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.

Structural ordering of diamond like carbon films by applied electric field

Diamond like carbon films deposited by RF magnetron sputter deposition technique contain both SP2 and SP3 hybridized carbons. These films are structurally disordered and inhomogeneous. By the application of electric field across the film, these films are transformed to a more orderly structured diamond like carbon, bringing homogenity in the film. This transformation has resulted in the increase of the reflectivity of the metal(Aluminum), which is used as one of the electrodes for applying the electric field, by 5 times.

A novel structural derivative of natural alkaloid ellipticine, MDPSQ, induces necrosis in leukemic cells

DNA intercalating molecules are promising chemotherapeutic agents. In the present study, a novel DNA intercalating compound of pyrimido4',5':4,5]selenolo(2,3-b)quinoline series having 8-methyl-4-(3 diethylaminopropylamino) side chain is studied for its chemotherapeutic properties. Our results showed that 8-methyl-4-(3 diethylaminopropylamino) pyrimido 4',5':4,5] selenolo(2,3-b)quinoline (MDPSQ) induces cytotoxicity in a time- and concentration-dependent manner on leukemic cell lines. Both cell cycle analysis and tritiated thymidine assays revealed that MDPSQ affects DNA replication. Treatment with MDPSQ resulted in both elevated levels of DNA strand breaks and repair proteins, further indicating its cytotoxic effects. Besides, Annexin V/PI staining revealed that MDPSQ induces cell death by triggering necrosis rather than apoptosis.

Instability, intermittency, and multiscaling in discrete growth models of kinetic roughening

We show by numerical simulations that discretized versions of commonly studied continuum nonlinear growth equations (such as the Kardar-Parisi-Zhangequation and the Lai-Das Sarma-Villain equation) and related atomistic models of epitaxial growth have a generic instability in which isolated pillars (or grooves) on an otherwise flat interface grow in time when their height (or depth) exceeds a critical value. Depending on the details of the model, the instability found in the discretized version may or may not be present in the truly continuum growth equation, indicating that the behavior of discretized nonlinear growth equations may be very different from that of their continuum counterparts. This instability can be controlled either by the introduction of higher-order nonlinear terms with appropriate coefficients or by restricting the growth of pillars (or grooves) by other means. A number of such ''controlled instability'' models are studied by simulation. For appropriate choice of the parameters used for controlling the instability, these models exhibit intermittent behavior, characterized by multiexponent scaling of height fluctuations, over the time interval during which the instability is active. The behavior found in this regime is very similar to the ''turbulent'' behavior observed in recent simulations of several one- and two-dimensional atomistic models of epitaxial growth.

Optical and structural properties of reactive ion beam sputter deposited CeO2 films

Optical and structural properties of reactive ion beam sputter deposited CeO2 films as a function of oxygen partial pressures (P-O2) and substrate temperatures (T-s) have been investigated. The films deposited at ambient temperature with P-O2 of 0.01 Pa have shown a refractive index of 2.36 which increased to 2.44 at 400 degrees C. Refractive index and extinction coefficient are sensitive up to a T-s of similar to 200 degrees C. Raman spectroscopy and X-ray diffraction (XRD) have been used to characterise the structural properties. A preferential orientation of (220) was observed up to a T-s of 200 degrees C and it changed to (200) at 400 degrees C: and above. Raman line broadening, peak shift and XRD broadening indicate the formation of nanocrystalline phase for the films deposited up to a substrate temperature of 300 degrees C. However, crystallinity of the films were better for T-s values above 300 degrees C. In general both optical and structural properties were unusual compared to the films deposited by conventional electron beam evaporation, but were similar in some aspects to those deposited by ion-assisted deposition. Apart from thermal effects, this behavior is also attributed to the bombardment of backscattered ions/neutrals on the growing film as well as the higher kinetic energy of the condensing species, together resulting in increased packing density. (C) 1997 Elsevier Science S.A.

