Disulfide conformation and design at helix N-termini

To understand structural and thermodynamic features of disulfides within an alpha-helix, a non-redundant dataset comprising of 5025 polypeptide chains containing 2311 disulfides was examined. Thirty-five examples were found of intrahelical disulfides involving a CXXC motif between the N-Cap and third helical positions. GLY and PRO were the most common amino acids at positions 1 and 2, respectively. The N-Cap residue for disulfide bonded CXXC motifs had average values of (-112 +/- 25.2 degrees, 106 +/- 25.4 degrees). To further explore conformational requirements for intrahelical disulfides, CYS pairs were introduced at positions N-Cap-3; 1,4; 7,10 in two helices of an Escherichia coli thioredoxin mutant lacking its active site disulfide (nSS Trx). In both helices, disulfides formed spontaneously during purification only at positions N-Cap-3. Mutant stabilities were characterized by chemical denaturation studies (in both oxidized and reduced states) and differential scanning calorimetry (oxidized state only). All oxidized as well as reduced mutants were destabilized relative to nSS Trx. All mutants were redox active, but showed decreased activity relative to wild-type thioredoxin. Such engineered disulfides can be used to probe helix start sites in proteins of unknown structure and to introduce redox activity into proteins. Conversely, a protein with CYS residues at positions N-Cap and 3 of an alpha-helix is likely to have redox activity.

Unraveling the packing pattern leading to gelation using SS NMR and X-ray diffraction: direct observation of the evolution of self-assembled fibers

A detailed understanding of the mode of packing patterns that leads to the gelation of low molecular mass gelators derived from bile acid esters was carried out using solid state NMR along with complementary techniques such as powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and polarizing optical microscopy (POM). Solid state C-13{H-1} cross polarization (CP) magic angle spinning (MAS) NMR of the low molecularmass gel in its native state was recorded for the first time. A close resemblance in the packing patterns of the gel, xerogel and bulk solid states was revealed upon comparing their C-13{H-1} CPMAS NMR spectral pattern. A doublet resonance pattern of C-13 signals in C-13{H-1}CPMAS NMR spectra were observed for the gelator molecules, whereas the non-gelators showed simple singlet resonance or resulted inthe formation of inclusion complexes/solvates. PXRD patterns revealed a close isomorphous nature of the gelators indicating the similarity in the mode of the packing pattern in their solid state. Direct imaging of the evolution of nanofibers (sol-gel transition) was carried out using POM, which proved the presence of self-assembled fibrillar networks (SAFINs) in the gel. Finally powder X-ray structure determination revealed the presence of two non-equivalent molecules in an asymmetric unit which is responsible for the doublet resonance pattern in the solid state NMR spectra.

Aggregation and mesomorphic properties of 'double-headed' carbohydrate amphiphiles

Sugar-based amphiphiles, consisting of two sugar head groups and an alkylene chain within the molecules, are synthesized and their aggregation and mesomorphic properties are evaluated. The hydrophilic sugar head groups, constituted with beta-D-glucopyranoside units, and the lyophilic alkylene units, are coupled to a glycerol backbone to afford the 'double-headed' sugar amphiphiles. Aggregation studies in aqueous solutions provided their critical micellar concentrations and the aggregation numbers. Mesophase characterizations by polarizing optical microscopy and differential scanning calorimetry (DSC) revealed the phase-transition behaviour of these new 'double-headed' glycolipids.

Effect of substituent on the thermodynamics of D-glucopyranoside binding to concanavalin A, pea (Pisum sativum) lectin and lentil (Lens culinaris) lectin

