Binding of BIS like and other ligands with the GSK-3 beta kinase: a combined docking and MM-PBSA study

Binding of several bisindolylmaleimide (BIS) like (BIS-3, BIS-8 and UCN1) and other ligands (H89, SB203580 and Y27632) with the glycogen synthase kinase-3 (GSK-3 beta) has been studied using combined docking, molecular dynamics and Poisson-Boltzmann surface area analysis approaches. The study generated novel binding modes of these ligands that can rationalize why some ligands inhibit GSK-3 beta while others do not. The relative binding free energies associated with these binding modes are in agreement with the corresponding measured specificities. This study further provides useful insight regarding possible existence of multiple conformations of some ligands like H89 and BIS-8. It is also found that binding modes of BIS-3, BIS-8 and UCN1 with GSK-3 beta and PDK1 kinases are similar. These new insights are expected to be useful for future rational design of novel, more potent GSK-3 beta-specific inhibitors as promising therapeutics.

Composites of Graphene and Other Nanocarbons with Organogelators Assembled through Supramolecular Interactions

Carbon nanomaterials (CNMs), such as exfoliated graphene (EG), long-chain functionalized EG, single-walled carbon nanotubes (SWNTs), and fullerene (C-60), have been investigated for their interaction with two structurally different gelators based on all-trans tri-p-phenylenevinylene bis-aldoxime (1) and n-lauroyl-L-alanine (2) both in solution and in supramolecular organogels. Gelation occurs in toluene through hydrogen bonding and van der Waals interactions for 1 and 2 in addition to pp stacking specifically in the case of 1. These nanocomposites provide a thorough understanding in terms of molecular-level interactions of dimensionally different CNMs with structurally different gelators. The presence of densely wrapped CNMs encapsulated fibrous network in the resulting composites is evident from various spectroscopic and microscopic studies, indicating the presence of supramolecular interactions. Concentration- and temperature-dependent UV/Vis and fluorescence spectra show that CNMs promote aggregation of the gelator molecules, leading to hypochromism and quenching of the fluorescence intensity. Thermotropic mesophases of 1 are altered by the inclusion of a small amount of CNMs. The gelCNM composites show increased electrical conductivity compared with that of the native organogel. Rheological studies of the composites demonstrate the formation of rigid and viscoelastic solidlike assembly due to reinforced aggregation of the gelators on CNMs. Synergistic behavior is observed in case of the composite gel of 1, containing a mixture of EG and SWNT, when compared with other mixtures of CNMs in all combinations with EG. This affords new nanocomposites with interesting optical, thermal, electrical, and mechanical properties.

Low-thermal-budget solution processing of thin films of zinc ferrite and other complex oxides

Further miniaturization of magnetic and electronic devices demands thin films of advanced nanomaterials with unique properties. Spinel ferrites have been studied extensively owing to their interesting magnetic and electrical properties coupled with stability against oxidation. Being an important ferrospinel, zinc ferrite has wide applications in the biological (MRI) and electronics (RF-CMOS) arenas. The performance of an oxide like ZnFe2O4 depends on stoichiometry (defect structure), and technological applications require thin films of high density, low porosity and controlled microstructure, which depend on the preparation process. While there are many methods for the synthesis of polycrystalline ZnFe2O4 powder, few methods exist for the deposition of its thin films, where prolonged processing at elevated temperature is not required. We report a novel, microwave-assisted, low temperature (<100°C) deposition process that is conducted in the liquid medium, developed for obtaining high quality, polycrystalline ZnFe2O4 thin films on technologically important substrates like Si(100). An environment-friendly solvent (ethanol) and non-hazardous oxide precursors (β-diketonates of Zn and Fe in 1:2 molar ratio), forming a solution together, is subjected to irradiation in a domestic microwave oven (2.45 GHz) for a few minutes, leading to reactions which result in the deposition of ZnFe2O4 films on Si (100) substrates suspended in the solution. Selected surfactants added to the reactant solution in optimum concentration can be used to control film microstructure. The nominal temperature of the irradiated solution, i.e., film deposition temperature, seldom exceeds 100°C, thus sharply lowering the thermal budget. Surface roughness and uniformity of large area depositions (50x50 mm2) are controlled by tweaking the concentration of the mother solution. Thickness of the films thus grown on Si (100) within 5 min of microwave irradiation can be as high as several microns. The present process, not requiring a vacuum system, carries a very low thermal budget and, together with a proper choice of solvents, is compatible with CMOS integration. This novel solution-based process for depositing highly resistive, adherent, smooth ferrimagnetic films on Si (100) is promising to RF engineers for the fabrication of passive circuit components. It is readily extended to a wide variety of functional oxide films.

