Structure Of 5'-Deoxy-5',6-Epithio-5,6-Dihydro-2',3'-O-Isopropylideneuridine, C12h16n2o5s

Mr=300.33 , triclinic, P1, a=5.635 (2), b=11.077(2), c=11.582(2)A, a= 70.48 (1), fl= 88.16 (3), y=80.56(3) ° , V= 670.325 A3, Z=2, D x = 1.49 Mg m -3, Cu Ka, n= 1.54184 ,A, g = 2.308mm -1, F(000)=316, T=301K, R=0.054, R w = 0.093 for 1944 observed counter reflections. The sulphur position with respect to the dihydrouracil ring, which is of possible relevance to the action of thymidylate synthetase, is axial in molecule A and equatorial in B. Both molecules show the anti conformation about the glycosidic bond [torsion angle C(6)-N(1)-C(1')-O(4'), 2'CN = 21.6 (9) and 29.4 (10) °] and have the C(4')-endo, O(4')-exo (40T) sugar conformation. The dioxolane-ring conformation is O(2')-endo in A and C(7)-endo in B. The dihydrouracil rings show self base pairing with hydrogen bondsN(3A)...O(ZB) and N(3B)...O(ZA).

The Structure of Monosodium Phosphoenolpyruvate

CDH406P-.Na +.H20 , M r = 208.0, is monoclinic, Cc, a = 11.423 (2), b = 23.253 (5), c - 6.604 (1) A, fl = 123.63 (1) °, U = 1460.6 A 3, D x =. 1.89 Mg m -a, Z = 8, 2(Mo Ka) = 0.7107 A, p(Mo Ka) = 0.44 mm -~, F(000) = 840. Final R = 0.063 for 1697 reflections.The two crystallographically independent molecules of phosphoenolpyruvate (PEP) (A and B) are almost mirror images of each other, the mirror being the planar enolpyruvate group. The torsion angle C(3)-C(2)- O(1)-P(1) is 122.6 in A and -112.0 ° in B, in contrast to -209.1 ° in PEP.K. The enolic C(2)-O(1) has a partial double-bond character [1.401 (A), 1.386A (B)]. The high-energy P~O bond (1.595 and 1.610A) is comparable to that in PEP.K (1.612 A). Na(1) has six nearest neighbours while Na(2) has only five. The Na + ions are involved in binding only the phosphates of different molecules, in contrast to the K ÷ ion in PEP. K, which binds to both the phosphate and carboxyl ends of the same molecule. The planar carboxyl groups stack on each other at an average distance of 3.2 A instead of forming hydrogen-bonded dimers usually found in carboxylate structures.

Sequence-dependent molecular conformation of polynucleotides: right and left-handed helices

Based upon a stereochemical guideline, two topologically distinct types of helicalduplexes have been deduced for a polynucleotide duplex with alternating purine pyrimidine sequence (PAPP): (a) right-handed uniform (RU) helix and (b) left-handed zig-zag (LZ) helix. Both structures have trinucleoside diphosphate as the basic unit wherein the purine pyrimidine fragment has a different conformation from the pyrimidine-purine fragment. Thus, RU and LZ helices represent two different classes of sequence-dependent molecular conformations for PAPP. The conformationalf eatures of an RU helix of PAPP in B-form and three LZ-helices for B-, D- and Z-forms are discussed.

The curvature invariant for a class of homogeneous operators

For an operator T in the class B-n(), introduced by Cowen and Douglas, the simultaneous unitary equivalence class of the curvature and the covariant derivatives up to a certain order of the corresponding bundle E-T determine the unitary equivalence class of the operator T. In a subsequent paper, the authors ask if the simultaneous unitary equivalence class of the curvature and these covariant derivatives are necessary to determine the unitary equivalence class of the operator T is an element of B-n(). Here we show that some of the covariant derivatives are necessary. Our examples consist of homogeneous operators in B-n(). For homogeneous operators, the simultaneous unitary equivalence class of the curvature and all its covariant derivatives at any point w in the unit disc are determined from the simultaneous unitary equivalence class at 0. This shows that it is enough to calculate all the invariants and compare them at just one point, say 0. These calculations are then carried out in number of examples. One of our main results is that the curvature along with its covariant derivative of order (0, 1) at 0 determines the equivalence class of generic homogeneous Hermitian holomorphic vector bundles over the unit disc.

NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures

Software packages NUPARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids, by analysis and generation of non-uniform structures. A set of local inter basepair parameters (viz. tilt, roll, twist, shift, slide and rise) have been defined, which use geometry and coordinates of two successive basepairs only and can be used to generate polymeric structures with varying geometries for each of the 16 possible dinucleotide steps. Intra basepair parameters, propeller, buckle, opening and the C6...C8 distance can also be varied, if required, while the sugar phosphate backbone atoms are fixed in some standard conformation ill each of the nucleotides. NUPARM can be used to analyse both DNA and RNA structures, with single as well as double stranded helices. The NUCGEN software generates double helical models with the backbone fixed in B-form DNA, but with appropriate modifications in the input data, it can also generate A-form DNA ar rd RNA duplex structures.

Crystal structure of dimeric FabZ of Plasmodium falciparum reveals conformational switching to active hexamers by peptide flips

The crystal structure of beta-hydroxyacyl acyl carrier protein dehydratase of Plasmodium falciparum (PfFabZ) has been determined at a resolution of 2.4 angstrom. PfFabZ has been found to exist as a homodimer (d-PfFabZ) in the crystals of the present study in contrast to the reported hexameric form (h-PfFabZ) which is a trimer of dimers crystallized in a different condition. The catalytic sites of this enzyme are located in deep narrow tunnel-shaped pockets formed at the dimer interface. A histidine residue from one subunit of the dimer and a glutamate residue from the other subunit lining the tunnel form the catalytic dyad in the reported crystal structures. While the position of glutamate remains unaltered in the crystal structure of d-PffabZ compared to that in b-PfFabZ, the histidine residue takes up an entirely different conformation and moves away from the tunnel leading to a His-Phe cis-trans peptide flip at the histidine residue. In addition, a loop in the vicinity has been observed to undergo a similar flip at a Tyr-Pro peptide bond. These alterations not only prevent the formation of a hexamer but also distort the active site geometry resulting in a dimeric form of FabZ that is incapable of substrate binding. The dimeric state and an altered catalytic site architecture make d-PfFabZ distinctly different from the FabZ structures described so far. Dynamic light scattering and size exclusion chromatographic studies clearly indicate a pH-related switching of the dimers to active hexamers. (c) 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserv.

Microstructural Evolution during Laser Resolidification of Fe-18 At. Pct Ge Alloy

The technique of laser resolidification has been used to study the rapid solidification behavior of concentrated Fe-18 at. pct Ge alloy. The microstructural evolution has been studied as a function of scanning rate of laser beam. Scanning electron microscopy (SEM) reveals the formation of a two-layer (designated as "A" and "B") microstructure in the remelted pool. The A layer shows a band consisting of a network of interconnected channels and walls, quite similar to cell walls. The B layer shows dendritic growth. Transmission electron microscopic observations reveal the formation of bcc alpha-FeGe in the B layer. Laser melting has been found to play an important role in formation of the A layer. Microstructural evolution in B has been analyzed using the competitive growth criterion, and formation of bcc alpha-FeGe has been rationalized in the remelted layers.

Interaction between the Z-type DNA duplex and 1,3-propanediamine:crystal structure of d(CACGTG)(2) at 1.2 angstrom resolution

The crystal structure of a hexamer duplex d(CACGTG)(2) has been determined and refined to an R-factor of 18.3% using X-ray data up to 1.2 angstrom resolution. The sequence crystallizes as a left-handed Z-form double helix with Watson-Crick base pairing. There is one hexamer duplex, a spermine molecule, 71 water molecules, and an unexpected diamine (Z-5, 1,3-propanediamine, C3H10N2)) in the asymmetric unit. This is the high-resolution non-disordered structure of a Z-DNA hexamer containing two AT base pairs in the interior of a duplex with no modifications such as bromination or methylation on cytosine bases. This structure does not possess multivalent cations such as cobalt hexaammine that are known to stabilize Z-DNA. The overall duplex structure and its crystal interactions are similar to those of the pure-spermine form of the d(CGCGCG)(2) structure. The spine of hydration in the minor groove is intact except in the vicinity of the T5A8 base pair. The binding of the Z-5 molecule in the minor grove of the d(CACGTG)(2) duplex appears to have a profound effect in conferring stability to a Z-DNA conformation via electrostatic complementarity and hydrogen bonding interactions. The successive base stacking geometry in d(CACGTG)(2) is similar to the corresponding steps in d(CG)(3). These results suggest that specific polyamines such as Z-5 could serve as powerful inducers of Z-type conformation in unmodified DNA sequences with AT base pairs. This structure provides a molecular basis for stabilizing AT base pairs incorporated into an alternating d(CG) sequence.

