Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution

Background: Glucosamine 6-phosphate deaminase from Escherichia coli is an allosteric hexameric enzyme which catalyzes the reversible conversion of D-glucosamine 6-phosphate into D-fructose 6-phosphate and ammonium ion and is activated by N-acetyl-D-glucosamine 6-phosphate. Mechanistically, it belongs to the group of aldose-ketose isomerases, but its reaction also accomplishes a simultaneous amination/deamination. The determination of the structure of this protein provides fundamental knowledge for understanding its mode of action and the nature of allosteric conformational changes that regulate its function. Results: The crystal structure of glucosamine 6-phosphate deaminase with bound phosphate ions is presented at 2.1 Å resolution together with the refined structures of the enzyme in complexes with its allosteric activator and with a competitive inhibitor. The protein fold can be described as a modified NAD-binding domain. Conclusions: From the similarities between the three presented structures, it is concluded that these represent the enzymatically active R state conformer. A mechanism for the deaminase reaction is proposed. It comprises steps to open the pyranose ring of the substrate and a sequence of general base-catalyzed reactions to bring about isomerization and deamination, with Asp72 playing a key role as a proton exchanger.

Crystallization of ZrF4-LaF3-AlF3 glasses

0.7125ZrF4-0.2375(1 - xLaF3 • xLnF3)-0.05AIF3 with x = 0.01, 0.02 and 0.03 for Ln = Er and x = 0.03 for Ln = Pr, Nd glasses were studied by differential thermal analysis (DTA), X-ray diffraction and optical spectroscopy. Avrami parameters (Ec and n) were obtained from DTA curves. With La3+ substitution a decrease in the stability against crystallization was observed. This decrease follows the order Er3+ > Nd3+ ≈ Pr3+ for 3% molar substitution. n values suggest an interface controlled growth mechanism with grain edge nucleation abler saturation. Two crystalline polymorphs of the LaZr3F15 phase were identified. With the substitution of 3 mol% of Pr3+, Nd3+ or Er3+ for La3+ only the crystallization of the rhombohedral α-LnZr3F15 phase was observed. An increase in Ω6 Judd's intensity parameter occurs with crystallization and also an increase in the 1.04 μm peak emission cross-section for Nd3+ 4I3/2 state suggesting the potential application of these glass ceramics in optical amplification devices. © 1997 Elsevier Science B.V.

On closed Einstein-de Sitter universes

We briefly summarize the idea of cosmological models with compact, flat spatial sections. It has been suggested that, because of the COBE satellite's maps of the microwave background, such models cannot be small in the sense of Ellis, and hence are no longer interesting. Here we use the method of cosmic crystallography by Lehoucq et al. to show that these models are physically meaningful even if the size of the spatial sections is of the same order of magnitude as the radius of the observational horizon. © 1998 Elsevier Science B.V.

Synthesis, characterization and spectroscopy of the europium doped lanthanum trimetaphosphate

Orthorhombic modification of europium doped lanthanum trimetaphosphate has been prepared. The compound was obtained by precipitation of rare earth chloride solution with trimetaphosphoric acid. The characterizations were made using X-ray diffractometry, chemical analysis and infrared spectroscopy. Excitation and emission spectra were recorded at liquid nitrogen and room temperatures. Assignments of the 5D0→7FJ (J=0, 1, 2, 3, 4, 5) transitions were made and an unusual high 5D0→7F4 transition intensity with six split lines has been observed. Structural distortion of the crystal lattice may be caused by the Eu3+ ion inclusion. The simple overlap model was applied for the calculation of the total splitting of the 5D0→7F1 transition, the 5D0→7F0/5D 0→7F2 transition intensity ratio and the Ωλ (λ=2.4) intensity parameters. Theoretical predictions showed to be in good accordance with the experimental data. © 1988 Elsevier Science S.A.

Study of KCl + x% in and KCl + y% TlCl thin films

The present work reports the study of KCl thin films doped with In+ or Tl+. Both systems show optical absorption bands similar to single crystals. As the impurity concentration increases, so does the absorption as also the half band width, unlike in KCl: Cu+ films. Further experimental techniques such as X-ray diffraction, scanning electron micrographs and energy dispersive X-ray observations were used and comparative analysis with KCl : Cu+ films reveals new conditions for better crystallinity of the samples.

