Structural diversity and ligand specificity of lectins. The Bangalore effort

Structural studies in this laboratory encompass four of the five major classes of plant lectins, including the one discovered by us. In addition to addressing issues specific to individual lectins, the work provided insights into protein folding, quaternary association and generation of ligand specificity. Legume and beta-prism fold lectins constitute families of proteins in which small alterations in essentially the same tertiary structure lead to large variations in quaternary structure, including that involving an open structure. Strategies for generating ligand specificity include water bridges, variation in loop length, post translational modification and oligomerization. Three of the structural classes investigated have subunits with three-fold symmetry. The symmetry in the structure is reflected in the sequence to different extents in different subclasses. The evolutionary implications of this observation have been explored. The work on lectins has now been extended to those from mycobacteria.

Combinatorial Crystal Synthesis: Structural Landscape of Phloroglucinol:1,2-bis(4-pyridyl)ethylene and Phloroglucinol:Phenazine

A large number of crystal forms, polymorphs and pseudopolymorphs, have been isolated in the phloroglucinol-dipyridylethylene (PGL:DPE) and phloroglucinol-phenazine (PGL:PHE) systems. An understanding of the intermolecular interactions and synthon preferences in these binary systems enables one to design a ternary molecular solid that consists of PGL, PHE, and DPE, and also others where DPE is replaced by other heterocycles. Clean isolation of these ternary cocrystals demonstrates synthon amplification during crystallization. These results point to the lesser likelihood of polymorphism in multicomponent crystals compared to single-component crystals. The appearance of several crystal forms during crystallization of a multicomponent system can be viewed as combinatorial crystal synthesis with synthon selection from a solution library. The resulting polymorphs and pseudopolymorphs that are obtained constitute a crystal structure landscape.

A bio-attuned ratiometric hydrogen sulfate ion selective receptor in aqueous solvent: structural proof of the H-bonded adduct

A new cell permeable quinazoline based receptor (1) selectively senses HSO4- ions of nanomolar region in 0.1 M HEPES buffer (ethanol-water: 1/5, v/v) at biological pH over other competitive ions through the proton transfer followed by hydrogen bond formation and subsequent anion coordination to yield the LHSO4]-LH+center dot 3H(2)O (2) ensemble, which has been crystallographically characterised to ensure the structure property relationship. This non-cytotoxic HSO4- ion selective biomarker has great potential to recognize the intercellular distribution of HSO4- ions in HeLa cells under fluorescence microscope.

Structural, Magnetic, and Electrical Properties of Microwave-Sintered Cr3+-Doped Sr Hexaferrites

SrCrxFe12-xO19 (x = 0.0, 0.1, 0.3, 0.5, 0.7, 0.9) hexaferrites were prepared by a microwave-hydrothermal method and subsequently sintered at 950 degrees C for 90 min using the microwave sintering method. The results show that, with increasing Cr3+ content, the lattice parameters changed anisotropically. The average grain sizes of sintered samples were in the range of 280 nm to 660 nm. The saturation magnetization systematically decreased with increasing Cr3+ doping, but the coercivity values increased. The electrical resistivity (log rho) decreased linearly with increasing temperature up to a certain temperature known as the transition temperature (T-c), and T-c decreased with further increase (x>0.5) of the Cr3+ content. This decrease in log rho and the activation energy (E-g) is due to electron hopping and occupancy of doped ions at different lattice sites. We found that the dielectric constant and dielectric loss for all the samples decreased with the Cr3+ content. The structural, magnetic, and electrical properties of Cr3+-doped SrFe12O19 hexaferrites have thus been investigated.

Use of a structural alphabet to find compatible folds for amino acid sequences

The structural annotation of proteins with no detectable homologs of known 3D structure identified using sequence-search methods is a major challenge today. We propose an original method that computes the conditional probabilities for the amino-acid sequence of a protein to fit to known protein 3D structures using a structural alphabet, known as Protein Blocks (PBs). PBs constitute a library of 16 local structural prototypes that approximate every part of protein backbone structures. It is used to encode 3D protein structures into 1D PB sequences and to capture sequence to structure relationships. Our method relies on amino acid occurrence matrices, one for each PB, to score global and local threading of query amino acid sequences to protein folds encoded into PB sequences. It does not use any information from residue contacts or sequence-search methods or explicit incorporation of hydrophobic effect. The performance of the method was assessed with independent test datasets derived from SCOP 1.75A. With a Z-score cutoff that achieved 95% specificity (i.e., less than 5% false positives), global and local threading showed sensitivity of 64.1% and 34.2%, respectively. We further tested its performance on 57 difficult CASP10 targets that had no known homologs in PDB: 38 compatible templates were identified by our approach and 66% of these hits yielded correctly predicted structures. This method scales-up well and offers promising perspectives for structural annotations at genomic level. It has been implemented in the form of a web-server that is freely available at http://www.bo-protscience.fr/forsa.

