Structural features of B-DNA dodecamer crystal structures: Influence of crystal packing versus base sequence

We have analyzed the set of inter and intra base pair parameters for each dinucleotide step in single crystal structures of dodecamers, solved at high and medium resolution and all crystallized in P2(1)2(1)2(1) space group. The objective was to identify whether all the structures which have either the Drew-Dickerson (DD) sequence d[CGCGAATTCGCG] with some base modification or related sequence (non-DD), would display the same sequence dependent structural variability about its palindromic sequence, despite the molecule being bent at one end because of similar crystal lattice packing effect. Most of the local doublet parameters for base pairs steps G2-C3 and G10-C11 positions, symmetrically situated about the lateral twofold, were significantly correlated between themselves. In non-DD sequences, significant correlations between these positional parameters were absent. The different range of local step parameter values at each sequence position contributed to the gross feature of smooth helix axis bending in all structures. The base pair parameters in some of the positions, for medium resolution DD sequence, were quite unlike the high-resolution set and encompassed a higher range of values. Twist and slide are the two main parameters that show wider conformational range for the middle region of non-DD sequence structures in comparison to DD sequence structures. On the contrary, the minor and major groove features bear good resemblance between DD and non-DD sequence crystal structure datasets. The sugar-phosphate backbone torsion angles are similar in all structures, in sharp contrast to base pair parameter variation for high and low resolution DD and non-DD sequence structures, consisting of unusual (epsilon =g(-), xi =t) B-II conformation at the 10(th) position of the dodecamer sequence. Thus examining DD and non-DD sequence structures packed in the same crystal lattice arrangement, we infer that inter and intra base pair parameters are as symmetrically equivalent in its value as the symmetry related step for the palindromic DD sequence about lateral two-fold axis. This feature would lead us to agree with the conclusion that DNA conformation is not substantially affected by end-to-end or lateral inter-molecular interaction due to crystal lattice packing effect. Non-DD sequence structures acquire step parameter values which reflect the altered sequence at each of the dodecamer sequence position in the orthorhombic lattice while showing similar gross features of DD sequence structures

Structural morphology of acoustically levitated and heated nanosilica droplet

We study the vaporization and precipitation dynamics of a nanosilica encapsulated water droplet by levitating it acoustically and heating it with a CO2 laser. For all concentrations, we observe three phases: solvent evaporation, surface agglomeration, and precipitation leading to bowl or ring shaped structures. At higher concentrations, ring reorientation and rotation are seen consistently. The surface temperature from an infrared camera is seen to be dependent on the final geometrical shape of the droplet and its rotation induced by the acoustic field of the levitator. With nonuniform particle distribution, these structures can experience rupture which modifies the droplet rotational speed. (C) 2010 American Institute of Physics. doi:10.1063/1.3493178]

Chemical toughening of epoxies. I. Structural modification of epoxy resins by reaction with hydroxy-terminated poly (butadiene-co-acrylonitrile)

In an attempt to toughen the epoxy resin matrix for fiber-reinforced composite applications, a chemical modification procedure of a commercially available bisphenol-A-based epoxy resin using reactive liquid rubber HTBN [hydroxy-terminated poly(butadiene-co-acrylonitrile)] and TDI (tolylene diisocyanate) is described. The progress of the reaction and the structural changes during modification process are studied using IR spectroscopy, viscosity data, and chemical analysis (epoxy value determination). The studies support the proposition that TDI acts as a coupling agent between the epoxy and HTBN, forming a urethane linkage with the former and an oxazolidone ring with the latter. The chemical reactions that possibly take place during the modification are discussed.

Chemical toughening of epoxies. I. Structural modification of epoxy resins by reaction with hydroxy-terminated poly(butadiene-co-acrylonitrile)

In an attempt to toughen the epoxy resin matrix for fiber-reinforced composite applications, a chemical modification procedure of a commercially available bisphenol-A-based epoxy resin using reactive liquid rubber HTBN [hydroxy-terminated poly(butadiene-co-acrylonitrile)] and TDI (tolylene diisocyanate) is described. The progress of the reaction and the structural changes during modification process are studied using IR spectroscopy, viscosity data, and chemical analysis (epoxy value determination). The studies support the proposition that TDI acts as a coupling agent between the epoxy and HTBN, forming a urethane linkage with the former and an oxazolidone ring with the latter. The chemical reactions that possibly take place during the modification are discussed.

