Autoinhibitory mechanism and activity-related structural changes in a mycobacterial adenylyl cyclase

An adenylyl cyclase from Mycobacterium avium, Mal 120, is a functional orthologue of a pseudogene Rv1120c from Mycobacterium tuberculosis. We report the crystal structure of Mal 120 in a monomeric form and its truncated construct as a dimer. Mal 120 exists as a monomer in solution and crystallized as a monomer in the absence of substrate or inhibitor. An additional alpha-helix present at the N-terminus of the monomeric structure blocks the active site by interacting with the substrate binding residues and occupying the dimer interface region. However, the enzyme has been found to be active in solution, indicating the movement of the helix away from the interface to facilitate the formation of active dimers in conditions favourable for catalysis. Thus, the N-terminal helix of Ma1120 keeps the enzyme in an autoinhibited state when it is not active. Deletion of this helix enabled us to crystallize the molecule as an active homodimer in the presence of a P-site inhibitor 2',5'-dideoxy-3'-ATP, or pyrophosphate along with metal ions. The substrate specifying lysine residue plays a dual role of interacting with the substrate and stabilizing the dimer. The dimerization loop region harbouring the second substrate specifying residue, an aspartate, shows significant differences in conformation and position between the monomeric and dimeric structures. Thus, this study has not only revealed that significant structural transitions are required for the interconversion of the inactive and the active forms of the enzyme, but also provided precise nature of these transitions. (C) 2015 Elsevier Inc. All rights reserved.

Intramolecular hydrogen bonds involving organic fluorine in the derivatives of hydrazides: an NMR investigation substantiated by DFT based theoretical calculations

The rare examples of intramolecular hydrogen bonds (HB) of the type the N-H center dot center dot center dot F-C, detected in a low polarity solvent in the derivatives of hydrazides, by utilizing one and two-dimensional solution state multinuclear NMR techniques, are reported. The observation of through-space couplings, such as, (1h)J(FH), and (1h)J(FN), provides direct evidence for the existence of intra-molecular HB. Solvent induced perturbations and the variable temperature NMR experiments unambiguously establish the presence of intramolecular HB. The existence of multiple conformers in some of the investigated molecules is also revealed by two dimensional HOESY and N-15-H-1 HSQC experiments. The H-1 DOSY experimental results discard any possibility of self or cross dimerization of the molecules. The derived NMR experimental results are further substantiated by Density Function Theory (DFT) based Non Covalent Interaction (NCI), and Quantum Theory of Atom in Molecule (QTAIM) calculations. The NCI calculations served as a very sensitive tool for detection of non-covalent interactions and also confirm the presence of bifurcated HBs.

Modeling Ultrasonic NDE and Guided Wave based Structural Health Monitoring

Structural Health Monitoring (SHM) systems require integration of non-destructive technologies into structural design and operational processes. Modeling and simulation of complex NDE inspection processes are important aspects in the development and deployment of SHM technologies. Ray tracing techniques are vital simulation tools to visualize the wave path inside a material. These techniques also help in optimizing the location of transducers and their orientation with respect to the zone of interrogation. It helps in increasing the chances of detection and identification of a flaw in that zone. While current state-of-the-art techniques such as ray tracing based on geometric principle help in such visualization, other information such as signal losses due to spherical or cylindrical shape of wave front are rarely taken into consideration. The problem becomes a little more complicated in the case of dispersive guided wave propagation and near-field defect scattering. We review the existing models and tools to perform ultrasonic NDE simulation in structural components. As an initial step, we develop a ray-tracing approach, where phase and spectral information are preserved. This enables one to study wave scattering beyond simple time of flight calculation of rays. Challenges in terms of theory and modelling of defects of various kinds are discussed. Various additional considerations such as signal decay and physics of scattering are reviewed and challenges involved in realistic computational implementation are discussed. Potential application of this approach to SHM system design is highlighted and by applying this to complex structural components such as airframe structures, SHM is demonstrated to provide additional value in terms of lighter weight and/or longevity enhancement resulting from an extension of the damage tolerance design principle not compromising safety and reliability.

