Functional characterization, homology modeling and docking studies of beta-glucosidase responsible for bioactivation of cyanogenic hydroxynitrile glucosides from Leucaena leucocephala (subabul)

Glycosyl hydrolase family 1 beta-glucosidases are important enzymes that serve many diverse functions in plants including defense, whereby hydrolyzing the defensive compounds such as hydroxynitrile glucosides. A hydroxynitrile glucoside cleaving beta-glucosidase gene (Llbglu1) was isolated from Leucaena leucocephala, cloned into pET-28a (+) and expressed in E. coli BL21 (DE3) cells. The recombinant enzyme was purified by Ni-NTA affinity chromatography. The optimal temperature and pH for this beta-glucosidase were found to be 45 A degrees C and 4.8, respectively. The purified Llbglu1 enzyme hydrolyzed the synthetic glycosides, pNPGlucoside (pNPGlc) and pNPGalactoside (pNPGal). Also, the enzyme hydrolyzed amygdalin, a hydroxynitrile glycoside and a few of the tested flavonoid and isoflavonoid glucosides. The kinetic parameters K (m) and V (max) were found to be 38.59 mu M and 0.8237 mu M/mg/min for pNPGlc, whereas for pNPGal the values were observed as 1845 mu M and 0.1037 mu M/mg/min. In the present study, a three dimensional (3D) model of the Llbglu1 was built by MODELLER software to find out the substrate binding sites and the quality of the model was examined using the program PROCHEK. Docking studies indicated that conserved active site residues are Glu 199, Glu 413, His 153, Asn 198, Val 270, Asn 340, and Trp 462. Docking of rhodiocyanoside A with the modeled Llbglu1 resulted in a binding with free energy change (Delta G) of -5.52 kcal/mol on which basis rhodiocyanoside A could be considered as a potential substrate.

Structural and mechanical properties of room temperature sputter deposited CrN coatings

Chromium nitride (CrN) thin films were deposited at room temperature on silicon and glass substrates using DC reactive magnetron sputtering in Ar + N-2 plasma. Structure and mechanical properties of these films were examined by using XRD, FESEM and nanoindentation techniques. XRD studies revealed that films are of mixed phase at lower nitrogen partial pressure (P-N2) and single phase at higher (P-N2). Microscopy results show that the films were composed of non-equiaxed columns with nanocrystallite morphology. The hardness and elastic modulus of the films increase with increasing nitrogen partial pressure (P-N2). A maximum hardness of similar to 29 GPa and elastic modulus of 341 GPa were obtained, which make these films useful for several potential applications. (C) 2012 Elsevier Ltd. All rights reserved.

Smoothed functional and Quasi-Newton algorithms for routing in multi-stage queueing network with constraints

We consider the problem of optimal routing in a multi-stage network of queues with constraints on queue lengths. We develop three algorithms for probabilistic routing for this problem using only the total end-to-end delays. These algorithms use the smoothed functional (SF) approach to optimize the routing probabilities. In our model all the queues are assumed to have constraints on the average queue length. We also propose a novel quasi-Newton based SF algorithm. Policies like Join Shortest Queue or Least Work Left work only for unconstrained routing. Besides assuming knowledge of the queue length at all the queues. If the only information available is the expected end-to-end delay as with our case such policies cannot be used. We also give simulation results showing the performance of the SF algorithms for this problem.

Vibrational spectroscopy and density functional theory analysis of 3-O-caffeoylquinic acid

Density functional theory (DFT) calculations are being performed to investigate the geometric, vibrational, and electronic properties of the chlorogenic acid isomer 3-CQA (1R,3R,4S,5R)-3-{(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-1,4, 5-trihydroxycyclohexanecarboxylic acid), a major phenolic compound in coffee. DFT calculations with the 6-311G(d,p) basis set produce very good results. The electrostatic potential mapped onto an isodensity surface has been obtained. A natural bond orbital analysis (NBO) has been performed in order to study intramolecular bonding, interactions among bonds, and delocalization of unpaired electrons. HOMO-LUMO studies give insights into the interaction of the molecule with other species. The calculated HOMO and LUMO energies indicate that a charge transfer occurs within the molecule. (C) 2012 Elsevier B.V. All rights reserved.

Multi-component, Self-assembled, Functional Soft Materials

Supramolecular chemistry is an emerging tool for devising materials that can perform specified functions. The self-assembly of facially amphiphilic bile acid molecules has been extensively utilized for the development of functional soft materials. Supramolecular hydrogels derived from the bile acid backbone act as useful templates for the intercalation of multiple components. Based on this, synthesis of gel-nanoparticle hybrid materials, photoluminescent coating materials, development of a new enzyme assay technique, etc. were achieved in the author's laboratory. The present account highlights some of these achievements.

