X-ray crystallographic and NMR studies of pantothenate synthetase provide insights into the mechanism of homotropic inhibition by pantoate

The structural basis for the homotropic inhibition of pantothenate synthetase by the substrate pantoate was investigated by X-ray crystallography and high-resolution NMR spectroscopic methods. The tertiary structure of the dimeric N-terminal domain of Escherichia coli pantothenate synthetase, determined by X-ray crystallography to a resolution of 1.7 Å, showed a second molecule of pantoate bound in the ATP-binding pocket. Pantoate binding to the ATP-binding site induced large changes in structure, mainly for backbone and side chain atoms of residues in the ATP binding HXGH(34–37) motif. Sequence-specific NMR resonance assignments and solution secondary structure of the dimeric N-terminal domain, obtained using samples enriched in 2H, 13C, and 15N, indicated that the secondary structural elements were conserved in solution. Nitrogen-15 edited two-dimensional solution NMR chemical shift mapping experiments revealed that pantoate, at 10 mm, bound at these two independent sites. The solution NMR studies unambiguously demonstrated that ATP stoichiometrically displaced pantoate from the ATP-binding site. All NMR and X-ray studies were conducted at substrate concentrations used for enzymatic characterization of pantothenate synthetase from different sources [Jonczyk R & Genschel U (2006) J Biol Chem 281, 37435–37446]. As pantoate binding to its canonical site is structurally conserved, these results demonstrate that the observed homotropic effects of pantoate on pantothenate biosynthesis are caused by competitive binding of this substrate to the ATP-binding site. The results presented here have implications for the design and development of potential antibacterial and herbicidal agents.

The 310 helical conformation of a pentapeptide containing a-aminoisobutyric acid (Aib): X-ray crystal structure of Tos-(Aib)5 OMe

The pentapeptide Tos-(Aib)5-OMe adopts a 310 helical conformation in the solid state, with three consecutive Type III B-turns stabilized by intramolecular hydrogen bonds.

X-Pro peptides: Synthesis and solution conformation of benzyloxycarbonyl-(Aib-Pro)4methyl ester. Evidence for a novel helical structure

The synthesis of the octapeptide, benzyloxycarbonyl-(-aminoisobutyryl-L-prolyl)4-methyl ester [Z-(Aib-Pro)4-OMe] and an analysis of its solution conformation is reported. The octapeptide is shown to possess three strong intramolecular hydrogen bonds on the basis of studies of the solvent and temperature dependence of NH chemical shifts and rates of hydrogen-deuterium exchange. 13C studies are consistent with a structure involving only trans Aib-Pro bonds, while ir experiments support a hydrogen-bonded conformation. The Aib 3, 5, and 7 NH groups are shown to participate in hydrogen bonding. A 310 helical conformation compatible with the spectroscopic data is suggested. The proposed conformation consists of three type III -turns with Aib and Pro at the corners and stabilized by 4 1 intramolecular hydrogen bonds.

Type II beta-turn conformation of pivaloyl-L-prolyl-a-aminoiso-butyryl-N-methylamide: Theoretical, spectroscopic and X-ray studies

Pivaloyl-L-Pro-Aib-N-methylamihdaes been shown to possess one intramolecular hydrogen bond in (CD&SO solution, by 'H-nmr methods, suggesting the existence of p-turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II P-turn conformations are about 2 kcal mol-' more stable than Type 111 structures. A crystallographic study has established the Type I1 /%turn in the solid state. The molecule crystallizes in the space group P21 with a = 5.865 8, b = 11.421 A, c = 12.966 A, /3 = 97.55", and 2 = 2. The structure has been refined to a final R value of 0.061. The Type I1 p-turn conformation is stabilized by an intramolecular 4 - 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are @pro= -57.8", $pro = 139.3', @Aib = 61.4', and $Ajb = 25.1'. The Type 11 /%turn conformation for Pro-Aib in this peptide is compared with the Type I11 structures observed for the same segment in larger peptides.

