Network properties of decoys and CASP predicted models: a comparison with native protein structures

Protein structure space is believed to consist of a finite set of discrete folds, unlike the protein sequence space which is astronomically large, indicating that proteins from the available sequence space are likely to adopt one of the many folds already observed. In spite of extensive sequence-structure correlation data, protein structure prediction still remains an open question with researchers having tried different approaches (experimental as well as computational). One of the challenges of protein structure prediction is to identify the native protein structures from a milieu of decoys/models. In this work, a rigorous investigation of Protein Structure Networks (PSNs) has been performed to detect native structures from decoys/ models. Ninety four parameters obtained from network studies have been optimally combined with Support Vector Machines (SVM) to derive a general metric to distinguish decoys/models from the native protein structures with an accuracy of 94.11%. Recently, for the first time in the literature we had shown that PSN has the capability to distinguish native proteins from decoys. A major difference between the present work and the previous study is to explore the transition profiles at different strengths of non-covalent interactions and SVM has indeed identified this as an important parameter. Additionally, the SVM trained algorithm is also applied to the recent CASP10 predicted models. The novelty of the network approach is that it is based on general network properties of native protein structures and that a given model can be assessed independent of any reference structure. Thus, the approach presented in this paper can be valuable in validating the predicted structures. A web-server has been developed for this purpose and is freely available at http://vishgraph.mbu.iisc.ernet.in/GraProStr/PSN-QA.html.

Pristine nanomaterials: synthesis, stability and applications

Capping-free and linker-free nanostructures/hybrids possess superior properties due to the presence of pristine surfaces and interfaces. In this review, various methods for synthesizing pristine nanomaterials are presented along with the general principles involved in their morphology control. In wet chemical synthesis, the interplay between various reaction parameters results in diverse morphology. The fundamental principles behind the evolution of morphology including nanoporous aggregates of metals and other inorganic materials, 2D nanocrystals of metals is elucidated by capping-free methods in aqueous medium. In addition, strategies leading to the attachment of bare noble metal nanoparticles to functional oxide supports/reduced graphene oxide has been demonstrated which can serve as a simple solution for obtaining thermally stable and efficient supported catalysts with free surfaces. Solution based synthesis of linker-free oxide-semiconductor hybrids and capping-free metal nanowires on substrates are also discussed in this context with ZnO/CdS and ultrathin Au nanowires as examples. A simple and rapid microwave-assisted method is highlighted for obtaining such hybrids which can be employed for high-yield production of similar materials.

Analysis of designed beta-hairpin peptides: molecular conformation and packing in crystals

The crystal structures of several designed peptide hairpins have been determined in order to establish features of molecular conformations and modes of aggregation in the crystals. Hairpin formation has been induced using a centrally positioned (D)Pro-Xxx segment (Xxx = (L)Pro, Aib, Ac(6)c, Ala; Aib = alpha-aminoisobutyric acid; Ac(6)c = 1-aminocyclohexane-1-carboxylic acid). Structures of the peptides Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (1), Boc-Leu-Tyr-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (2, polymorphic forms labeled as 2a and 2b), Boc-Leu-Val-Val-(D)Pro-(L)Pro-Leu-Val-Val-OMe (3), Boc-Leu-Phe-Val-(D)Pro-Aib-Leu-Phe-Val-OMe (4, polymorphic forms labeled as 4a and 4b), Boc-Leu-Phe-Val-(D)Pro-Ac(6)c-Leu-Phe-Val-OMe (5) and Boc-Leu-Phe-Val-(D)Pro-Ala-Leu-Phe-Val-OMe (6) are described. All the octapeptides adopt type II' beta-turn nucleated hairpins, stabilized by three or four cross-strand intramolecular hydrogen bonds. The angle of twist between the two antiparallel strands lies in the range of -9.8 degrees to -26.7 degrees. A detailed analysis of packing motifs in peptide hairpin crystals is presented, revealing three broad modes of association: parallel packing, antiparallel packing and orthogonal packing. An attempt to correlate aggregation modes in solution with observed packing motifs in crystals has been made by indexing of crystal faces in the case of three of the peptide hairpins. The observed modes of hairpin aggregation may be of relevance in modeling multiple modes of association, which may provide insights into the structure of insoluble polypeptide aggregates.

Yield stress, thixotropy and shear banding in a dilute aqueous suspension of few layer graphene oxide platelets

We demonstrate a rigidity percolation transition and the onset of yield stress in a dilute aqueous dispersion of graphene oxide platelets (aspect ratio similar to 5000) above a critical volume fraction of 3.75 x 10(-4) with a percolation exponent of 2.4 +/- 0.1. The viscoelastic moduli of the gel at rest measured as a function of time indicate the absence of structural evolution of the 3D percolated network of disks. However a shear-induced aging giving rise to a compact jammed state and shear rejuvenation indicating a homogenous flow is observed when a steady shear stress (sigma) is imposed in creep experiments. We construct a shear diagram (sigma vs. volume fraction phi) and the critical stress above which shear rejuvenation occurs is identified as the yield stress sigma(y) of the gel. The minimum steady state shear rate (gamma) over dot(m) obtained from creep experiments agrees well with the end of the plateau region in a controlled shear rate flow curve, indicating a shear localization below (gamma) over dot(m). A steady state shear banding in the plateau region of the flow curve observed in particle velocimetry measurements in a Couette geometry confirms that the dilute suspensions of GO platelets form a thixotropic yield stress fluid.