Analogous stress and electric field driven structural transformation and decrease in polarization coherence on poling around the morphotropic phase boundary in BiScO3-PbTiO3

The nature of the stress and electric field driven structural and microstructural transformations in the morphotropic phase boundary (MPB) compositions of the high Curie point piezoelectric system BiScO3-PbTiO3 has been examined by ex situ based techniques. Using a powder poling technique, which is based on the concept of exploiting the irreversible structural change that occurs after the application of a strong electric field and stress independently, it was possible to ascertain that both moderate stress and electric field induce identical structural transformation-a fraction of the monoclinic phase transforms irreversibly to the tetragonal phase. Moreover, analysis of the dielectric response before and after poling revealed a counterintuitive phenomenon of poling induced decrease in the spatial coherence of polarization for compositions around the MPB and not so for compositions far away from the MPB range. Exploiting the greater sensitivity of this technique, we demonstrate that the criticality associated with the interferroelectric transition spans a wider composition range than what is conventionally reported in the literature based on bulk x-ray/neutron powder diffraction techniques.

An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles

Rich data bearing on the structural and evolutionary principles of protein protein interactions are paving the way to a better understanding of the regulation of function in the cell. This is particularly the case when these interactions are considered in the framework of key pathways. Knowledge of the interactions may provide insights into the mechanisms of crucial `driver' mutations in oncogenesis. They also provide the foundation toward the design of protein protein interfaces and inhibitors that can abrogate their formation or enhance them. The main features to learn from known 3-D structures of protein protein complexes and the extensive literature which analyzes them computationally and experimentally include the interaction details which permit undertaking structure-based drug discovery, the evolution of complexes and their interactions, the consequences of alterations such as post-translational modifications, ligand binding, disease causing mutations, host pathogen interactions, oligomerization, aggregation and the roles of disorder, dynamics, allostery and more to the protein and the cell. This review highlights some of the recent advances in these areas, including design, inhibition and prediction of protein protein complexes. The field is broad, and much work has been carried out in these areas, making it challenging to cover it in its entirety. Much of this is due to the fast increase in the number of molecules whose structures have been determined experimentally and the vast increase in computational power. Here we provide a concise overview. (C) 2014 Elsevier Ltd. All rights reserved.

Structural, magnetic and electrochemical investigation of novel binary Na2-x(Fe1-yMny)P2O7 (0 <= y <= 1) pyrophosphate compounds for rechargeable sodium-ion batteries

Pyrophosphate cathodes have been recently reported as a competent family of insertion compounds for sodium-ion batteries. In the current study, we have investigated the binary Na2 - x(Fe1 - yMny)P2O7 (0 <= y <= 1) pyrophosphate family, synthesized by the classical solid-state method. They form a continuous solid solution maintaining triclinic P-1 (#2) symmetry. The local structural coordination differs mainly by different degrees of Na site occupancy and preferential occupation of the Fe2 site by Mn. The structural and magnetic properties of these mixed-metal pyrophosphate phases have been studied. In each case, complete Fe3+/Fe2+ redox activity has been obtained centered at 3 V vs. Na. The Fe3+/Fe2+ redox process involves multiple steps between 2.5 and 3 V owing to Na-cation ordering during electrochemical cycling, which merge to form a broad single Fe3+/Fe2+ redox peak upon progressive Mn-doping. (C) 2014 Elsevier B.V. All rights reserved.

