Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7

Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

Synthesis, structure and physicochemical properties of zinc and copper complexes based on sulfonamides containing 8-aminoquinoline ligands

Sulfonamides obtained by reaction of 8-aminoquinoline with 4-nitrobenzenesulfonylchloride and 2,4,6-triisopropylbenzenesulfonyl chloride were used to synthesize coordination compounds with CuII and ZnII with a ML2 composition. Determination of the crystal structures of the resulting zinc and copper complexes by X-ray diffraction show a distorted tetrahedral environment for the [Cu(qnbsa)2], [Cu(qibsa)2] and [Zn(qibsa)2] complexes in which the sulfonamide group acts as a bidentate ligand through the nitrogen atoms from the sulfonamidate and quinoline groups. The complex [Zn(qnbsa)2] crystallizes with a water molecule from the solvent and the Zn is five-coordinated and shows a bipyramidal-trigonal geometry. The electrochemical and electronic spectroscopy properties of the copper complexes are also discussed.

Alpha2-adrenoceptors: Structure and ligand binding properties at the molecular level

Alpha₂-Adrenoceptors: structure and ligand binding properties at the molecular level The mouse is the most frequently used animal model in biomedical research, but the use of zebrafish as a model organism to mimic human diseases is on the increase. Therefore it is considered important to understand their pharmacological differences from humans also at the molecular level. The zebrafish Alpha_2-adrenoceptors were expressed in mammalian cells and the binding affinities of 20 diverse ligands were determined and compared to the corresponding human receptors. The pharmacological properties of the human and zebrafish Alpha_2--adrenoceptors were found to be quite well conserved. Receptor models based on the crystal structures of bovine rhodopsin and the human Beta₂-adrenoceptor revealed that most structural differences between the paralogous and orthologous Alpha_2--adrenoceptors were located within the second extracellular loop (XL2). Reciprocal mutations were generated in the mouse and human Alpha_2--adrenoceptors. Ligand binding experiments revealed that substitutions in XL2 reversed the binding profiles of the human and mouse Alpha_2--adrenoceptors for yohimbine, rauwolscine and RS-79948-197, evidence for a role for XL2 in the determination of species-specific ligand binding. Previous mutagenesis studies had not been able to explain the subtype preference of several large Alpha_2--adrenoceptor antagonists. We prepared chimaeric Alpha_2--adrenoceptors where the first transmembrane (TM1) domain was exchanged between the three human Alpha_2--adrenoceptor subtypes. The binding affinities of spiperone, spiroxatrine and chlorpromazine were observed to be significantly improved by TM1 substitutions of the Alpha_2a--adrenoceptor. Docking simulations indicated that indirect effects, such as allosteric modulation, are more likely to be involved in this phenomenon rather than specific side-chain interactions between ligands and receptors.

Bacterial community structure and petroleum hydrocarbon degradation in the Baltic Sea

The Baltic Sea is unique by its biological, geochemical and physical features. The number of species of larger organisms is small and the species composition is distinctive. On the contrary microbial communities are diverse. Because of the low salinity levels, bacterial communities differ from the ones in the oceans. Knowing the structure of these communities better and how they response to different environmental conditions helps us to estimate how different factors affect the balance and function of the Baltic Sea ecosystem. Bacteria are the key players when it comes to natural biogeochemical processes and human-induced phenomena like eutrophication, oil spills or disposal of other harmful substances to the sea ecosystem. In this thesis, bacterial community structure in the sea surface microlayer and subsurface water of the Archipelago Sea were compared. In addition, the effect of diatom derived polyunsaturated aldehydes on bacterial community structure was studied by a mesocosm experiment. Diesel, crude oil and polycyclic aromatic hydrocarbon degradation capacity of the Baltic Sea bacteria was studied in smaller scale microcosm experiments. In diesel oil experiments bacteria from water phase of the Archipelago Sea was studied. Sediment and iron manganese concretions collected from the Gulf of Finland were used in the crude oil and polycyclic aromatic hydrocarbon experiments. The amount of polycyclic aromatic hydrocarbon degradation genes was measured in all of the oil degradation experiments. The results show how differences in bacterial community structure can be seen in the sea surface when compared to the subsurface waters. The mesocosm experiment demonstrated how diatom-bacteria interactions depend on other factors than diatom derived polyunsaturated aldehydes, which do not seem to have an effect on the bacterial community structure as has been suggested in earlier studies. The dominant bacterial groups in the diesel microcosms differed in samples taken from a pristine site when compared to a site with previous oil exposure in the Archipelago Sea area. Results of the study with sediment and iron-manganese concretions indicate that there are diverse bacterial communities, typical to each bottom type, inhabiting the bottoms of the Gulf of Finland capable to degrade oil and polycyclic aromatic hydrocarbon compounds.  