Titration calorimetry measurements of the binding of phenyl-alpha (alpha PhOGlu), 3-methoxy (3MeOGlu), fluorodeoxy and deoxy derivatives of alpha-D-glucopyranose (Glu) to concanavalin A (conA), pea lectin and lentil lectin were performed at approx. 10 and 25 degrees C in 0.01 M dimethylglutaric acid/NaOH buffer, pH 6.9, containing 0.15 M NaCl and Mn2+ and Ca2+ ions. Apparently the 3-deoxy, 4-deoxy and 6-deoxy as well as the 4-fluorodeoxy and 6-fluorodeoxy derivatives of Glu do not bind to the lectins because no heat release was observed on the addition of aliquots of solutions of these derivatives to the lectin solutions. The binding enthalpies, delta H0b, and entropies, delta S0b, determined from the measurements were compared with the same thermodynamic binding parameters for Glu, D-mannopyranoside and methyl-alpha- D-glucopyranoside (alpha MeOGlu). The binding reactions are enthalpically driven with little change in the heat capacity on binding, and exhibit enthalpy-entropy compensation. Differences between the thermodynamic binding parameters can be rationalized in terms of the interactions apparent in the known crystal structures of the methyl-alpha-D-mannopyranoside-conA [Derewenda, Yariv, Helliwell, Kalb (Gilboa), Dodson, Papiz, Wan and Campbell (1989) EMBO J. 8, 2189-2193] and pea lectin-trimanno-pyranoside [Rini, Hardman, Einspahr, Suddath and Carber (1993) J. Biol. Chem. 268, 10126-10132] complexes. Increases in the entropy change on binding are observed for alpha MeOGlu binding to pea and lentil lectin, for alpha PhOGlu binding to conA and pea lectin, and for 3MeOGlu binding to pea lectin relative to the entropy change for Glu binding, and imply that the phenoxy and methoxy substituents provide additional hydrophobic interactions in the complex. Increases in the binding enthalpy relative to that of Glu are observed for deoxy and fluoro derivatives in the C-1 and C-2 positions and imply that these substituents weaken the interaction with the surrounding water, thereby strengthening the interaction with the binding site.

Energetics of carbohydrate binding by a 14 kDa S-type mammalian lectin

The thermodynamics of the binding of derivatives of galactose and lactose to a 14 kDa beta-galactoside-binding lectin (L-14) from sheep spleen has been studied in 10 nM phosphate/150 mM NaCl/10 mM beta-mercaptoethanol buffer, pH 7.4, and in the temperature range 285-300 K using titration calorimetry. The single-site binding constants of various sugars for the lectin were in the following order: N-acetyl-lactosamine thiodigalactoside > 4-methylumbelliferyl lactoside > lactose > 4-methylumbelliferyl alpha-D-galactoside > methyl-alpha-galactose > methyl-beta-galactose. Reactions were essentially enthalpically driven with the binding enthalpies ranging from -53.8 kJ/mol for thiodigalactoside at 301 K to -2.2 kJ/mol for galactose at 300 K, indicating that hydrogen-bonding and van der Waals interactions provide the major stabilization for these reactions. However, the binding of 4-methylumbelliferyl-alpha-D-galactose displays relatively favourable entropic contributions, indicating the existence of a non-polar site adjacent to the galactose-binding subsite. From the increments in the enthalpies for the binding of lactose, N-acetyl-lactosamine and thiodigalactoside relative to methyl-beta-galactose, the contribution of glucose binding in the subsite adjacent to that for galactose shows that glucose makes a major contribution to the stability of L-14 disaccharide complexes. Observation of enthalpy-entropy compensation for the recognition of saccharides such as lactose by L-14 and the absence of it for monosaccharides such as galactose, together with the lack of appreciable changes in the heat capacity (delta Cp), indicate that reorganization of water plays an important role in these reactions.

Thermodynamics of monosaccharide binding to concanavalin A, pea (Pisum sativum) lectin, and lentil (Lens culinaris) lectin

