Detecting similarities among distant homologous proteins by comparison of domain flexibilities

Aim of this work is to assess the informativeness of protein dynamics in the detection of similarities among distant homologous proteins. To this end, an approach to perform large-scale comparisons of protein domain flexibilities is proposed. CONCOORD is confirmed as a reliable method for fast conformational sampling. The root mean square fluctuation of alpha carbon positions in the essential dynamics subspace is employed as a measure of local flexibility and a synthetic index of similarity is presented. The dynamics of a large collection of protein domains from ASTRAL/SCOP40 is analyzed and the possibility to identify relationships, at both the family and the superfamily levels, on the basis of the dynamical features is discussed. The obtained picture is in agreement with the SCOP classification, and furthermore suggests the presence of a distinguishable familiar trend in the flexibility profiles. The results support the complementarity of the dynamical and the structural information, suggesting that information from dynamics analysis can arise from functional similarities, often partially hidden by a static comparison. On the basis of this first test, flexibility annotation can be expected to help in automatically detecting functional similarities otherwise unrecoverable.     

Structural studies of coal extracts

The reductive alkylation of a medium-volatile bituminous coal was carried out using potassium and naphthalene in tetrahydrofuran, and using methyl, ethyl and butyl iodides to alkylate the resultant polyanion. The soluble products of the reductive alkylation reaction were isolated by extraction with n-pentane and benzene. The extracts were characterized by i.r. and ¹H n.m.r. spectroscopy, molecular mass and ultimate analyses.     

Structural studies of collagen-like sequential polypeptides

Sequential polyhexapeptides, synthesised by combination of sequences from collagen type Gly-X-Y (X = Ala, Pro, Ser; Y = Ala, Gly, Lys, Pro), were characterized by the temperature dependence of circular dichroism spectra. Under comparable conditions these studies revealed that alternating triplets of Gly-Pro-Pro or Gly-Pro-Ala combined with Gly-Pro-Lys or Gly-Pro-Glu exhibit collagen-like structures in aqueous solutions. In case of unstructured chains of (Gly-Pro-Ala) ≈ 12 it can be shown that N-terminal crosslinking of three chains produces a similar ordered structure.     

Some studies on thermal treatments of polyester fibers: Structural changes

The development of the changes of structure during thermal treatment of polyester fiber is studied. Critical dissolution time (CDT) was evaluated to trace the changes in crystallinity and crystal morphology of polyester fibers. CDT increased as the time of thermal treatment was increased. The change in CDT was less effective for samples thermally treated at temperatures up to 160°C, which may indicate a nucleation tendency of tiny crystals. CDT of polyester treated at 200°C in air was found to be relatively high, while silicon oil medium can affect both amorphous and crystalline regions, increasing the structure disorder. The effect of treatment under constant length revealed smaller CDT values than those attained by samples treated in free conditions. An indication to crystal size increase was traced by a decrease in peak width in X-ray diffraction pattern. Thermal treatment increased the crystallinity of polyester fibers up to 160°C. Dry air medium was more effective in increasing the disorder in amorphous regions than silicon oil medium. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 65: 2773–2780, 1997     

Structural studies of electrodeposited tin—cobalt alloys

The cast tin—cobalt alloys γ′Co₃Sn₂ (hexagonal) and CoSn₂ (tetragonal) were prepared and studied using Mössbauer and X-ray measurements. These results were used in the indentification of the components of electrodeposited tin—cobalt alloys obtained from mildly alkaline sulphate baths. γ′Co₃Sn₂ (hexagonal), CoSn (cubic) and metallic tin were detected as components of the electrodeposited alloys. The relative amounts of the components is highly dependent on the bath operation conditions, and no γ′Co₃Sn₂ was observed when the concentration of electroactive tin in the plating bath was high. The Mössbauer parameters of all the studied alloys are given and are well within the observed values for binary tin alloys.     