Copper(II) complexes of N(4)-substituted thiosemicarbazones derived from pyridine-2-carbaldehyde: Crystal structure of a binuclear complex

Ten copper(II) complexes {[CuL1Cl] (1), [CuL1NO3]2 (2), [CuL1N3]2 · 2/3H2O (3), [CuL1]2(ClO4)2 · 2H2O (4), [CuL2Cl]2 (5), [CuL2N3] (6), [Cu(HL2)SO4]2 · 4H2O (7), [Cu(HL2)2] (ClO4)2 · 1/2EtOH (8), [CuL3Cl]2 (9), [CuL3NCS] · 1/2H2O (10)} of three NNS donor thiosemicarbazone ligands {pyridine-2-carbaldehyde-N(4)-p-methoxyphenyl thiosemicarbazone [HL1], pyridine-2-carbaldehyde-N(4)-2-phenethyl thiosemicarbazone [HL2] and pyridine-2-carbaldehyde N(4)-(methyl), N(4)-(phenyl) thiosemicarbazone [HL3]} were synthesized and physico-chemically characterized. The crystal structure of compound 9 has been determined by X-ray diffraction studies and is found that the dimer consists of two square pyramidal Cu(II) centers linked by two chlorine atoms.

Influence of sulphate content on the physico-chemical properties and catalytic activity of some sulphated zirconia systems

The present work attempts a systematic examination of the effect of sulphate content on the physico-chemical properties and catalytic activity of sulphated zirconia and iron promoted sulphated zirconia systems. Sulphate content is estimated by EDX analysis. The amount of sulphate incorporated has been found to influence the surface area, crystal structure and the acid strength distribution. Ammonia TPD and adsorption studies using perylene have enabled the determination of surface acidic properties. The results are supported by the thermodesorption studies using pyridine and 2,6-dimethylpyridine. The catalytic activity towards benzoylation reaction has been correlated with the surface acidity of the systems.

Structure and far-infrared edge modes of quantum antidots at zero magnetic field

We have investigated edge modes of different multipolarity sustained by quantum antidots at zero magnetic field. The ground state of the antidot is described within a local-density-functional formalism. Two sum rules, which are exact within this formalism, have been derived and used to evaluate the energy of edge collective modes as a function of the surface density and the size of the antidot.

Investigations on the structural, optical and Magnetic properties of nanostructured cerium oxide in pure and doped forms and its polymer nanocomposiets

