The Structure of the Thioredoxin−Triosephosphate Isomerase Complex Provides Insights into the Reversible Glutathione-Mediate Regulation of Triosephosphate Isomerase

Protein−protein interactions are crucial for many biological functions. The redox interactome encompasses numerous weak transient interactions in which thioredoxin plays a central role. Proteomic studies have shown that thioredoxin binds to numerous proteins belonging to various cellular processes, including energy metabolism. Thioredoxin has cross talk with other redox mechanisms involving glutathionylation and has functional overlap with glutaredoxin in deglutathionylation reactions. In this study, we have explored the structural and biochemical interactions of thioredoxin with the glycolytic enzyme, triosephosphate isomerase. Nuclear magnetic resonance chemical shift mapping methods and molecular dynamics-based docking have been applied in deriving a structural model of the thioredoxin−triosephosphate isomerase complex. The spatial proximity of active site cysteine residues of thioredoxin to reactive thiol groups on triosephosphate isomerase provides a direct link to the observed deglutathionylation of cysteine 217 in triosephosphate isomerase, thereby reversing the inhibitory effect of S-glutathionylation of triosephosphate isomerase.

Scale effects on buckling analysis of orthotropic nanoplates based on nonlocal two-variable refined plate theory

This article presents the buckling analysis of orthotropic nanoplates such as graphene using the two-variable refined plate theory and nonlocal small-scale effects. The two-variable refined plate theory takes account of transverse shear effects and parabolic distribution of the transverse shear strains through the thickness of the plate, hence it is unnecessary to use shear correction factors. Nonlocal governing equations of motion for the monolayer graphene are derived from the principle of virtual displacements. The closed-form solution for buckling load of a simply supported rectangular orthotropic nanoplate subjected to in-plane loading has been obtained by using the Navier's method. Numerical results obtained by the present theory are compared with first-order shear deformation theory for various shear correction factors. It has been proven that the nondimensional buckling load of the orthotropic nanoplate is always smaller than that of the isotropic nanoplate. It is also shown that small-scale effects contribute significantly to the mechanical behavior of orthotropic graphene sheets and cannot be neglected. Further, buckling load decreases with the increase of the nonlocal scale parameter value. The effects of the mode number, compression ratio and aspect ratio on the buckling load of the orthotropic nanoplate are also captured and discussed in detail. The results presented in this work may provide useful guidance for design and development of orthotropic graphene based nanodevices that make use of the buckling properties of orthotropic nanoplates.

Functional regulation of PVBV Nuclear Inclusion protein-a protease activity upon interaction with Viral Protein genome-linked and phosphorylation

Regulation of NIa-Pro is crucial for polyprotein processing and hence, for successful infection of potyviruses. We have examined two novel mechanisms that could regulate NIa-Pro activity. Firstly, the influence of VPg domain on the proteolytic activity of NIa-Pro was investigated. It was shown that the turnover number of the protease increases when these two domains interact (as: two-fold; trans: seven-fold) with each other. Secondly, the protease activity of NIa-Pro could also be modulated by phosphorylation at Ser129. A mutation of this residue either to aspartate (phosphorylation-mimic) or alanine (phosphorylation-deficient) drastically reduces the protease activity. Based on these observations and molecular modeling studies, we propose that interaction with VPg as well as phosphorylation of Ser129 could relay a signal through Trp143 present at the protein surface to the active site pocket by subtle conformational changes, thus modulating protease activity of NIa-Pro. (C) 2011 Elsevier Inc. All rights reserved.

Simulation-driven design of helmets for head impact protection using an injury-based criterion

The current paper suggests a new procedure for designing helmets for head impact protection for users such as motorcycle riders. According to the approach followed here, a helmet is mounted on a featureless Hybrid 3 headform that is used in assessing vehicles for compliance to the FMVSS 201 regulation in the USA for upper interior head impact safety. The requirement adopted in the latter standard, i.e. not exceeding a threshold HIC(d) limit of 1000, is applied in the present study as a likely criterion for adjudging the efficacy of helmets. An impact velocity of 6 m/s (13.5 mph) for the helmet-headform system striking a rigid target can probably be acceptable for ascertaining a helmet's effectiveness as a countermeasure for minimizing the risk of severe head injury. The proposed procedure is demonstrated with the help of a validated LS-DYNA model of a featureless Hybrid 3 headform in conjunction with a helmet model comprising an outer polypropylene shell to the inner surface of which is bonded a protective polyurethane foam padding of a given thickness. Based on simulation results of impact on a rigid surface, it appears that a minimum foam padding thickness of 40 mm is necessary for obtaining an acceptable value of HIC(d).

