fashion leading to a supramolecular columnar assembly along the crystallographic a-axis. In this assembly, triethylammonium ions are sandwiched between successive Co-bisphenolate units and act as gluing agents joining Co-bisphenolate units on either side through C-H center dot center dot center dot pi interactions. In sharp contrast to trans-1, Co-bisphenolate units and triethylammonium ions in cis-1 are arranged in a helical supramolecular assembly through similar C-H center dot center dot center dot pi interactions along the crystallographic b-axis. The Se center dot center dot center dot Se van der Waals interactions may be responsible for the predominant occurrence of the cis-isomer. The cyclic voltammetric studies showed quasi-reversible waves for the cobalt(III) -> cobalt(II) reductions with E-1/2 = 0.635 and 0.628 V vs. Ag/AgCl for cis-1 (at similar to 5 degrees C) and trans-1 (at similar to 25 degrees C), respectively. DFT calculations show that the trans-form is the thermodynamic product with higher stability than the cis-one, which is consistent with the variable temperature H-1 NMR studies

Structure, rheology and shear alignment of Pluronic block copolymer mixtures

The structure and flow behaviour of binary mixtures of Pluronic block copolymers P85 and P123 is investigated by small-angle scattering, rheometry and mobility tests. Micelle dimensions are probed by dynamic light scattering. The micelle hydrodynamic radius for the 50/50 mixture is larger than that for either P85 or P123 alone, Clue to the formation of mixed micelles with a higher association number. The phase diagram for 50/50 mixtures contains regions Of Cubic and hexagonal phases similar to those for the parent homopolymers, however the region of stability of the cubic phase is enhanced at low temperature and concentrations above 40 wt%. This is ascribed to favourable packing of the mixed micelles containing core blocks with two different chain lengths, but similar corona chain lengths. The shear flow alignment of face-centred cubic and hexagonal phases is probed by in situ small-angle X-ray or neutron scattering with simultaneous rheology. The hexagonal phase can be aligned using steady shear in a Couette geometry, however the high modulus Cubic phase cannot be aligned well in this way. This requires the application of oscillatory shear or compression. (C) 2008 Elsevier Inc. All rights reserved.

Supramolecular beta-sheet and nanofibril formation by self-assembling tripeptides containing an N-terminally located gamma-aminobutyric acid residue

Three terminally protected tripeptides Boc-gamma-Abu-Val-Leu-OMe 1, Boc-gamma-Abu-Leu-Phe-OMe 2 and Boc-gamma-Abu-Val-Tyr-OMe 3 (gamma-Abu = gamma-aminobutyric acid) each containing an N-terminally positioned gamma-aminobutyric acid residue have been synthesized, purified and studied. FT-IR studies of all these peptides revealed that these peptides form intermolecularly hydrogen bonded supramolecular beta-sheet structures. Peptides 1, 2 and 3 adopt extended backbone beta-strand molecular structures in crystals. Crystal packing of all these peptides demonstrates that these beta-strand structures self-assemble to form intermolecularly H-bonded parallel beta-sheet structures. Peptide 3 uses a side chain tyrosyl -OH group as an additional hydrogen bonding functionality in addition to the backbone CONH groups to pack in crystals. Transmission electron microscopic studies of all peptides indicate that they self-assemble to form nanofibrillar structures of an average diameter of 65 nm. These peptide fibrils exhibit amyloid-like behavior as they bind to a physiological dye Congo red and show a characteristic green-gold birefringence under polarizing microscope.

Synthesis, crystal structure and reactivity of copper(II) complexes of tetradentate N2S2 donor ligands

Two new hexa-coordinated mononuclear copper(II) complexes of two ligands L-1 and L-2 containing NSSN donor sets formulated as [Cu(L)(H2O)(2)](NO3)(2) [1a, L = 1,2-bis(2-pyridylmethylthio)ethane (L-1), 1b L = 1,3-bis(2-pyridyl-methylthio)propane (L-2)] were synthesized and characterized by physico-chemical and spectroscopic methods. In 1a the single crystal X-ray crystallography analysis showed a distorted octahedral geometry about copper(II) ion. The crystal packing evidences pairs of complexes arranged about a center of symmetry and connected through a H-bond occurring between aquo ligands and nitrate anions. On reaction with chloride and pseudohalides (N-3(-) and SCN-), in acetonitrile at ambient temperature. complexes 1 changed to monocationic penta-coordinated mononuclear copper(H) species formulated as [Cu(L)(Cl)]NO3 (2), [Cu(L)(N-3)]NO3 (3). and [Cu(L)(SCN)]NO3 (4). These copper(II) complexes have been isolated in pure form from the reaction mixtures and characterized by physico-chemical and spectroscopic tools. The solid-state structure of 2a, established by X-ray crystallography, shows a trigonal bipyramidal geometry about the metal ion with a trigonality index (tau) of 0.561. (C) 2009 Elsevier B.V. All rights reserved.