Structural studies of nanodiamond by high-energy X-ray diffraction

The atomic scale structure of explosive diamond nanoparticles has been studied using high-energy X-ray diffraction. The diffraction data have been converted to the real space representation in the form of the radial distribution function. Spherical and truncated octahedron nanodiamond clusters containing from 729 to 1182 atoms have been computer generated and then relaxed using the molecular dynamics method with the reactive empirical bond order potential for carbon-carbon interaction and the Lennard–Jones potential with parameters for inter-layer interactions. Validity of such constructed models has been verified by comparison of the simulations and the experimental data in both real and reciprocal space. The obtained results show that the structure of the investigated diamond nanoparticles cannot be satisfactorily described in terms of the model based on the perfect diamond lattice. The core-shell model with an average size of 22.5–23.4 Å, consisting of the diamond core and the graphite-like shell, accounts very well for the experimental data.     

Substituent effects of iron porphyrins: Structural, kinetic, and theoretical studies

Substituent effects of iron porphyrin complexes on the structures and kinetic processes have been examined for the first time. Basing on the premise that iron porphyrin is functional analogous to heme, a series of iron porphyrin derivatives bearing different substituents at the meso positions of the corrole ring are investigated as to their electrochemistry, the relationships among the electron transfer (ET) processes, their structures, and orbital energies. The good coherence between the experiment and theory indicates that the ET rate can be accelerated when electron-donating substituents are introduced to the iron porphyrin ring. Finally, the implications of the results are discussed in the influence of stability of iron porphyrin complexes on the ability to carry molecular oxygen, which may suggest it possible to dominate the biological activity of heme by selecting the appropriate substituents to iron porphyrin ring.     

Molecular association complex of urea with polyethylene: 3. Structural studies of the complex

The crystal structure of urea-polyethylene complex in the hexagonal form, obtained by one of our preparation methods, is analysed by X-ray power diffractometry. In this analysis, the fixed molecular parameters of urea are used, and three models with respect to rotational disorder of the guest polyethylene molecule are assumed. It is shown that the host lattice structure constructed by urea molecules is essentially the same as that of urea-n-paraffin complex. Effects of the disorder structure of the guest on X-ray scattering of the complex are presented. However, there is a difficulty in identifying the disorder structure by X-ray analysis. With the aid of a potential energy calculation between the hexagonal urea tunnel and the guest molecule, a rotational disorder model is preferred.     

Structural studies of carbon prepared by electrochemical reduction of polytetrafluoroethylene

The methods of electron microscopy and X-ray scattering were used in the investigation of the structure of carbon JADO, prepared by the electrochemical reduction of polytetrafluoroethylene, and of the intermediate system C-LiF. The carbon JADO was found to be nongraphitc with a typical nodular morphology. The structure parameters as assessed by both methods were in good agreement and suggested that the carbon ordering in polytetrafluoroethylene did not change substantially during the reduction. The obtained results explained also the abnormally high specific surface area of the carbon. The electrochemical reaction allowed to decompose a bulk polymer into lamellae and to make visible its nodular morphology.     

Low-density polyethylene modified by thermal polymerization of 4-vinylpyridine and methyl methacrylate: Structural studies

The structures of low-density polyethylene (LDPE) modified by in situ sorption and thermal polymerization of 4-vinylpyridine (4VP) and of methyl methacrylate (MMA) were studied. The phase behavior of these materials was investigated by means of X-ray diffraction, scanning electron microscopy (SEM), and by thermal measurements (DSC). The diffraction studies indicated that the polymerization occurs at the amorphous domains of the matrix, except for the case of 4VP (168.0%), in which polymerization at the crystalline domains of LDPE matrix was also observed. These materials showed at least two T_g values, indicating microphase separation. The morphology of LDPE-P4VP was different from that of LDPE-PMMA.     

