Structure of bis(thiocyanato-N)bis(thiosemicarbazide-N1,S)nickel(II): a redetermination

[Ni(NCS)2(CHsN3S)2], Mr = 356.7, monoclinic, P21/c , a = 5-297 (1), b = 7.869 (1), c - 16-078 (2) A,/3 = 91.53 (1) °, V-= 669.9 A 3, Z= 2, Om = 1"76, Dx = 1"771 g cm -3, A(Mo Ka) = 0-71069 ]k, /.~ = 19"9 cm-l, F(000) = 364, T = 295 K, final R = 0.026 for 1576 significant [F > 10g(F)] reflections. The complex lies on a crystallographic centre of symmetry. The Ni atom is octahedrally coordinated by two thiocyanates (through N atoms) and by two thiosemicarbazide molecules (through hydrazinic N and S atoms). The crystal structure is stabilized by N--H...S hydrogen bonds. Early work on this structure [Garaj & Dunaj-Jurco (1968). Chem. Commun. p. 518] used photographic data and was refined to R = 0-13 for 512 reflections.

Reproduction and population structure in European aspen

The European aspen (Populus tremula) is a keystone species for biodiversity in boreal forests. However, the future of aspen may be threatened, because large aspens have mostly been removed from managed forests, whereas regeneration and the long-term persistence of mature trees are subjects of concern in protected areas. Aspen is a pioneer tree, and it can reproduce both sexually by seed and asexually by root suckers. Through asexual reproduction aspen forms clones, groups of genetically identical trees (ramets). In my thesis, I have studied the structure of aspen populations in terms of number, size, clonal and demographic properties. Additionally, I have investigated the emergence and survival of seedlings as well as the seed quantity and quality in crosses between the European and hybrid aspen. To study the regeneration and population structure, mature aspens were recorded in old-growth and managed forests in eastern Finland based on a large-scale inventory (11 400 ha). In addition, small aspen trees were surveyed on sample plots. Clonal structure was investigated both by morphological characters and by DNA-based markers (microsatellites). Seedling emergence and survival was studied with two sowing experiments. With crosses between European and hybrid aspens we wanted to study whether elevated temperatures due to climate change would benefit the different crosses of European and hybrid aspen unequally and thus affect the gene flow between the two species. The average volumes of mature aspen were 5.3 m3/ha in continuous old-growth, and 0.8 m3/ha in managed forests. Results indicate also that large aspen trees in managed forests are a legacy of the past less intensively managed forest landscapes. Long-term persistence of aspen in protected areas can only be secured by restoration measures creating sufficiently large gaps for regeneration. More emphasis should be given to sparing aspens in thinnings and to retaining of mature aspens in regeneration cutting in managed forests. Aspen was found to be spatially aggregated in the landscape. This could be explained by site type, disturbance history and / or limitations in seed dispersal. Clonal structure does not explain the spatial aggregation, since average size of the clones was only 2.3 ramets, and most clones (70 %) consisted of just one ramet. The small size of the clones suggests that most of them are relatively young. Therefore, sexual reproduction may be more common than has previously been thought. Seedling emergence was most successful in mineral soil especially, when the site had been burned. Only few seedlings occurred on humus. Survival of the seedlings was low, and strongly dependent on moisture, but also on seedbed conditions. The seeds were found to maintain their germinability longer than has earlier been thought to be possible. Interspecific crosses produced more seeds with higher quality than intraspecific crosses. When temperature was elevated, germination of hybrid aspen seeds increased more than seeds from P. tremula x P. tremula crosses. These results suggest that hybrid aspen may have a significant genetic impact on the European aspen, and this effect may become strengthened by climate warming.

Evaluating viewpoint entropy for ribbon representation of protein structure

While many measures of viewpoint goodness have been proposed in computer graphics, none have been evaluated for ribbon representations of protein secondary structure. To fill this gap, we conducted a user study on Amazon’s Mechanical Turk platform, collecting human viewpoint preferences from 65 participants for 4 representative su- perfamilies of protein domains. In particular, we evaluated viewpoint entropy, which was previously shown to be a good predictor for human viewpoint preference of other, mostly non-abstract objects. In a second study, we asked 7 molecular biology experts to find the best viewpoint of the same protein domains and compared their choices with viewpoint entropy. Our results show that viewpoint entropy overall is a significant predictor of human viewpoint preference for ribbon representations of protein secondary structure. However, the accuracy is highly dependent on the complexity of the structure: while most participants agree on good viewpoints for small, non-globular structures with few secondary structure elements, viewpoint preference varies considerably for complex structures. Finally, experts tend to choose viewpoints of both low and high viewpoint entropy to emphasize different aspects of the respective structure.