Novel supramolecular network in tri- and mono-nuclear oxovanadium(V)-salicyl-hydroximate: Synthesis, structure and catalytic oxidation of hydrocarbons using H2O2 as terminal oxidant

oxovanadium(V) salicylhydroximate complexes, [VO(SHA)(H2O)]center dot 1.58H(2)O (1) and [V3O3(CSHA)(3) (H2O)(3)]center dot 3CH(3)COCH(3) (2) have been synthesized by reaction of VO43- with N-salicyl hydroxamic acid (SHAHS) and N-(5-chlorosalicyl) hydroxamic acid (CSHAH(3)), respectively, in methanol medium. Compound 1 on reaction with pyridine 2,6-dicarboxylic acid (PyDCH2) yields mononuclear complex [VO(SHAH(2))(PyDC)] (3). Treatment of compound 3 with hydrogen peroxide at low pH (2-3) and low temperature (0-5 degrees C) yields a stable oxoperoxovanadium(V) complex H[VO(O-2)(PyDC)(H2O)]center dot 2.5H(2)O (4). All four complexes (1-4) have been characterized by spectroscopic (IR, UV-Vis, V-51 NMR) and single crystal X-ray analyses. Intermolecular hydrogen bonds link complex 1 into hexanuclear clusters consisting of six {VNO5} octahedra surrounded by twelve {VNO5} octahedra to form an annular ring. While the molecular packing in 2 generates a two-dimensional framework hydrogen bonds involving the solvent acetone molecules, the mononuclear complexes 3 and 4 exhibit three-dimensional supramolecular architecture. The compounds 1 and 2 behave as good catalysts for oxygenation of benzylic, aromatic, carbocyclic and aliphatic hydrocarbons to their corresponding hydroxylated and oxygenated products using H2O2 as terminal oxidant; the process affords very good yield and turnover number. The catalysis work shows that cyclohexane is a very easily oxidizable substrate giving the highest turnover number (TON) while n-hexane and n-heptane show limited yield, longer time involvement and lesser TON than other hydrocarbons. (C) 2008 Elsevier Ltd. All rights reserved.

Effect of Stretching on the Structure of Cylinder- and Sphere-Forming Styrene-Isoprene-Styrene Block Copolymers

Two styrene-isoprene-styrene block copolymers Vector 4111 and 4113, exhibiting cylindrical (18 wt % PS) and spherical (16 wt % PS) morphology, respectively, have been examined under uniaxial elongation up to 200% strain. On the basis of stress-strain data, mechanical properties are compared for isotropic and oriented polystyrene domains. The structure at various stages of deformation has been determined from SAXS patterns in three planes and two principal deformation directions with respect to orientation. Samples showed a very high degree of hexagonal packing, resulting in an X-ray pattern taken parallel to the cylinder alignment approaching single crystal ordering. Cylinders were aligned with the closest packed planes parallel to film surface. Particular attention has been paid to a lattice deformation process occurring during the first stretching and relaxation cycle. For a copolymer with oriented cylindrical morphology the deformation was affine up to 120% strain. The microdomain spacing was calculated parallel and perpendicular to the stretching direction. The cylindrical microstructure orientation, quantified by Hermans' orientation factor reduced during elongation of oriented polymer, while the elongation of isotropic sample caused an increase of orientation. Deformation of all studied morphologies was reversible.

