Three-dimensional solution structure of alpha-conotoxin MII by NMR spectroscopy: Effects of solution environment on helicity

alpha-Conotoxin MII, a 16-residue polypeptide from the venom of the piscivorous cone snail Conus magus, is a potent and highly specific blocker of mammalian neuronal nicotinic acetylcholine receptors composed of alpha 3 beta 2 subunits. The role of this receptor type in the modulation of neurotransmitter release and its relevance to the problems of addiction and psychosis emphasize the importance of a structural understanding of the mode of interaction of MII with the alpha 3 beta 2 interface. Here we describe the three-dimensional solution structure of MIT determined using 2D H-1 NMR spectroscopy. Structural restraints consisting of 376 interproton distances inferred from NOEs and 12 dihedral restraints derived from spin-spin coupling constants were used as input for simulated annealing calculations and energy minimization in the program X-PLOR. The final set of 20 structures is exceptionally well-defined with mean pairwise rms differences over the whole molecule of 0.07 Angstrom for the backbone atoms and 0.34 Angstrom for all heavy atoms. MII adopts a compact structure incorporating a central segment of alpha-helix and beta-turns at the N- and C-termini. The molecule is stabilized by two disulfide bonds, which provide cross-links between the N-terminus and both the middle and C-terminus of the structure. The susceptibility of the structure to conformational change was examined using several different solvent conditions. While the global fold of MII remains the same, the structure is stabilized in a more hydrophobic environment provided by the addition of acetonitrile or trifluoroethanol to the aqueous solution. The distribution of amino acid side chains in MII creates distinct hydrophobic and polar patches on its surface that may be important for the specific interaction with the alpha 3 beta 2 neuronal nAChR. A comparison of the structure of MII with other neuronal-specific alpha-conotoxins provides insights into their mode of interaction with these receptors.

X-ray properties of the Parkes sample of flat-spectrum radio sources: dust in radio-loud quasars?

We investigate the X-ray properties of the Parkes sample of Bat-spectrum radio sources using data from the ROSAT All-Sky Survey and archival pointed PSPC observations. In total, 163 of the 323 sources are detected. For the remaining 160 sources, 2 sigma upper limits to the X-ray flux are derived. We present power-law photon indices in the 0.1-2.4 keV energy band for 115 sources, which were determined either with a hardness ratio technique or from direct fits to pointed PSPC data if a sufficient number of photons were available. The average photon index is <Gamma > = 1.95(-0.12)(+0.13) for flat-spectrum radio-loud quasars, <Gamma > = 1.70(-0.24)(+0.23) for galaxies, and <Gamma > = 2.40(-0.31)(+0.12) for BL Lac objects. The soft X-ray photon index is correlated with redshift and with radio spectral index in the sense that sources at high redshift and/or with flat (or inverted) radio spectra have flatter X-ray spectra on average. The results are in accord with orientation-dependent unification schemes for radio-loud active galactic nuclei. Webster et al. discovered many sources with unusually red optical continua among the quasars of this sample, and interpreted this result in terms of extinction by dust. Although the X-ray spectra in general do not show excess absorption, we find that low-redshift optically red quasars have significantly lower soft X-ray luminosities on average than objects with blue optical continua. The difference disappears for higher redshifts, as is expected for intrinsic absorption by cold gas associated with the dust. In addition, the scatter in log(f(x)/f(o)) is consistent with the observed optical extinction, contrary to previous claims based on optically or X-ray selected samples. Although alternative explanations for the red optical continua cannot be excluded with the present X-ray data, we note that the observed X-ray properties are consistent with the idea that dust plays an important role in some of the radio-loud quasars with red optical continua.

