Catalytic pathway, substrate binding and stability in SAICAR synthetase: A structure and molecular dynamics study

The de novo purine biosynthesis is one of the highly conserved pathways among all organisms and is essential for the cell viability. A clear understanding of the enzymes in this pathway would pave way for the development of antimicrobial and anticancer drugs. Phosphoribosylaminoimidazole-succinocar boxamide (SAICAR) synthetase is one of the enzymes in this pathway that catalyzes ATP dependent ligation of carboxyaminoimidazole ribotide (CAIR) with L-aspartate (ASP). Here, we describe eight crystal structures of this enzyme, in C222(1) and H3 space groups, bound to various substrates and substrate mimics from a hyperthermophilic archaea Pyrococcus horikoshii along with molecular dynamics simulations of the structures with substrates. Complexes exhibit minimal deviation from its apo structure. The CAIR binding site displays a preference for pyrimidine nucleotides. In the ADP.TMP-ASP complex, the ASP binds at a position equivalent to that found in Saccharomyces cerevisiae structure (PDB: 2CNU) and thus, clears the ambiguity regarding ASP's position. A possible mode for the inhibition of the enzyme by CTP and UTP, observed earlier in the yeast enzyme, is clearly illustrated in the structures bound to CMP and UMP. The ADP.Mg2+.PO4.CD/MP complex having a phosphate ion between the ATP and CAIR sites strengthens one of the two probable pathways (proposed in Escherichia coli study) of catalytic mechanism and suggests the possibility of a phosphorylation taking place before the ASP's attack on CAIR. Molecular dynamic simulations of this enzyme along with its substrates at 90 degrees C reveal the relative strengths of substrate binding, possible antagonism and the role of Mg2+ ions. (C) 2015 Elsevier Inc. All rights reserved.

Improved capacity and stability of integrated Li and Mn rich layered-spinel Li1.17Ni0.25Mn1.08O3 cathodes for Li-ion batteries

A Li-rich layered-spinel material with a target composition Li1.17Ni0.25Mn1.08O3 (xLiLi1/3Mn2/3]O-2.(1 - x) LiNi0.5Mn1.5O4, (x = 0.5)) was synthesized by a self-combustion reaction (SCR), characterized by XRD, SEM, TEM, Raman spectroscopy and was studied as a cathode material for Li-ion batteries. The Rietveld refinement results indicated the presence of monoclinic (LiLi1/3Mn2/3]O-2) (52%), spinel (LiNi0.5Mn1.5O4) (39%) and rhombohedral LiNiO2 (9%). The electrochemical performance of this Li-rich integrated cathode material was tested at 30 degrees C and compared to that of high voltage LiNi0.5Mn1.5O4 spinel cathodes. Interestingly, the layered-spinel integrated cathode material exhibits a high specific capacity of about 200 mA h g(-1) at C/10 rate as compared to 180 mA h g(-1) for LiNi0.5Mn1.5O4 in the potential range of 2.4-4.9 V vs. Li anodes in half cells. The layered-spinel integrated cathodes exhibited 92% capacity retention as compared to 82% for LiNi0.5Mn1.5O4 spinel after 80 cycles at 30 degrees C. Also, the integrated cathode material can exhibit 105 mA h g(-1) at 2 C rate as compared to 78 mA h g(-1) for LiNi0.5Mn1.5O4. Thus, the presence of the monoclinic phase in the composite structure helps to stabilize the spinel structure when high specific capacity is required and the electrodes have to work within a wide potential window. Consequently, the Li1.17Ni0.25Mn1.08O3 composite material described herein can be considered as a promising cathode material for Li ion batteries.

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.

Imidazolium based ionic liquid type surfactant improves activity and thermal stability of lipase of Rhizopus oryzae

Lipase and surfactant together form a potent pair in various biotransformation, industrial application and biotechnological studies. The present investigation deals with changes in the activity, stability and structure of lipase from Rhizopus oryzae NRRL 3562 in presence of long chain ionic liquid-type imidazolium surfactant. Both the activity and stability were found to be enhanced in presence of the surfactant at low concentration (1-125 mu M) followed by inhibition at high concentration. The activity increased by 80% and thermal deactivation temperature raised by 2.5 degrees C. Investigations by ultraviolet-visible spectroscopy and circular dichroism revealed structural changes leading to rise in beta-sheet content and lowering of a-helix at low surfactant concentrations. Deactivation at high concentration correlated with greater structural changes depicted by spectroscopic studies. Isothermal titration calorimetric studies showed the binding to be spontaneous in nature involving non-covalent interactions. High negative value of entropy signifies exposure of hydrophobic domains and increase in structural rigidity, which correlates with active site being more accessible and rigid in presence of the surfactant. Application of these surfactants hold greater potential in the field of lipase based biotransformations, enzyme structural modifications and studies. (C) 2015 Elsevier B.V. All rights reserved.