Pressure-induced structural phase transitions and phonon anomalies in ReO3: Raman and first-principles study

We report high-pressure Raman-scattering studies on single-crystal ReO3 up to 26.9 GPa at room temperature, complemented by first-principles density functional calculations to assign the modes and to develop understanding of the subtle features of the low-pressure phase transition. The pressure (P) dependence of phonon frequencies (omega) reveals three phase transitions at 0.6, 3, and 12.5 GPa with characteristic splitting and changes in the slope of omega(P). Our first-principles theoretical analysis confirms the role of the rotational modes of ReO6, M-3, to the lowest pressure structural transition, and shows that the transition from the Pm3m to the Im3 structure is a weak first-order transition, originating from the strong anharmonic coupling of the M-3 modes with the acoustic modes (strain).

Structural crossover from nonmodulated to long-period modulated tetragonal phase and anomalous change in ferroelectric properties in the lead-free piezoelectric Na1/2Bi1/2TiO3-BaTiO3

The highly complex structure-property interrelationship in the lead-free piezoelectric (x) Na1/2Bi1/2TiO3 - (1 - x) BaTiO3 is a subject of considerable contemporary debate. Using comprehensive x-ray, neutron diffraction, dielectric, and ferroelectric studies, we have shown the existence of a new criticality in this system at x = 0.80, i.e., well within the conventional tetragonal phase field. This criticality manifests as a nonmonotonic variation of the tetragonality and coercivity and is shown to be associated with a crossover from a nonmodulated tetragonal phase (for x < 0.8) to a long-period modulated tetragonal phase (for x > 0.80). It is shown that the stabilization of long-period modulation introduces a characteristic depolarization temperature in the system. While differing qualitatively from the two-phase model often suggested for the critical compositions of this system, our results support the view with regard to the tendency in perovskites to stabilize long-period modulated structures as a result of complex interplay of antiferrodistortive modes Bellaiche and Iniguez, Phys. Rev. B 88, 014104 ( 2013); Prosandeev, Wang, Ren, Iniguez, ands Bellaiche, Adv. Funct. Mater. 23, 234 (2013)].

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.

Investigations on doping induced changes in structural, electronic structure and magnetic behavior of spintronic Cr-ZnS nanoparticles

Dilute magnetic semiconducting Zn1-xCrxS (x = 0.00, 0.01, 0.03, 0.05, 0.07) nanoparticles were synthesized by the co-precipitation technique using thioglycerol as the capping agent. Powder X-ray diffraction studies showed that Zn1-xCrxS nanoparticles exhibit zinc blende structure with no secondary phase, indicating that Cr ions are substituted at the Zn sites. Photoluminescence and Raman studies show the incorporation of Cr in ZnS nanoparticles. X-ray absorption studies depict that the valence of Zn remains unchanged and maintained in the divalent state, upon doping with Cr. The M-H curves at room temperature indicate the presence of weak ferromagnetism at room temperature due to structural defects. The increase in ferromagnetism with increasing Cr content up to 3%, demonstrates the possibility of tailoring the weak ferromagnetism in ZnS by appropriate Cr doping. (C) 2015 Elsevier Ltd. All rights reserved.