Structure determination and biochemical studies on Bacillus stearothermophilus E53Q serine hydroxymethyltransferase and its complexes provide insights on function and enzyme memory

Serine hydroxymethyltransferase (SHMT) belongs to the alpha-family of pyridoxal 5'-phosphate-dependent enzymes and catalyzes the reversible conversion of L-Ser and etrahydrofolate to Gly and 5,10-methylene tetrahydrofolate. 5,10-Methylene tetrahydrofolate serves as a source of one-carbon fragment in many biological processes. SHMT also catalyzes the tetrahydrofolate-independent conversion of L-allo-Thr to Gly and acetaldehyde. The crystal structure of Bacillus stearothermophilus SHMT (bsSHMT) suggested that E53 interacts with the substrate, L-Ser and etrahydrofolate. To elucidate the role of E53, it was mutated to Q and structural and biochemical studies were carried out with the mutant enzyme. The internal aldimine structure of E53QbsSHMT was similar to that of the except for significant changes at Q53, Y60 and Y61. The wild-type enzyme, carboxyl of Gly and side chain of L-Ser were in two conformations in the respective external aldimine structures. The mutant enzyme was completely inactive for tetrahydrofolate-depen dent cleavage of L-Ser, whereas there was a 1.5-fold increase in the rate of tetrahydrofolate-independent reaction with L-allo-Thr. The results obtained from these studies suggest that E53 plays an essential role in tetrahydrofolate/5-formyl tetrahydrofolate binding and in the proper positioning of C beta of L-Ser for direct attack by N5 of tetrahydrofolate. Most interestingly, the structure of the complex obtained by cocrystallization of E53QbsSHMT with Gly and 5-formyl tetrahydrofolate revealed the gem-diamine form of pyridoxal 5'-phosphate bound to Gly and active site Lys. However, density for 5-formyl tetrahydrofolate was not observed. Gly carboxylate was in a single conformation, whereas pyridoxal 5'-phosphate had two distinct conformations. The differences between the structures of this complex and Gly external aldimine suggest that the changes induced by initial binding of 5-formyl tetrahydrofolate are retained even though 5-formyl tetrahydrofolate is absent in the final structure. Spectral studies carried out with this mutant enzyme also suggest that 5-formyl tetrahydrofolate binds to the E53QbsSHMT-Gly complex forming a quinonoid intermediate and falls off within 4 h of dialysis, leaving behind the mutant enzyme in the gemdiamine form. This is the first report to provide direct evidence for enzyme memory based on the crystal structure of enzyme complexes.

A Device to Crystallize Organic Solids: Structure of Ciprofloxacin, Midazolam, and Ofloxacin as Targets

The crystal structure determination of the anhydrous form of any organic compound has been a challenge because of solvent incorporation during crystallization. A device to grow anhydrous forms of low melting organic solids based on vaporization and condensation by a gradient cooling technique has been designed. Its utility has been evaluated by growing anhydrous forms of ciprofloxacin, midazolam, and ofloxacin. Ciprofloxacin crystallizes in triclinic P (1) over bar, midazolam in monoclinic P2(1)/n, and ofloxacin in the C2/c space group. Comparative studies on the conformational features with solvated structure show no significant variation in the aromatic moieties.

Multiple support excitations of open-plane frames by a filtered white noise and soil-structure interaction