Biotin-conjugated tumour-targeting photocytotoxic iron(III) complexes

Iron(III) complexes FeL(B)] (1-4) of a tetradentate phenolate-based ligand (H3L) and biotin-conjugated dipyridophenazine bases (B), viz. 7-aminodipyrido 3,2-a: 2',3'-c]-phenazine (dppza in 1), (N-dipyrido3,2-a: 2',3'-c]-phenazino) amidobiotin (dppzNB in 2), dipyrido 3,2-a: 2',3'-c]-phenazine-11-carboxylic acid (dppzc in 3) and 2-((2-biotinamido) ethyl) amidodipyrido 3,2-a: 2',3'-c]-phenazine (dppzCB in 4) are prepared, characterized and their interaction with streptavidin and DNA and their photocytotoxicity and cellular uptake in various cells studied. The high-spin iron(III) complexes display Fe(III)/Fe(II) redox couple near -0.7V versus saturated calomel electrode in dimethyl sulfoxide-0.1M tetrabutylammonium perchlorate. The complexes show non-specific interaction with DNA as determined from the binding studies. Complexes with appended biotin moiety show similar binding to streptavidin as that of free biotin, suggesting biotin conjugation to dppz does not cause any loss in its binding affinity to streptavidin. The photocytotoxicity of the complexes is tested in HepG2, HeLa and HEK293 cell lines. Complex 2 shows higher photocytotoxicity in HepG2 cells than in HeLa or HEK293, forming reactive oxygen species. This effect is attributed to the presence of overexpressed sodium-dependent multi-vitamin transporters in HepG2 cells. Microscopic studies in HepG2 cells show internalization of the biotin complexes 2 and 4 essentially occurring by receptor-mediated endocytosis, which is similar to that of native biotin and biotin fluorescein isothiocyanate conjugate.

Interconnected, ultrafine osmium nanoclusters: preparation and surface enhanced Raman scattering activity

Interconnected Os nanochains consisting of ultrafine particles prepared using a simple procedure yield a coupled surface plasmon peak in the visible region and can be used as substrates for surface enhanced Raman scattering of various analytes.

Origin of enhanced photocatalytic activity and photoconduction in high aspect ratio ZnO nanorods

Faceted ZnO nanorods with different aspect ratios were synthesized by a solvothermal method by tuning the reaction time. Increased reaction leads to the formation of high aspect ratio ZnO nanorods largely bound by the prism planes. The high aspect ratio rods showed significantly higher visible light photocatalytic activity when compared to the lower aspect ratio structures. It is proposed that the higher activity is due to better charge separation in the elongated 1D structure. In addition, the fraction of unsaturated Zn2+ sites is higher on the {10 (1) over bar0} facets, leading to better adsorption of oxygen-containing species. These species enhance the production of reactive radicals that are responsible for photodegradation. The photocurrent for these ZnO nanostructures under solar light was measured and a direct correlation between photocurrent and aspect ratio was observed. Since the underlying mechanisms for photodegradation and photocurrent generation are directly related to the efficiency of electron-hole creation and separation, this observation corroborates that the charge separation processes are indeed enhanced in the high aspect ratio structures. The efficiency of photoconduction (electron-hole pair separation) could be further improved by attaching Au nanoparticles on ZnO, which can act as a sink for the electrons. This heterostructure exhibits a high chemisorption of oxygen, which facilitates the production of highly reactive radicals contributing to the high photoreactivity. The suggested mechanisms are applicable to other n-type semiconductor nanostructures with important implications for applications relating to energy and the environment.

Analytical theory and stability analysis of an elongated nanoscale object under external torque

We consider the rotational motion of an elongated nanoscale object in a fluid under an external torque. The experimentally observed dynamics could be understood from analytical solutions of the Stokes equation, with explicit formulae derived for the dynamical states as a function of the object dimensions and the parameters defining the external torque. Under certain conditions, multiple analytical solutions to the Stokes equations exist, which have been investigated through numerical analysis of their stability against small perturbations and their sensitivity towards initial conditions. These experimental results and analytical formulae are general enough to be applicable to the rotational motion of any isolated elongated object at low Reynolds numbers, and could be useful in the design of non-spherical nanostructures for diverse applications pertaining to microfluidics and nanoscale propulsion technologies.