Scheelite-type MWO4 (M = Ca, Sr, and Ba) nanophosphors: Facile synthesis, structural characterization, photoluminescence, and photocatalytic properties

Scheelite-type MWO4 (M = Ca, Sr, and Ba) nanophosphors were synthesized by the precipitation method. All compounds crystallized in the tetragonal structure with space group 141/a (No. 88). Scherrer's and TEM results revealed that the average crystallite size varies from 32 to 55 nm. FE-SEM illustrate the spherical (CaWO4), bouquet (SrWO4), and fish (BaWO4) like morphologies. PL spectra indicate the broad emission peak maximum at 436 (CaWO4), 440 (SrWO4), and 433 nm (BaWO4) under UV excitation. The calculated CIE color coordinates of MWO4 nanophosphors are close to the commercial BAM and National Television System Committee blue phosphor. The photocatalytic activities of MWO4 were investigated for the degradation of methylene blue dye under UV illumination. At pH 3, BaWO4 nanocatalyst showed 100% dye degradation within 60 min. The photocatalytic activity was in the decreasing order of BaWO4> CaWO4>SrWO4 under both neutral and acidic conditions. (C) 2014 Elsevier Ltd. All rights reserved.

Structural transition and enhanced phase transition properties of Se doped Ge2Sb2Te5 alloys

Amorphous Ge2Sb2Te5 (GST) alloy, upon heating crystallize to a metastable NaCl structure around 150 degrees C and then to a stable hexagonal structure at high temperatures (>= 250 degrees C). It has been generally understood that the phase change takes place between amorphous and the metastable NaCl structure and not between the amorphous and the stable hexagonal phase. In the present work, it is observed that the thermally evaporated (GST)(1-x)Se-x thin films (0 <= x <= 0.50) crystallize directly to the stable hexagonal structure for x >= 0.10, when annealed at temperatures >= 150 degrees C. The intermediate NaCl structure has been observed only for x, 0.10. Chemically ordered network of GST is largely modified for x >= 0.10. Resistance, thermal stability and threshold voltage of the films are found to increase with the increase of Se. The contrast in electrical resistivity between the amorphous and crystalline phases is about 6 orders of magnitude. The increase in Se shifts the absorption edge to lower wavelength and the band gap widens from 0.63 to 1.05 eV. Higher resistance ratio, higher crystallization temperature, direct transition to the stable phase indicate that (GST)(1-x)Se-x films are better candidates for phase change memory applications.

First-Principles Study on Structural Stability of Belite

A first-principles study was carried out to investigate the stability of the crystal structure of beta-form belite (beta-C2S) substituted by Sr atoms as trace impurities for Ca atoms in CaOx polyhedra. The effect of the connection types of CaOx polyhedral, in the form of common-edge bond and common-face bond, upon the crystal stability is described. The Ca-Ca interatomic distance closely relates to the hydraulic activity of beta-C2S. The beta-C2S substituted by an Sr atom for Ca(1) atoms having seven Ca-O bonds is energetically more stable than that substituted by an Sr atom for Ca(2) atoms having eight Ca-O bonds. The Sr-doped beta-C2S having a common face bond with SrOx polyhedra is energetically more favorable and results in structural stability compared with that having a common edge bond with SrOx polyhedra.

Unraveling the nature of electric field- and stress- induced structural transformations in soft PZT by a new powder poling technique

A `powder-poling' technique was developed to study electric field induced structural transformations in ferroelectrics exhibiting a morphotropic phase boundary (MPB). The technique was employed on soft PZT exhibiting a large longitudinal piezoelectric response (d(33) similar to 650 pCN(-1)). It was found that electric poling brings about a considerable degree of irreversible tetragonal to monoclinic transformation. The same transformation was achieved after subjecting the specimen to mechanical stress, which suggests an equivalence of stress and electric field with regard to the structural mechanism in MPB compositions. The electric field induced structural transformation was also found to be accompanied by a decrease in the spatial coherence of polarization.

High Proton Mobility, Solvent Induced Single Crystal to Single Crystal Structural Transformation, and Related Studies on a Family of Compounds Formed from Mn-3 Oxo-Clusters