The solution structure of a copper(II) compound of a new cyclic octapeptide by EPR spectroscopy and force field calculations

A new cyclic octapeptide, cyclo(Ile-Ser-(Gly)Thz-Ile-Thr-(Gly)Thz) (PatN), related to patellamide A, has been synthesized and reacted with copper(II) and base to form mono- and dinuclear complexes. The coordination environments around copper(TI) have been characterized by EPR spectroscopy. The solution structure of the thermodynamically most stable product, a purple dicopper(TI) compound, has been examined by simulating weakly dipole-dipole coupled EPR spectra based upon structural parameters obtained from force field (MM and MD) calculations. The MM-EPR method produces a saddle-shaped structure for [Cu-2(PatN)(OH2)(6)] that is similar to the known solution structure of patellamide A and the known solid-state structure of [Cu-2(AscidH(2))CO3(OH2)(2)]. Compared with the latter, [Cu-2(PatN)] has no carbonate bridge and a significantly flatter topology. The MM-EPR approach to solution-structure determination for paramagnetic metallopeptides may find wide applications to other metallopeptides and metalloproteins.

Red Parkes quasars: Evidence for soft X-ray absorption

The Parkes Half-Jansky Flat-Spectrum Sample contains a large number of sources with unusually red optical-to-near-infrared (NIR) continua. If this is to be interpreted as extinction by dust in the line of sight, then associated material might also give rise to absorption in the soft X-ray regime. This hypothesis is tested using broadband (0.1-2.4 keV) data from the ROSAT All-Sky Survey. Significant (>3 sigma confidence level) correlations between the optical (and NIR)-to-soft X-ray continuum slope and optical extinction are found in the data, consistent with absorption by material with metallicity and a range in the gas-to-dust ratio as observed in the local ISM. Under this simple model, the soft X-rays are absorbed at a level consistent with the range of extinctions (0 < A(V) < 6 mag) implied by the observed optical reddening. Excess X-ray absorption by warm (ionized) gas, (i.e., a warm absorber) is not required by the data.

The solution structure of the N-terminal zinc finger of GATA-1 reveals a specific binding face for the transcriptional co-factor FOG

Zinc fingers (ZnFs) are generally regarded as DNA-binding motifs. However, a number of recent reports have implicated particular ZnFs in the mediation of protein-protein interactions. The N-terminal ZnF of GATA-1 (NF) is one such finger, having been shown to interact with a number of other proteins, including the recently discovered transcriptional co-factor FOG. Here we solve the three-dimensional structure of the NF in solution using multidimensional H-1/N-15 NMR spectroscopy, and we use H-1/N-15 spin relation measurements to investigate its backbone dynamics. The structure consists of two distorted beta-hairpins and a single alpha-helix, and is similar to that of the C-terminal ZnF of chicken GATA-1. Comparisons of the NF structure with those of other C-4-type zinc binding motifs, including hormone receptor and LIM domains, also reveal substantial structural homology. Finally, we use the structure to map the spatial locations of NF residues shown by mutagenesis to be essential for FOG binding, and demonstrate that these residues all lie on a single face of the NE Notably, this face is well removed from the putative DNA-binding face of the NE an observation which is suggestive of simultaneous roles for the NF; that is, stabilisation of GATA-1 DNA complexes and recruitment of FOG to GATA-1-controlled promoter regions.

Observation of a cubic phase in mesoporous silicate films grown at the air/water interface

X-Ray diffraction is reported from mesoporous silicate films grown at the air/water interface. The films were studied both as powdered films, and oriented on silicon or mica sheets. At early stages of growth we observe Bragg diffraction from a highly ordered cubic phase, with both long and short d-spacing peaks. We have assigned this as a discontinuous micellar Pm3n phase in which the silica is partly ordered. Later films retain only the known hexagonal p6m peaks and have lost any order both at short d-spacings and the longer d-spacing Bragg peaks characteristic of the cubic structure. The silica framework is considerably expanded from that in bulk amorphous silica, average Si Si distances are some 30% greater. Incorporation of glycerol or polyethylene glycol preserves the earlier cubic structure. To be consistent with earlier, in situ, X-ray and neutron reflectivity data we infer that both structures are produced after a phase transition from a less-ordered him structure late in the induction phase. The structural relations between the film Pm3n and p6m phase(s) and the known bulk SBA-1 and MCM-41 phases are briefly discussed.