This thesis Entitled INVESTIGATIONS ON THE STRUCTURAL, OPTICAL AND MAGNETIC PROPERTIES OF NANOSTRUCTURED CERIUM OXIDE IN PURE AND DOPED FORMS AND ITS POLYMER NANOCOMPOSITES.Synthesis and processing of nanomatelials and nanostmctures are the essential aspects of nanotechnology. Studies on new physical properties and applications of nanomaterials and nanostructures are possible only when nanostructured materials are made available with desired size, morphology,crystal structure and chemical composition.Recently, several methods have been developed to prepare pure and doped CeO2 powder, including wet chemical synthesis, thermal hydrolysis, flux method, hydrothermal synthesis, gas condensation method, microwave technique etc. In all these, some special reaction conditions, such as high temperature, high pressure, capping agents, expensive or toxic solvents etc. have been involved.Another hi gh-li ght of the present work is room temperature ferromagnetism in cerium oxdie thin films deposited by spray pyrolysis technique.The observation of self trapped exciton mediated PL in ceria nanocrystals is another important outcome of the present study. STE mediated mechanism has been proposed for CeO2 nanocrystals based on the dependence of PL intensity on the annealing temperature. It would be interesting to extent these investigations to the doped forms of cerium oxide and cerium oxide thin films to get deeper Insight into STE mechanism.Due to time constraints detailed investigations could not be canied out on the preparation and properties of free standing films of polymer/ceria nanocomposites. It has been observed that good quality free standing films of PVDF/ceria, PS/C61‘l8, PMMA/ceria can be obtained using solution casting technique. These polymer nanocomposite films show high dielectric constant around 20 and offer prospects of applications as gate electrodes in metal-oxide semiconductor devices.

Studies on Energy Exchange and Upper Ocean Thermat Structure in Arabian Sea and Heat Transport in Northern Indian Ocean

The thesis focused Studies on Energy Exchange and Upper Ocean Thermal Structure in Arabian Sea and Heat Transport in Northern Indian Ocean. The present thesis is an attempt to understand the upper ocean thermal characteristics at selected areas in the western and eastern Arabian Sea in relation to surface energy exchange and dynamics, on a climatological basis. It is also aimed to examine, the relative importance of different processes in the evolution of SST at the western and eastern Arabian Sea. Short-term variations of energy exchange and upper ocean thermal structure are also investigated. Climatological studies of upper ocean thermal structure and surface energy exchange in the western and eastern parts of Arabian Sea bring out the similarities/differences and the causative factors for the observed features. Annual variation of zonally averaged heat advection in north Indian Ocean shows that maximum export of about 100 W/m2 occurs around 15ON during southwest monsoon season. This is due to large negative heat storage caused by intense upwelling in several parts of northern Indian Ocean. By and large, northern Indian Ocean is an area of heat export

Transition metal complexes of some N4-phenylsemicarbazones: crystal structures and spectral studies

The unusual coordination modes of semicarbazones when bound to metals, the wide applications and structural diversity of metal complexes of semicarbazones provoked us to synthesize and characterize the tridentate ONO and NNO-donor semicarbazones and their transition metal complexes. This work is focused on the studies on complexes of three N4-phenylsemicarbazones synthesized by changing the carbonyl compounds. This work is concerned with the studies of two new semicarbazones, 2- formylpyridine-N4-phenylsemicarbazone (HL1) and 3-ethoxysalicylaldehyde- N4-phenylsemicarbazone (H2L2) and a reported semicarbazone 2-benzoylpyridine-N4-phenylsemicarbazone (HL3) [29]. The compositions of these semicarbazones were determined by the CHN analyses and IR, UV and NMR spectral studies were used for the characterization of these compounds. The molecular structure of 3-ethoxysalicylaldehyde-N4-phenylsemicarbazone (H2L2) was obtained by single crystal X-ray diffraction studies. Also, we have synthesized Cu(II), Cd(II), Zn(II) and Ni(II) complexes of these three semicarbazones. The complexes were characterized by various spectroscopic techniques, magnetic and conductivity studies. We could isolate single crystals of some complexes of all metals suitable for X-ray diffraction studies. This thesis is divided into six chapters.

Transition metal complexes derived from ketone based N(4)-substituted thiosemicarbazones: Crystal structures and spectral studies

