Structure of 5-methyl-2'-deoxycytidine 5'-monophosphate dihydrate

CloHI6N307P.2H20 , Mr = 357.2, triclinic, P1, a = 4-8520 (8), b = 8"3703 (8), c = 10.0199 (12) A, a= 104.578 (9),/3= 102.332 (13), 7=93.670(11) o, V = 381"75 A 3, Z = 1, Dx = 1"55, Dm = 1"53 Mg m -3, a(Cu Ka) = 1.5418 A,/z = 2.01 mm- l, F(000) = 188, T= 290 K, R = 0-049 for 1568 unique reflections.

Solution structure of O-glycosylated C-terminal leucine zipper domain of human salivary mucin (MUC7)

Solution structures of a 23 residue glycopeptide II (KIS* RFLLYMKNLLNRIIDDMVEQ, where * denotes the glycan Gal-beta-(1-3)-alpha-GalNAc) and its deglycosylated counterpart I derived from the C-terminal leucine zipper domain of low molecular weight human salivary mucin (MUC7) were studied using CD, NMR spectroscopy and molecular modeling. The peptide I was synthesized using the Fmoc chemistry following the conventional procedure and the glycopeptide II was synthesized incorporating the O-glycosylated building block (N alpha-Fmoc-Ser-[Ac-4,-beta-D-Gal-(1,3)-Ac(2)alpha-D-GalN(3)]-OPfp) at the appropriate position in stepwise assembly of peptide chain. Solution structures of these glycosylated and nonglycosylated peptides were studied in water and in the presence of 50% of an organic cosolvent, trifluoroethanol (TFE) using circular dichroism (CD), and in 50% TFE using two-dimensional proton nuclear magnetic resonance (2D H-1 NMR) spectroscopy. CD spectra in aqueous medium indicate that the apopeptide I adapts, mostly, a beta-sheet conformation whereas the glycopeptide II assumes helical structure. This transition in the secondary structure, upon glycosylation, demonstrates that the carbohydrate moiety exerts significant effect on the peptide backbone conformation. However, in 50% TFE both the peptides show pronounced helical structure. Sequential and medium range NOEs, C alpha H chemical shift perturbations, (3)J(NH:C alpha H) couplings and deuterium exchange rates of the amide proton resonances in water containing 50% TFE indicate that the peptide I adapts alpha-helical structure from Ile2-Val21 and the glycopeptide II adapts alpha-helical structure from Ser3-Glu22. The observation of continuous stretch of helix in both the peptides as observed by both NMR and CD spectroscopy strongly suggests that the C-terminal domain of MUC7 with heptad repeats of leucines or methionine residues may be stabilized by dimeric leucine zipper motif. The results reported herein may be invaluable in understanding the aggregation (or dimerization) of MUC7 glycoprotein which would eventually have implications in determining its structure-function relationship.

X-Ray structure of a ternary complex, copper(II)–lnosine 5-monophosphate–benzimidazole. The first example for the absence of direct metal–nucleotide interaction

The unprecedented absence of direct metal–nucleotide interaction has been observed in the X-ray structure of the ternary metal nucleotide system [Cu(bzim)(H2O)5]2+[IMP]2–·3H2O [IMP = inosine 5-monophosphate(2–), bzim = benzimidazole). The complex crystallizes in the space group P21 with a= 7.013(2), b= 13.179(9), c= 14.565(9)Å, = 94.82(4)°, and Z= 2. The structure was solved by the heavy-atom method and refined by full-matrix least squares on the basis of 1 761 observed (I? 3i) reflections to final R and R values of 0.034 and 0.036 respectively. The CuII has a distorted octahedral co-ordination with a nitrogen of the bzim ligand [Cu–N 1.947(5)Å] and three oxygens of water molecules in the basal plane [mean Cu–O 2.017(3)Å] and two more water oxygens at axial positions [Cu–O 2.194(6) and 2.732(5)Å]. The nucleotide base stacks with the bzim ligand at an average distance of 3.5 Å and an angle of 22°. In the lattice, N(7) of the base is linked to a lattice water through a hydrogen bond, while all the phosphate oxygens are involved in hydrogen bonds with co-ordinated as well as lattice water molecules. The co-ordination behaviour of IMP to CuII is compared in structures containing different -aromatic amines in order to assess the influence of the ternary ligand in complex formation. The present results indicate that, apart from the commonly observed phosphate binding, other modes of co-ordination are possible, these being influenced mainly by the -accepting properties of the ternary ligand.