Phases in the (1-x)Na0.5Bi0.5TiO3-(x)CaTiO3 system

The structures of (1 - x) Na0.5Bi0.5TiO3-(x) CaTiO3 at room temperature have been investigated using neutron powder diffraction and dielectric studies. The system exhibits an orthorhombic (Pbnm) structure for x >= 0.15 and rhombohedral (R3c) for x <= 0.05. For x = 0.10, though the neutron diffraction pattern shows features of the orthorhombic (Pbnm) structure, Rietveld refinement using this structure shows a drastic reduction in the in-phase tilt angle (similar to 4 degrees) as compared to the corresponding value (similar to 8 degrees) for a neighbouring composition x = 0.15. The neutron diffraction pattern of x = 0.10 could be fitted equally well using a two-phase model (R3c + Pbnm) with orthorhombic as the minor phase (22%), without the need for a drastic decrease in the in-phase tilt angle. The dielectric studies of x = 0.10 revealed the presence of the polar R3c phase, thereby favouring the phase coexistence model, instead of a single-phase Pbnm structure, for this composition.

Expression, purification and X-ray analysis of 1,3-propanediol dehydrogenase (Aq_1145) from Aquifex aeolicus VF5

1,3-Propanediol dehydrogenase is an enzyme that catalyzes the oxidation of 1,3-propanediol to 3-hydroxypropanal with the simultaneous reduction of NADP(+) to NADPH. SeMet-labelled 1,3-propanediol dehydrogenase protein from the hyperthermophilic bacterium Aquifex aeolicus VF5 was overexpressed in Escherichia coli and purified to homogeneity. Crystals of this protein were grown from an acidic buffer with ammonium sulfate as the precipitant. Single-wavelength data were collected at the selenium peak to a resolution of 2.4 angstrom. The crystal belonged to space group P3(2), with unit-cell parameters a = b = 142.19, c = 123.34 angstrom. The structure contained two dimers in the asymmetric unit and was solved by the MR-SAD approach.

A 100MHz to 1GHz, 0.35V to 1.5V supply 256 x 64 SRAM mock using symmetrized 9T SRAM cell with controlled read

In this paper, we present Dynamic Voltage and Frequency Managed 256 x 64 SRAM block in 65nm technology, for frequency ranging from 100MHz to 1GHz. The total energy is minimized for any operating frequency in the above range and leakage energy is minimized during standby mode. Since noise margin of SRAM cell deteriorates at low voltages, we propose Static Noise Margin improvement circuitry, which symmetrizes the SRAM cell by controlling the body bias of pull down NMOS transistor. We used a 9T SRAM cell that isolates Read and Hold Noise Margin and has less leakage. We have implemented an efficient technique of pushing address decoder into zigzag-super-cut-off in stand-by mode without affecting its performance in active mode of operation. The Read Bit Line (RBL) voltage drop is controlled and pre-charge of bit lines is done only when needed for reducing power wastage.

Apparent shortening of the Csp(3)-Csp(3) bond analysed via a variable-temperature X-ray diffraction study in racemic 1,1 '-binaphthalene-2,2 '-diyl diethyl bis(carbonate)

Crystal structure determination at room temperature [292 (2) K] of racemic 1,1'-binaphthalene-2,2'-diyl diethyl bis(carbonate), C26H22O6, showed that one of the terminal carbon-carbon bond lengths is very short [Csp(3)-Csp(3) = 1.327 (6) angstrom]. The reason for such a short bond length has been analysed by collecting data sets on the same crystal at 393, 150 and 90 K. The values of the corrected bond lengths clearly suggest that the shortening is mainly due to positional disorder at two sites, with minor perturbations arising as a result of thermal vibrations. The positional disorder has been resolved in the analysis of the 90 K data following the changes in the unit-cell parameters for the data sets at 150 and 90 K, which appear to be an artifact of a near centre of symmetry relationship between the two independent molecules in the space group P (1) over bar at these temperatures. Indeed, the unit cell at low temperature (150 and 90 K) is a supercell of the room-temperature unit cell.

