Bio-inspired route for the synthesis of spherical shaped MgO:Fe3+ nanoparticles: Structural, photoluminescence and photocatalytic investigation

MgO:Fe3+ (0.1-5 mol%) nanoparticles (NPs) were synthesized via eco-friendly, inexpensive and simple low temperature solution combustion route using Aloe vera gel as fuel. The final products were characterized by SEM, TEM and HRTEM. PXRD data and Rietveld analysis revealed the formation of cubic system. The influence of Fe3+ ion concentration on the structure morphology, UV absorption, PL emission and photocatalytic activity of MgO:Fe3+ NPs were investigated. The yellow emission with CIE chromaticity coordinates (0.44, 0.52) and average correlated color temperature value was found to be 3540 K which corresponds to warm light of NPs. The control of Fe3+. on MgO matrix influences the photocatalytic decolorization of methylene blue (MB) under UV light. The enhanced photocatalytic activity of MgO:Fe3+ (4 mol%) was attributed to dopant concentration, effective crystallite size, textural properties, decreased band gap and capability for reducing the electron hole pair recombination. Further, the trends of inhibitory effect in the presence of different radical scavengers were explored. These findings open up new avenues for the exploration of Fe-doped MgO in eco-friendly water applications and in the process of display devices. (C) 2015 Elsevier B.V. All rights reserved.

Graphene scavenges free radicals to synergistically enhance structural properties in a gamma-irradiated polyethylene composite through enhanced interfacial interactions

A unique strategy for scavenging free radicals in situ on exposure to gamma irradiation in polyethylene (PE) nanocomposites is presented. Blends of ultra-high molecular weight PE and linear low-density PE (PEB) and their nanocomposites with graphene (GPEB) were prepared by melt mixing to develop materials for biomedical implants. The effect of gamma irradiation on the microstructure and mechanical properties was systematically investigated. The neat blend and the nanocomposite were subjected to gamma-ray irradiation in order to improve the interfacial adhesion between PE and graphene sheets. Structural and thermal characterization revealed that irradiation induced crosslinking and increased the crystallinity of the polymer blend. The presence of graphene further enhanced the crystallinity via crosslinks between the polymer matrix and the filler on irradiation. Graphene was found to scavenge free radicals as confirmed by electron paramagnetic resonance spectroscopy. Irradiation of graphene-containing polymer composites resulted in the largest increase in modulus and hardness compared to either irradiation or addition of graphene to PEB alone. This study provides new insight into the role of graphene in polymer matrices during irradiation and suggests that irradiated graphene-polymer composites could emerge as promising materials for use as articulating surfaces in biomedical implants.

Anomalous Dielectric Features and Structural Implications in Gallic Acid-lsoniazid Cocrystal Mediated by Lattice Water

An organic supramolecular ternary salt (gallic acid:isoniazid:water; GINZH) examined earlier for its proton conducting characteristics is observed to display step-like dielectric behavior across the structural phase transition mediated by loss of water of hydration at 389 K. The presence of hydration in the crystal lattice along with proton mobility between acid base pairs controls the ``ferroelectric like'' behavior until the phase transition temperature.

SInCRe-structural interactome computational resource for Mycobacterium tuberculosis

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein-protein and protein-small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein-protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host-pathogen protein-protein interactions. Together they provide prerequisites for identification of off-target binding.

The effect of structural dimensionality on the electrocatalytic properties of the nickel selenide phase

Nickel selenide (NiSe) nanostructures possessing different morphologies of wires, spheres and hexagons are synthesized by varying the selenium precursors, selenourea, selenium dioxide (SeO2) and potassium selenocyanate (KSeCN), respectively, and are characterized using X-ray diffraction, X-ray photoelectron spectroscopy, Raman spectroscopy, transmission electron microscopy and scanning electron microscopy techniques. Electrical measurements of a single nanowire and a hexagon carried out on devices fabricated by the focused ion beam (FIB) technique depict the semiconducting nature of NiSe and its ability to act as a visible light photodetector. The three different morphologies are used as catalysts for hydrogen evolution (HER), oxygen reduction (ORR) and glucose oxidation reactions. The wire morphology is found to be better than that of spheres and hexagons for all the reactions. Among the reactions studied, NiSe is found to be good for HER and glucose oxidation while ORR seems to terminate at the peroxide stage.

A Simple Label Switching Algorithm for Semisupervised Structural SVMs

In structured output learning, obtaining labeled data for real-world applications is usually costly, while unlabeled examples are available in abundance. Semisupervised structured classification deals with a small number of labeled examples and a large number of unlabeled structured data. In this work, we consider semisupervised structural support vector machines with domain constraints. The optimization problem, which in general is not convex, contains the loss terms associated with the labeled and unlabeled examples, along with the domain constraints. We propose a simple optimization approach that alternates between solving a supervised learning problem and a constraint matching problem. Solving the constraint matching problem is difficult for structured prediction, and we propose an efficient and effective label switching method to solve it. The alternating optimization is carried out within a deterministic annealing framework, which helps in effective constraint matching and avoiding poor local minima, which are not very useful. The algorithm is simple and easy to implement. Further, it is suitable for any structured output learning problem where exact inference is available. Experiments on benchmark sequence labeling data sets and a natural language parsing data set show that the proposed approach, though simple, achieves comparable generalization performance.