Stability of Poiseuille flow in a fluid overlying an anisotropic and inhomogeneous porous layer

We present the linear stability analysis of horizontal Poiseuille flow in a fluid overlying a porous medium with anisotropic and inhomogeneous permeability. The generalized Darcy model is used to describe the flow in the porous medium with the Beavers-Joseph condition at the interface of the two layers and the eigenvalue problem is solved numerically. The effect of major system parameters on the stability characteristics is addressed in detail. It is shown that the anisotropic and inhomogeneous modulation of the permeability of the underlying porous layer provides an effective means for passive control of the flow stability.

A Few Case Studies on the Correlation of Particle Network and Its Stability on the Ionic Conductivity of Solid-Liquid Composite Electrolytes

We discuss here the crucial role of the particle network and its stability on the long-range ion transport in solid liquid composite electrolytes. The solid liquid composite electrolytes chosen for the study here comprise nanometer sized silica (SiO2) particles having various surface chemical functionalities dispersed in nonaqueous lithium salt solutions, viz, lithium perchlorate (LiClO4) in two different polyethylene glycol based solvents. These systems constitute representative examples of an independent class of soft matter electrolytes known as ``soggy sand'' electrolytes, which have tremendous potential in diverse electrochemical devices. The oxide additive acts as a heterogeneous dopant creating free charge carriers and enhancing the local ion transport. For long-range transport, however, a stable spanning particle network is needed. Systematic experimental investigations here reveal that the spatial and time dependent characteristics of the particle network in the liquid solution are nontrivial. The network characteristics are predominantly determined by the chemical makeup of the electrolyte components and the chemical interactions between them. It is noteworthy that in this study the steady state macroscopic ionic conductivity and viscosity of the solid liquid composite electrolyte are observed to be greatly determined by the additive oxide surface chemical functionality, solvent chemical composition, and solvent dielectric constant.

Efficient visible light photocatalytic activity and enhanced stability of BiOBr/Cd(OH)(2) heterostructures

Novel BioBr/Cd(OH)(2) heterostructures were synthesized by a facile chemical bath method under ambient conditions. A series of BiOBr/Cd(OH)(2) heterostructures were obtained by tuning the Bi/Cd molar ratios. The obtained heterostructures were characterized by powder X-ray diffraction (PXRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and energy dispersive spectroscopy (EDS). Optical properties were studied by UV-visible spectroscopy, diffuse reflectance spectroscopy and photoluminescence (PL). Photocatalytic studies on rhodamine B (RhB) under visible light irradiation showed that the heterostructures are very efficient photocatalysts in mild basic medium. Scavenger test studies confirmed that the photogenerated holes and superoxide radicals (O-2(center dot-)) are the main active species responsible for RhB degradation. Comparison of photoluminescence (PL) intensity suggested that an inhibited charge recombination is crucial for the degradation process over these photocatalysts. Moreover, relative positioning of the valence and conduction band edges of the semiconductors, O-2/O-2(center dot-) and (OH)-O-center dot/H2O redox potentials and HOMO-LUMO levels of RhB appear to be responsible for the hole-specificity of degradation. Photocatalytic recycling experiments indicated the high stability of the catalysts in the reaction medium without any significant loss of activity. This study hence concludes that the heterojunction constructed between Cd(OH)(2) and BiOBr interfaces play a crucial role in influencing the charge carrier dynamics and subsequent photocatalytic activity.

Influence of soil pedological properties on termite mound stability

This study investigated the influence of soil properties on the density and shape of epigeous fungus-growing termite nests in a dry deciduous forest in Karnataka, India. In this environment, Odontotermes obesus produces cathedral shaped mounds. Their density, shape (height and volume) and soil physicochemical properties were analyzed in ferralsol and vertisol environments. No significant difference was observed in O. obesus mound density (n = 2.7 mound ha(-1) on average in the vertisol and ferralsol areas). This study also showed that O. obesus has a limited effect on soil physical properties. No differences in soil particle size, pH, or the C:N ratio and base saturation were measured whereas the C and N contents were reduced and CEC was higher in termite nest soils in both environments. Clay mineralogical composition was also measured, and showed the presence of higher amounts of smectite clays in termite nest soils, which thus explained the increasing CEC despite the reduced C and N content. However, the main difference was the shape of the termite mounds. The degradation of the nests created a hillock of eroded soil at the base of termite mounds in the vertisol while only a thin layer of eroded soil was observed in the ferralsol. The increased degradation of termite mounds in the vertisol is explained by the presence of smectites (2:1 swelling clays), which confer macroscopic swelling and shrinking characteristics to the soil. Soil shrinkage during the dry season leads to the formation of deep cracks in the termite mounds that allow rain to rapidly penetrate inside the mound wall and then breakdown unstable aggregates. In conclusion, it appears that despite a similar abundance, termite mound properties depend to a large extent on the soil properties of their environments. (C) 2015 Elsevier B.V. All rights reserved.