Titration calorimetry measurements of the binding of methyl alpha-D-mannopyranoside (Me alpha Man), D-mannopyranoside (Man), methyl alpha-D-glucopyranoside (Me alpha Glu), and D-glucopyranoside (Glu) to concanavalin A (Con A), pea lectin, and lentil lectin were performed at 281 and 292 K in 0.01 M dimethylglutaric acid-NaOH buffer (pH 6.9) containing 0.15 M NaCl and Mn+2 and Ca+2 ions. The site binding enthalpies, delta H, are the same at both temperatures and range from -28.4 +/- 0.9 (Me alpha Man) to -16.6 +/- 0.5 kJ mol-1 (Glu) for Con A, from -26.2 +/- 1.1 (Me alpha Man) to -12.8 +/- 0.4 kJ mol-1 (Me alpha Glu) for pea lectin, and from -16.6 +/- 0.7 (Me alpha Man) to -8.0 +/- 0.2 kJ mol-1 (Me alpha Glu) for lentil lectin. The site binding constants range from 17 +/- 1 x 10(3) M-1 (Me alpha Man to Con A at 281.2 K) to 230 +/- 20 M-1 (Glu to lentil lectin at 292.6 K) and exhibit high specificity for Con A where they are in the Me alpha Man:Man:Me alpha Glu:Glu ratio of 21:4:5:1, while the corresponding ratio is 5:2:1.5:1 for pea lectin and 4:2:2:1 for lentil lectin. The higher specificity for Con A indicates more interactions between the amino acid residues at the binding site and the carbohydrate ligand than for the pea and lentil lectin-carbohydrate complexes. The carbohydrate-lectin binding results exhibit enthalpy-entropy compensation in that delta Hb (kJ mol-1) = -1.67 +/- 0.06 x 10(4) + (1.30 +/- 0.12)T(K) delta Sb (J mol-1K-1). Differential scanning calorimetry measurements on the thermal denaturation of the lectins and their carbohydrate complexes show that the Con A tetramer dissociates into monomers, while the pea and lentil lectin dimers dissociate into two submonomer fragments. At the denaturation temperature, one carbohydrate binds to each monomer of Con A and the pea and lentil lectins. Complexation with the carbohydrate increases the denaturation temperature of the lectin and the magnitude of the increases yield binding constants in agreement with the determinations from titration calorimetry.

Thermodynamics of the binding of galactopyranoside derivatives to the basic lectin from winged bean (Psophocarpus tetrogonolobus)

The thermodynamics of the binding of D-galactopyranoside (Gal), 2-acetamido-2-deoxygalactopyranoside (GalNAc), methyl-alpha-D-galactopyranoside, and methyl-beta-D-galactopyranoside to the basic agglutinin from winged bean (WBAI) in 0.02 M sodium phosphate and 0.15 M sodium chloride buffer have been investigated from 298.15 to 333.15 K by titration calorimetry and at the denaturation temperature by differential scanning calorimetry (DSC). WBAI is a dimer with two binding sites. The titration calorimetry yielded single-site binding constants ranging from 0.56 +/- 0.14 x 10(3) M-1 for Gal at 323.15 K to 7.2 +/- 0.5 x 10(3) M-1 for GalNAc at 298.15 K and binding enthalpies ranging from -28.0 +/- 2.0 kJ mol-1 for GalNAc at 298.15 K to -14.3 +/- 0.1 kJ mol-1 for methyl-beta-D-galactopyranoside at 322.65 K. The denaturation transition consisted of two overlapping peaks over the pH range 5.6-7.4. Fits of the differential scanning calorimetry data to a two-state transition model showed that the low temperature transition (341.6 +/- 0.4 K at pH 7.4) consisted of two domains unfolding as a single entity while the higher temperature transition (347.8 +/- 0.6 K at pH 7.4) is of the remaining WBAI dimer unfolding into two monomers. Both transitions shift to higher temperatures and higher calorimetric enthalpies with increase in added ligand concentration at pH 7.4. Analysis of the temperature increase as a function of added ligand concentration suggests that one ligand binds to the two domains unfolding at 341.6 +/- 0.6 K and one ligand binds to the domain unfolding at 347.8 +/- 0.6 K.

Low density polyethylene and grafted lignin polyblends using epoxy-functionalized compatibilizer: mechanical and thermal properties

Lignin was graft copolymerized with methyl methacrylate using manganic pyrophosphate as initiator. This modified lignin was then blended (up to 50 wt%) with low density polyethylene (LDPE) using a small quantity of poly[ethylene-co-(glycidyl methacrylate)] (PEGMA) compatibilizer. The mechanical properties of the blend were substantially improved by using modified lignin in contrast to untreated lignin. Differential scanning calorimetry studies showed loss of crystallinity of the LDPE phase owing to the interaction between the blend components. Thermogravimetric analysis showed higher thermal stability of modified lignin in the domain of blend processing. This suggested that there is scope for useful utilization of lignin, which could also lead to the development of eco-friendly products. (c) 2005 Society of Chemical Industry.