Thermal vibration analysis of orthotropic nanoplates based on nonlocal continuum mechanics

This paper presents the thermal vibration analysis of orthotropic nanoplates such as graphene, using the two variable refined plate theory and nonlocal continuum mechanics for small scale effects. The nanoplate is modeled based on two variable refined plate theory and the axial stress caused by the thermal effects is also considered. The two variable refined plate theory takes account of transverse shear effects and parabolic distribution of the transverse shear strains through the thickness of the plate, hence it is unnecessary to use shear correction factors. Nonlocal governing equations of motion for the nanoplate are derived from the principle of virtual displacements. The closed form solution for thermal-vibration frequencies of a simply supported rectangular nanoplate has been obtained by using Navier's method of solution. Numerical results obtained by the present theory are compared with available solutions in the literature and the molecular dynamics results. The influences of the small scale coefficient, the room or low temperature, the high temparature, the half wave number and the aspect ratio of nanoplate on the natural frequencies are considered and discussed in detail. It can be concluded that the present theory, which does not require shear correction factor, is not only simple but also comparable to the first-order and higher order shear deformation theory. The present analysis results can be used for the design of the next generation of nanodevices that make use of the thermal vibration properties of the nanoplates. (C) 2012 Elsevier B.V. All rights reserved.

Improvement in Bone Properties by Using Risedronate Adsorbed Hydroxyapatite Novel Nanoparticle Based Formulation in a Rat Model of Osteoporosis

A superior drug formulation capable of achieving efficient osteogenesis is in imperative demand for the treatment of osteoporosis. In the present study we investigated the potential of using novel risedronate-hydroxyapatite (HA) nanoparticle based formulation in an animal model of established osteoporosis. Nanoparticles of HA loaded with risedronate (NHLR) of various sizes (80-130 nm) were generated for bone targeted drug delivery. Three months after ovariectomy, 36 ovariectomized (OVX) rats were divided into 6 equal groups and treated with various doses of NHLR (500,350 and 250 mu g/kg intravenous single dose) and sodium risedronate (500 mu g/kg, intravenous single dose). Untreated OVX and sham OVX served as controls. One month after drug administration, the left tibia and femur were tested for bone mechanical properties and histology, respectively. In the right femur, bone density was measured by method based on Archimedes principle and bone porosity analyses were performed using X-ray imaging. NHLR (250 mu g/kg) showed a significant increase in bone density and reduced bone porosity when compared with OVX control. Moreover, NHLR (250 mu g/kg) significantly increased bone mechanical properties and bone quality when compared with OVX control. The results strongly suggest that the NHLR, which is a novel nanoparticle based formulation, has a therapeutic advantage over risedronate sodium monotherapy for the treatment of osteoporosis in a rat model of postmenopausal osteoporosis.

Force and ATP hydrolysis dependent regulation of RecA nucleoprotein filament by single-stranded DNA binding protein

In Escherichia coli, the filament of RecA formed on single-stranded DNA (ssDNA) is essential for recombinational DNA repair. Although ssDNA-binding protein (SSB) plays a complicated role in RecA reactions in vivo, much of our understanding of the mechanism is based on RecA binding directly to ssDNA. Here we investigate the role of SSB in the regulation of RecA polymerization on ssDNA, based on the differential force responses of a single 576-nucleotide-long ssDNA associated with RecA and SSB. We find that SSB outcompetes higher concentrations of RecA, resulting in inhibition of RecA nucleation. In addition, we find that pre-formed RecA filaments de-polymerize at low force in an ATP hydrolysis- and SSB-dependent manner. At higher forces, re-polymerization takes place, which displaces SSB from ssDNA. These findings provide a physical picture of the competition between RecA and SSB under tension on the scale of the entire nucleoprotein SSB array, which have broad biological implications particularly with regard to competitive molecular binding.