Structural and surface morphology characterizations of oriented LiNbO3 thin films grown by polymeric precursor method

Polymeric precursor solution was used to deposit LiNbO3 thin films by dip coating on sapphire substrates. The effects of processing variables, such as heat treatment conditions and number of deposited layers, on crystallinity and morphology of the final films were investigated. X-ray diffraction patterns show the oriented growth of the films. The rocking curves, obtained around the (006) LiNbO3 peak, revealed that the shape peak and the FWHM value were influenced by the processing variables. According to these parameters, some films presented very homogeneous dense and smooth surfaces, as shown by the SEM and AFM studies.

Direct amorphous-to-cubic perovskite phase transformation for lead titanate

The phase evolution of lead titanate processed by the polymeric precursor method was investigated by thermal analysis, X-ray diffraction, and high-resolution transmission electron microscopy. The results showed that the cubic perovskite PbTiO3 (PT) phase is formed from an inorganic amorphous precursor at a temperature of 444 °C. A gradual transition from cubic to tetragonal perovskite PT was observed with the increase of calcination time at this temperature. HRTEM results showed that the cubic PT particles have a size of around 5 nm. The identification of cubic PT as an intermediate phase supports the hypothesis that the chemical homogeneity was kept at the molecular level during the synthesis process, with no cation segregation.

Structure of tick anticoagulant peptide at 1.6 Å resolution complexed with bovine pancreatic trypsin inhibitor

The structure of tick anticoagulant peptide (TAP) has been determined by X-ray crystallography at t.6 Å resolution complexed with bovine pancreatic trypsin inhibitor (BPTI). The TAP-BPTI crystals are tetragonal, a = b = 46.87, c = 50.35 Å, space group P41, four complexes per unit cell. The TAP molecules are highly dipolar and form an intermolecular helical array along the c-axis with a diameter of about 45 Å. Individual TAP units interact in a head-to-tail fashion, the positive end of one molecule associating with the distal negative end of another, and vice versa. The BPTI molecules have a uniformly distributed positively charged surface that interacts extensively through 14 hydrogen bonds and two hydrogen bonded salt bridges with the helical groove around the helical TAP chains. Comparing the structure of TAP in TAP-BPTI with TAP bound to factor Xa(Xa) suggests a massive reorganization in the N-terminal tetrapeptide and the first disulfide loop of TAP (CyS5(T)- Cys 15(T)) upon binding to Xa. The Tyr1(T)OH atom of TAP moves 14.2 Å to interact with Asp189 of the S1 specificity site, Arg3(T)CZ moves 5.0 Å with the guanidinium group forming a cation-π-electron complex in the S4 subsite of Xa, while Lys7(T)NZ differs in position by 10.6 Å in TAP-BPTI and TAP-Xa, all of which indicates a different pre-Xa-bound conformation for the N- terminal of TAP in its native state. In contrast to TAP, the BPTI structure of TAP-BPTI is practically the same as all those of previously determined structures of BPTI, only arginine and lysine side-chain conformations showing significant differences.

Structure of thrombin complexed with selective non-electrophilic inhibitors having cyclohexyl moieties at P1

The crystal structures of five new non-electrophilic β-strand-templated thrombin active-site inhibitors have been determined bound to the enzyme. Four co-crystallize with hirugen and inhibitor isomorphously to produce thrombin-hirugen crystals (monoclinic, space group C2), while one co-crystallizes in the hexagonal system, space group P65. A 1,4-substituted cyclohexyl moiety is conserved at the P1 position of all the inhibitors, along with a fused hetero-bicyclic five- and six-membered ring that occupies the P2 site. Amino, amidino and aminoimidazole groups are attached to the cyclohexyl ring for recognition at the S1 specificity site, while benzylsulfonyl and diphenyl groups enhance the binding at the S3 subsite. The cyclohexyl groups at the P1 positions of three of the inhibitors appear to be in the energetically favored chair conformation, while the imidazole-substituted cyclohexyl rings are in a boat conformation. Somewhat unexpectedly, the two cyclohexyl-aminoimidazole groups bind differently in the specificity site; the unique binding of one is heretofore unreported. The other inhibitors generally mimic arginyl binding at S1. This group of inhibitors combines the nonelectrophilicity and selectivity of DAPA-like compounds and the more optimal binding features of the S1-S3 sites of thrombin for peptidic molecules, which results in highly potent (binding constants 12 nM-16 pM, one being 1.1 μM) and selective (ranging from 140 to 20 000 times more selective compared with trypsin) inhibitors of thrombin. The binding modes of these novel inhibitors are correlated with their binding constants, as is their selectivity, in order to provide further insight for the design of therapeutic antithrombotic agents that inhibit thrombin directly at the active site.

