X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase

To be effective as antiviral agent, AZT (3′-azido-3′-deoxythymidine) must be converted to a triphosphate derivative by cellular kinases. The conversion is inefficient and, to understand why AZT diphosphate is a poor substrate of nucleoside diphosphate (NDP) kinase, we determined a 2.3-Å x-ray structure of a complex with the N119A point mutant of Dictyostelium NDP kinase. It shows that the analog binds at the same site and, except for the sugar ring pucker which is different, binds in the same way as the natural substrate thymidine diphosphate. However, the azido group that replaces the 3′OH of the deoxyribose in AZT displaces a lysine side chain involved in catalysis. Moreover, it is unable to make an internal hydrogen bond to the oxygen bridging the β- and γ-phosphate, which plays an important part in phosphate transfer.

Identification, retinoid binding, and x-ray analysis of a human retinol-binding protein

Two cellular retinol-binding proteins (CRBP I and II) with distinct tissue distributions and retinoid-binding properties have been recognized thus far in mammals. Here, we report the identification of a human retinol-binding protein resembling type I (55.6% identity) and type II (49.6% identity) CRBPs, but with a unique H residue in the retinoid-binding site and a distinctively different tissue distribution. Additionally, this binding protein (CRBP III) exhibits a remarkable sequence identity (62.2%) with the recently identified ι-crystallin/CRBP of the diurnal gecko Lygodactylus picturatus [Werten, P. J. L., Röll, B., van Alten, D. M. F. & de Jong, W. W. (2000) Proc. Natl. Acad. Sci. USA 97, 3282–3287 (First Published March 21, 2000; 10.1073/pnas.050500597)]. CRBP III and all-trans-retinol form a complex (Kd ≈ 60 nM), the absorption spectrum of which is characterized by the peculiar fine structure typical of the spectra of holo-CRBP I and II. As revealed by a 2.3-Å x-ray molecular model of apo-CRBP III, the amino acid residues that line the retinol-binding site in CRBP I and II are positioned nearly identically in the structure of CRBP III. At variance with the human CRBP I and II mRNAs, which are most abundant in ovary and intestine, respectively, the CRBP III mRNA is expressed at the highest levels in kidney and liver thus suggesting a prominent role for human CRBP III as an intracellular mediator of retinol metabolism in these tissues.

No anticorrelation between cyclotron line energy and X-ray flux in 4U 0115+634

We report on an outburst of the high mass X-ray binary 4U 0115+634 with a pulse period of 3.6 s in 2008 March/April as observed with RXTE and INTEGRAL. During the outburst the neutron star’s luminosity varied by a factor of 10 in the 3–50 keV band. In agreement with earlier work we find evidence of five cyclotron resonance scattering features at ~10.7, 21.8, 35.5, 46.7, and 59.7 keV. Previous work had found an anticorrelation between the fundamental cyclotron line energy and the X-ray flux. We show that this apparent anticorrelation is probably due to the unphysical interplay of parameters of the cyclotron line with the continuum models used previously, e.g., the negative and positive exponent power law (NPEX). For this model, we show that cyclotron line modeling erroneously leads to describing part of the exponential cutoff and the continuum variability, and not the cyclotron lines. When the X-ray continuum is modeled with a simple exponentially cutoff power law modified by a Gaussian emission feature around 10 keV, the correlation between the line energy and the flux vanishes, and the line parameters remain virtually constant over the outburst. We therefore conclude that the previously reported anticorrelation is an artifact of the assumptions adopted in the modeling of the continuum.

Crystallization and preliminary X-ray analysis of sulfite dehydrogenase from Stargeya novella

Crystals of purified heterodimeric sulfite dehydrogenase from Starkeya novella have been grown using vapour diffusion. X-ray diffraction data have been collected from crystals of the native protein at lambda=1.0 Angstrom and close to the iron absorption edge at lambda=1.737 Angstrom. The crystals belong to space group P2(1)2(1)2, with unit-cell parameters a=97.5, b=92.5, c=55.9 Angstrom. Native data have been recorded to 1.8 Angstrom resolution and Fe-edge data to 2.5 Angstrom.