Thermal vibration analysis of monolayer graphene embedded in elastic medium based on nonlocal continuum mechanics

This paper presents the thermal vibration analysis of single-layer graphene sheet embedded in polymer elastic medium, using the plate theory and nonlocal continuum mechanics for small scale effects. The graphene is modeled based on continuum plate theory and axial stress caused by the thermal effects is also considered. Nonlocal governing equation of motion for this graphene sheet system is derived from the principle of virtual displacements. The closed form solution for thermal-vibration frequencies of a simply supported rectangular nanoplate has been obtained by using the Navier's method of solution. Numerical results obtained by the present theory are compared with available solutions in the literature and the molecular dynamics results. The influences of the small scale coefficient, the room or low temperature, the high temperature, the half wave number and the aspect ratio of nanoplate on the natural frequencies are considered and discussed in detail. The thermal vibration analysis of single- and double-layer graphene sheets are considered for the analysis. The mode shapes of the respective graphene system are also captured in this work. The present analysis results can be used for the design of the next generation of nanodevices that make use of the thermal vibration properties of the graphene.

``On-the-fly'' kinetics of enzymatic racemization using deuterium NMR in DNA-based chiral oriented media

We report the in situ and real-time monitoring of the interconversion of L- and D-alanine-d(3) by alanine racemase from Bacillus stearothermophilus directly observed by H-2 NMR spectroscopy in anisotropic phase. The enantiomers are distinguished by the difference of their H-2 quadrupolar splittings in a chiral liquid crystal containing short DNA fragments. The proof-of-principle, the reliability, and the robustness of this new method is demonstrated by the determination of the turnover rates of the enzyme using the Michaelis Menten model.

Modified current space vector based powerline communication method for distributed inverters interfaced smart grids

The following paper presents a Powerline Communication (PLC) Method for grid interfaced inverters, for smart grid application. The PLC method is based on the concept of the composite vector which involves multiple components rotating at different harmonic frequencies. The pulsed information is modulated on the fundamental component of the grid current as a specific repeating sequence of a particular harmonic. The principle of communication is same as that of power flow, thus reducing the complexity. The power flow and information exchange are simultaneously accomplished by the interfacing inverters based on current programmed vector control, thus eliminating the need for dedicated hardware. Simulation results have been shown for inter-inverter communication, both under ideal and distorted conditions, using various harmonic modulating signals.

Aza-induced cardiomyocyte differentiation of P19 EC-cells by epigenetic co-regulation and ERK signaling

Stem cells in cell based therapy for cardiac injury is being potentially considered. However, genetic regulatory networks involved in cardiac differentiation are not clearly understood. Among stem cell differentiation models, mouse P19 embryonic carcinoma (EC) cells, are employed for studying (epi)genetic regulation of cardiomyocyte differentiation. Here, we comprehensively assessed cardiogenic differentiation potential of 5-azacytidine (Aza) on P19 EC-cells, associated gene expression profiles and the changes in DNA methylation, histone acetylation and activated-ERK signaling status during differentiation. Initial exposure of Aza to cultured EC-cells leads to an efficient (55%) differentiation to cardiomyocyte-rich embryoid bodies with a threefold (16.8%) increase in the cTnI(+) cardiomyocytes. Expression levels of cardiac-specific gene markers i.e., Isl-1, BMP-2, GATA-4, and alpha-MHC were up-regulated following Aza induction, accompanied by differential changes in their methylation status particularly that of BMP-2 and alpha-MHC. Additionally, increases in the levels of acetylated-H3 and pERK were observed during Aza-induced cardiac differentiation. These studies demonstrate that Aza is a potent cardiac inducer when treated during the initial phase of differentiation of mouse P19 EC-cells and its effect is brought about epigenetically and co-ordinatedly by hypo-methylation and histone acetylation-mediated hyper-expression of cardiogenesis-associated genes and involving activation of ERK signaling.