Thiosemicarbazones have recently attracted considerable attention due to their ability to form tridentate chelates with transition metal ions through either two nitrogen and sulfur atoms, N–N–S or oxygen, nitrogen and sulfur atoms, O–N–S. Considerable interest in thiosemicarbazones and their transition metal complexes has also grown in the areas of biology and chemistry due to biological activities such as antitumoral, fungicidal, bactericidal, antiviral and nonlinear optical properties. They have been used for metal analyses, for device applications related to telecommunications, optical computing, storage and information processing.The versatile applications of metal complexes of thiosemicarbazones in various fields prompted us to synthesize the tridentate NNS-donor thiosemicarbazones and their metal complexes. As a part of our studies on transition metal complexes with these ligands, the researcher undertook the current work with the following objectives. 1. To synthesize and physico-chemically characterize the following thiosemicarbazone ligands: a. Di-2-pyridyl ketone-N(4)-methyl thiosemicarbazone (HDpyMeTsc) b. Di-2-pyridyl ketone-N(4)-ethyl thiosemicarbazone (HDpyETsc) 2. To synthesize oxovanadium(IV), manganese(II), nickel(II), copper(II), zinc(II) and cadmium(II) complexes using the synthesized thiosemicarbazones as principal ligands and some anionic coligands. 3. To study the coordination modes of the ligands in metal complexes by using different physicochemical methods like partial elemental analysis, thermogravimetry and by different spectroscopic techniques. 4. To establish the structure of compounds by single crystal XRD studies

MgO/Ag(001) interface structure and STM images from first principles

The interface of MgO/Ag(001) has been studied with density functional theory applied to slabs. We have found that regular MgO films show a small adhesion to the silver substrate, the binding can be increased in off-stoichiometric regimes, either by the presence of O vacancies at the oxide film or by a small excess of O atoms at the interface between the ceramic to the metal. By means of theoretical methods, the scanning tunneling microscopy signatures of these films is also analyzed in some detail. For defect free deposits containing 1 or 2 ML and at low voltages, tunnelling takes place from the surface Ag substrate, and at large positive voltages Mg atoms are imaged. If defects, oxygen vacancies, are present on the surface of the oxide they introduce much easier channels for tunnelling resulting in big protrusions and controlling the shape of the image, the extra O stored at the interface can also be detected for very thin films.

Swift heavy ion induced surface and microstructural evolution in metallic glass thin films

Swift heavy ion induced changes in microstructure and surface morphology of vapor deposited Fe–Ni based metallic glass thin films have been investigated by using atomic force microscopy, X-ray diffraction and transmission electron microscopy. Ion beam irradiation was carried out at room temperature with 103 MeV Au9+ beam with fluences ranging from 3 1011 to 3 1013 ions/cm2. The atomic force microscopy images were subjected to power spectral density analysis and roughness analysis using an image analysis software. Clusters were found in the image of as-deposited samples, which indicates that the film growth is dominated by the island growth mode. As-deposited films were amorphous as evidenced from X-ray diffraction; however, high resolution transmission electron microscopy measurements revealed a short range atomic order in the samples with crystallites of size around 3 nm embedded in an amorphous matrix. X-ray diffraction pattern of the as-deposited films after irradiation does not show any appreciable changes, indicating that the passage of swift heavy ions stabilizes the short range atomic ordering, or even creates further amorphization. The crystallinity of the as-deposited Fe–Ni based films was improved by thermal annealing, and diffraction results indicated that ion beam irradiation on annealed samples results in grain fragmentation. On bombarding annealed films, the surface roughness of the films decreased initially, then, at higher fluences it increased. The observed change in surface morphology of the irradiated films is attributed to the interplay between ion induced sputtering, volume diffusion and surface diffusion

Structural And Surface Morphological Investigation Of Formation Stages Of Highly (002) Oriented Zno Films On Glass Substrates By Spray Pyrolysis Method

ZnO thin films were coated on amorphous glass substrate at various temperatures in the range 160-500 0C by spray pyrolysis method. The as deposited films were characterised by using XRD and SEM. Wurtzite phase of ZnO was formed at a substrate temperature of 400 0C, highly oriented (002) phase was developed with respect to increase of substrate temperature from 450 to 500 0C. Morphological and growth mode of these films were analyzed with respect to structural orientation of films from wurtzite to highly (002) oriented phase. Present study reveals that substrate temperature was one of the important parameters which determine the crystalline quality, population of defects, grain size, orientation and morphology of the films