Evolutionary and structural analyses of heterodimeric proteins composed of subunits with same fold

Heterodimeric proteins with homologous subunits of same fold are involved in various biological processes. The objective of this study is to understand the evolution of structural and functional features of such heterodimers. Using a non-redundant dataset of 70 such heterodimers of known 3D structure and an independent dataset of 173 heterodimers from yeast, we note that the mean sequence identity between interacting homologous subunits is only 23-24% suggesting that, generally, highly diverged paralogues assemble to form such a heterodimer. We also note that the functional roles of interacting subunits/domains are generally quite different. This suggests that, though the interacting subunits/domains are homologous, the high evolutionary divergence characterize their high functional divergence which contributes to a gross function for the heterodimer considered as a whole. The inverse relationship between sequence identity and RMSD of interacting homologues in heterodimers is not followed. We also addressed the question of formation of homodimers of the subunits of heterodimers by generating models of fictitious homodimers on the basis of the 3D structures of the heterodimers. Interaction energies associated with these homodimers suggests that, in overwhelming majority of the cases, such homodimers are unlikely to be stable. Majority of the homologues of heterodimers of known structures form heterodimers (51.8%) and a small proportion (14.6%) form homodimers. Comparison of 3D structures of heterodimers with homologous homodimers suggests that interfacial nature of residues is not well conserved. In over 90% of the cases we note that the interacting subunits of heterodimers are co-localized in the cell. Proteins 2015; 83:1766-1786. (c) 2015 Wiley Periodicals, Inc.

Structural diversities in Cu(I) and Ag(I) sulfonate coordination polymers and their anion exchange properties

Two new Cu(I) compounds, namely Cu-2(bds)(bpy)(2)]center dot 2H(2)O (1) and Cu-4(bds)(2)(azpy)(4)]center dot 6H(2)O (3) (where bds = benzene-1,3-disulfonate, bpy = 4,4'-bipyridine and azpy = 4,4'-azopyridine), and four Ag(I) compounds, namely Ag-2(bds)(bpy)(2)]center dot 2H(2)O (2), Ag-2(bds)(azpy)(2)]center dot 4H(2)O (4), Ag(bds)(1/2)(bpe)]center dot 3H(2)O (5), and Ag-4(bds)(2)(tmdp)(4)]center dot 9H(2)O (6) (where bpe = 1,2-di(4-pyridyl) ethylene and tmdp = 4,4'trimethylenedipyridine), have been synthesized, and their structures were determined and characterized by elemental analysis, IR, UV-vis and thermal studies. The structure of the compounds changed from 1D (1 and 2) to 2D (3-5) and interpenetrated 3D (6). In the case of 5, a solid-state 2 + 2] photochemical cycloaddition reaction has been performed. Compound 2 exhibits a reversible anion exchange for perchlorate and permanganate, whereas the other compounds (1, 3-6) exhibit an irreversible anion exchange behaviour for perchlorate. Catalytic studies on 2 indicate Lewis acidity.

Solution structural features of N-acyl homoserine lactones

Here we demonstrate that in interbacterial quorum signal moderators, N-acylhomoserine lactones (AHLs), the stabilization of bioactive pharmacophore lactone against lysis is through the e(-) withdrawing N-acyl motif which reduces lactone carbonyl polarization. This lysis is assisted by weak (<0.05 kcal mol(-1)) contacts between N-acyl O and lactone C'. The interactions that preclude this weak contact, in the free and receptor-bound AHLs, improve lactone halflife and hence are key to the design of the antibacterial AHL analogues. (C) 2015 Elsevier Ltd. All rights reserved.

The X-ray photoelectron spectroscopy and high-temperature structural studies of Zn1-xNixO/NiO two-phase composites

Detailed investigation of the chemical states and local atomic environment of Ni and Zn in the two-phase composites of Zn1-xNixO/NiO was reported. The X-ray photoelectron spectra of both Ni-2p and Zn-2p revealed the existence of a doublet with spin-orbit splitting approximate to 17.9 and 23.2eV, respectively confirming the divalent oxidation state of both Ni and Zn. However, the samples fabricated under oxygen-rich conditions exhibit significant difference in the binding energy approximate to 18.75eV between the 2p3/2 and 2p1/2 states of Ni. The shift in the satellite peaks of Ni-2p with increasing the Ni composition x within the Zn1-xNixO/NiO matrix signifies the attenuation of nonlocal screening because of reduced site occupancy of two adjacent Zn ions. The temperature dependence of X-ray diffraction analysis reveals a large distortion in the axial-rhombohedral angle for oxygen-rich NiO. Conversely, no significant distortion was noticed in the NiO system present as a secondary phase within Zn1-xNixO. Nevertheless, the unit-cell volume of both wurtzite h.c.p. Zn1-xNixO and f.c.c. NiO exhibits an anomalous behavior between 150 and 300 degrees C. The origin of such unusual change in the unit-cell volume was discussed in terms of oxygen stoichiometry.

