The crystal structure of a lectin from Butea monosperma: Insight into its glycosylation and binding of ligands

Crystal structure of a lectin purified from Butea monosperma seeds was determined by Molecular Replacement method. Its primary structure was determined by Tandem Mass Spectroscopy and electron density maps from X-ray diffraction data. Its quaternary structure was tetrameric, formed of two monomers, alpha and beta, beta appearing as truncated alpha. The occurrence of two tetramers in the asymmetric unit of the crystal might be a consequence of asymmetric contacts due to difference in glycosylation and variable loops structures, to form an `octamer-structure'. The crystal structure showed binding pockets for gamma Abu, having a proposed role in plant defense, at the interface of canonical dimer-partners. Hemagglutination studies, enzyme kinetics, isothermal titration calorimetry and molecular dynamics showed that the lectin is specific to N-acetyl D-galactosamine, galactose and lactose in decreasing order, and alpha-amylase inhibitor. (C) 2014 Elsevier B.V. All rights reserved.

New structural forms of a mycobacterial adenylyl cyclase Rv1625c

Rv1625c is one of 16 adenylyl cyclases encoded in the genome of Mycobacterium tuberculosis. In solution Rv1625c exists predominantly as a monomer, with a small amount of dimer. It has been shown previously that the monomer is active and the dimeric fraction is inactive. Both fractions of wild-type Rv1625c crystallized as head-to-head inactive domain-swapped dimers as opposed to the head-to-tail dimer seen in other functional adenylyl cyclases. About half of the molecule is involved in extensive domain swapping. The strain created by a serine residue located on a hinge loop and the crystallization condition might have led to this unusual domain swapping. The inactivity of the dimeric form of Rv1625c could be explained by the absence of the required catalytic site in the swapped dimer. A single mutant of the enzyme was also generated by changing a phenylalanine predicted to occur at the functional dimer interface to an arginine. This single mutant exists as a dimer in solution but crystallized as a monomer. Analysis of the structure showed that a salt bridge formed between a glutamate residue in the N-terminal segment and the mutated arginine residue hinders dimer formation by pulling the N-terminal region towards the dimer interface. Both structures reported here show a change in the dimerization-arm region which is involved in formation of the functional dimer. It is concluded that the dimerization arm along with other structural elements such as the N-terminal region and certain loops are vital for determining the oligomeric nature of the enzyme, which in turn dictates its activity.

On the Room Temperature Ferromagnetic and Ferroelectric Properties of Pb(Fe1/2Nb1/2)O-3

We report the origin of room temperature (RT) ferromagnetic and ferroelectric properties of Pb(Fe1/2Nb1/2)O-3 (PFN) ceramic sample prepared by modified solid-state reaction synthesis by a single-step method, based on X-ray diffraction (XRD), neutron diffraction (ND), Mossbauer spectroscopy and electron paramagnetic resonance (EPR) spectroscopy results. Formation of single-phase monoclinic PFN ceramic with Cm space group was confirmed by XRD and ND at RT. The morphology studied by scanning electron microscopy (SEM) confirmed uniform microstructure of the sample with average grain size of similar to 2 mu m. The ND, Mossbauer spectroscopy, M-H loop and EPR studies were carried out to confirm the existence of weak ferromagnetism at RT. A clear opening of hysteresis (M-H) loop is evidenced as the existence of weak ferromagnetism at RT. EPR spectrum clearly shows the ferromagnetism through a good resonance signal. The symmetric EPR line shape with g = 1.9895 observed in PFN sample was identified to be due to Fe3+ ions. Mossbauer spectroscopy at RT shows superparamagnetic behaviour with presence of Fe in 3+ valence state. Ferroelectric P-E loops on PFN at RT confirm the existing ferroelectric ordering. Our observation is in agreement with literature, and it supports that the origin of ferromagnetism and ferroelectricity is isolated, i.e. from different regions in the sample. Our results do not support the multiferroic nature of PFN at RT.