Detection of lead(II) and silver(I) in aqueous solution using a piezoelectric device

The gold surface of a quartz crystal microbalance was modified by the attachment of silica particles derivatised with N-[(3-trimethoxysilyl)propyl] ethylenediaminetriacetic acid. The device was employed to study the kinetics of the interaction of aqueous solutions of lead(II) nitrate and silver(I) nitrate with the surface and for the selective separation of the metal ions.

Solution structure of alpha-conotoxin ImI by H-1 nuclear magnetic resonance

alpha-Conotoxin ImI derives from the venom of Conus imperialis and is the first and only small-peptide ligand that selectively binds to the neuronal alpha(7) homopentameric subtype of the nicotinic acetylcholine receptor (nAChR). This receptor subtype is a possible drug target for several neurological disorders. The cysteines are connected in the pairs Cys2-Cys8 and Cys3-Cys12, To date it is the only alpha-conotoxin with a 4/3 residue spacing between the cysteines, The structure of ImI has been determined by H-1 NMR spectroscopy in aqueous solution, The NMR structure is of high quality, with a backbone pairwise rmsd of 0.34 Angstrom for a family of 19 structures, and comprises primarily a series of nested beta turns. Addition of organic solvent does not perturb the solution structure. The first eight residues of ImI are identical to the larger, but related, conotoxin EpI and adopt a similar structure, despite a truncated second loop. Residues important for binding of ImI to the alpha 7 nAChR are all clustered on one face of the molecule. Once further binding data for EPI and ImI are available, the ImI structure will allow for design of novel alpha(7) nAChR-specific agonists and antagonists with a wide range of potential pharmaceutical applications.

A consistent point-searching algorithm for solution interpolation in unstructured meshes consisting of 4-node bilinear quadrilateral elements

To translate and transfer solution data between two totally different meshes (i.e. mesh 1 and mesh 2), a consistent point-searching algorithm for solution interpolation in unstructured meshes consisting of 4-node bilinear quadrilateral elements is presented in this paper. The proposed algorithm has the following significant advantages: (1) The use of a point-searching strategy allows a point in one mesh to be accurately related to an element (containing this point) in another mesh. Thus, to translate/transfer the solution of any particular point from mesh 2 td mesh 1, only one element in mesh 2 needs to be inversely mapped. This certainly minimizes the number of elements, to which the inverse mapping is applied. In this regard, the present algorithm is very effective and efficient. (2) Analytical solutions to the local co ordinates of any point in a four-node quadrilateral element, which are derived in a rigorous mathematical manner in the context of this paper, make it possible to carry out an inverse mapping process very effectively and efficiently. (3) The use of consistent interpolation enables the interpolated solution to be compatible with an original solution and, therefore guarantees the interpolated solution of extremely high accuracy. After the mathematical formulations of the algorithm are presented, the algorithm is tested and validated through a challenging problem. The related results from the test problem have demonstrated the generality, accuracy, effectiveness, efficiency and robustness of the proposed consistent point-searching algorithm. Copyright (C) 1999 John Wiley & Sons, Ltd.

X-ray computed tomography to quantify tree rooting spatial distributions

Poor root development due to constraining soil conditions could be an important factor influencing health of urban trees. Therefore, there is a need for efficient techniques to analyze the spatial distribution of tree roots. An analytical procedure for describing tree rooting patterns from X-ray computed tomography (CT) data is described and illustrated. Large irregularly shaped specimens of undisturbed sandy soil were sampled from Various positions around the base of trees using field impregnation with epoxy resin, to stabilize the cohesionless soil. Cores approximately 200 mm in diameter by 500 mm in height were extracted from these specimens. These large core samples were scanned with a medical X-ray CT device, and contiguous images of soil slices (2 mm thick) were thus produced. X-ray CT images are regarded as regularly-spaced sections through the soil although they are not actual 2D sections but matrices of voxels similar to 0.5 mm x 0.5 mm x 2 mm. The images were used to generate the equivalent of horizontal root contact maps from which three-dimensional objects, assumed to be roots, were reconstructed. The resulting connected objects were used to derive indices of the spatial organization of roots, namely: root length distribution, root length density, root growth angle distribution, root spatial distribution, and branching intensity. The successive steps of the method, from sampling to generation of indices of tree root organization, are illustrated through a case study examining rooting patterns of valuable urban trees. (C) 1999 Elsevier Science B.V. All rights reserved.