The reaction between 4,4'-sulfonyldibenzoic acid (H(2)SDBA) and manganese under mild conditions resulted in the isolation of two new three-dimensional compounds, Mn-4(C14H8O6S)(4)(DMA)(2)]center dot 3DMA, I, and Mn-3(C14H8O6S)(3)(DMA)(2)(MeOH)]center dot DMA, IIa. Both structures have Mn-3 trimer oxo cluster units. While the Mn-3 oxoclusters are connected through octahedral manganese forming one-dimensional Mn-O-Mn chains in I, the Mn-3 units are isolated in IIa. The SDBA units connect the Mn-O-Mn chains and the Mn-3 clusters giving rise to the three-dimensional structure. Both compounds have coordinated and free solvent molecules. In IIa, two different solvent molecules are coordinated, of which one solvent can be reversibly exchanged by a variety of other similar solvents via a solvent-mediated single crystal to single crystal (SCSC) transformation. The free lattice DMA solvent molecules in I can be exchanged by water molecules resulting in hydrophilic channels. Proton conductivity studies on I reveals a high proton mobility with conductivity values of similar to 0.87 x 10(-3) Omega(-1) cm(-1) at 34 degrees C and 98% RH, which is comparable to some of the good proton conductivity values observed in inorganic coordination polymers. We have also shown structural transformation of I to IIa through a possible dissolution and recrystallization pathway. In addition, both I and IIa appear to transform to two other manganese compounds H3O]Mn-3(mu(3)-OH)(C14H8O6S)(3)(H2O)](DMF)(5) and H3O](2)Mn-7(mu 3-OH)(4)(C14H8O6S)(6)(H2O)(4)](H2O)(2)(DMF)(8) under suitable reaction conditions. We have partially substituted Co in place of Mn in the Mn-3 trimer clusters forming CoMn2(C14H8O6S)(3)(DMA)(2)(EtOH)]center dot DMA, III, a structure that is closely related to IIa. All the compounds reveal antiferromagnetic behavior. On heating, the cobalt substituted phase (compound III) forms a CoMn2O4 spinel phase with particle sizes in the nanometer range.

Facile green fabrication of iron-doped cubic ZrO2 nanoparticles by Phyllanthus acidus: Structural, photocatalytic and photoluminescent properties

Cubic ZrO2: Fe3+ (0.5-4 mol%) nanoparticles (NPs) were synthesized via bin-inspired, inexpensive and simple route using Phyllanthus acidus as fuel. PXRD, SEM, TEM, FTIR, UV absorption and PL studies were performed to ascertain the formation of NPs. Rietveld analysis confirmed the formation of cubic structure. The influence of Fe3+ on the structure, morphology, UV absorption, PL emission and photocatalytic activity of NPs were investigated. The CIE chromaticity coordinates (0.36, 0.41) show that NPs could be a promising candidate for white LEDs. The influence of Fe3+ on ZrO2 matrix for photocatalytic degradation of AO7 was evaluated under UVA and Sunlight irradiation. The enhanced photocatalytic activity of spherical shaped ZrO2: Fe3+ (2 mol%) under UVA light was attributed to dopant concentration, crystallite size, narrow band gap, textural properties and capability for reducing the electron-hole pair recombination. The trend of inhibitory effect in the presence of different radical scavengers were followed the order SO42- > Cl- > C2H5OH > HCO3- > CO32-. The recycling catalytic ability of the ZrO2: Fe3+ (2 mol%) was also evaluated with a negligible decrease in the degradation efficiency even after the sixth successive run. (C) 2014 Elsevier B.V. All rights reserved.

Structural investigation of resorcinol based symmetrical banana mesogens by XRD, NMR and polarization measurements

Synthesis and structural characterization of two novel symmetrical banana mesogens built from resorcinol with seven phenyl rings linked by ester and imine with a terminal dodecyl/dodecyloxy chain has been carried out. Density functional theory (DFT) has been employed for obtaining the geometry optimized structures, the dipole moments and C-13 NMR chemical shifts. The HOPM and DSC studies revealed enantiotropic B-2 and B-7 phases for the dodecyl and dodecyloxy homologs respectively. The powder X-ray studies of both the mesogens indicate the presence of layer ordering. The polarization measurements reveal an anti-ferroelectric switching for the B-2 phase of the dodecyl homolog whose structure has been identified as SmCSPA. The B-7 phase of the dodecyloxy homolog was found to be non-switchable. High resolution C-13 NMR study of the dodecyl homolog in its mesophase has been carried out. C-13-H-1 dipolar couplings obtained from the 2-dimensional separated local field spectroscopy experiment were used to obtain the orientational order parameters of the different segments of the mesogen. Very large C-13-H-1 dipolar couplings observed for the carbons of the central phenyl ring (9.7-12.3 kHz) in comparison to the dipolar couplings of those of the side arm phenyl rings (less than 3 kHz) are a direct consequence of the ordering in the banana phase and the shape of the molecule. From the ratio of the local order parameter values, the bent-angle of the mesogen could be determined in a straight forward manner to be 120.5 degrees.