Flow-enhanced pairing and other unusual effects in Fermi gases in synthetic gauge fields

Recent experiments on fermions in synthetic gauge fields result in systems with a spin-orbit coupling along one spatial axis, a detuning field, and a Zeeman field. We show theoretically that the presence of all three results in interesting and unusual phenomena in a system of interacting fermions (interactions described by a scattering length). For two fermions, bound states appear only over a certain range of the center-of-mass momenta. The deepest bound state appears at a nonzero center-of-mass momentum. For center-of-mass momenta without a bound state, the gauge field induces a resonance-like feature in the scattering continuum resulting in a large scattering phase shift. In the case of many particles, we demonstrate that the system, in a parameter range, shows flow-enhanced pairing, i.e., a Fulde-Farrell-Larkin-Ovchnnikov superfluid state made of robust pairs with a finite center-of-mass momentum. Yet another regime of parameters offers the opportunity to study strongly interacting normal states of spin-orbit-coupled fermionic systems utilizing the resonance-like feature induced by the synthetic gauge field.

Computational Study of the Migration of Rhenium from One Enantioface of an Olefin to the Other Facilitated by (C-H)center dot center dot center dot Re Interactions

The migration of a metal atom in a metal olefin complex from one pi face of the olefin to the opposite pi face has been rarely documented. Gladysz and co-workers showed that such a movement is indeed possible in monosubstituted chiral Re olefin complexes, resulting in diastereomerization. Interestingly, this isomerization occurred without dissociation, and on the basis of kinetic isotope effects, the involvement of a trans C-H bond was indicated. Either oxidative addition or an agostic interaction of the vinylic C-H(D) bond with the metal could account for the experimentally observed kinetic isotope effect. In this study we compute the free energy of activation for the migration of Re from one enantioface of the olefin to the other through various pathways. On the basis of DFT calculations at the B3LYP level we show that a trans (C-H)center dot center dot center dot Re interaction and trans C-H oxidative addition provide a nondissociative path for the diastereomerization. The trans (C-H)center dot center dot center dot Re interaction path is computed to be more favorable by 2.3 kcal mol(-1) than the oxidative addition path. While direct experimental evidence was not able to discount the migration of the metal through the formation of a eta(2)-arene complex (conducted tour mechanism), computational results at the B3LYP level show that it is energetically more expensive. Surprisingly, a similar analysis carried out at the M06 level computes a lower energy path for the conducted tour mechanism and is not consistent with the experimental isotope effects observed. Metal-(C-H) interactions and oxidative additions of the metal into C-H bonds are closely separated in energy and might contribute to unusual fluxional processes such as this diastereomerization.

Synthesis, properties and applications of graphene doped with boron, nitrogen and other elements

Chemical doping of graphene becomes necessary to create a band gap which is useful for various applications. Furthermore, chemical doping of elements like boron and nitrogen in graphene gives rise to useful properties. Since chemically doped graphene is both of academic and technical importance, we have prepared this article on the present status of various aspects of this important class of materials. In doing so, we have covered the recent literature on this subject citing all the major references. Some of the aspects that we have covered are the synthesis of chemically doped graphene followed by properties and applications. The applications discussed relate to gas adsorption, lithium batteries, supercapacitors, oxygen reduction reaction, field emission and photochemical water splitting. Characterization of chemically doped graphene also included. We believe that the article will be useful to all those interested in graphene and related materials and provides the present status of the subject. (C) 2014 Elsevier Ltd. All rights reserved.

Co-benefits, trade-offs, barriers and policies for greenhouse gas mitigation in the agriculture, forestry and other land use (AFOLU) sector

The agriculture, forestry and other land use (AFOLU) sector is responsible for approximately 25% of anthropogenic GHG emissions mainly from deforestation and agricultural emissions from livestock, soil and nutrient management. Mitigation from the sector is thus extremely important in meeting emission reduction targets. The sector offers a variety of cost-competitive mitigation options with most analyses indicating a decline in emissions largely due to decreasing deforestation rates. Sustainability criteria are needed to guide development and implementation of AFOLU mitigation measures with particular focus on multifunctional systems that allow the delivery of multiple services from land. It is striking that almost all of the positive and negative impacts, opportunities and barriers are context specific, precluding generic statements about which AFOLU mitigation measures have the greatest promise at a global scale. This finding underlines the importance of considering each mitigation strategy on a case-by-case basis, systemic effects when implementing mitigation options on the national scale, and suggests that policies need to be flexible enough to allow such assessments. National and international agricultural and forest (climate) policies have the potential to alter the opportunity costs of specific land uses in ways that increase opportunities or barriers for attaining climate change mitigation goals. Policies governing practices in agriculture and in forest conservation and management need to account for both effective mitigation and adaptation and can help to orient practices in agriculture and in forestry towards global sharing of innovative technologies for the efficient use of land resources. Different policy instruments, especially economic incentives and regulatory approaches, are currently being applied however, for its successful implementation it is critical to understand how land-use decisions are made and how new social, political and economic forces in the future will influence this process.

