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.

Remarkable Selectivity and Photo-Cytotoxicity of an Oxidovanadium(IV) Complex of Curcumin in Visible Light

Oxidovanadium(IV) complexes of 2-(2'-pyridyl)-1,10-phenanthroline (pyphen), viz. VO(pyphen)(acac)](ClO4) (1), VO(pyphen)(anacac)](ClO4) (2) and VO(pyphen)(cur)](ClO4) (3), where acac is acetylacetonate (in 1), anacac is anthracenylacetylacetonate (in 2) and cur is curcumin monoanion (in 3) were synthesized, characterized and their photo-induced DNA cleavage activities and photo-cytotoxicities studied. The complexes are 1: 1 electrolytes in DMF. The one-electron paramagnetic complexes show a d-d band near 760 nm in DMF. Complexes 2 and 3 are blue and green emissive, respectively, in DMSO. The complexes exhibit irreversible V-IV/V-III reductive responses near -1.1 V and V-V/V-IV oxidative responses near 0.85 V vs. SCE in DMF-0.1 M TBAP. Complexes 2 and 3 display significant and selective photo-cytotoxicity upon irradiation with visible light giving an IC50 value of about 5 mu M against HeLa and MCF-7 cancer cells; they are significantly less-toxic against normal 3T3 control cells and in the absence of light. Complex 1 was used as a control. Both cytosolic and nuclear localization of the complexes were observed on the basis of fluorescence imaging. The complexes, avid binders to calf thymus (ct) DNA, were found to photocleave supercoiled pUC19 DNA upon irradiation with near-IR light (785 nm) by generating hydroxyl radical (OH) as the reactive oxygen species (ROS). Cell death events noted with HeLa and MCF-7 cell lines likely are attributable to apoptotic pathways involving light-assisted generation of intracellular ROS.

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.

Structural, thermal and quantum chemical studies of p-coumaric and caffeic acids

Two hydroxycinnamic acids viz., p-coumaric, and caffeic acids have been extracted and purified from Parthenium hysterophorus, subsequently characterized by elemental analysis, FT-IR, NMR, single crystal X-ray crystallography. The optimized structures of these acids were calculated in terms of density functional theory by Gaussian 09. The validation of experimental and theoretically obtained data for structural parameters such as bond lengths and bond angles has have been carried out to analyze the statistical significance by curve fitting analysis and the values of correlation coefficient found to be 0.985, 0.992, and 0.984, 0.975 in p-coumaric, and caffeic acids, respectively. The calculated HOMO and LUMO energies show the eventual charge transfer interaction within the molecule. Thermal studies were also carried out by thermogravimetry (TG), differential thermogravimetric analysis (DTA), and derivative thermogravimetry (DTG). (C) 2014 Elsevier B.V. All rights reserved.

Structural studies on Mycobacterium tuberculosis RecA: Molecular plasticity and interspecies variability

Structures of crystals of Mycobacterium tuberculosis RecA, grown and analysed under different conditions, provide insights into hitherto underappreciated details of molecular structure and plasticity. In particular, they yield information on the invariant and variable features of the geometry of the P-loop, whose binding to ATP is central for all the biochemical activities of RecA. The strengths of interaction of the ligands with the P-loop reveal significant differences. This in turn affects the magnitude of the motion of the `switch' residue, Gln195 in M. tuberculosis RecA, which triggers the transmission of ATP-mediated allosteric information to the DNA binding region. M. tuberculosis RecA is substantially rigid compared with its counterparts from M smegmatis and E. coli, which exhibit concerted internal molecular mobility. The interspecies variability in the plasticity of the two mycobacterial proteins is particularly surprising as they have similar sequence and 3D structure. Details of the interactions of ligands with the protein, characterized in the structures reported here, could be useful for design of inhibitors against M. tuberculosis RecA.

Multifunctional magnetic reduced graphene oxide dendrites: Synthesis, characterization and their applications

In this paper, for the first time, we have reported the novel synthesis of reduced graphene oxide (r-GO) dendrite kind of nanomaterial. The proposed r-GO dendrite possesses multifunctional properties in various fields of sensing and separation. The dendrite was synthesized by chemical reaction in different steps. Initially, the r-GO sheet was conjugated with silane group modified magnetic nanoparticle, resulting in nanoparticle decorated r-GO. The above r-GO sheet was further reacted with a new r-GO sheet, resulting in the formation of r-GO dendrite type of structure. Multifunctional behavior of this r-GO dendrite structure was studied by different methods. First, magnetic properties were studied by vibrating sample magnetometer (VSM) and it was found that dendrite structure shows good magnetic susceptibility (180.2 emu/g). The proposed r-GO dendrite also shows a very good antibacterial behavior for Escherichia coli and excellent electrochemical behavior towards ferrocyanide probe molecule. Along with these, it also acts as a substrate for the synthesis of molecularly imprinted polymer for europium metal ion, a lanthanide. The proposed imprinted sensor shows a very high selectivity and sensitivity for europium metal ion (limit of detection= 0.019 mu g L-1) in aqueous as well as real samples. (C) 2015 Elsevier B.V. All rights reserved.

Hierarchical sampling for metastable conformers determines biomolecular recognition: the case of malectin and diglucosylated N-glycan interactions

Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin's exquisite selectivity for diglucosylated N-glycan (Dig-N-glycan), a highly flexible oligosaccharide comprising of numerous dihedral torsion angles, are described as an example. For this purpose, a novel approach based on hierarchical sampling for acquiring metastable molecular conformations constituting low-energy minima for understanding the structural features involved in a biologic recognition is proposed. For this purpose, four variants of principal component analysis were employed recursively in both Cartesian space and dihedral angles space that are characterized by free energy landscapes to select the most stable conformational substates. Subsequently, k-means clustering algorithm was implemented for geometric separation of the major native state to acquire a final ensemble of metastable conformers. A comparison of malectin complexes was then performed to characterize their conformational properties. Analyses of stereochemical metrics and other concerted binding events revealed surface complementarity, cooperative and bidentate hydrogen bonds, water-mediated hydrogen bonds, carbohydrate-aromatic interactions including CH-pi and stacking interactions involved in this recognition. Additionally, a striking structural transition from loop to beta-strands in malectin CRD upon specific binding to Dig-N-glycan is observed. The interplay of the above-mentioned binding events in malectin and Dig-N-glycan supports an extended conformational selection model as the underlying binding mechanism.

Water-responsive carbon nanotubes for selective detection of toxic gases

Ammonia plays an important role in our daily lives and hence its quantitative and qualitative sensing has become necessary. Bulk structure of carbon nanotubes (CNTs) has been employed to detect the gas concentration of 10 ppm. Hydrophobic CNTs were turned to hydrophilic via the application of a ramp electric field that allowed confinement of a controlled amount of water inside CNT microstructure. These samples were then also used to detect different gases. A comparative study has been performed for sensing three reducing gases, namely, ammonia, sulphur-di-oxide, and hydrogen sulphide to elaborate the selectivity of the sensor. A considerable structural bending in the bulk CNT was observed on evaporation of the confined water, which can be accounted to the zipping of individual nanotubes. However, the rate of the stress induced on these bulk microstructures increased on the exposure of ammonia due to the change in the surface tension of the confined solvent. A prototype of an alarm system has been developed to illustrate sensing concept, wherein the generated stress in the bulk CNT induces a reversible loss in electrical contact that changes the equivalent resistance of the electrical circuit upon exposure to the gas. (C) 2015 AIP Publishing LLC.