Extended integrability regime for the supersymmetric U model

An extension of the supersymmetric U model for correlated electrons is given and integrability is established by demonstrating that the model can he constructed through the quantum inverse scattering method using an R-matrix without the difference property. Some general symmetry properties of the model are discussed and from the Bethe ansatz solution an expression for the energies is presented.

Nickel complexes with tris(2-aminoethyl)amine (tren): [Ni-3(tren)(4)(H2O)(2)][Cr(ox)(3)](2)center dot 6H(2)O (ox = oxalate), {[Ni-2(tren)(3)][ClO4](4)center dot H2O}(n), and [Ni-2(tren)(2)(aepd)][ClO4](4)center dot 2H(2)O (aepd = N-(2-aminoethyl)pyrrolidi

Reaction of K-3[Cr(ox)(3)] (ox = oxalate) with nickel(II) and tris(2-aminoethyl)amine (tren) in aqueous solution resulted in isolation of the bimetallic assembly [Ni-3(tren)(4)(H2O)(2)][Cr(ox)(3)](2). 6H(2)O. The polymeric complex {[Ni-2(tren)(3)][ClO4](4). H2O}(n) has been prepared by reaction of nickel(II) perchlorate and tren in aqueous solution. From the same reaction mixture the complex [Ni-2(tren)(2)(aepd)][ClO4](4). 2H(2)O (aepd = N-(2-aminoethyl)pyrrolidine-3,4-diamine), in which a bridging tren ligand contains a carbon-carbon bond between two arms forming a substituted pyrrolidine, has been isolated. The complexes have been characterized by X-ray crystallography. The magnetic susceptibility (300-4.2 K) and magnetization data (2, 4 K, H = 0-5 T) for {[Ni-2(tren)(3)][ClO4](4). H2O}(n) (300 K , 4.23 mu(B)) exhibit evidence of weak antiferromagnetic coupling and zero field splitting (2J = -1.8 cm(-1); \ D\ = 2 cm(-1)) at low temperature. For [Ni-3(tren)(4)(H2O)(2)][Cr(ox)(3)](2). 6H(2)O the susceptibility data at 300 K are indicative of uncoupled nickel(II) and chromium(III) sites with zero-field splitting and intramolecular antiferromagnetic coupling predicted at low temperature.

Solution structure of a defensin-like peptide from platypus venom

Three defensin-like peptides (DLPs) were isolated from platypus venom and sequenced. One of these peptides, DLP-1, was synthesized chemically and its three-dimensional structure was determined using NMR spectroscopy. The main structural elements of this 42-residue peptide were an anti-parallel beta-sheet comprising residues 15-18 and 37-40 and a small 3(10) helix spanning residues 10-12. The overall three-dimensional fold is similar to that of beta-defensin-12, and similar to the sodium-channel neurotoxin ShI (Stichodactyla helianthus neurotoxin I). However, the side chains known to be functionally important in beta-defensin-12 and ShI are not conserved in DLP-1, suggesting that it has a different biological function. Consistent with this contention, we showed that DLP-1 possesses no anti-microbial properties and has no observable activity on rat dorsal-root-ganglion sodium-channel currents.

Crystallization and preliminary X-ray diffraction studies of mammalian purple acid phosphatase

The oxidized form of purple acid phosphatase from pig allantoic fluid has been crystallized in the presence of phosphate using the hanging-drop technique. The crystals belong to the space group P2(1)2(1)2(1) and have unit-cell parameters a = 66.8, b = 70.3, c = 78.7 Angstrom. Diffraction data collected from a cryocooled crystal using a conventional X-ray source extend to 1.55 Angstrom resolution. A knowledge of the three-dimensional structure of mammalian purple acid phosphatase will aid in understanding the substrate specificity of the enzyme and will be important in the rational design of inhibitors, with potential in the treatment of bone diseases.