Molecular and crystal structure of 4-ethynylcyanobenzene. An example of Csingle bondHcdots, three dots, centeredN hydrogen bonding

The molecular and crystal structures of 4-ethynylcyanobenzene arereported. The packing of molecules in the crystal is found to be homologous with the crystal structures of HCN, cyanoacetylene and 4-cyano-4'-ethynylbiphenyl. Alternatively, these four crystals could be said to constitute a structural homologous series. The influence of C-H center dot center dot center dot N hydrogen bonding in directing a linear supramolecular arrangement of molecules with ethynyl and cyano groups at opposite ends, is illustrated. (C) 2010 Elsevier B.V. All rights reserved.

Crystal structure of L-lysyl-L-glutamic acid dihydrate

L-Lysyl-L-glutamic acid dihydrate, C11N3O5H21·2H2O, crystallizes in the monoclinic space group P21 with a = 12.474(2), b = 5.020(1), c = 13.157(2) Å, β= 114.69(1)° and Z = 2. The crystal structure was solved by direct methods and refined to an R value of 0.037 using full matrix least-squares method. The molecule exists as a double zwitterion with both the amino and carboxyl groups ionised. The peptide has a folded conformation with its Lys residue trans and Glu residue gauche−gauche+. The side chains of the Lys and Glu residues correspond to all trans and folded (g−g−g−) conformations respectively. The terminal carboxyl group forms hydrogen bonds with the ξ-amino group of the lysine side chain. The head-to-tail interaction often seen in peptide crystals is absent in the present structure. In the extended crystal structure water molecules form channels along the b direction and are enclosed within helically arranged hydrogen bonds formed by the lysine side chain and the peptide backbone.

Ideal Structure of the Silver Code

The Silver code has captured a lot of attention in the recent past,because of its nice structure and fast decodability. In their recent paper, Hollanti et al. show that the Silver code forms a subset of the natural order of a particular cyclic division algebra (CDA). In this paper, the algebraic structure of this subset is characterized. It is shown that the Silver code is not an ideal in the natural order but a right ideal generated by two elements in a particular order of this CDA. The exact minimum determinant of the normalized Silver code is computed using the ideal structure of the code. The construction of Silver code is then extended to CDAs over other number fields.

Dynamics and local structure of colossal magnetoresistance manganites

We report Extended X-ray Absorption Fine Structure and anelastic spectroscopy measurements on on hole doped manganese oxides La1-xCaxMnO3 which present the colossal magnetoresistance effect. EXAFS measurements were realized both in the absence and presence of an applied magnetic field of 1.1 Tesla, in a wide temperature range (between 330 and 77 K) and at various dopings (x = 0.25 and x = 0.33). The magnetic field orders the magnetic moments so favouring the electron mobility and the reduction of Mn-O octahedra distortions. We observe the presence of four short and two long Mn-O distances (1.93 and 2.05 Angstrom respectively) above and also below the metal-insulator phase transition. The overall distortion decreases but does not completely disappear in the metallic phase suggesting the possible coexistence of metallic and insulating regions at low temperatures. The magnetic field reduces the lattice distortions showing evidence of a microscopic counterpart of the macroscopic colossal magnetoresistance. We also present preliminary anelastic relaxation spectra in a wide temperature range from 900 K to 1 K on a sample with x = 0.40, in order to study the structural phase transitions and the lattice dynamics. A double peak has been observed at the metal-insulator transition in the imaginary part of Young's modulus. This double peak indicates that the metal-insulator transition could be a more complex phenomenon than a simple second order phase transition. In particular the peak at lower temperatures can be connected with the possible presence of inhomogeneous phase structures. Another intense dissipation peak has been observed corresponding to the structural orthorhombic-trigonal transition around 750 K.