Synthesis and structural characterization of two nostoclide analogues

The vinylogous aldol reaction between appropriate aldehydes and furan-based silyloxy diene synthon generated from 3-benzyl-5H-furan-2-one (3) afforded two truncated lactone analogues [compounds (4) and (5)] of nostoclides (2). The compounds were fully characterized by IR, NMR (H-1 and C-13), 2D NMR spectroscopy experiments (HMBC, HSQC and NOESY), MS spectrometry and X-ray crystallography. Compounds (4) and (5) crystallized in the space group P2(1)2(1)2(1) and P2(1)/c, respectively. Although expected correlations between hydrogen atoms in spatial close proximity were not observed for compound (5) using NMR, the stereochemistry of the exocyclic double bond of both (4) and (5) was unambiguously determined to be Z and E, respectively, using X-ray crystallography. The packing of both compounds within the crystal are stabilized by non-classical inter-molecular hydrogen bonds. DFT calculations (B3LYP/6-31+G* level) confirmed that the crystal structures possessed the lowest energies in the gas phase when compared to their geometric isomers. (c) 2006 Elsevier B.V. All rights reserved.

Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution

Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 Angstrom. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.

Deprotection, tethering, and activation of a one-legged metalloporphyrin on a chemically active metal surface: NEXAFS, Synchrotron XPS, and STM study of [SAc]P-Mn(III)Cl on Ag(100)

The structural and reactive properties of the acetyl-protected "one-legged" manganese porphyrin [SAc]P-Mn(III)Cl on Ag(100) have been studied by NEXAFS, synchrotron XPS and STM Spontaneous surface-mediated deprotection occurs at 300 K accompanied by spreading of the resulting thio-tethered porphyrin across the metal surface Loss of the axial chlorine ligand occurs at 498 K, without any demetalation of the macrocycle, leaving the Mn center in a low co-ordination state At low coverages the macrocycle is markedly tilted toward the silver surface, as is the phenyl group that forms part of the tethering "leg". In the monolayer region a striking transition occurs whereby the molecule rolls over, preserving the tilt angle of the phenyl group, strongly increasing that of the macrocycle, decreasing the apparent height of the molecule and decreasing its footprint, thus enabling closer packing These findings are in marked contrast with those previously reported for the corresponding more rigidly bound four-legged porphyrin [Turner, M., Vaughan, O. P. H., Kyriakou, G., Watson, D. J., Scherer, L. J; Davidson, G J. E, Sanders, J. K. M.; Lambert, R. M J. Am. Chem Soc 2009, 131, 1910] suggesting that the physicochemical :)properties and potential applications of these versatile systems should be strongly dependent on the mode of tethering to the surface.

Evaluation of data for atmospheric models: master equation/RRKM calculations on the combination reaction, BrO+NO2 -> BrONO2, a conundrum

Experimental data for the title reaction were modeled using master equation (ME)/RRKM methods based on the Multiwell suite of programs. The starting point for the exercise was the empirical fitting provided by the NASA (Sander, S. P.; Finlayson-Pitts, B. J.; Friedl, R. R.; Golden, D. M.; Huie, R. E.; Kolb, C. E.; Kurylo, M. J.; Molina, M. J.; Moortgat, G. K.; Orkin, V. L.; Ravishankara, A. R. Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation Number 15; Jet Propulsion Laboratory: Pasadena, California, 2006)(1) and IUPAC (Atkinson, R.; Baulch, D. L.; Cox, R. A.: R. F. Hampson, J.; Kerr, J. A.; Rossi, M. J.; Troe, J. J. Phys. Chem. Ref. Data. 2000, 29, 167) 2 data evaluation panels, which represents the data in the experimental pressure ranges rather well. Despite the availability of quite reliable parameters for these calculations (molecular vibrational frequencies (Parthiban, S.; Lee, T. J. J. Chem. Phys. 2000, 113, 145)3 and a. value (Orlando, J. J.; Tyndall, G. S. J. Phys. Chem. 1996, 100,. 19398)4 of the bond dissociation energy, D-298(BrO-NO2) = 118 kJ mol(-1), corresponding to Delta H-0(circle) = 114.3 kJ mol(-1) at 0 K) and the use of RRKM/ME methods, fitting calculations to the reported data or the empirical equations was anything but straightforward. Using these molecular parameters resulted in a discrepancy between the calculations and the database of rate constants of a factor of ca. 4 at, or close to, the low-pressure limit. Agreement between calculation and experiment could be achieved in two ways, either by increasing Delta H-0(circle) to an unrealistically high value (149.3 kJ mol(-1)) or by increasing , the average energy transferred in a downward collision, to an unusually large value (> 5000 cm(-1)). The discrepancy could also be reduced by making all overall rotations fully active. The system was relatively insensitive to changing the moments of inertia in the transition state to increase the centrifugal effect. The possibility of involvement of BrOONO was tested and cannot account for the difficulties of fitting the data.