Damage quantification under sliding and seizure condition using first-of-a-kind fretting machine

In a practical situation, it is difficult to model exact contact conditions clue to challenges involved in the estimation of contact forces, and relative displacements between the contacting bodies. Sliding and seizure conditions were simulated on first-of-a-kind displacement controlled system. Self-mated stainless steels have been investigated in detail. Categorization of contact conditions prevailing at the contact interface has been carried out based on the variation of coefficient of friction with number of cycles, and three-dimensional fretting loops. Surface and subsurface micro-cracks have been observed, and their characteristic shows strong dependence on loading conditions. Existence of shear bands in the subsurface region has been observed for high strain and low strain rate loading conditions. Studies also include the influence of initial surface roughness on the damage under two extreme contact conditions. (C) 2013 Elsevier B.V. All rights reserved.

Impact of glycosylation on stability, structure and unfolding of soybean agglutinin (SBA): an insight from thermal perturbation molecular dynamics simulations

Glycosylation has been recognized as one of the most prevalent and complex post-translational modifications of proteins involving numerous enzymes and substrates. Its effect on the protein conformational transitions is not clearly understood yet. In this study, we have examined the effect of glycosylation on protein stability using molecular dynamics simulation of legume lectin soybean agglutinin (SBA). Its glycosylated moiety consists of high mannose type N-linked glycan (Man(9)GlcNAc(2)). To unveil the structural perturbations during thermal unfolding of these two forms, we have studied and compared them to the experimental results. From the perspective of dynamics, our simulations revealed that the nonglycosylated monomeric form is less stable than corresponding glycosylated form at normal and elevated temperatures. Moreover, at elevated temperature thermal destabilization is more prominent in solvent exposed loops, turns and ends of distinct beta sheets. SBA maintains it folded structure due to some important saltbridges, hydrogen bonds and hydrophobic interactions within the protein. The reducing terminal GlcNAc residues interact with the protein residues VAL161, PRO182 and SER225 via hydrophobic and via hydrogen bonding with ASN 9 and ASN 75. Our simulations also revealed that single glycosylation (ASN75) has no significant effect on corresponding cis peptide angle orientation. This atomistic description might have important implications for understanding the functionality and stability of Soybean agglutinin.

Taming Control Divergence in GPUs through Control Flow Linearization

Branch divergence is a very commonly occurring performance problem in GPGPU in which the execution of diverging branches is serialized to execute only one control flow path at a time. Existing hardware mechanism to reconverge threads using a stack causes duplicate execution of code for unstructured control flow graphs. Also the stack mechanism cannot effectively utilize the available parallelism among diverging branches. Further, the amount of nested divergence allowed is also limited by depth of the branch divergence stack. In this paper we propose a simple and elegant transformation to handle all of the above mentioned problems. The transformation converts an unstructured CFG to a structured CFG without duplicating user code. It incurs only a linear increase in the number of basic blocks and also the number of instructions. Our solution linearizes the CFG using a predicate variable. This mechanism reconverges the divergent threads as early as possible. It also reduces the depth of the reconvergence stack. The available parallelism in nested branches can be effectively extracted by scheduling the basic blocks to reduce the effect of stalls due to memory accesses. It can also increase execution efficiency of nested loops with different trip counts for different threads. We implemented the proposed transformation at PTX level using the Ocelot compiler infrastructure. We evaluated the technique using various benchmarks to show that it can be effective in handling the performance problem due to divergence in unstructured CFGs.