Seismic structural design is essentially the estimation of structural response to a forced motion, which may be deterministic or stochastic, imposed on the ground. The assumption that the same ground motion acts at every point of the base of the structure (or at every support) is not always justifiable; particularly in case of very large structures when considerable spatial variability in ground motion can exist over significant distances example long span bridges. This variability is partly due to the delay in arrival of the excitation at different supports (which is called the wave passage effect) and due to heterogeneity in the ground medium which results in incoherency and local effects. The current study examines the influence of the wave passage effect (in terms of delay in arrival of horizontal ground excitation at different supports and neglecting transmission through the structure) on the response of a few open-plane frame building structures with soil-structure interaction. The ground acceleration has been modeled by a suitably filtered white noise. As a special case, the ground excitation at different supports has also been treated as statistically independent to model the extreme case of incoherence due to local effects and due to modifications to the ground motion resulting from wave reflections and refractions in heterogeneous soil media. The results indicate that, even for relatively short spanned building frames, wave passage effect can be significant. In the absence of soil-structure interaction, it can significantly increase the root mean square (rms) value of the shear in extreme end columns for the stiffer frames but has negligible effect on the flexible frames when total displacements are considered. It is seen that pseudo-static displacements increasingly contribute to the rms value of column shear as the time delay increases both for the stiffer and for the more flexible frames. When soil-structure interaction is considered, wave passage effect (in terms of total displacements) is significant only for low soil shear modulus, G. values (where soil-structure interaction significantly lowers the fundamental frequency) and for stiff frames. The contribution of pseudo-static displacement to these rms values is found to decrease with increase in G. In general, wave passage effect for most interactive frames is insignificant compared to the attenuating effect a decrease in G, has on the response of the interactive structure to uniform support excitation. When the excitations at different supports are statistically independent, it is seen that for both the stiff and flexible frames, the rms value of the column shear in extreme end columns is several times larger (more for the stiffer frames) than the value corresponding to uniform base excitation with the pseudo-static displacements contributing over 99% of the rms value of column shear. Soil-structure interaction has an attenuating effect on the rms value of the column shear, the effect decreasing with increase in G,. Here too, the pseudo-static displacements contribute very largely to the column shear. The influence of the wave passage effect on the response of three 2-bay frames with and without soil-structure interaction to a recorded horizontal accelerogram is also examined. (C) 2010 Elsevier Ltd. All rights reserved.

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.

Structure of 6-acetoxycoumarin: topochemical photodimerization and analysis of acetoxy...acetoxy interactions in the solid state

C~HaO 4, Mr=204.2, monoclinic, P2Jn,a=3.900(1), =37.530(6), c=6.460(1)A, fl=103.7 (1) °, V= 918.5 (5) A 3, Z = 4, D m = 1.443, D x --- 1.476 Mg m -3, Cu Ks, 2 = 1.5418 ,/k, /t = 0.86 mm -~, F(000) = 424, T= 293 K, R = 0.075 for 1019 significant reflections. Molecules pack in fl-type stacking mode which is characterized by the close packing of parallel and nearly planar reactive double bonds with a separation of 3.900/~ along the a axis.The syn head-head dimer obtained is the direct consequence of this packing arrangement. Molecular packing is stabilized by intermolecular C-H...O hydrogen bonding. Analysis of acetoxy...acetoxy interactions in the acetoxy compounds retrieved from the Cambridge Structural Database reveal that the majority of them are anti-dipolar.

Structure-Reactivity Correlations of Benzoin Alkyl Ethers. Structures of 2-Methoxy-1,2-diphenylethanone (I) and 2-Isopropoxy-1,2-diphenylethanone (II)

(I): C15H1402, Mr---226.27, triclinic, Pi,a=8.441 (2), b= 10.276 (1), c= 15.342 (2)A, a=91.02 (2), ~ t= 79.26 (2), y= 105.88 (2) °, V=1256.8 (4)A 3, Z=4, D,,= 1.209 (flotation in KI),D x - 1.195 g cm -3, #(Mo, 2 = 0.7107/~) = 0.44 cm -~,F(000) = 480, T= 293 K, R -- 0.060 for 1793 significant reflections. (II): C~THlsO2, Mr= 254.83, orthorhombic, Pca21, a=8.476 (1); b= 16.098 (3), c=10.802(3)A, V=1473.9 (5) A s, Z=4, Dm=1.161 (flotation in KI), Dx= 1.148gem -3, /~(Mo, 2=0.7107 A) =0.41 cm -~, F(000) = 544, T= 293 K, R = 0.071 for 867 significant reflections. Both (I) and (II) crystallize in a cisoid conformation for the carbonyl group and alkoxy groups. Compounds (I) and (II) are photostable on irradiation in the solid state in spite of the favourable conformation of the functional groups for intramolecular H abstraction. Absence of photoreaction of (I)and (II) in the solid state is rationalized in the light of unfavourable intramolecular geometry.

Studies in nonlinear optical materials: structure of di-2-menthyl 2-(N,N'-dimethyl-2-imidazolidinylidene)malonate monohydrate

C28H48N2Oa.H2 O, Mr=494.7, orthorhombic,P2~2~2~, a = 7.634 (2), b = 11.370 (2), c=34. 167 (4) A, V = 2966 (2) A 3, Z = 4, D m = 1.095,D x -- 1. 108 g cm -3, Mo Kct, 2 -- 0.7107 ,/k, ~ =0.43 cm -~, F(000) = 1088.0, T= 293 K, R = 0.061 for 1578 significant reflections. The second-harmonicgeneration (SHG) efficiency of this compound is negligible (1/100th of the urea standard). The observed low second-order nonlinear response has been attributed to the unfavourable packing of the molecules in the crystal lattice.