Photometric calibration of the CCD camera of 1-m telescope at VBO

Calibration of the CCD camera of the 1-m telescope at the Vainu Bappu Observatory, Kavalur, to the BVR system is reported here based on the observations of stars in the 'dipper asterism' in the open cluster M 67 (NGC 2682). Transformations involving B and V have negligible colour terms, while those involving R are slightly colour dependent. The possibility of using scale-down R band fluxes to estimate the continuum flux at H-alpha is investigated by comparing the counts in R band with those through an interference filter centred at H-alpha. The scaling factor is found to remain constant over a wide range of colours. The sensitivity of the telescope-filter-CCD combination is estimated to be 2.0 per cent, 8.3 per cent and 9.7 per cent in B, V and R bands, respectively. The star F117 appears to be a small-amplitude (approximately 0.05 mag) variable.

DNA Polymerase4 from the Silk Glands of Bombyx mori

The silk gland of Bombyx mori is a terminally differentiated tissue in which DNA replication continues without cell or nuclear division during larval development. DNA polymerase-delta activity increases in the posterior and middle silk glands during the development period, reaching maximal levels in the middle of the fifth instar larvae. The enzyme has been purified to homogeneity by a series of column chromatographic and affinity purification steps. It is a multimer comprising of three heterogeneous subunits, M(r) 170,000, 70,000, and 42,000. An auxiliary protein from B. mori silk glands, analogous to the proliferating cell nuclear antigen, enhances the processivity of the enzyme and stimulates catalytic activity by 3-fold. This auxiliary protein has also been purified to homogeneity. It is a dimer comprised of a single type M(r) 40,000 subunit. Polymerase-delta possesses an intrinsic 3' --> 5' exonuclease activity which participates in proofreading by mismatch match repair during DNA synthesis and is devoid of any primase activity. DNA polymerase-delta activity could be further distinguished from polymerase-alpha from the same tissue based on its sensitivity to various inhibitors and polyclonal antibodies to the individual enzymes. Like DNA polymerase-alpha, polymerase-delta is also tightly associated with the nuclear matrix. The polymerase alpha-primase complex could be readily separated from polymerase-delta (exonuclease) in the purification protocol adopted. DNA polymerase-delta from B. mori silk glands resembles the mammalian delta-polymerases. Considering that both DNA polymerase-delta and -alpha are present in nearly equal amounts in this highly replicative tissue and their close association with the nuclear matrix, the involvement of both the enzymes in the chromosomal endoreplication process in B. mori is strongly implicated.

Investigation on the Magnetic Anomaly and the Role of Orbital Moment on the Magnetic Properties of LaMn0.5Co0.5O3

Two distinct ferromagnetic phases are present in LaMn0.5Co0.5O3 for which the spin-only magnetic moment calculated from the high temperature dc susceptibility is found to be unusually high. Such a high moment can only be accounted for by assigning the valence state of the cations to Mn2+-Co4+. This is unrealistic as the earlier report based on X-ray absorption spectroscopy (XAS) has suggested the valence state to be mainly Mn4+-Co2+ with traces of Co3+. Also from our studies using XAS, it is found that the valence state is mainly Mn4+-Co2+. In addition, no notable difference is observed in the minor Co3+ present in both phases. Our results based on X-ray magnetic circular dichroism studies (XMCD) reveal the presence of ``distinct'' high orbital moment associated with Co2+ for both phases. Thus it is found that the distinctness of the orbital moment also plays a vital role in determining the magnetic moment and T-c of both phases of LaMn0.5Co0.5O3. By considering the orbital moment obtained from XMCD, the anomaly in the paramagnetic susceptibility is resolved and thus we are able to assign the valence state to Mn4+-Co2+ configuration. The difference in the magnitude of orbital moment in both phases is believed to be due to the crystal field effects.