Electric field induced short range to long range structural ordering and its influence on the Eu+3 photoluminescence in the lead-free ferroelectric Na1/2Bi1/2TiO3

Eu+3 was incorporated into the lattice of a lead-free ferroelectric Na1/2Bi1/2TiO3 (NBT) as per the nominal formula Na0.5Bi0.5-xEuxTiO3. This system was investigated with regard to the Eu+3 photoluminescence (PL) and structural behaviour as a function of composition and electric field. Electric field was found to irreversibly change the features in the PL spectra and also in the x-ray diffraction patterns below the critical composition x = 0.025. Detailed analysis revealed that below the critical composition, electric field irreversibly suppresses the structural heterogeneity inherent of the host matrix NBT and brings about a long range ferroelectric state with rhombohedral (R3c) distortion. It is shown that the structural disorder on the nano-scale opens a new channel for radiative transition which manifests as a new emission line branching off from the main D-5(0)-> F-7(0) line along with a concomitant change in the relative intensity of the other crystal field induced Stark lines with different J values. The study suggests that Eu+3 luminescence can be used to probe the relative degree of field induced structural ordering in relaxor ferroelectrics and also in high performance piezoelectric alloys where electric field couples very strongly with the lattice and structural degrees of freedom. (C) 2015 AIP Publishing LLC.

Measurement of Large Dipolar Couplings of a Liquid Crystal with Terminal Phenyl Rings and Estimation of the Order Parameters

NMR spectroscopy is a powerful means of studying liquid-crystalline systems at atomic resolutions. Of the many parameters that can provide information on the dynamics and order of the systems, H-1-C-13 dipolar couplings are an important means of obtaining such information. Depending on the details of the molecular structure and the magnitude of the order parameters, the dipolar couplings can vary over a wide range of values. Thus the method employed to estimate the dipolar couplings should be capable of estimating both large and small dipolar couplings at the same time. For this purpose, we consider here a two-dimensional NMR experiment that works similar to the insensitive nuclei enhanced by polarization transfer (INEPT) experiment in solution. With the incorporation of a modification proposed earlier for experiments with low radio frequency power, the scheme is observed to enable a wide range of dipolar couplings to be estimated at the same time. We utilized this approach to obtain dipolar couplings in a liquid crystal with phenyl rings attached to either end of the molecule, and estimated its local order parameters.

Composition dependent multiple structural transformations of myoglobin in aqueous ethanol solution: A combined experimental and theoretical study

Experimental studies (circular dichroism and ultra-violet (UV) absorption spectra) and large scale atomistic molecular dynamics simulations (accompanied by order parameter analyses) are combined to establish a number of remarkable (and unforeseen) structural transformations of protein myoglobin in aqueous ethanol mixture at various ethanol concentrations. The following results are particularly striking. (1) Two well-defined structural regimes, one at x(EtOH) similar to 0.05 and the other at x(EtOH) similar to 0.25, characterized by formation of distinct partially folded conformations and separated by a unique partially unfolded intermediate state at x(EtOH) similar to 0.15, are identified. (2) Existence of non-monotonic composition dependence of (i) radius of gyration, (ii) long range contact order, (iii) residue specific solvent accessible surface area of tryptophan, and (iv) circular dichroism spectra and UV-absorption peaks are observed. Interestingly at x(EtOH) similar to 0.15, time averaged value of the contact order parameter of the protein reaches a minimum, implying that this conformational state can be identified as a molten globule state. Multiple structural transformations well known in water-ethanol binary mixture appear to have considerably stronger effects on conformation and dynamics of the protein. We compare the present results with studies in water-dimethyl sulfoxide mixture where also distinct structural transformations are observed along with variation of co-solvent composition. (C) 2015 AIP Publishing LLC.

Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications

17 independent crystal structures of family I uracil-DNA glycosylase from Mycobacterium tuberculosis (MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 50 position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.