High-resolution methyl edited GFT NMR experiments for protein resonance assignments and structure determination

Three-dimensional (3D) structure determination of proteins is benefitted by long-range distance constraints comprising the methyl groups, which constitute the hydrophobic core of proteins. However, in methyl groups (of Ala, Ile, Leu, Met, Thr and Val) there is a significant overlap of C-13 and H-1 chemical shifts. Such overlap can be resolved using the recently proposed (3,2)D HCCH-COSY, a G-matrix Fourier transform (GFT) NMR based experiment, which facilitates editing of methyl groups into distinct spectral regions by combining their C-13 chemical shifts with that of the neighboring, directly attached, C-13 nucleus. Using this principle, we present three GFT experiments: (a) (4,3)D NOESY-HCCH, (b) (4,3)D H-1-TOCSY-HCCH and (c) (4,3)D C-13-TOCSY-HCCH. These experiments provide unique 4D spectral information rapidly with high sensitivity and resolution for side-chain resonance assignments and NOE analysis of methyl groups. This is exemplified by (4,3)D NOESY-HCCH data acquired for 17.9 kDa non-deuterated cytosolic human J-protein co-chaperone, which provided crucial long-range distance constraints for its 3D structure determination.

Structure of the putative mutarotase YeaD from Salmonella typhimurium in two different forms: in vivo binding of a sugar phosphate

Salmonella typhimurium YeaD (stYeaD), annotated as a putative aldose 1-epimerase, has a very low sequence identity to other well characterized mutarotases. Sequence analysis suggested that the catalytic residues and a few of the substrate-binding residues of galactose mutarotases (GalMs) are conserved in stYeaD. Determination of the crystal structure of stYeaD in an orthorhombic form at 1.9 angstrom resolution and in a monoclinic form at 2.5 angstrom resolution revealed this protein to adopt the beta-sandwich fold similar to GalMs. Structural comparison of stYeaD with GalMs has permitted the identification of residues involved in catalysis and substrate binding. In spite of the similar fold and conservation of catalytic residues, minor but significant differences were observed in the substrate- binding pocket. These analyses pointed out the possible role of Arg74 and Arg99, found only in YeaD-like proteins, in ligand anchoring and suggested that the specificity of stYeaD may be distinct from those of GalMs

Studies on nonlinear optical materials: structure of diphenylmethyl (Z)-1-(1-methylthio-2-nitrovinyl)tetrahydropyrrole-2-carboxylate

C21H22N2045, M r = 398.5, orthorhombic, P212~21, a = 9.799 (1), b = 11.853 (1), c = 17.316(2)/~, V=2011.4A 3, Z=4, Dm=l.320, Dx=1.314Mgm -3, CuKa, A=1.5418A, Iz= 1.63 ram-1, F(000) = 840.0, T = 293 K, R = 0.055 for 1735 significant reflections. In the 1-methylthio-2- nitrovinyl moiety the C--C bond, 1.368 (7)A, is significantly longer than in ethylene, 1.336 (2)/~. The second harmonic generation (SHG) efficiency of this compound is only 0.25 of the urea standard. The correlation between the molecular packing and SHG is discussed.

Crystal and Molecular Structure of N-acetyl-L-glutamine

The crystal and molecular structure of the title compound has been determined by direct methods from diffractometer data. Crystals are orthorhombic, with Z= 4 in a unit cell of dimensions : a= 13.811 (10), b= 5.095(5), c= 12.914(10)Å, space group P212121. The structure was refined by least-squares to R 3.31% for 868 observed reflections. There is significant non-planarity of the peptide group and its nitrogen atom is significantly pyramidal. There is no correlation between the double-bond character and reactivity of the C–N bond of the terminal amide group in glutamine and acetamide

Conformational Variability in Modified Nucleosides. Crystal and Molecular Structure of 2',3'-O-Isopropylidene Inosine

The crystal structure of 2',3'-O-isopropylidene inosine shows a number of interesting features. The four independent molecules in the asymmetric unit exhibit significant conformational variations. Ribose puckers fall in the O(4')-exo region, unfavourable in unsubstituted nucleosides. Hypoxanthine bases show base-pairing (I.I) in a manner analogous to the guanine self pairs (G.G) in 2',3'-O-isopropylidene guanosine but with a C(2)-H…O(6) hydrogen bond instead of N(2)-H…O(6).