Structural insights into N-terminal to C-terminal interactions and implications for thermostability of a (beta/alpha)(8)-triosephosphate isomerase barrel enzyme

Although several factors have been suggested to contribute to thermostability, the stabilization strategies used by proteins are still enigmatic. Studies on a recombinant xylanase from Bacilllus sp. NG-27 (RBSX), which has the ubiquitous (beta/alpha)(8)-triosephosphate isomerase barrel fold, showed that just a single mutation, V1L, although not located in any secondary structural element, markedly enhanced the stability from 70 degrees C to 75 degrees C without loss of catalytic activity. Conversely, the V1A mutation at the same position decreased the stability of the enzyme from 70 degrees C to 68 degrees C. To gain structural insights into how a single extreme N-terminus mutation can markedly influence the thermostability of the enzyme, we determined the crystal structure of RBSX and the two mutants. On the basis of computational analysis of their crystal structures, including residue interaction networks, we established a link between N-terminal to C-terminal contacts and RBSX thermostability. Our study reveals that augmenting N-terminal to C-terminal noncovalent interactions is associated with enhancement of the stability of the enzyme. In addition, we discuss several lines of evidence supporting a connection between N-terminal to C-terminal noncovalent interactions and protein stability in different proteins. We propose that the strategy of mutations at the termini could be exploited with a view to modulate stability without compromising enzymatic activity, or in general, protein function in diverse folds where N and C termini are in close proximity. Database The coordinates of RBSX, V1A and V1L have been deposited in the PDB database under the accession numbers 4QCE, 4QCF, and 4QDM, respectively

Structural modification and enhanced magnetic properties with two phonon modes in Ca-Co codoped BiFeO3 nanoparticles

Bi1-xCaxFe1-xCoxO3 nanoparticles with x=0.0, 0.05, 0.10 and 0.15 were successfully synthesized by cost effective tartaric acid based sol gel route. The alkali earth metal Ca2+ ions and transition metal Co3+ ions codoping at A and B-sites of BiFeO3 results in structural distortion and phase transformation. Rietveld refinement of XRD patterns suggested the coexistence of rhombohedral and orthorhombic phases in codoped BiFeO3 samples. Both XRD and Raman scattering studies showed the compressive lattice distortion in the samples induced by codoping of Ca2+ and Co3+ ions. Two-phonon Raman spectra exhibited the improvement of magnetization in these samples. X-ray photoelectron spectroscopy (XPS) showed the dominancy of Fe3+ and Co3+ oxidation states along with the shifting of the binding energy of Bi 4f orbital which confirms the substitution Ca2+ at Bi-site. The magnetic study showed the enhancement in room temperature ferromagnetic behavior with co-substitution consistent with Rama analysis. The gradual change in line shape of electron spin resonance spectra indicated the local distortion induced by codoping. (C) 2015 Published by Elsevier Ltd and Techna Group S.r.l.

Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes

Residue types at the interface of protein-protein complexes (PPCs) are known to be reasonably well conserved. However, we show, using a dataset of known 3-D structures of homologous transient PPCs, that the 3-D location of interfacial residues and their interaction patterns are only moderately and poorly conserved, respectively. Another surprising observation is that a residue at the interface that is conserved is not necessarily in the interface in the homolog. Such differences in homologous complexes are manifested by substitution of the residues that are spatially proximal to the conserved residue and structural differences at the interfaces as well as differences in spatial orientations of the interacting proteins. Conservation of interface location and the interaction pattern at the core of the interfaces is higher than at the periphery of the interface patch. Extents of variability of various structural features reported here for homologous transient PPCs are higher than the variation in homologous permanent homomers. Our findings suggest that straightforward extrapolation of interfacial nature and inter-residue interaction patterns from template to target could lead to serious errors in the modeled complex structure. Understanding the evolution of interfaces provides insights to improve comparative modeling of PPC structures.

First Structural View of a Peptide Interacting with the Nucleotide Binding Domain of Heat Shock Protein 90

The involvement of Hsp90 in progression of diseases like cancer, neurological disorders and several pathogen related conditions is well established. Hsp90, therefore, has emerged as an attractive drug target for many of these diseases. Several small molecule inhibitors of Hsp90, such as geldanamycin derivatives, that display antitumor activity, have been developed and are under clinical trials. However, none of these tested inhibitors or drugs are peptide-based compounds. Here we report the first crystal structure of a peptide bound at the ATP binding site of the N-terminal domain of Hsp90. The peptide makes several specific interactions with the binding site residues, which are comparable to those made by the nucleotide and geldanamycin. A modified peptide was designed based on these interactions. Inhibition of ATPase activity of Hsp90 was observed in the presence of the modified peptide. This study provides an alternative approach and a lead peptide molecule for the rational design of effective inhibitors of Hsp90 function.