Synthesis and structural characterization of perovskite 0.65Pb(Mg1/3Nb2/3)O-3-0.35PbTiO(3) nanotubes

We report the synthesis and structural characterization of 0.65Pb(Mg1/3Nb2/3)O-3-0.35PbTiO(3) (PMN-PT) nanotubes prepared by a novel sal-gel template method. X-ray diffraction (XRD) and selected-area electron diffraction (SAED) investigations demonstrated that the postannealed (650 degrees C for 1 h) PMN-PT nanotubes were polycrystalline with perovskite crystal structure. The field emission scanning electron microscope (FE-SEM) shows that as prepared PMN-PT nanotubes were hollow with diameter to be about 200 nm. High resolution transmission electron microscope (HRTEM) analysis confirmed that the obtained PMN-PT nanotubes made up of nanoparticles (10-20 nm) which were randomly aligned in the nanotubes. Energy-dispersive X-ray spectroscopy (EDX) analysis confirmed the stoichiometric 0.65Pb(Mg1/3Nb2/3)O-3-0.35PbTiO(3). The possible formation mechanism of PMN-PT nanotubes was proposed at the end. (C) 2011 Elsevier B.V. All rights reserved.

Structural studies of protein unfolding

Methods for macromolecular structure determination (NMR and crystallography) are now being used to get structural information on partially folded and unfolded states of proteins. These techniques, in combination with proton hydrogen exchange studies are powerful tools to extract information on non-native states of proteins. This review discusses progress In this area of protein folding.

Structural characterisation of a uracil containing hairpin DNA by NMR and molecular dynamics

Three-dimensional (3D) structure of a hairpin DNA d-CTAGAGGATCCTTTUGGATCCT (22mer; abbreviated as U4-hairpin), which has a uracil nucleotide unit at the fourth position from the 5' end of the tetra-loop has been solved by NMR spectroscopy. The H-1 resonances of this hairpin have been assigned almost completely. NMR restrained molecular dynamics and energy minimisation procedures have been used to describe the 3D structure of the U4 hairpin. This study establishes that the stem of the hairpin adopts a right handed B-DNA conformation while the T-12 and U-15 nucleotide stack upon 3' and 5' ends of the stem, respectively. Further, T-14 stacks upon both T-12 and U-15 while T-13 partially stacks upon T-14. Very weak stacking interaction is observed between T-13 and T-12. All the individual nucleotide bases adopt 'anti' conformation with respect to their sugar moiety. The turning phosphate in the loop is located between T-13 and T-14. The stereochemistry of U-15 mimics the situation where uracil would stack in a B-DNA conformation. This could be the reason as to why the U4-hairpin is found to be the best substrate for its interaction with uracil DNA glycosylase (UDG) compared to the other substrates in which the uracil is at the first, second and third positions of the tetra-loop from its 5' end, as reported previously.

Structural instability of the charge ordered compound Nd0.5Sr0.5MnO3 under a magnetic field

We report an anomalous magnetostriction behavior of the charge ordered compound Nd0.5Sr0.5MnO3. We have found that the applied magnetic field not only gives rise to a large negative magnetoresistance but also produces a huge positive magnetovolume effect. This unusual effect is explained considering that the applied magnetic field induces a structural transition at which the volume drastically increases. This effect is also seen in the anisotropic magnetostriction which shows clear anomalies at the field induced transition.

Assessment of conditional moment closure models of turbulent autoignition using DNS data

A systematic assessment of the submodels of conditional moment closure (CMC) formalism for the autoignition problem is carried out using direct numerical simulation (DNS) data. An initially non-premixed, n-heptane/air system, subjected to a three-dimensional, homogeneous, isotropic, and decaying turbulence, is considered. Two kinetic schemes, (1) a one-step and (2) a reduced four-step reaction mechanism, are considered for chemistry An alternative formulation is developed for closure of the mean chemical source term , based on the condition that the instantaneous fluctuation of excess temperature is small. With this model, it is shown that the CMC equations describe the autoignition process all the way up to near the equilibrium limit. The effect of second-order terms (namely, conditional variance of temperature excess sigma(2) and conditional correlations of species q(ij)) in modeling is examined. Comparison with DNS data shows that sigma(2) has little effect on the predicted conditional mean temperature evolution, if the average conditional scalar dissipation rate is properly modeled. Using DNS data, a correction factor is introduced in the modeling of nonlinear terms to include the effect of species fluctuations. Computations including such a correction factor show that the species conditional correlations q(ij) have little effect on model predictions with a one-step reaction, but those q(ij) involving intermediate species are found to be crucial when four-step reduced kinetics is considered. The "most reactive mixture fraction" is found to vary with time when a four-step kinetics is considered. First-order CMC results are found to be qualitatively wrong if the conditional mean scalar dissipation rate is not modeled properly. The autoignition delay time predicted by the CMC model compares excellently with DNS results and shows a trend similar to experimental data over a range of initial temperatures.