A Disulfide Stabilized beta-Sandwich Defines the Structure of a New Cysteine Framework M-Superfamily Conotoxin

The structure of a new cysteine framework (-C-CC-C-C-C) ``M''-superfamily conotoxin, Mo3964, shows it to have a beta-sandwich structure that is stabilized by inter-sheet cross disulfide bonds. Mo3964 decreases outward K+ currents in rat dorsal root ganglion neurons and increases the reversal potential of the Na(V)1.2 channels. The structure of Mo3964 (PDB ID: 2MW7) is constructed from the disulfide connectivity pattern, i.e., 1-3, 2-5, and 4-6, that is hitherto undescribed for the ``M''-superfamily conotoxins. The tertiary structural fold has not been described for any of the known conus peptides. NOE (549), dihedral angle (84), and hydrogen bond (28) restraints, obtained by measurement of (h3)J(NC') scalar couplings, were used as input for structure calculation. The ensemble of structures showed a backbone root mean square deviation of 0.68 +/- 0.18 angstrom, with 87% and 13% of the backbone dihedral (phi, psi) angles lying in the most favored and additional allowed regions of the Ramachandran map. The conotoxin Mo3964 represents a new bioactive peptide fold that is stabilized by disulfide bonds and adds to the existing repertoire of scaffolds that can be used to design stable bioactive peptide molecules.

Bio-inspired route for the synthesis of spherical shaped MgO:Fe3+ nanoparticles: Structural, photoluminescence and photocatalytic investigation

MgO:Fe3+ (0.1-5 mol%) nanoparticles (NPs) were synthesized via eco-friendly, inexpensive and simple low temperature solution combustion route using Aloe vera gel as fuel. The final products were characterized by SEM, TEM and HRTEM. PXRD data and Rietveld analysis revealed the formation of cubic system. The influence of Fe3+ ion concentration on the structure morphology, UV absorption, PL emission and photocatalytic activity of MgO:Fe3+ NPs were investigated. The yellow emission with CIE chromaticity coordinates (0.44, 0.52) and average correlated color temperature value was found to be 3540 K which corresponds to warm light of NPs. The control of Fe3+. on MgO matrix influences the photocatalytic decolorization of methylene blue (MB) under UV light. The enhanced photocatalytic activity of MgO:Fe3+ (4 mol%) was attributed to dopant concentration, effective crystallite size, textural properties, decreased band gap and capability for reducing the electron hole pair recombination. Further, the trends of inhibitory effect in the presence of different radical scavengers were explored. These findings open up new avenues for the exploration of Fe-doped MgO in eco-friendly water applications and in the process of display devices. (C) 2015 Elsevier B.V. All rights reserved.

Graphene scavenges free radicals to synergistically enhance structural properties in a gamma-irradiated polyethylene composite through enhanced interfacial interactions

A unique strategy for scavenging free radicals in situ on exposure to gamma irradiation in polyethylene (PE) nanocomposites is presented. Blends of ultra-high molecular weight PE and linear low-density PE (PEB) and their nanocomposites with graphene (GPEB) were prepared by melt mixing to develop materials for biomedical implants. The effect of gamma irradiation on the microstructure and mechanical properties was systematically investigated. The neat blend and the nanocomposite were subjected to gamma-ray irradiation in order to improve the interfacial adhesion between PE and graphene sheets. Structural and thermal characterization revealed that irradiation induced crosslinking and increased the crystallinity of the polymer blend. The presence of graphene further enhanced the crystallinity via crosslinks between the polymer matrix and the filler on irradiation. Graphene was found to scavenge free radicals as confirmed by electron paramagnetic resonance spectroscopy. Irradiation of graphene-containing polymer composites resulted in the largest increase in modulus and hardness compared to either irradiation or addition of graphene to PEB alone. This study provides new insight into the role of graphene in polymer matrices during irradiation and suggests that irradiated graphene-polymer composites could emerge as promising materials for use as articulating surfaces in biomedical implants.

Anomalous Dielectric Features and Structural Implications in Gallic Acid-lsoniazid Cocrystal Mediated by Lattice Water

An organic supramolecular ternary salt (gallic acid:isoniazid:water; GINZH) examined earlier for its proton conducting characteristics is observed to display step-like dielectric behavior across the structural phase transition mediated by loss of water of hydration at 389 K. The presence of hydration in the crystal lattice along with proton mobility between acid base pairs controls the ``ferroelectric like'' behavior until the phase transition temperature.