Deformation and crystallization of Zr-based amorphous alloys in homogeneous flow regime

The purpose of this study is to experimentally investigate the interaction of inelastic deformation and microstructural changes of two Zr-based bulk metallic glasses (BMGs): Zr41.25Ti13.75Cu12.5Ni10Be22.5 (commercially designated as Vitreloy 1 or Vit1) and Zr46.75Ti8.25Cu7.5Ni10Be27.5 (Vitreloy 4, Vit4). High-temperature uniaxial compression tests were performed on the two Zr alloys at various strain rates, followed by structural characterization using differential scanning calorimetry (DSC) and transmission electron microscopy (TEM). Two distinct modes of mechanically induced atomic disordering in the two alloys were observed, with Vit1 featuring clear phase separation and crystallization after deformation as observed with TEM, while Vit4 showing only structural relaxation with no crystallization. The influence of the structural changes on the mechanical behaviors of the two materials was further investigated by jump-in-strain-rate tests, and flow softening was observed in Vit4. A free volume theory was applied to explain the deformation behaviors, and the activation volumes were calculated for both alloys.

Dielectric relaxation and electrical conductivity in Bi5NbO10 oxygen ion conductors prepared by a modified sol–gel process

Crystalline Bi5NbO10 nanoparticles have been achieved through a modified sol–gel process using a mixture of ethylenediamine and ethanolamine as a solvent. The Bi5NbO10 nanoparticles were characterized by X-ray diffraction (XRD), differential scanning calorimetry/thermogravimetry (DSC/TG), Fourier transform infrared spectroscopy (FT-IR), transmission electron microscopy (TEM) and Raman spectroscopy. The results showed that well-dispersed 5–60 nm Bi5NbO10 nanoparticles were prepared through heat-treating the precursor at 650 °C and the high density pellets were obtained at temperatures lower than those commonly employed. The frequency and temperature dependence of the dielectric constant and the electrical conductivity of the Bi5NbO10 solid solutions were investigated in the 0.1 Hz to 1 MHz frequency range. Two distinct relaxation mechanisms were observed in the plots of dielectric loss and the imaginary part of impedance (Z″) versus frequency in the temperature range of 200–350 °C. The dielectric constant and the loss in the low frequency regime were electrode dependent. The ionic conductivity of Bi5NbO10 solid solutions at 700 °C is 2.86 Ω−1 m−1 which is in same order of magnitude for Y2O3-stabilized ZrO2 ceramics at same temperature. These results suggest that Bi5NbO10 is a promising material for an oxygen ion conductor.

Degradation Kinetics of Poly(HDDA-co-MMA)

1,6-hexanediol diacrylate (HDDA) and methyl methacrylate (MMA) were copolymerized in different weight ratios using UV light induced photo-polymerization to give poly(HDDA-co-MMA). Differential scanning calorimetry shows that copolymer was formed. The thermogravimetric and differential scanning calorimetric studies with different heating rates were carried out on these copolymers to understand the nature of degradation and to determine its kinetics. Different kinetic models were adopted to evaluate various parameters like the activation energy, the order, and the frequency factor. These analyses are important to study the binder removal from 3D-shaped ceramic objects made by techniques like Solid free form fabrication. (C) 2010 Wiley Periodicals, Inc. J Appl Polym Sci 117: 2444-2453, 2010.