Crystallization and preliminary X-ray analysis of a Kunitz-type inhibitor, textilinin-1 from Pseudonaja textilis textilis

Textilinin-1 (Txln-1), a Kunitz-type serine protease inhibitor, is a 59-amino-acid polypeptide isolated from the venom of the Australian Common Brown snake Pseudonaja textilis textilis. This molecule has been suggested as an alternative to aprotinin, also a Kunitz-type serine protease inhibitor, for use as an anti-bleeding agent in surgical procedures. Txln-1 shares only 47% amino-acid identity to aprotinin; however, six cysteine residues in the two peptides are in conserved locations. It is therefore expected that the overall fold of these molecules is similar but that they have contrasting surface features. Here, the crystallization of recombinant textilinin-1 (rTxln-1) as the free molecule and in complex with bovine trypsin (229 amino acids) is reported. Two organic solvents, phenol and 1,4-butanediol, were used as additives to facilitate the crystallization of free rTxln-1. Crystals of the rTxln-1-bovine trypsin complex diffracted to 2.0 angstrom resolution, while crystals of free rTxln-1 diffracted to 1.63 angstrom resolution.

Room temperature ferroelectric and magnetic investigations and detailed phase analysis of Aurivillius phase Bi 5Ti 3Fe 0.7Co 0.3O 15 thin films

Aurivillius phase Bi 5Ti 3Fe 0.7Co 0.3O 15 (BTF7C3O) thin films on α-quartz substrates were fabricated by a chemical solution deposition method and the room temperature ferroelectric and magnetic properties of this candidate multiferroic were compared with those of thin films of Mn 3 substituted, Bi 5Ti 3Fe 0.7Mn 0.3O 15 (BTF7M3O). Vertical and lateral piezoresponse force microscopy (PFM) measurements of the films conclusively demonstrate that BTF7C3O and BTF7M3O thin films are piezoelectric and ferroelectric at room temperature, with the major polarization vector in the lateral plane of the films. No net magnetization was observed for the in-plane superconducting quantum interference device (SQUID) magnetometry measurements of BTF7M3O thin films. In contrast, SQUID measurements of the BTF7C3O films clearly demonstrated ferromagnetic behavior, with a remanent magnetization, B r, of 6.37 emu/cm 3 (or 804 memu/g), remanent moment 4.99 × 10 -5 emu. The BTF7C3O films were scrutinized by x-ray diffraction, high resolution transmission electron microscopy, scanning transmission electron microscopy, and energy dispersive x-ray analysis mapping to assess the prospect of the observed multiferroic properties being intrinsic to the main phase. The results of extensive micro-structural phase analysis demonstrated that the BTF7C3O films comprised of a 3.95 Fe/Co-rich spinel phase, likely CoFe 2 - xTi xO 4, which would account for the observed magnetic moment in the films. Additionally, x-ray magnetic circular dichroism photoemission electron microscopy (XMCD-PEEM) imaging confirmed that the majority of magnetic response arises from the Fe sites of Fe/Co-rich spinel phase inclusions. While the magnetic contribution from the main phase could not be determined by the XMCD-PEEM images, these data however imply that the Bi 5Ti 3Fe 0.7Co 0.3O 15 thin films are likely not single phase multiferroics at room temperature. The PFM results presented demonstrate that the naturally 2D nanostructured Bi 5Ti 3Fe 0.7Co 0.3O 15 phase is a novel ferroelectric and has potential commercial applications in high temperature piezoelectric and ferroelectric memory technologies. The implications for the conclusive demonstration of ferroelectric and ferromagnetic properties in single-phase materials of this type are discussed.

Crystallization, preliminary X-ray analysis and molecular-replacement solution of haemoglobin-II from the fish matrinxa (Brycon cephalus)

Haemoglobins constitute a set of proteins with interesting structural and functional properties, especially when the two large animal groups reptiles and fishes are focused on. Here, the crystallization and preliminary X-ray analysis of haemoglobin-II from the South American fish matrinxa (Brycon cephalus) is reported. X-ray diffraction data have been collected to 3.0 Angstrom resolution using synchrotron radiation (LNLS). Crystals were determined to belong to space group P2(1) and preliminary structural analysis revealed the presence of two tetramers in the asymmetric unit. The structure was determined using the standard molecular-replacement technique.