Snaps and mends: DNA breaks and chromosomal translocations

Integrity in entirety is the preferred state of any organism. The temporal and spatial integrity of the genome ensures continued survival of a cell. DNA breakage is the first step towards creation of chromosomal translocations. In this review, we highlight the factors contributing towards the breakage of chromosomal DNA. It has been well-established that the structure and sequence of DNA play a critical role in selective fragility of the genome. Several non-B-DNA structures such as Z-DNA, cruciform DNA, G-quadruplexes, R loops and triplexes have been implicated in generation of genomic fragility leading to translocations. Similarly, specific sequences targeted by proteins such as Recombination Activating Genes and Activation Induced Cytidine Deaminase are involved in translocations. Processes that ensure the integrity of the genome through repair may lead to persistence of breakage and eventually translocations if their actions are anomalous. An insufficient supply of nucleotides and chromatin architecture may also play a critical role. This review focuses on a range of events with the potential to threaten the genomic integrity of a cell, leading to cancer.

Sampling Period Selection of Control Application Connected to FlexRay Bus

Flexray is a high speed communication protocol designed for distributive control in automotive control applications. Control performance not only depends on the control algorithm but also on the scheduling constraints in communication. A balance between the control performance and communication constraints must required for the choice of the sampling rates of the control loops in a node. In this paper, an optimum sampling period of control loops to minimize the cost function, satisfying the scheduling constraints is obtained. An algorithm to obtain the delay in service of each task in a node of the control loop in the hyper period has been also developed. (C) 2015 The Authors. Published by Elsevier B.V.

Future collider signatures of the possible 750 GeV state

If the recent indications of a possible state I broken vertical bar with mass similar to 750 GeV decaying into two photons reported by ATLAS and CMS in LHC collisions at 13 TeV were to become confirmed, the prospects for future collider physics at the LHC and beyond would be affected radically, as we explore in this paper. Even minimal scenarios for the I broken vertical bar resonance and its gamma gamma decays require additional particles with masses . We consider here two benchmark scenarios that exemplify the range of possibilities: one in which I broken vertical bar is a singlet scalar or pseudoscalar boson whose production and gamma gamma decays are due to loops of coloured and charged fermions, and another benchmark scenario in which I broken vertical bar is a superposition of (nearly) degenerate CP-even and CP-odd Higgs bosons in a (possibly supersymmetric) two-Higgs doublet model also with additional fermions to account for the gamma gamma decay rate. We explore the implications of these benchmark scenarios for the production of I broken vertical bar and its new partners at colliders in future runs of the LHC and beyond, at higher-energy pp colliders and at e (+) e (-) and gamma gamma colliders, with emphasis on the bosonic partners expected in the doublet scenario and the fermionic partners expected in both scenarios.

Net-like Ferromagnetic Mnsb Film Deposited on Porous Silicon Substrates

MnSb films were deposited on porous silicon substrates by physical vapor deposition (PVD) technique. Modulation effects due to the substrate on microstructure and magnetic properties of the MnSb film's were studied by scanning electron microscope (SEM), X-ray diffraction (XRD) and measurements of hysteresis loops. SEM images of the MnSb films indicate that net-like structures were obtained because of the special morphology of the substrates. The net-like MnSb films exhibit some novel magnetic properties different from the unpatterned referenced samples. For example, in the case of net-like morphology, the coercive field is as low as 60 Oe.

Room-temperature ferromagnetic semiconductor MnxGa1-xSb

Ferromagnetic semiconductor MnxGa1-xSb single crystals were fabricated by Mn-ions implantation, deposition, and the post annealing. Magnetic hysteresis-loops in the MnxGa1-xSb single crystals were obtained at room temperature (300 K). The structure of the ferromagnetic semiconductor MnxGa1-xSb single crystal was analyzed by Xray diffraction. The distribution of carrier concentrations in MnxGa1-xSb was investigated by electrochemical capacitance- voltage profiler. The content of Mn in MnxGa1-xSb varied gradually from x = 0.09 near the surface to x = 0 in the wafer inner analyzed by X-ray diffraction. Electrochemical capacitance-voltage profiler reveals that the concentration of p-type carriers in MnxGa1-xSb is as high as 1 1021 cm-3, indicating that most of the Mn atoms in MnxGa1-xSb take the site of Ga, and play a role of acceptors.

Correct biological timing in Arabidopsis requires multiple light-signaling pathways.