Stability analysis of thick piezoelectric metal based FGM plate using first order and higher order shear deformation theory

This paper presents the stability analysis of functionally graded plate integrated with piezoelectric actuator and sensor at the top and bottom face, subjected to electrical and mechanical loading. The finite element formulation is based on first order and higher order shear deformation theory, degenerated shell element, von-Karman hypothesis and piezoelectric effect. The equation for static analysis is derived by using the minimum energy principle and solutions for critical buckling load is obtained by solving eigenvalue problem. The material properties of the functionally graded plate are assumed to be graded along the thickness direction according to simple power law function. Two types of boundary conditions are used, such as SSSS (simply supported) and CSCS (simply supported along two opposite side perpendicular to the direction of compression and clamped along the other two sides). Sensor voltage is calculated using present analysis for various power law indices and FG (functionally graded) material gradations. The stability analysis of piezoelectric FG plate is carried out to present the effects of power law index, material variations, applied mechanical pressure and piezo effect on buckling and stability characteristics of FG plate.

Mapping Key Residues of ISD11 Critical for NFS1-ISD11 Subcomplex Stability IMPLICATIONS IN THE DEVELOPMENT OF MITOCHONDRIAL DISORDER, COXPD19

Biogenesis of the iron-sulfur (Fe-S) cluster is an indispensable process in living cells. In mammalian mitochondria, the initial step of the Fe-S cluster assembly process is assisted by the NFS1-ISD11 complex, which delivers sulfur to scaffold protein ISCU during Fe-S cluster synthesis. Although ISD11 is an essential protein, its cellular role in Fe-S cluster biogenesis is still not defined. Our study maps the important ISD11 amino acid residues belonging to putative helix 1 (Phe-40), helix 3 (Leu-63, Arg-68, Gln-69, Ile-72, Tyr-76), and C-terminal segment (Leu-81, Glu-84) are critical for in vivo Fe-S cluster biogenesis. Importantly, mutation of these conserved ISD11 residues into alanine leads to its compromised interaction with NFS1, resulting in reduced stability and enhanced aggregation of NFS1 in the mitochondria. Due to altered interaction with ISD11 mutants, the levels of NFS1 and Isu1 were significantly depleted, which affects Fe-S cluster biosynthesis, leading to reduced electron transport chain complex (ETC) activity and mitochondrial respiration. In humans, a clinically relevant ISD11 mutation (R68L) has been associated in the development of a mitochondrial genetic disorder, COXPD19. Our findings highlight that the ISD11 R68A/R68L mutation display reduced affinity to form a stable subcomplex with NFS1, and thereby fails to prevent NFS1 aggregation resulting in impairment of the Fe-S cluster biogenesis. The prime affected machinery is the ETC complex, which showed compromised redox properties, causing diminished mitochondrial respiration. Furthermore, the R68L ISD11 mutant displayed accumulation of mitochondrial iron and reactive oxygen species, leading to mitochondrial dysfunction, which correlates with the phenotype observed in COXPD19 patients.

Effect of Surface Energy Anisotropy on the Stability of Growth Fronts in Multiphase Alloys

Eutectic growth offers a variety of examples for pattern formation which are interesting both for theoreticians as well as experimentalists. One such example of patterns is ternary eutectic colonies which arise as a result of instabilities during growth of two solid phases. Here, in addition to the two major components being exchanged between the solid phases during eutectic growth, there is an impurity component which is rejected by both solid phases. During progress of solidification, there develops a boundary layer of the third impurity component ahead of the solidification front of the two solid phases. Similar to Mullins-Sekerka type instabilities, such a boundary layer tends to make the global solidification envelope unstable to morphological perturbations giving rise to two-phase cells. This phenomenon has been studied numerically in two dimensions for the conditions of directional solidification, by Plapp and Karma (Phys Rev E 66:061608, 2002) using phase-field simulations. While, in the work by Plapp and Karma (Phys Rev E 66:061608, 2002) all interfaces are isotropic, in our presentation, we extend the phase-field model by considering interfacial anisotropy in the solid-solid and solid-liquid interfaces and characterize the role of interfacial anisotropy on the stability of the growth front through phase-field simulations in two dimensions.