Biophysical Characterization of Interactions Involving Importin-α during Nuclear Import

Proteins containing the classical nuclear localization sequences (NLSs) are imported into the nucleus by the importin-α/β heterodimer. Importin-α contains the NLS binding site, whereas importin-β mediates the translocation through the nuclear pore. We characterized the interactions involving importin-α during nuclear import using a combination of biophysical techniques (biosensor, crystallography, sedimentation equilibrium, electrophoresis, and circular dichroism). Importin-α is shown to exist in a monomeric autoinhibited state (association with NLSs undetectable by biosensor). Association with importin-β (stoichiometry, 1:1; K D = 1.1 × 10 -8 M) increases the affinity for NLSs; the importin-α/β complex binds representative monopartite NLS (simian virus 40 large T-antigen) and bipartite NLS (nucleoplasmin) with affinities (K D = 3.5 × 10 -8 M and 4.8 × 10 -8 M, respectively) comparable with those of a truncated importin-α lacking the autoinhibitory domain (T-antigen NLS, K D = 1.7 × 10 -8 M; nucleoplasmin NLS, K D = 1.4 × 10 -8 M). The autoinhibitory domain (as a separate peptide) binds the truncated importin-α, and the crystal structure of the complex resembles the structure of full-length importin-α. Our results support the model of regulation of nuclear import mediated by the intrasteric autoregulatory sequence of importin-α and provide a quantitative description of the binding and regulatory steps during nuclear import.

Crystallographic, dielectric and optical properties of SrBi 2Ta2O9 thin films prepared by the polymeric precursor method

Strontium bismuth tantalate thin films were prepared on several substrates (platinized silicon (Pt/Ti/SiO 2 /Si), n -type (100)-oriented and p -type (111)-oriented silicon wafers, and fused silica) by the solution deposition method. The resin was obtained by the polymeric precursor method, based on the Pechini process, using strontium carbonate, bismuth oxide, and tantalum ethoxide as starting reagents. Characterizations by XRD and SEM were performed for structural and microstructural evaluations. The electrical measurements, carried on the MFM configuration, showed P r values of 6.24 μC/cm 2 and 31.5 kV/cm for the film annealed at 800 C. The film deposited onto fused silica and treated at 700 C presented around 80% of transmittance. © 2002 Taylor & Francis.

Crystallographic and spectroscopic studies on palladium(II) complexes containing pyrazole and thiocyanate ligands

Mononuclear palladium(II) complexes containing both pyrazole-type ligands and thiocyanate, of general formula [Pd(SCN) 2(L) 2] {L = pyrazole (HPz) and l-phenyl-3-methylpyrazole (phmPz)} have been prepared and characterized by elemental analysis, i.r. and n.m.r. spectroscopy and by single crystal X-ray diffraction methods. The Pd atom in these structures lies on the crystallographic inversion center; in a square-planar coordination geometry made by two sulfur and two nitrogen atoms of the ligands, both in trans positions.

Spectroscopic characteristics of Er3+ in the two crystallographic sites of Gd2SiO5

Gd2SiO5 is among the interesting and suitable hosts for Er3+ which find extensive applications in the infrared, visible and ultraviolet spectral regions. In order to investigate its potentialities, a prior study of the spectroscopic behaviour of Er3+ substituting for Gd3+ ions in the two crystallographic sites of the host was performed. Absorption, excitation, site-selective emission and time-resolved spectroscopies were employed in the visible spectral region to study transitions between excited 4S3/2 and ground 4I15/2 states. These levels multiplets were attributed to each site separately, and their corresponding 4S3/2 lifetimes (1.8 ± 0.1 μs for site 1 and 3.2 ± 0.1 μs for site 2) were determined.