A numerical study of the role of the vertical structure of vorticity during tropical cyclone genesis

An eight-level axisymmetric model with simple parameterizations for clouds and the atmospheric boundary layer was developed to examine the evolution of vortices that are precursors to tropical cyclones. The effect of vertical distributions of vorticity, especially that arising from a merger of mid-level vortices, was studied by us to provide support for a new vortex-merger theory of tropical cyclone genesis. The basic model was validated with the analytical results available for the spin-down of axisymmetric vortices. With the inclusion of the cloud and boundary layer parameterizations, the evolution of deep vortices into hurricanes and the subsequent decay are simulated quite well. The effects of several parameters such as the initial vortex strength, radius of maximum winds, sea-surface temperature and latitude (Coriolis parameter) on the evolution were examined. A new finding is the manner in which mid-level vortices of the same strength decay and how, on simulated merger of these mid-level vortices, the resulting vortex amplifies to hurricane strength in a realistic time frame. The importance of sea-surface temperature on the evolution of full vortices was studied and explained. Also it was found that the strength of the surface vortex determines the time taken by the deep vortex to amplify to hurricane strength.

Primary structure of belladonna mottle virus coat protein.

The coat protein of belladonna mottle virus (a tymovirus) was cleaved by trypsin and chymotrypsin, and the peptides were separated by high performance liquid chromatography using a combination of gel permeation, reverse phase, and ion pair chromatography. The peptides were sequenced manually using the 4-N, N-dimethylaminoazobenzene-4'-isothiocyanate/phenyl isothiocyanate double-coupling method. The chymotryptic peptides were aligned by overlapping sequences of tryptic peptides and by homology with another tymovirus, eggplant mosaic virus. The belladonna mottle virus is more closely related to eggplant mosaic virus than to turnip yellow mosaic virus, the type member of this group, as evident from the sequence homologies of 57 and 32%, respectively. The accumulation of basic residues at the amino terminus implicated in RNA-protein interactions in many spherical plant viruses was absent in all the three sequences. Interestingly, the amino-terminal region is the least conserved among the tymoviruses. The longest stretch of conserved sequence between belladonna mottle virus and eggplant mosaic virus was residues 34-44, whereas it was residues 96-102 in the case of belladonna mottle virus and turnip yellow mosaic virus. A tetrapeptide in the region (residues 154-157) was found to be common for all the three sequences. It is possible that these conserved regions (residues 34-44, 96-102, 154-157) are involved in either intersubunit or RNA-protein interactions.

Electronic structure of high-Tc Ba0.6K0.4BiO3 by x-ray photoelectron spectroscopy

We have investigated the electronic structure of Ba1-xKxBiO3 (0of +3 as in Bi2O3 and we find no evidence for the disproportionation of Bi4+ to Bi3+ and Bi5+. Instead, we find that BaBiO3 has mixed valent O2- and O1- ions. As the potassium doping is increased, the binding energy of the O2- ions in the O(1s) photoelectron spectra steadily decreases from 529.7 to 528.8 eV. The effect of lowering the O(1s) binding energy is to raise the O(2p) band towards EF and at the superconducting composition a finite density of O(2p) states is observed near EF. Similarly, the Ba(5p) binding energies decrease with potassium doping, indicating increased metallicity. The behavior of the O(1s), Ba(5p), and the valence band resembles that of all the cuprate superconductors and we conclude that in all these oxide superconductors, a hole in the (filled) O(2p) band is the carrier responsible for superconductivity, which predicts hole conduction in the Ba-K-Bi-O and Ba-Pb-Bi-O systems.

Structure of columbin, a diterpenoid furanolactone from Tinospora cordifolia Miers

(1S,4R,5R,8S, IOR,12S)-4-Hydroxy-15,16-epoxycleroda-2,13 (16), 14-trieno- 17,12:18,1-biscarbolactone,C20H2206, Mr = 358.2, m.p. = 453-454 K,orthorhombic, P212121, a = 7.3869 (6), b = 11.986 (1),c=19.896(2) A, V=1761.65A 3, Z=4, D x=1.351, Din(by flotation)= 1.349gem -3, 2(CuKa)=1.5418 A, /l = 8.36 cm -1, F(000) = 760, T= 295 K,R = 0.0432 for 1662 observed reflections. Two terpenerings, two ~-lactones, two methyl groups, a tertiary hydroxyl group and a fl-substituted furan ring are present in the structure. The H atoms at C(12) and C(8) are a- and fl-oriented. The terpene ring A is locked into a boat conformation by the C(1)-C(4) lactone bridge. The furan ring is attached equatoriaUy at atom C(12). The hydroxyl group is involved in intramolecular hydrogen bonding.