Structures of apo and GTP-bound molybdenum cofactor biosynthesis protein MoaC from Thermus thermophilus HB8

The first step in the molybdenum cofactor (Moco) biosynthesis pathway involves the conversion of guanosine triphosphate (GTP) to precursor Z by two proteins (MoaA and MoaC). MoaA belongs to the S-adenosylmethioninedependent radical enzyme superfamily and is believed to generate protein and/or substrate radicals by reductive cleavage of S-adenosylmethionine using an Fe-S cluster. MoaC has been suggested to catalyze the release of pyrophosphate and the formation of the cyclic phosphate of precursor Z. However, structural evidence showing the binding of a substrate-like molecule to MoaC is not available. Here, apo and GTP-bound crystal structures of MoaC from Thermus thermophilus HB8 are reported. Furthermore, isothermal titration calorimetry experiments have been carried out in order to obtain thermodynamic parameters for the protein-ligand interactions. In addition, molecular-dynamics (MD) simulations have been carried out on the protein-ligand complex of known structure and on models of relevant complexes for which X-ray structures are not available. The biophysical, structural and MD results reveal the residues that are involved in substrate binding and help in speculating upon a possible mechanism.

Simple kinetic sensor to structural transitions

Driven nonequilibrium structural phase transformation has been probed using time-varying resistance fluctuations or noise. We demonstrate that the non-Gaussian component (NGC) of noise obtained by evaluating the higher-order statistics of fluctuations, serves as a simple kinetic detector of these phase transitions. Using the Martensite transformation in free-standing wires of nickel-titanium binary alloys as a prototype, we observe clear deviations from the Gaussian background in the transformation zone, indicative of the long-range correlations in the system as the phase transforms. The viability of non-Gaussian statistics as a robust probe to structural phase transition was also confirmed by comparing the results from differential scanning calorimetry measurements. We further studied the response of the NGC to the modifications in the microstructure on repeated thermal cycling, as well as the variations in the temperature-drive rate, and explained the results using established simplistic models based on the different competing time scales. Our experiments (i) suggest an alternative method to estimate the transformation temperature scales with high accuracy and (ii) establish a connection between the material-specific evolution of microstructure to the statistics of its linear response. Since the method depends on an in-built long-range correlation during transformation, it could be portable to other structural transitions, as well as to materials of different physical origin and size.

Thermal ignition studies on metallized fuel-oxidizer systems

The thermal ignition behaviour of various mixtures of organic fuels, magnesium and ammonium nitrate (AN) has been examined by differential thermal analysis technique. It has been observed that the thermal decomposition/ignition of organic fuel-AN mixtures is modified significantly in the presence of magnesium metal. The decomposition characteristics of the binary mixtures of AN with various metals indicate the specific action of magnesium and zinc in lowering the decomposition temperature. A possible explanation for the low temperature decomposition is given in terms of the solid state reaction causing the fusion of AN which further reacts with the metal resulting in a highly exothermic reaction.

Increasing ionic conductivity of polymer-sodium salt complex by addition of a non-ionic plastic crystal

Ionic conductivity and other physico-chemical properties of a soft matter composite electrolyte comprising of a polymer-sodium salt complex and a non-ionic plastic crystal are discussed here. The electrolyte under discussion comprises of polyethyleneoxide (PEO)-sodium triflate (NaCF3SO3) and succinonitrile (SN). Addition of SN to PEO-NaCF3SO3 resulted in significant enhancement in ionic conductivity. At 50% SN concentration (with respect to weight of polymer), the polymer-plastic composite electrolyte room temperature (= 25 degrees C) ionic conductivity was similar to 1.1 x 10(-4) Omega(-1) cm(-1), approximately 45 times higher than PEO-NaCF3SO3. Observations from ac-impedance spectroscopy along with X-ray diffraction, differential scanning calorimetry and Fourier transform inrared spectroscopy strongly suggest the enhancement in the composite is ionicconductivity due to enhanced ion mobility via decrease in crystallinity of PEO. The free standing composite polymer-plastic electrolytes were more compliable than PEO-NaCF3SO3 thus exhibiting no detrimental effects of succinonitrile addition on the mechanical stability of PEO-NaCF3SO3. We propose that the exploratory PEO-NaCF3SO3-SN system.discussed here will eventually be developed as a prototype electrolyte.for sodium-sulfur batteries capable of operating at ambient and.sub-ambient conditions. (C) 2010 Elsevier B.V. All rights reserved.