X-ray analysis of local mid-infrared selected Compton-thick AGN candidates

Cosmic X-ray background synthesis models (Gilli 2007) require a significant fraction of obscured AGN, some of which are expected to be heavily obscured (Compton-thick), but the number density of observationally found obscured sources is still an open issue (Vignali 2010, 2014). This thesis work takes advantage of recent NuSTAR data and is based on a multiwavelength research approach. Gruppioni et al. 2016 compared the AGN bolometric luminosity, for a sample of local 12 micron Seyfert galaxies, derived from the SED decomposition to the same quantity obtained by the 2-10 keV luminosity (IPAC-NED). A difference up to two orders of magnitude resulted between these quantities for some sources. Thus, the intrinsic X-ray luminosity obtained correcting for the obscuration may be underestimated. In this thesis we have tested this hypothesis by re-analysing the X-ray spectra of three of the sources (UGC05101, NGC1194 and NGC3079), for which observations from NuSTAR and Chandra and/or XMM-Newton were available. This is meant to extend our analysis to energies above 10 keV and thus estimate the AGN column density as reliable as possible. For spectral fitting we made use of both the commonly used XSPEC package and the two very recent MYtorus and BNtorus physical models. The available wide bandpass allowed us to achieve new and more solid insights into the X-ray spectral properties of these sources. The measured absorption column densities are highly suggestive of heavy obscuration. Once corrected the X-ray AGN luminosity for the obscuration estimated through our spectral analysis, we compared the L(X) values in the 2-10 keV band with those derived from the MIR band, by means of the relation by Gandhi, 2009. As expected, the values derived from this relation are in good agreement with those we measured, indicating that the column densities were underestimated in the previous literature works.

The encapsulation of gold nanoparticles using RAFT, ATRP and miniemulsion polymerisation techniques

The investigation into the encapsulation of gold nanoparticles (AuNPs) by poly(methyl methacrylate) (PMMA) was undertaken. This was performed by three polymerisation techniques including: grafting PMMA synthesised by reversible addition-fragmentation chain transfer (RAFT) polymerisation to AuNPs, grafting PMMA synthesised by atom transfer radical polymerisation (ATRP) from the surface of functionalised AuNPs and by encapsulation of AuNPs within PMMA latexes produced through photo-initiated oil-in-water (o/w) miniemulsion polymerisation. The grafting of RAFT PMMA to AuNPs was performed by the addition of the RAFT functionalised PMMA to citrate stabilised AuNPs. This was conducted with a range of PMMA of varying molecular weight distribution (MWD) as either the dithioester or thiol end-group functionalities. The RAFT PMMA polymers were characterised by gel permeation chromatography (GPC), ultraviolet-visible (UV-vis), Fourier transform infrared-attenuated total reflectance (FTIR-ATR), Fourier transform Raman (FT-Raman) and proton nuclear magnetic resonance (1H NMR) spectroscopies. The attachment of PMMA to AuNPs showed a tendency for AuNPs to associate with the PMMA structures formed, though significant aggregation occurred. Interestingly, thiol functionalised end-group PMMA showed very little aggregation of AuNPs. The spherical polymer-AuNP structures did not vary in size with variations in PMMA MWD. The PMMA-AuNP structures were characterised using scanning electron microscopy (SEM), transition electron microscopy (TEM), energy dispersive X-ray analysis (EDAX) and UV-vis spectroscopy. The surface confined ATRP grafting of PMMA from initiator functionalised AuNPs was polymerised in both homogeneous and heterogeneous media. 11,11’- dithiobis[1-(2-bromo-2-methylpropionyloxy)undecane] (DSBr) was used as the surface-confined initiator and was synthesised in a three step procedure from mercaptoundecanol (MUD). All compounds were characterised by 1H NMR, FTIR-ATR and Raman spectroscopies. The grafting in homogeneous media resulted in amorphous PMMA with significant AuNP aggregation. Individually grafted AuNPs were difficult to separate and characterise, though SEM, TEM, EDAX and UV-vis spectroscopy was used. The heterogeneous polymerisation did not produce grafted AuNPs as characterised by SEM and EDAX. The encapsulation of AuNPs within PMMA latexes through the process of photoinitiated miniemulsion polymerisation was successfully achieved. Initially, photoinitiated miniemulsion polymerisation was conducted as a viable low temperature method of miniemulsion initiation. This proved successful producing a stable PMMA with good conversion efficiency and narrow particle size distribution (PSD). This is the first report of such a system. The photo-initiated technique was further optimised and AuNPs were included into the miniemulsion. AuNP encapsulation was very effective, producing reproducible AuNP encapsulated PMMA latexes. Again, this is the first reported case of this. The latexes were characterised by TEM, SEM, GPC, gravimetric analysis and dynamic light scattering (DLS).