Polyethylene glycol assisted facile sol-gel synthesis of lanthanum oxide nanoparticles: Structural characterizations and photoluminescence studies

In this study, lanthanum oxide nanoparticles (La₂O₃ NPs) synthesised via the facile sol-gel method, using a solution of micro-sized lanthanum oxide powders containing 20% nitric acid and high molecular weight polyethylene glycol (PEG). The as synthesised La₂O₃ NPs were then characterized using X-ray diffraction (XRD), environmental scanning electron microscopy (ESEM), energy-dispersive X-ray (EDS) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and photoluminescence (PL) spectroscopy. Our findings indicated that the concentration of PEG strongly influences the particle size and the lattice strain of the La₂O₃ NPs. A single phase hexagonal crystal structure was confirmed via XRD studies with lattice constants, a =?b =?0.3973?nm and c =?0.6129?nm. The average crystallite size and lattice strains estimated were in the range of approximately 25–28?nm and 0.0050–0.0055 respectively. The incremental nature of the crystallinity and lattice strains of the NPs was observed with the subsequent enhancement of PEG-contents, while the average particle size was reduced. The average particle size of La₂O₃ NPs estimated from ESEM imaging was consistent with that obtained from the XRD data. The photoluminescence spectra revealed a strong emission band located at a wavelength of 365?nm (typical green band) for all La₂O₃NPsamples. This is ascribed to the recombination of delocalized electrons around the conduction band with a single charged state of a surface oxygen vacancy.     

Fatty acid hydroperoxide isomerase inSaprolegnia parasitica: Structural studies of epoxy alcohols formed from isomeric hydroperoxyoctadecadienoates

The major part (80%) of the fatty acid hydroperoxide isomerase activity present in homogenates of the fungus,Saprolegnia parasitica, was localized in the particle fraction sedimenting at 105,000×g. 13(S)-Hydroperoxy-9(Z),11(E)-octadecadienoic acid and 9(S)-hydroperoxy-10(E),12(Z)-octadecadienoic acid were both good substrates for the particle-bound hydroperoxide isomerase. The products formed from the 13(S)-hydroperoxide were identified as an α,β- and a γ,δ-epoxy alcohol, i.e., 11(R),12(R)-epoxy-13(S)-hydroxy-9(Z)-octadecenoic acid and 9(S),10(R)-epoxy-13(S)-hydroxy-11(E)-octadecenoic acid, respectively. The 9(S)-hydroperoxide was converted in an analogous way into an α,β-epoxy alcohol, 10(R),11(R)-epoxy-9(S)-hydroxy-12(Z)-octadecenoic acid and a γ,δ-epoxy alcohol, 12(R),13(S)-epoxy-9(S)-hydroxy-10(E)-octadecenoic acid. 9(R,S)-Hydroperoxy-10(E),12(E)-octadecadienoic acid and 13(R,S)-hydroperoxy-9(E),11(E)-octadecadienoic acid were poor substrates for theS. parasitica hydroperoxide isomerase. Experiments with 13(R,S)-hydroperoxy-9(Z),11(E)-octadecadienoic acid showed that the 13(R)-hydroperoxy enantiomer was slowly isomerized by the enzyme. The major product was identified as α,β-epoxy alcohol 11(R),12(R)-epoxy-13(R)-hydroxy-9(Z)-octadecenoic acid.     

Structural studies of electrospun nylon 6 fibers from solution and melt

Nylon 6 (N6) fibers have been fabricated via two different electrospinning schemes, from solution of N6 and formic acid at room temperature as well as from N6 melt at elevated temperature. The crystal structures of electrospun N6 fibers from solution and melt, and the annealing effect on the structures were studied by using various techniques. Combined analysis of the differential scanning calorimetry (DSC) at various heating rates, temperature-dependent X-ray diffraction (XRD), and Fourier-transform infrared (FTIR) spectroscopy indicates that N6 fibers from melt predominantly exhibit the meta-stable γ-crystalline forms and low molecular orientation, while solution electrospun fibers from slowly evaporating solvent show both α- and γ-form crystals and higher degree of molecular orientation. At high annealing temperature, the meta-stable γ-crystals in melt electrospun fibers easily transform into thermodynamically stable α-form crystals, while crystals in solution electrospun fibers exhibit higher thermal stability. Nonisothermal modeling and in-situ measurements of jet temperature indicate that rapid quenching due to enhanced heat transfer by electrohydrodynamically driven air flow near the jet is responsible for the less stable γ-crystals and lower degree of molecular orientation in melt electrospun fibers.     