A practical approach for cross-functional vehicle body weight optimization

The goal of optimization in vehicle design is often blurred by the myriads of requirements belonging to attributes that may not be quite related. If solutions are sought by optimizing attribute performance-related objectives separately starting with a common baseline design configuration as in a traditional design environment, it becomes an arduous task to integrate the potentially conflicting solutions into one satisfactory design. It may be thus more desirable to carry out a combined multi-disciplinary design optimization (MDO) with vehicle weight as an objective function and cross-functional attribute performance targets as constraints. For the particular case of vehicle body structure design, the initial design is likely to be arrived at taking into account styling, packaging and market-driven requirements. The problem with performing a combined cross-functional optimization is the time associated with running such CAE algorithms that can provide a single optimal solution for heterogeneous areas such as NVH and crash safety. In the present paper, a practical MDO methodology is suggested that can be applied to weight optimization of automotive body structures by specifying constraints on frequency and crash performance. Because of the reduced number of cases to be analyzed for crash safety in comparison with other MDO approaches, the present methodology can generate a single size-optimized solution without having to take recourse to empirical techniques such as response surface-based prediction of crash performance and associated successive response surface updating for convergence. An example of weight optimization of spaceframe-based BIW of an aluminum-intensive vehicle is given to illustrate the steps involved in the current optimization process.

Pressure induced structural phase transformation in TiN: a first-principles study

Titanium nitride (TiN), which is widely used for hard coatings, reportedly undergoes a pressure-induced structural phase transformation, from a NaCl to a CsCl structure, at similar to 7 GPa. In this paper, we use first-principles calculations based on density functional theory with a generalized gradient approximation of the exchange correlation energy to determine the structural stability of this transformation. Our results show that the stress required for this structural transformation is substantially lower (by more than an order of magnitude) when it is deviatoric in nature vis-a-vis that under hydrostatic pressure. Local stability of the structure is assessed with phonon dispersion determined at different pressures, and we find that CsCl structure of TiN is expected to distort after the transformation. From the electronic structure calculations, we estimate the electrical conductivity of TiN in the CsCl structure to be about 5 times of that in NaCl structure, which should be observable experimentally. (C) 2013 American Institute of Physics. http://dx.doi.org/10.1063/1.4798591]

A Comparison of mechanical and tribological behavior of nanostructured and conventional WC-12Co detonation-sprayed coatings

In the present study, WC-12Co coatings were deposited by detonation-spraying technique using conventional and nanostructured WC-12Co feedstock at four different oxy/fuel ratios (OF ratio). The coatings exhibited the presence of phases like W2C and W due to the decarburization of the WC phase, and the proportions of these phases were higher in the nano WC-12Co coatings compared with conventional WC-12Co coatings. Coating hardness and fracture toughness were measured. The tribological performance of coatings was examined under dry sand rubber wheel abrasion wear, and solid particle erosion wear conditions. The mechanical and wear properties of coatings were influenced by degree of decarburization and more so in the case of nanostructured WC-Co coatings. The results indicate that the extent of decarburization has a substantial influence on the elastic modulus of the coating which in turn is related to the extent of intersplat cracking of the coating.

Phase synchronization in brain networks derived from correlation between probabilities of recurrences in functional MRI data

It is increasingly being recognized that resting state brain connectivity derived from functional magnetic resonance imaging (fMRI) data is an important marker of brain function both in healthy and clinical populations. Though linear correlation has been extensively used to characterize brain connectivity, it is limited to detecting first order dependencies. In this study, we propose a framework where in phase synchronization (PS) between brain regions is characterized using a new metric ``correlation between probabilities of recurrence'' (CPR) and subsequent graph-theoretic analysis of the ensuing networks. We applied this method to resting state fMRI data obtained from human subjects with and without administration of propofol anesthetic. Our results showed decreased PS during anesthesia and a biologically more plausible community structure using CPR rather than linear correlation. We conclude that CPR provides an attractive nonparametric method for modeling interactions in brain networks as compared to standard correlation for obtaining physiologically meaningful insights about brain function.

Cytochrome P450-mediated metabolism in brain: functional roles and their implications

Introduction: Cytochromes P450 (P450) and associated monooxygenases are a family of heme proteins involved in metabolism of endogenous compounds (arachidonic acid, eicosanoids and prostaglandins) as also xenobiotics including drugs and environmental chemicals. Liver is the major organ involved in P450-mediated metabolism and hepatic enzymes have been characterized. Extrahepatic organs, such as lung, kidney and brain have the capability for biotransformation through P450 enzymes. Brain, including human brain, expresses P450 enzymes that metabolize xenobiotics and endogenous compounds. Areas covered: An overview of P450-mediated metabolism in brain is presented focusing on distinct differences seen in expression of P450 enzymes, generation of unique P450 enzymes in brain through alternate splicing and their consequences in terms of metabolism of psychoactive drugs and inflammatory prompts, such as leukotrienes, thus modulating inflammatory response. Expert opinion: The brain possesses unique P450s that metabolize drugs and endogenous compounds through pathways that are markedly different from that seen in liver indicating that extrapolation directly from liver to brain is not appropriate. It is therefore necessary to characterize the unique brain P450s and their ability to metabolize xenobiotics and endogenous compounds to better understand the functions of this important class of enzymes in brain, especially human brain.