Predicting single-layer technetium dichalcogenides (TcX2, X = S, Se) with promising applications in photovoltaics and photocatalysis

One of the least known compounds among transition metal dichalcogenides (TMDCs) is the layered triclinic technetium dichalcogenides (TcX2, X = S, Se). In this work, we systematically study the structural, mechanical, electronic, and optical properties of TcS2 and TcSe2 monolayers based on density functional theory (DFT). We find that TcS2 and TcSe2 can be easily exfoliated in a monolayer form because their formation and cleavage energy are analogous to those of other experimentally realized TMDCs monolayer. By using a hybrid DFT functional, the TcS2 and TcSe2 monolayers are calculated to be indirect semiconductors with band gaps of 1.91 and 1.69 eV, respectively. However, bilayer TcS2 exhibits direct-bandgap character, and both TcS2 and TcSe2 monolayers can be tuned from semiconductor to metal under effective tensile/compressive strains. Calculations of visible light absorption indicate that 2D TcS2 and TcSe2 generally possess better capability of harvesting sunlight compared to single-layer MoS2 and ReSe2, implying their potential as excellent light-absorbers. Most interestingly, we have discovered that the TcSe2 monolayer is an excellent photocatalyst for splitting water into hydrogen due to the perfect fit of band edge positions with respect to the water reduction and oxidation potentials. Our predictions expand the two-dimensional (2D) family of TMDCs, and the remarkable electronic/optical properties of monolayer TcS2 and TcSe2 will place them among the most promising 2D TMDCs for renewable energy application in the future.

High-level expression of biologically active glycoprotein hormones in Pichia pastoris strains—selection of strain GS115, and not X-33, for the production of biologically active N-glycosylated 15N-labeled phCG

The methylotrophic yeast Pichia pastoris is widely used for the production of recombinant glycoproteins. With the aim to generate biologically active 15N-labeled glycohormones for conformational studies focused on the unravelling of the NMR structures in solution, the P. pastoris strains GS115 and X-33 were explored for the expression of human chorionic gonadotropin (phCG) and human follicle-stimulating hormone (phFSH). In agreement with recent investigations on the N-glycosylation of phCG, produced in P. pastoris GS115, using ammonia/glycerol-methanol as nitrogen/carbon sources, the N-glycosylation pattern of phCG, synthesized using NH4Cl/glucose–glycerol–methanol, comprised neutral and charged, phosphorylated high-mannose-type N-glycans (Man8–15GlcNAc2). However, the changed culturing protocol led to much higher amounts of glycoprotein material, which is of importance for an economical realistic approach of the aimed NMR research. In the context of these studies, attention was also paid to the site specific N-glycosylation in phCG produced in P. pastoris GS115. In contrast to the rather simple N-glycosylation pattern of phCG expressed in the GS115 strain, phCG and phFSH expressed in the X-33 strain revealed, besides neutral high-mannose-type N-glycans, also high concentrations of neutral hypermannose-type N-glycans (Manup-to-30GlcNAc2). The latter finding made the X-33 strain not very suitable for generating 15N-labeled material. Therefore, 15N-phCG was expressed in the GS115 strain using the new optimized protocol. The 15N-enrichment was evaluated by 15N-HSQC NMR spectroscopy and GLC-EI/MS. Circular dichroism studies indicated that 15N-phCG/GS115 had the same folding as urinary hCG. Furthermore, 15N-phCG/GS115 was found to be similar to the unlabeled protein in every respect as judged by radioimmunoassay, radioreceptor assays, and in vitro bioassays.