Circadian oscillators provide rhythmic temporal cues for a range of biological processes in plants and animals, enabling anticipation of the day/night cycle and enhancing fitness-associated traits. We have used engineering models to understand the control principles of a plant's response to seasonal variation. We show that the seasonal changes in the timing of circadian outputs require light regulation via feed-forward loops, combining rapid light-signaling pathways with entrained circadian oscillators. Linear time-invariant models of circadian rhythms were computed for 3,503 circadian-regulated genes and for the concentration of cytosolic-free calcium to quantify the magnitude and timing of regulation by circadian oscillators and light-signaling pathways. Bioinformatic and experimental analysis show that rapid light-induced regulation of circadian outputs is associated with seasonal rephasing of the output rhythm. We identify that external coincidence is required for rephasing of multiple output rhythms, and is therefore important in general phase control in addition to specific photoperiod-dependent processes such as flowering and hypocotyl elongation. Our findings uncover a fundamental design principle of circadian regulation, and identify the importance of rapid light-signaling pathways in temporal control.

Phase Evolution and its Effect on Magnetic Properties of Nd60Al10Fe20Co10 Bulk Metallic Glass

The thermal stability of nanocrystalline clusters, the phase evolution, and their effects on magnetic Propertieswere studied for as-cast Nd60Al10Fe20Co10 alloy using differential scanning calorimetry curves, x-ray diffraction patterns, scanning electron microscopy, and high-resolution transition electron microscopy. Thermomagnetic curves and hysteresis loops of the bulk metallic glass were measured during the annealing process. The high thermostability of the hardmagnetic properties of the samples observed is attributed to the stability of the nanocrystalline clusters upon annealing, while the slight enhancement in the magnetization is due to the precipitation of some Nd-rich metastable phases. The mechanism of thermostability of the nanocrystalline clusters and the formation of the metastable phases are discussed.

Nonlinear Constitutive Behavior Of Ferroelectric Materials

The ferroelectric specimen is considered as an aggregation of many randomly oriented domains. According to this mechanism, a multi-domain mechanical model is developed in this paper. Each domain is represented by one element. The applied stress and electric field are taken to be the stress and electric field in the formula of the driving force of domain switching for each element in the specimen. It means that the macroscopic switching criterion is used for calculating the volume fraction of domain switching for each element. By using the hardening relation between the driving force of domain switching and the volume fraction of domain switching calibrated, the volume fraction of domain switching for each element is calculated. Substituting the stress and electric field and the volume fraction of domain switching into the constitutive equation of ferroelectric material, one can easily get the strain and electric displacement for each element. The macroscopic behavior of the ferroelectric specimen is then directly calculated by volume averaging. Meanwhile, the nonlinear finite element analysis for the ferroelectric specimen is carried out. In the finite element simulation, the volume fraction of domain switching for each element is calculated by using the same method mentioned above. The interaction between different elements is taken into account in the finite element simulation and the local stress and electric field for each element is obtained. The macroscopic behavior of the specimen is then calculated by volume averaging. The computation results involve the electric butterfly shaped curves of axial strain versus the axial electric field and the hysteresis loops of electric displacement versus the electric field for ferroelectric specimens under the uniaxial coupled stress and electric field loading. The present theoretical prediction agrees reasonably with the experimental results.

Theory Of Phase Transformation And Reorientation In Single Crystalline Shape Memory Alloys

A constitutive model, based on an (n + 1)-phase mixture of the Mori-Tanaka average theory, has been developed for stress-induced martensitic transformation and reorientation in single crystalline shape memory alloys. Volume fractions of different martensite lattice correspondence variants are chosen as internal variables to describe microstructural evolution. Macroscopic Gibbs free energy for the phase transformation is derived with thermodynamics principles and the ensemble average method of micro-mechanics. The critical condition and the evolution equation are proposed for both the phase transition and reorientation. This model can also simulate interior hysteresis loops during loading/unloading by switching the critical driving forces when an opposite transition takes place.