Carbon recombination lines between 34.5 and 770 MHz toward Cassiopeia A

We present observations of low-frequency recombination lines of carbon toward Cas A near 34.5 MHz (n similar to 575) using the Gauribidanur radio telescope and near 560 MHz (n similar to 225) and 770 MHz (n similar to 205) using the NRAO 140 foot (43 m) telescope in Greenbank. We also present high angular resolution (1') observations of the C270 alpha line near 332 MHz using the Very Large Array in B-configuration. A high signal-to-noise ratio spectrum is obtained at 34.5 MHz, which clearly shows a Voigt profile with distinct Lorentzian wings, resulting from significant pressure and radiation broadening at such high quantum numbers. The emission lines detected near 332, 550, and 770 MHz, on the other hand, are narrow and essentially Doppler-broadened. The measured Lorentzian width at 34.5 MHz constrains the allowed combinations of radiation temperature, electron density, and electron temperature in the line-forming region. Radiation broadening at 34.5 MHz places a lower limit of 115 pc on the separation between Cas A and the line-forming clouds. Modeling the variation in the integrated line-to-continuum ratio with frequency indicates that the region is likely to be associated with the cold atomic hydrogen component of the interstellar medium, and the physical properties of this region are likely to be T-e = 75 K, n(e) = 0.02 cm(-3), T-R100 = 3200 K, and n(H) T-e = 10,000 cm(-3) K. Comparison of the distribution of the C270 alpha recombination line emission across Cas A with that of (CO)-C-12 and H I also supports the above conclusion.

Molecular cloning and expression pattern of a Cubitus interruptus homologue from the mulberry silkworm Bombyx mori

A homologue of the segment polarity gene Cubitus interruptus from Bombyx Mori, (BmCi) has been cloned and characterized. This region harbouring Zn2+ finger motif is highly conserved across species. In B. Mori, BmCi RNA expression was first detected at stage 6 of embryogenesis, which reached maximum levels at stage 21C and was maintained until larval hatching. The segmentally reiterated striped pattern of transcript distribution in stage 21C embryos was in conformity with its predicted segment polarity nature. BmCi was expressed in the fore- and hind-wing discs, ovaries, testes and gut during fifth larval intermolt, reminiscent of its expression domains in Drosophila. Besides, BmCi expression was seen in the. anterior part of the middle silkglands in late embryonic stages, and this pattern was maintained during larval development. The transition from third to fourth and fifth larval intermolts was accompanied by an increase in the transcript levels in the middle silkglands. Our results demonstrate the presence of a novel expression domain for Ci in Bombyx. (C) 2002 Elsevier Science Ireland Ltd. All rights reserved.

Efficient visible light induced nuclease activity of a ternary mono-1,10-phenanthroline copper(II) complex containing 2-(methylthio)ethylsalicylaidimine

Ternary Schiff base copper(II) complex [CuL(phen)](ClO4), where HL is 2-(methylthio)ethylsalicylaldimine and phen is 1,10-phenanthroline, has been prepared and structurally characterized by X-ray crystallography. The complex shows a CuN3OS coordination in a square-pyramidal (4 + 1) geometry with the sulfur as an equatorial ligand. The complex is an avid binder to double-stranded DNA in the minor groove and exhibits both photonuclease and chemical nuclease activity. When exposed to UV light of 312 nm (96 W) or visible light of 532 nm (125 W) under aerobic conditions, the complex causes significant cleavage of supercoiled pUC19 DNA in the absence of any externally added reducing agent or H2O2.

From the Icosahedron to Natural Triangulations of CP(2) and S(2) x S(2)

We present two constructions in this paper: (a) a 10-vertex triangulation CP(10)(2) of the complex projective plane CP(2) as a subcomplex of the join of the standard sphere (S(4)(2)) and the standard real projective plane (RP(6)(2), the decahedron), its automorphism group is A(4); (b) a 12-vertex triangulation (S(2) x S(2))(12) of S(2) x S(2) with automorphism group 2S(5), the Schur double cover of the symmetric group S(5). It is obtained by generalized bistellar moves from a simplicial subdivision of the standard cell structure of S(2) x S(2). Both constructions have surprising and intimate relationships with the icosahedron. It is well known that CP(2) has S(2) x S(2) as a two-fold branched cover; we construct the triangulation CP(10)(2) of CP(2) by presenting a simplicial realization of this covering map S(2) x S(2) -> CP(2). The domain of this simplicial map is a simplicial subdivision of the standard cell structure of S(2) x S(2), different from the triangulation alluded to in (b). This gives a new proof that Kuhnel's CP(9)(2) triangulates CP(2). It is also shown that CP(10)(2) and (S(2) x S(2))(12) induce the standard piecewise linear structure on CP(2) and S(2) x S(2) respectively.