Characterization and microhardness of Co-W coatings electrodeposited at different pH using gluconate bath: a comparative study

Electrodeposition of Co-W alloy coatings has been carried out with DC and PC using gluconate bath at different pH. These coatings are characterized for their structure, morphology and chemical composition by X-ray diffraction, field emission scanning electron microscopy, differential scanning calorimetry and X-ray photoelectron spectroscopy (XPS). Alloy coatings plated at pH8 are crystalline, whereas coatings electrodeposited at pH5 are nanocrystalline in nature. XPS studies have demonstrated that as-deposited alloy plated at pH8 with DC contain only Co2+ and W6+ species, whereas that alloy plated at pH5 has significant amount of Co-0 and W-0 along with Co2+ and W6+ species. Again, Co2+ and W6+ are main species in all as-deposited PC plated alloys in both pH. Co-0 concentration increases upon successive sputtering of all alloy coatings. In contrast, mainly W6+ species is detected in the following layers of all alloys plated with PC. Alloys plated at pH5 show higher microhardness compared to their pH8 counterparts.

Heat and SDS insensitive NDK dimers are largely stabilised by hydrophobic interaction to form functional hexamer in Mycobacterium smegmatis

The primary structure and function of nucleoside diphosphate kinase (NDK), a substrate non-specific enzyme involved in the maintenance of nucleotide pools is also implicated to play pivotal roles in many other cellular processes. NDK is conserved from bacteria to human and forms a homotetramer or hexamer to exhibit its biological activity. However, the nature of the functional oligomeric form of the enzyme differs among different organisms. The functional form of NDKs from many bacterial systems, including that of the human pathogen, Mycobacterium tuberculosis (MtuNDK), is a hexamer, although some bacterial NDKs are tetrameric in nature. The present study addresses the oligomeric property of MsmNDK and how a dimer, the basic subunit of a functional hexamer, is stabilized by hydrogen bonds and hydrophobic interactions. Homology modeling was generated using the three-dimensional structure of MtuNDK as a template; the residues interacting at the monomer-monomer interface of MsmNDK were mapped. Using recombinant enzymes of wild type, catalytically inactive mutant, and monomer-monomer interactive mutants of MsmNDK, the stability of the dimer was verified under heat, SDS, low pH, and methanol. The predicted residues (Gln17, Ser24 and Glu27) were engaged in dimer formation, however the mutated proteins retained the ATPase and GTPase activity even after introducing single (MsmNDK- Q17A, MsmNDK-E27A, and MsmNDK-E27Q) and double (MsmNDK-E27A/Q17A) mutation. However, the monomer monomer interaction could be abolished using methanol, indicating the stabilization of the monomer-monomer interaction by hydrophobic interaction.

Gap renormalization of molecular crystals from density-functional theory

Fundamental gap renormalization due to electronic polarization is a basic phenomenon in molecular crystals. Despite its ubiquity and importance, all conventional approaches within density-functional theory completely fail to capture it, even qualitatively. Here, we present a new screened range-separated hybrid functional, which, through judicious introduction of the scalar dielectric constant, quantitatively captures polarization-induced gap renormalization, as demonstrated on the prototypical organic molecular crystals of benzene, pentacene, and C-60. This functional is predictive, as it contains system-specific adjustable parameters that are determined from first principles, rather than from empirical considerations.

Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.

Laser receptive polyelectrolyte thin films doped with biosynthesized silver nanoparticles for antibacterial coatings and drug delivery applications

We report a simple method to fabricate multifunctional polyelectrolyte thin films to load and deliver the therapeutic drugs. The multilayer thin films were assembled by the electrostatic adsorption of poly (allylamine hydrochloride) (PAH) and dextran sulfate (DS). The silver nanoparticles (Ag NPs) biosynthesized from novel Hybanthus enneaspermus leaf extract as the reducing agent were successfully incorporated into the film. The biosynthesized Ag NPs showed excellent antimicrobial activity against the range of enteropathogens, which could be significantly enhanced when used with commercial antibiotics. The assembled silver nano composite multilayer films showed rupture and deformation when they are exposed to laser. The Ag NPs act as an energy absorption center, locally heat up the film and rupture it under laser treatment. The antibacterial drug, moxifloxacin hydrochloride (MH) was successfully loaded into the multilayer films. The total amount of MH release observed was about 63% which increased to 85% when subjected to laser light exposure. Thus, the polyelectrolyte thin film reported in our study has significant potential in the field of remote activated drug delivery, antibacterial coatings and wound dressings. (C) 2013 Elsevier B.V. All rights reserved.