Vibrational spectroscopy of the silicate mineral plumbotsumite Pb5(OH)10Si4O8 : an assessment of the molecular structure

We have used scanning electron microscopy with energy dispersive X-ray analysis to determine the precise formula of plumbotsumite, a rare lead silicate mineral of formula Pb5(OH)10Si4O8. This study forms the first systematic study of plumbotsumite from the Bigadic deposits, Turkey. Vibrational spectroscopy was used to assess the molecular structure of plumbotsumite as the structure is not known. The mineral is characterized by sharp Raman bands at 1047, 1055 and 1060 cm−1 assigned to SiO stretching vibrational modes and sharp Raman bands at 673, 683 and 697 cm−1 assigned to OSiO bending modes. The observation of multiple bands offers support for a layered structure with variable SiO3 structural units. Little information may be obtained from the infrared spectra because of broad spectral profiles. Intense Raman bands at 3510, 3546 and 3620 cm−1 are ascribed to OH stretching modes. Evidence for the presence of water in the plumbotsumite structure was inferred from the infrared spectra.

A vibrational spectroscopic study of the sulphate mineral glauberite

The mineral glauberite is one of many minerals formed in evaporite deposits. The mineral glauberite has been studied using a combination of scanning electron microscopy with energy dispersive X-ray analysis and infrared and Raman spectroscopy. Qualitative chemical analysis shows a homogeneous phase, composed by sulphur, calcium and sodium. Glauberite is characterized by a very intense Raman band at 1002 cm-1 with Raman bands observed at 1107, 1141, 1156 and 1169 cm-1 attributed to the sulphate ν3 antisymmetric stretching vibration. Raman bands at 619, 636, 645 and 651 cm-1 are assigned to the ν4 sulphate bending modes. Raman bands at 454, 472 and 486 cm-1 are ascribed to the ν2 sulphate bending modes. The observation of multiple bands is attributed to the loss of symmetry of the sulphate anion. Raman spectroscopy is superior to infrared spectroscopy for the determination of glauberite.

A vibrational spectroscopic study of the silicate mineral lomonosovite Na5Ti2(Si2O7)(PO4)O2

The mineral lomonosovite has been studied using a combination of scanning electron microscopy with energy dispersive X-ray analysis and vibrational spectroscopy. Qualitative chemical analysis gave Si, P, Na and Ti as the as major elements with small amounts of Mn, Ca, Fe and Al. The mineral lomonosovite has a formula Na5Ti2(Si2O7)(PO4)O2. Raman bands observed at 909, 925 and 939 cm−1 are associated with phosphate units. Raman bands found at 975, 999, 1070, 1080 and 1084 cm−1 are attributed to siloxane stretching vibrations. The observation of multiple bands in both the phosphate stretching and bending regions supports the concept that the symmetry of the phosphate anion in the structure of lomonosovite is significantly reduced. Infrared spectroscopy identifies bands in the water stretching and bending regions, thus suggesting that water is involved with the structure of lomonosovite either through adsorption on the surface or by bonding to the phosphate units.

Infrared and Raman spectroscopic characterization of the carbonate bearing silicate mineral aerinite – Implications for the molecular structure

The mineral aerinite is an interesting mineral because it contains both silicate and carbonate units which is unusual. It is also a highly colored mineral being bright blue/purple. We have studied aerinite using a combination of techniques which included scanning electron microscopy, energy dispersive X-ray analysis, Raman and infrared spectroscopy. Raman bands at 1049 and 1072 cm−1 are assigned to the carbonate symmetric stretching mode. This observation supports the concept of the non-equivalence of the carbonate units in the structure of aerinite. Multiple infrared bands at 1354, 1390 and 1450 cm−1 supports this concept. Raman bands at 933 and 974 cm−1 are assigned to silicon–oxygen stretching vibrations. Multiple hydroxyl stretching and bending vibrations show that water is in different molecular environments in the aerinite structure.