An enthalpy-based model of dendritic growth in a convecting binary alloy melt

Purpose-In the present work, a numerical method, based on the well established enthalpy technique, is developed to simulate the growth of binary alloy equiaxed dendrites in presence of melt convection. The paper aims to discuss these issues. Design/methodology/approach-The principle of volume-averaging is used to formulate the governing equations (mass, momentum, energy and species conservation) which are solved using a coupled explicit-implicit method. The velocity and pressure fields are obtained using a fully implicit finite volume approach whereas the energy and species conservation equations are solved explicitly to obtain the enthalpy and solute concentration fields. As a model problem, simulation of the growth of a single crystal in a two-dimensional cavity filled with an undercooled melt is performed. Findings-Comparison of the simulation results with available solutions obtained using level set method and the phase field method shows good agreement. The effects of melt flow on dendrite growth rate and solute distribution along the solid-liquid interface are studied. A faster growth rate of the upstream dendrite arm in case of binary alloys is observed, which can be attributed to the enhanced heat transfer due to convection as well as lower solute pile-up at the solid-liquid interface. Subsequently, the influence of thermal and solutal Peclet number and undercooling on the dendrite tip velocity is investigated. Originality/value-As the present enthalpy based microscopic solidification model with melt convection is based on a framework similar to popularly used enthalpy models at the macroscopic scale, it lays the foundation to develop effective multiscale solidification.

Trans-spliced Heat Shock Protein 90 Modulates Encystation in Giardia lamblia

Background: Hsp90 from Giardia lamblia is expressed by splicing of two independently transcribed RNA molecules, coded by genes named HspN and HspC located 777 kb apart. The reasons underlying such unique trans-splicing based generation of GlHsp90 remain unclear. Principle Finding: In this study using mass-spectrometry we identify the sequence of the unique, junctional peptide contributed by the 5' UTR of HspC ORF. This peptide is critical for the catalytic function of Hsp90 as it harbours an essential ``Arg'' in its sequence. We also show that full length GlHsp90 possesses all the functional hall marks of a canonical Hsp90 including its ability to bind and hydrolyze ATP. Using qRT-PCR as well as western blotting approach we find the reconstructed Hsp90 to be induced in response to heat shock. On the contrary we find GlHsp90 to be down regulated during transition from proliferative trophozoites to environmentally resistant cysts. This down regulation of GlHsp90 appears to be mechanistically linked to the encystation process as we find pharmacological inhibition of GlHsp90 function to specifically induce encystation. Significance: Our results implicate the trans-spliced GlHsp90 from Giardia lamblia to regulate an essential stage transition in the life cycle of this important human parasite.

Role of DNA sequence based structural features of promoters in transcription initiation and gene expression

D Regulatory information for transcription initiation is present in a stretch of genomic DNA, called the promoter region that is located upstream of the transcription start site (TSS) of the gene. The promoter region interacts with different transcription factors and RNA polymerase to initiate transcription and contains short stretches of transcription factor binding sites (TFBSs), as well as structurally unique elements. Recent experimental and computational analyses of promoter sequences show that they often have non-B-DNA structural motifs, as well as some conserved structural properties, such as stability, bendability, nucleosome positioning preference and curvature, across a class of organisms. Here, we briefly describe these structural features, the differences observed in various organisms and their possible role in regulation of gene expression.

Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors

The nucleoid-associated protein HU plays an important role in maintenance of chromosomal architecture and in global regulation of DNA transactions in bacteria. Although HU is essential for growth in Mycobacterium tuberculosis (Mtb), there have been no reported attempts to perturb HU function with small molecules. Here we report the crystal structure of the N-terminal domain of HU from Mtb. We identify a core region within the HU-DNA interface that can be targeted using stilbene derivatives. These small molecules specifically inhibit HU-DNA binding, disrupt nucleoid architecture and reduce Mtb growth. The stilbene inhibitors induce gene expression changes in Mtb that resemble those induced by HU deficiency. Our results indicate that HU is a potential target for the development of therapies against tuberculosis.