A novel index for identification of weak nodes for reactive compensation to improve voltage stability

In this study, a new reactive power loss index (RPLI) is proposed for identification of weak buses in the system. This index is further used for determining the optimal locations for placement of reactive compensation devices in the power system for additional voltage support. The new index is computed from the reactive power support and loss allocation algorithm using Y-bus method for the system under intact condition and as well as critical/severe network contingencies cases. Fuzzy logic approach is used to select the important and critical/severe line contingencies from the contingency list. The inherent characteristics of the reactive power in system operation is properly addressed while determining the reactive power loss allocation to load buses. The proposed index is tested on sample 10-bus equivalent system and 72-bus practical equivalent system of Indian southern region power grid. The validation of the weak buses identification from the proposed index with that from other existing methods in the literature is carried out to demonstrate the effectiveness of the proposed index. Simulation results show that the identification of weak buses in the system from the new RPLI is completely non-iterative, thus requires minimal computational efforts as compared with other existing methods in the literature.

On the Structural Stability of Melt Spun Ribbons of Fe95-x Zr (x) B4Cu1 (x=7 and 9) Alloys and Correlation with Their Magnetic Properties

Melt spun ribbons of Fe95-x Zr (x) B4Cu1 with x = 7 (Z7B4) and 9 (Z9B4) alloys have been prepared, and their structure and magnetic properties have been evaluated using XRD, DSC, TEM, VSM, and Mossbauer spectroscopy. The glass forming ability (GFA) of both alloys has been calculated theoretically using thermodynamical parameters, and Z9B4 alloy is found to possess higher GFA than that of Z7B4 alloy which is validated by XRD results. On annealing, the amorphous Z7B4 ribbon crystallizes into nanocrystalline alpha-Fe, whereas amorphous Z9B4 ribbon shows two-stage crystallization process, first partially to bcc solid solution which is then transformed to nanocrystalline alpha-Fe and Fe2Zr phases exhibiting bimodal distribution. A detailed phase analysis using Mossbauer spectroscopy through hyperfine field distribution of phases has been carried out to understand the crystallization behavior of Z7B4 and Z9B4 alloy ribbons. In order to understand the phase transformation behavior of Z7B4 and Z9B4 ribbons, molar Gibbs free energies of amorphous, alpha-Fe, and Fe2Zr phases have been evaluated. It is found that in case of Z7B4, alpha-Fe is always a stable phase, whereas Fe2Zr is stable at higher temperature for Z9B4. (C) The Minerals, Metals & Materials Society and ASM International 2015

Rapid synthesis of hybrids and hollow PdO nanostructures by controlled in situ dissolution of a ZnO nanorod template: insights into the formation mechanism and thermal stability

Hollow nanomaterials have attracted a lot of interest by virtue of their wide range of applications that arise primarily due to their unique architecture. A common strategy to synthesize hollow nanomaterials is by nucleation of the shell material over a preformed core and subsequent dissolution of the core in the second step. Herein an ultrafast, microwave route has been demonstrated, to synthesize PdO nanotubes in a single step using ZnO as a sacrificial template. The mechanism of the nanotube formation has been investigated in detail using control experiments. By tuning the starting ratio of PdCl2 : ZnO, hollow to hybrid PdO nanostructures could be obtained using the same method. Conversion of the PdO to Pd nanotubes has been shown by simple NaBH4 treatment. The thermal stability of the PdO nanotubes has been studied. The insights presented here are general and applicable for the synthesis of hybrids/hollow structures in other systems as well.

Substituent Effects on the Stability and Antioxidant Activity of Spirodiazaselenuranes

Spirodiazaselenuranes are structurally interesting compounds and the stability of these compounds depends highly on the nature of the substituents attached to the nitrogen atoms. Aromatic substituents are known to play important roles in stabilizing the Se-N bonds in spiro compounds. In this study, several spirodiazaselenuranes are synthesized by introducing benzylic and aliphatic substituents to understand their effect on the stability of the Se-N bonds and the antioxidant activity. Replacement of phenyl substituent by benzyl/alkyl groups significantly reduces the stability of the spirodiazaselenuranes and slows down the oxidative cyclization process. The selenium centre in the spiro compounds undergoes further oxidation to produce the corresponding selenurane oxides, which are stable at room temperature. Comparison of the glutathione peroxidase (GPx) mimetic activity of the compounds showed that the diaryl selenides having heterocyclic rings are significantly more active due to the facile oxidation of the selenium centre. However, the activity is reduced significantly for compounds having aliphatic substituents. In addition to GPx activity, the compounds also inhibit peroxynitrite-mediated nitration and oxidation reaction of protein and small molecules, respectively. The experimental observations suggest that the antioxidant activity is increased considerably upon substitution of the aromatic group with the benzylic/aliphatic substituents on the nitrogen atoms.