Manifestation of geometric frustration on magnetic and thermodynamic properties of the pyrochlores Sm2X2O7 (X=Ti,Zr)

We present here magnetization, specific heat, and Raman studies on single-crystalline specimens of the first pyrochlore member Sm2Ti2O7 of the rare-earth titanate series. Its analogous compound Sm2Zr2O7 in the rare-earth zirconate series is also investigated in the polycrystalline form. The Sm spins in Sm2Ti2O7 remain unordered down to at least T=0.5 K. The absence of magnetic ordering is attributed to very small values of exchange (θcw∼−0.26 K) and dipolar interaction (μeff∼0.15 μB) between the Sm3+ spins in this pyrochlore. In contrast, the pyrochlore Sm2Zr2O7 is characterized by a relatively large value of Sm-Sm spin exchange (θcw∼−10 K); however, long-range ordering of the Sm3+ spins is not established at least down to T=0.67 K due to frustration of the Sm3+ spins on the pyrochlore lattice. The ground state of Sm3+ ions in both pyrochlores is a well-isolated Kramers doublet. The higher-lying crystal field excitations are observed in the low-frequency region of the Raman spectra of the two compounds recorded at T=10 K. At higher temperatures, the magnetic susceptibility of Sm2Ti2O7 shows a broad maximum at T=140 K, while that of Sm2Zr2O7 changes monotonically. Whereas Sm2Ti2O7 is a promising candidate for investigating spin fluctuations on a frustrated lattice, as indicated by our data, the properties of Sm2Zr2O7 seem to conform to a conventional scenario where geometrical frustration of the spin excludes their long-range ordering.

X-ray scattering and diffraction enhanced imaging studies of in vitro breast tissues

This thesis is a study of the x-ray scattering properties of tissues and tumours of the breast. Clinical radiography is based on the absorption of the x-rays when passing right through the human body and gives information about the densities of the tissues. Besides being absorbed, x-rays may change their direction within the tissues due to elastic scattering or even to refraction. The phenomenon of scattering is a nuisance to radiography in general, and to mammography in particular, because it reduces the quality of the images. However, scattered x-rays bear very useful information about the structure of the tissues at the supra-molecular level. Some pathologies, like breast cancer, produce alterations to the structures of the tissues, being especially evident in collagen-rich tissues. On the other hand, the change of direction due to refraction of the x-rays on the tissue boundaries can be mapped. The diffraction enhanced imaging (DEI) technique uses a perfect crystal to convert the angular deviations of the x-rays into intensity variations, which can be recorded as images. This technique is of especial interest in the cases were the densities of the tissues are very similar (like in mammography) and the absorption images do not offer enough contrast. This thesis explores the structural differences existing in healthy and pathological collagen in breast tissue samples by the small-angle x-ray scattering (SAXS) technique and compares these differences with the morphological information found in the DEI images and the histo-pathology of the same samples. Several breast tissue samples were studied by SAXS technique in the European Synchrotron Radiation Facility (ESRF) in Grenoble, France. Scattering patterns of the different tissues of the breast were acquired and compared with the histology of the samples. The scattering signals from adipose tissue (fat), connective tissue (collagen) and necrotic tissue were identified. Moreover, a clear distinction could be done between the scattering signals from healthy collagen and from collagen from an invasive tumour. Scattering from collagen is very characteristic. It includes several scattering peaks and scattering features that carry information about the size and the spacing of the collagen fibrils in the tissues. It was found that the collagen fibrils in invaded tumours were thinner and had a d-spacing length 0,7% longer that fibrils from healthy tumours. The scattering signals from the breast tissues were compared with the histology by building colour-coded maps across the samples. They were also imaged with the DEI technique. There was a total agreement between the scattering maps, the morphological features seen in the images and the information of the histo- pathological examination. The thesis demonstrates that the x-ray scattering signal can be used to characterize tissues and that it carries important information about the pathological state of the breast tissues, thus showing the potential of the SAXS technique as a possible diagnostic tool for breast cancer.