Folding of chains with random and edited sequences: similarities and differences

We have investigated the process of protein folding by Monte-Carlosimulation of folding occurring in a simple 3D lattice modelof a protein globule. We have found the range of ‘optimal’temperatures where the native fold is achieved by the Monte-Carloprocess much faster than that by exhaustive sorting of all thechain folds. The ‘optimal’ temperatures are essentiallythe same for different random and lsquo;edited’ sequences(for the latter, the native fold energy is separated by a considerablegap from the energies of other low-energy folds; for randomsequences, this gap is negligible). At the ‘optimal’temperatures, the ‘edited’ chains attain their nativefold faster than the random ones. However, the essence is thatthe native folds of ‘edited’ chains are thermodynamicallystable at temperatures optimal for fast folding, while the nativefolds of random chains are unstable at the temperatures optimalfor fast folding; also, at low temperatures where the nativefolds of random chains are stable, folding kinetics is veryslow. Consequently, stable native folds are formed slowly byrandom sequences and rapidly by the ‘edited’ ones     

Structural and complex impedance spectroscopic studies of Mg-substituted CoFe2O4

In this work, we present the effect of Mg substitution on the structural and impedance spectroscopic characteristics of Co_1−xMg_xFe₂O₄ (x=0.0, 0.3, 0.6, 0.9 and 1.0) samples, prepared by sol-gel auto-combustion method. As-burnt and fluffy powder samples were grinded and subsequently calcined at 600 °C for 6 h to change single phase cubic spinel structure, as confirmed by X-ray diffraction. The data obtained from diffraction was also utilized to perform Rietveld's refinement which provided detailed information on the structural changes occurred during the substitution. Frequency and temperature dependent electrical, and impedance studies were performed using an impedance analyzer in a wide frequency and temperature range. The behavior of characteristic dielectric parameters has been investigated using Maxwell-Wagner's model and Koop's theory. The impedance plot was used to define electro-active regions of the prepared samples, useful in modelling an equivalent circuit for each region. Frequency dependent Nyquist plot revealed the effect of grain, grain boundaries and electrode effect. Samples exhibited distinct grain and grain boundary contributions to the conductivity. Temperature dependent electrical characterization revealed that samples had negative temperature coefficient of resistance. The binding energies at different temperatures have also been estimated.     

Structural studies on thin organic coatings built by repeated adsorption of polyelectrolytes

Polyelectrolyte multilayers are obtained by repeated physisorption of oppositely charged polyions. We report on the effect of the linear charge density of a series of aromatic ionenes on the growth of stable ionene/poly(vinyl sulfate) multilayers. Stable multilayers could not be grown in water below a critical linear charge density, corresponding to a charge parameter of about 0.7 (in water at 20°C). We then present two potential ways to overcome the critical charge density limitation. The first one relies on the existence of a specific matching between a polycation and a polyanion, partly based on non-electrostatic intramolecular interactions, giving rise to a surface-constrained complexation leading to multilayers of extremely high supramolecular order. The growth mechanism of the multilayers is different from what is the usual case for stronger polyelectrolytes, since it occurs in a loose unstructured boundary layer at the sample surface, and involves organization processes similar to those occurring upon formation of insoluble structured polyelectrolyte complexes. The relationship between thickness and number of deposition cycles (d vs. n) could be described by an n^1.36 scaling law. The second way is to use a chemical reactivation of the outermost polyelectrolyte layer after its deposition by electrostatic adsorption, in order to regenerate a net charge at the interface allowing further adsorption. This technique is larger in scope, since it may lead to interesting properties such as non-centrosymmetry of the multilayers.