Multispecies coexistence of trees in tropical forests: spatial signals of topographic niche differentiation increase with environmental heterogeneity

Neutral and niche theories give contrasting explanations for the maintenance of tropical tree species diversity. Both have some empirical support, but methods to disentangle their effects have not yet been developed. We applied a statistical measure of spatial structure to data from 14 large tropical forest plots to test a prediction of niche theory that is incompatible with neutral theory: that species in heterogeneous environments should separate out in space according to their niche preferences. We chose plots across a range of topographic heterogeneity, and tested whether pairwise spatial associations among species were more variable in more heterogeneous sites. We found strong support for this prediction, based on a strong positive relationship between variance in the spatial structure of species pairs and topographic heterogeneity across sites. We interpret this pattern as evidence of pervasive niche differentiation, which increases in importance with increasing environmental heterogeneity.

Extraordinary supercapacitor performance of heavily nitrogenated graphene oxide obtained by microwave synthesis

Heavily nitrogenated graphene oxide containing similar to 18 wt% nitrogen, prepared by microwave synthesis with urea as the nitrogen source, shows outstanding performance as a supercapacitor electrode material, with the specific capacitance going up to 461 F g(-1).

Molecular dynamics simulations of PPI dendrimer-drug complexes

Dendrimeric nanoparticles are potential drug delivery devices which can enhance the solubility of hydrophobic drugs, thus increasing their bioavailability and sustained release action. A quantitative understanding of the dendrimer-drug interactions can give valuable insight into the solubility and release profile of hydrophobic drug molecules in various solvent conditions. Fully atomistic molecular dynamics (MD) simulations have been performed to study the interactions of G5 PPIEDA (G5 ethylenediamine cored poly(propylene imine)) dendrimer and two well known drugs (Famotidine and Indomethacin) at different pH conditions. The study suggested that at low pH the dendrimer-drug complexes are thermodynamically unstable as compared to neutral and high pH conditions. Calculated Potential of Mean Force (PMF) by umbrella sampling showed that the release of drugs from the dendrimer at low pH is spontaneous, median release at neutral pH and slow release at high pH. In addition, Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding free energy calculations were also performed at each umbrella sampling window to identify the various energy contributions. To understand the effect of dendrimer chemistry and topology on the solubility and release profile of drugs, this study is extended to explore the solubility and release profile of phenylbutazone drug complexed with G3 poly(amidoamine) and G4 diaminobutane cored PPI dendrimers. The results indicate that the pH-induced conformational changes in dendrimer, ionization states, dendrimer type and pK(a) of the guest molecules influence the free energy barrier and stability of complexation, and thus regulate drug loading, solubility and release.

Ellagic acid - a novel organic electrode material for high capacity lithium ion batteries

Ellagic acid, a naturally occurring polyphenol, extracted from pomegranate husk, is found to be a very good organic electrode material for rechargeable lithium batteries with high reversible capacities of similar to 450 and 200 mA h g(-1) at C/10 and C/2.5 discharge rates, respectively; ex situ NMR studies reveal possible lithiation-delithiation modes at different stages of the charge-discharge process.

Instantaneous reduction of graphene oxide at room temperature

We report an environment friendly and green approach to obtain few-layer graphene by the almost instantaneous reduction of graphene oxide using Mg ribbons in acidic solution with a hydrogen spillover mechanism. The typical time is 1-5 min, which is much faster than the reduction by other metal catalysts.

Flexible poly(vinyl alcohol-co-ethylene)/modified MMT moisture barrier composite for encapsulating organic devices

Flexible, nano-composite moisture barrier films of poly(vinyl alcohol-co-ethylene) with surface modified montmorillonite fabricated by solution casting were used to encapsulate organic devices. The composite films were characterized by FTIR, UV-visible spectroscopy and SEM imaging. Thermal and mechanical properties of the composite films were studied by DSC and UTM. Calcium degradation test was used to determine the transmission rate of water vapour through the composite films, which showed a gradual reduction from similar to 0.1 g m(-2) day(-1) to 0.0001 g m(-2) day(-1) with increasing modified montmorillonite loading in the neat copolymer. The increase in moisture barrier performance is attributed to the decreased water vapour diffusivity due to matrix-filler interactions in the composite. The accelerated aging test was carried out for non-encapsulated and encapsulated devices to evaluate the efficiency of the encapsulants. The encapsulated devices exhibited longer lifetimes indicating the efficacy of the encapsulant.

Molecular flexibility tuned emission in ``V'' shaped naphthalimides: Hg(II) detection and aggregation-induced emission enhancement (AIEE)

Four ``V'' shaped 1,8-naphthalimides (1-4) have been synthesized and their fluorescence quantum-yields correlated to their molecular flexibility. The correlation was used for detection of Hg(II) via a chemodosimetric approach. 4 was found to be an AIE active molecule with the formation of fluorescent nanoaggregates.