Ligand 5,10,15,20-Tetra(N-methyl-4-pyridyl)porphine (TMPyP4) Prefers the Parallel Propeller-Type Human Telomeric G-Quadruplex DNA over Its Other Polymorphs

The binding of ligand 5,10,15,20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) with telomeric and genomic G-quadruplex DNA has been extensively studied. However, a comparative study of interactions of TMPyP4 with different conformations of human telomeric G-quadruplex DNA, namely, parallel propeller-type (PP), antiparallel basket-type (AB), and mixed hybrid-type (MH) G-quadruplex DNA, has not been done. We considered all the possible binding sites in each of the G-quadruplex DNA structures and docked TMPyP4 to each one of them. The resultant most potent sites for binding were analyzed from the mean binding free energy of the complexes. Molecular dynamics simulations were then carried out, and analysis of the binding free energy of the TMPyP4-G-quadruplex complex showed that the binding of TMPyP4 with parallel propeller-type G-quadruplex DNA is preferred over the other two G-quadruplex DNA conformations. The results obtained from the change in solvent excluded surface area (SESA) and solvent accessible surface area (SASA) also support the more pronounced binding of the ligand with the parallel propeller-type G-quadruplex DNA.

Typical and atypical domain combinations in human protein kinases: functions, disease causing mutations and conservation in other primates

Ser/Thr and Tyr protein kinases orchestrate many signalling pathways and hence loss in this balance leads to many disease phenotypes. Due to their high abundance, diversity and importance, efforts have been made in the past to classify kinases and annotate their functions at both gross and fine levels. These kinases are conventionally classified into subfamilies based on the sequences of catalytic domains. Usually the domain architecture of a full-length kinase is consistent with the subfamily classification made based on the sequence of kinase domain. Important contributions of modular domains to the overall function of the kinase are well known. Recently occurrence of two kinds of outlier kinases-''Hybrid'' and ``Rogue'' has been reported. These show considerable deviations in their domain architectures from the typical domain architecture known for the classical kinase subfamilies. This article provides an overview of the different subfamilies of human kinases and the role of non-kinase domains in functions and diseases. Importantly this article provides analysis of hybrid and rogue kinases encoded in the human genome and highlights their conservation in closely related primate species. These kinases are examples of elegant rewiring to bring about subtle functional differences compared to canonical variants.

Translation Induction on Indian Language Corpora Using Translingual Themes from Other Languages

Identifying translations from comparable corpora is a well-known problem with several applications, e.g. dictionary creation in resource-scarce languages. Scarcity of high quality corpora, especially in Indian languages, makes this problem hard, e.g. state-of-the-art techniques achieve a mean reciprocal rank (MRR) of 0.66 for English-Italian, and a mere 0.187 for Telugu-Kannada. There exist comparable corpora in many Indian languages with other ``auxiliary'' languages. We observe that translations have many topically related words in common in the auxiliary language. To model this, we define the notion of a translingual theme, a set of topically related words from auxiliary language corpora, and present a probabilistic framework for translation induction. Extensive experiments on 35 comparable corpora using English and French as auxiliary languages show that this approach can yield dramatic improvements in performance (e.g. MRR improves by 124% to 0.419 for Telugu-Kannada). A user study on WikiTSu, a system for cross-lingual Wikipedia title suggestion that uses our approach, shows a 20% improvement in the quality of titles suggested.

Comparison of Matching Pursuit Algorithm with Other Signal Processing Techniques for Computation of the Time-Frequency Power Spectrum of Brain Signals

Signals recorded from the brain often show rhythmic patterns at different frequencies, which are tightly coupled to the external stimuli as well as the internal state of the subject. In addition, these signals have very transient structures related to spiking or sudden onset of a stimulus, which have durations not exceeding tens of milliseconds. Further, brain signals are highly nonstationary because both behavioral state and external stimuli can change on a short time scale. It is therefore essential to study brain signals using techniques that can represent both rhythmic and transient components of the signal, something not always possible using standard signal processing techniques such as short time fourier transform, multitaper method, wavelet transform, or Hilbert transform. In this review, we describe a multiscale decomposition technique based on an over-complete dictionary called matching pursuit (MP), and show that it is able to capture both a sharp stimulus-onset transient and a sustained gamma rhythm in local field potential recorded from the primary visual cortex. We compare the performance of MP with other techniques and discuss its advantages and limitations. Data and codes for generating all time-frequency power spectra are provided.