A structural study of Li2S---B2S3 glasses by neutron diffraction

The radial distribution functions (RDFs) of five xLi2S.(1 - x)B2S3 glasses (x = 0.55, 0.60, 0.67, 0.71 and 0.75) have been determined from neutron diffraction experiments performed at the Institut Laue-Langevin, Grenoble. These glasses are prepared by casting a molten mixture of boron, sulphur and Li2S inside a controlled atmosphere glovebox. Addition of the Li2S Modifier is found gradually to suppress all peaks corresponding to interatomic distances > 3.5 angstrom, which implies that the structural entities present in these glasses become segmented, and therefore more ionic, as x increases. The assumption of the existence of four main structural entities based on four- and three-coordinated borons (the latter carrying bridging and/or non-bridging sulphurs) accounts for all the peaks present in the RDFs as a function of composition. Furthermore, in the most modified glass (x = 0.75), that which contains only 'isolated' BS33- triangles, there seems to be evidence for either octahedral or tetrahedral coordination of Li+ by S- ions

Structural Behavior of Story-High Cement-Stabilized Rammed-Earth Walls under Compression

A rammed-earth wall is a monolithic construction made by compacting processed soil in progressive layers in a rigid formwork. There is a growing interest in using this low-embodied-carbon building material in buildings. The paper investigates the strength and structural behavior of story-high cement-stabilized rammed-earth (CSRE) walls, reviews literature on the strength of CSRE, and discusses results of the compressive strength of CSRE prisms, wallettes, and story-high walls. The strength of the story-high wall was compared with the strength of wallettes and prisms. There is a nearly 30% reduction in strength as the height-to-thickness ratio increases from about 5 to 20. The ultimate compressive strength of CSRE walls predicted using the tangent modulus theory is in close agreement with the experimental values. The shear failures noticed in the story-high walls resemble the shear failures of short-height prism and wallette specimens. The paper ends with a discussion of structural design and characteristic compressive strength of CSRE walls. DOI: 10.1061/(ASCE)MT.1943-5533.0000155. (C) 2011 American Society of Civil Engineers.

Structural characterization of gel-grown neodymium copper oxalate single crystals

Sparingly soluble neodymium copper oxalate (NCO) single crystals were grown by gel method, by the diffusion of a mixture of neodymium nitrate and cupric nitrate into the set gel containing oxalic acid. Tabular crystal, revealing well-defined dissolution figures has been recorded. X-ray diffraction studies of the powdered sample reveal that NCO is crystalline. Infrared absorption spectrum confirmed the formation of oxalato complex with water of crystallization, while energy dispersive X-ray analysis established the presence of neodymium dominant over copper in the sample. X-ray photoelectron spectroscopic studies established the presence of Nd and Cu in oxide states besides (C2O4)(2-) oxalate group. The intensities of Nd (3d(5/2)) and Cu (2p(3/2)) peaks measured in terms of maximum photoelectron count rates also revealed the presence of Nd in predominance. The inductively coupled plasma analysis supports the EDAX and XPS data by the estimation of neodymium percentage by weight to that of copper present in the NCO sample. On the basis of these findings, an empirical structure for NCO has been proposed. The implications are discussed.

Structural proteins of mycobacteriophage I3: cloning, expression and sequence analysis of a gene encoding a 70-kDa structural protein

The structural proteins of mycobacteriophage I3 have been analysed by sodium dodecyl sulfate-polyacrylamide-gel electrophoresis (SDS-PAGE), radioiodination and immunoblotting. Based on their abundance the 34- and 70-kDa bands appeared to represent the major structural proteins. Successful cloning and expression of the 70-kDa protein-encoding gene of phage I3 in Escherichia coli and its complete nucleotide sequence determination have been accomplished, A second (partial) open reading frame following the stop codon for the 70-kDa protein was also identified within the cloned fragment. The deduced amino-acid sequence of the 70-kDa protein and the codon usage patterns indicated the preponderance of codons, as predicted from the high G+C content of the genomic DNA of phage I3.

Studies on molecular evolution and structural features of double-headed inhibitors of ?-amylase and trypsin in plants

Plant seeds usually have high concentrations of proteinase and amylase inhibitors. These inhibitors exhibit a wide range of specificity, stability and oligomeric structure. In this communication, we report analysis of sequences that show statistically significant similarity to the double-headed alpha-amylase/trypsin inhibitor of ragi (Eleusine coracana). Our aim is to understand their evolutionary and structural features. The 14 sequences of this family that are available in the SWISSPROT database form three evolutionarily distinct branches. The branches relate to enzyme specificities and also probably to the oligomeric state of the proteins and not to the botanical class of the plant from which the enzymes are derived. This suggests that the enzyme specificities of the inhibitors evolved before the divergence of commercially cultivated cereals. The inhibitor sequences have three regions that display periodicity in hydrophobicity. It is likely that this feature reflects extended secondary structure in these segments. One of the most variable regions of the polypeptide corresponds to a loop, which is most probably exposed in the native structure of the inhibitors and is responsible for the inhibitory property.

Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S

Two fragments of pancreatic ribonuclease A, a truncated version of S-peptide (residues 1-15) and S-protein (residues 21-124), combine to give a catalytically active complex. We have substituted the wild-type residue at position 13, methionine (Met), with norleucine (Nle), where the only covalent change is the replacement of the sulfur atom with a methylene group. The thermodynamic parameters associated with the binding of this variant to S-protein, determined by titration calorimetry in the temperature range 10-40 degrees C, are reported and compared to values previously reported [Varadarajan, R., Connelly, P. R., Sturtevant, J. M., & Richards, F. M. (1992) Biochemistry 31, 1421-1426] for other position 13 analogs. The differences in the free energy and enthalpy of binding between the Met and Nle peptides are 0.6 and 7.9 kcal/mol at 25 degrees C, respectively. These differences are slightly larger than, but comparable to, the differences in the values for the Met/Ile and Met/Leu pairs. The structure of the mutant complex was determined to 1.85 Angstrom resolution and refined to an R-factor of 17.4% The structures of mutant and wild-type complexes are practically identical although the Nle side chain has a significantly higher average B-factor than the corresponding Met side chain. In contrast, the B-factors of the atoms of the cage of residues surrounding position 13 are all somewhat lower in the Nle variant than in the Met wild-type. Thus, the large differences in the binding enthalpy appear to reside entirely in the difference in chemical properties or dynamic behavior of the -S- and -CH2- groups and not in differences in the geometry of the side chains or the internal cavity surface. In addition, a novel method of obtaining protein stability data by means of isothermal titration calorimetry is introduced.

Neutron diffraction study of the coupling between spin, lattice, and structural degrees of freedom in 0.8BiFeO(3)-0.2PbTiO(3)

A powder neutron diffraction study was carried out on 0.8BiFeO(3)-0.2PbTiO(3) in the temperature range 27-1000 degrees C. The system exhibits magnetic transition at similar to 300 degrees C and a rhombohedral (R3c)-cubic (Pm3m) ferroelectric phase transition at similar to 650 degrees C. Anomalous variation in the lattice parameters and the octahedral tilt angle is observed across the magnetic transition temperature. In the magnetic phase, the c parameter is contracted and the octahedral tilt angle is slightly increased. The results suggest coupling between the spin, lattice and structural degrees of freedom. (C) 2011 American Institute of Physics. doi:10.1063/1.3555093]

Structural variants of hyperbranched polyesters

Hyperbranched polyesters based on 3,5-dihydroxybenzoic acid and its derivatives were prepared by self-condensation of the corresponding ester under standard trans-esterification conditions. The spacer segment length that connects the branching points was systematically varied by starting from the appropriate ethyl 3,5-bis(omega-hydroxyoligo(ethyleneoxy))benzoate. The thermal properties of the hyperbranched polyesters were studied using DSC, and they have been compared with those of the linear analogues prepared from the corresponding p-hydroxybenzoic acid derivatives and also with the molecularly ''kinked'' analogues prepared from the meta isomers. These hyperbranched polyesters were also terminally functionalized by using a potentially mesogenic 4-butoxybiphenylcarboxylic acid derivative in an attempt to prepare novel hyperbranched liquid crystalline polyesters. This was achieved by copolymerization of the AB(2) monomer with the mesogenic A-type capping unit. These polymers were found to be amorphous and did not exhibit any liquid crystalline phases, probably due to the random distribution of the mesogenic segments on the polymer framework, making it difficult to both crystallize and form mesophases.

Structural dependence of density in high molecular weight esters

The effect of molecular structure on density has been examined in high molecular weight esters (molecular weight 300-900), having varying degrees of branching. Densities were calculated from an empirical equation, which agrees well with the experimental values (error +/-1.5%), irrespective of branching. Since density is related to molecular packing and hence to the molecular rotation, in n-alkanes, the glass transition temperature (T(g)) and density both increase with molecular weight, and hence T(g) is directly related to the density. The esters exhibit a complex behavior. In linear esters the T(g) decreases with molecular weight which is explained from group contribution and molecular interactions. In the +-branched esters, however, T(g) decreases with molecular weight until the molecular weight reaches 600 and increases sharply thereafter. The Y-branched esters show an intermediate behavior. The dependence of T(g) on molecular weight has been explained from the segmental motion.