Theoretical study of the mechanisms of substrate recognition by catalase

A variety of theoretical methods including classical molecular interaction potentials, classical molecular dynamics, and activated molecular dynamics have been used to analyze the substrate recognition mechanisms of peroxisomal catalase from Saccharomyces cerevisiae. Special attention is paid to the existence of channels connecting the heme group with the exterior of the protein. On the basis of these calculations a rationale is given for the unique catalytic properties of this enzyme, as well as for the change in enzyme efficiency related to key mutations. According to our calculations the water is expected to be a competitive inhibitor of the enzyme, blocking the access of hydrogen peroxide to the active site. The main channel is the preferred route for substrate access to the enzyme and shows a cooperative binding to hydrogen peroxide. However, the overall affinity of the main channel for H(2)O(2) is only slightly larger than that for H(2)O. Alternative channels connecting the heme group with the monomer interface and the NADP(H) binding site are detected. These secondary channels might be important for product release.     

Investigation of magnetic phase transformations in a system of Nd1−x BaxMnO3−δ (0≤x≤0.50) depending on the conditions of preparation

Investigations are performed of the crystal structure and magnetic and electromagnetic properties of single crystals (0.23 ≤x≤0.34) and polycrystals (0 ≤x ≤0.50) of an Nd_1?x Ba_xMnO_3?δ system of solid solutions. It is found that, for samples prepared in the air, the maximal Curie temperature (T _C ) does not exceed 150 K, while, in the case of polycrystalline samples in the concentration range of 0.34 ≤x ≤0.50, prepared in a reducing medium (a gaseous mixture of argon and carbon monoxide), T _C increases to 320 K. As a result of the reducing medium effect on the compositions, the type of the magnetic phase transition to the paramagnetic state changes from the first to second order. The electrical resistivity of reduced polycrystalline samples (0.34≤x ≤0.50) decreases in magnitude and correlates with the behavior of magnetization. Both series of samples, prepared both in the air and in a reducing medium, exhibit a transition from the metal to dielectric state at a temperature below T _C . The temperature and field dependences of magnetization for the stoichiometric polycrystalline com-position of Nd_0.50Ba_0.50MnO₃ are measured under conditions of hydrostatic pressure. It is demonstrated that the hydrostatic pressure induces in Nd_0.50Ba_0.50MnO₃ the transition from the antiferromagnetic to ferromagnetic state. Based on the measurement results, hypothetical magnetic phase diagrams are constructed for the system of solid solutions being treated, depending on the concentration of barium and the method of preparation. It is found that no T _TC increase is observed in single crystals (0.23≤x≤0.34) such as is observed in polycrystals. It is assumed that the abrupt increase in T _C of polycrystalline samples prepared in a reducing medium is a result of the emergence of extended defects and microstresses in the crystal lattice.     

Photophysical properties and photocytotoxicity of novel phthalocyanines - potentially useful for their application in photodynamic therapy

Two novel zinc(II) phthalocyanines bearing non-peripheral ester-alkyloxy substituents (Pc-4 and Pc-5) were synthesized, by a two-step procedure starting from 2,3-dicyanohydroquinone. Both sensitizers show promising photophysical properties, including solvatochromic study, qualitative evaluation of emission, aggregation behavior and singlet oxygen generation. It was proven that the photodynamic activity of the compounds studied depends on the molecular oxygen level. Comparison of the quantum yields of singlet oxygen generation as well as the oxidation rate constants using 1,3-diphenylisobenzofurane before and after deaeration proved the photodynamic effect of Pc-4 and Pc-5 to be governed by the photosensitization mechanism II. Changes in the quantities of the compounds exposed to irradiation were also estimated. Upon their exposure to light the changes in intensity of the Q band were monitored. The photodecomposition of Pc-4 and Pc-5 in DMSO or DMF solutions was found to proceed according to the first order kinetic reaction in two stages.The photosensitizing effect of Pc-4 in HSC-3 cells was significantly lower than that of ZnPc. Pc-4 was ineffective at 0.1 μM, while a low, approx. 15% photocytotoxicity was observed at 5 μM, at a distance of 5 and 10 cm. The efficacy of Pc-4 in photokilling of cultured cells is affected by hydrophobicity and the aggregation status of the photosensitizer.     

Magnetic field effect on the susceptibility of a Heisenberg ferromagnet CuK2Cl4.2H2O near the critical point

The results on the investigation of the susceptibility for the Heisenberg ferromagnet CuK₂Cl₄.2H₂O in the magnetic field are reported. The susceptibility divergence at the critical temperature in the magnetic field is shown to transform into susceptibility anomalies of two types, their shifts being approximated by the power functions with indices ω = 2.6 and ? = 0.58. The experimental data support the assumption about the complex critical temperature. The regions for the existence of phases with uniform and non-uniform magnetizations are determined.     

Pressure-induced suppression of ferromagnetic phase in LaCoO3 nanoparticles

Magnetic and structural properties of nanocrystalline LaCoO₃ with particle size ranging from 25 to 38 nm, prepared by the citrate method, were investigated. All nanoparticles exhibit ferromagnetism below T_C ≈ 85 K. It was found that the unit-cell volume increases monotonically with decreasing particle size and ferromagnetic (FM) moment increases simultaneously with lattice expansion, whereas T_C remains nearly unchanged. It appears that both magnetic and structural properties of LaCoO₃ nanoparticles are size-dependent due to the surface effect. On the other hand, an applied pressure suppresses strongly the FM phase leading to its disappearance at ～11 kbar. Remarkably, the T_C does not change visibly under pressure. Our data reveal that the ferromagnetism in LaCoO₃ nanoparticles, likely related to the intermediate-spin (IS) Co³⁺ state, is simply controlled by the unit-cell volume. Within this scenario, the FM coupled IS states appear/disappear with expanding/compressing the lattice and/or Co–O bonds.     

The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations

The structures of Helicobacter pylori (HPC) and Penicillium vitale (PVC) catalases, each with two subunits in the crystal asymmetric unit, oxidized with peroxoacetic acid are reported at 1.8 and 1.7 A resolution, respectively. Despite the similar oxidation conditions employed, the iron-oxygen coordination length is 1.72 A for PVC, close to what is expected for a Fe=O double bond, and 1.80 and 1.85 A for HPC, suggestive of a Fe-O single bond. The structure and electronic configuration of the oxoferryl heme and immediate protein environment is investigated further by QM/MM density functional theory calculations. Four different active site electronic configurations are considered, Por*+-FeIV=O, Por*+-FeIV=O...HisH+, Por*+-FeIV-OH+ and Por-FeIV-OH (a protein radical is assumed in the latter configuration). The electronic structure of the primary oxidized species, Por*+-FeIV=O, differs qualitatively between HPC and PVC with an A2u-like porphyrin radical delocalized on the porphyrin in HPC and a mixed A1u-like "fluctuating" radical partially delocalized over the essential distal histidine, the porphyrin, and, to a lesser extent, the proximal tyrosine residue. This difference is rationalized in terms of HPC containing heme b and PVC containing heme d. It is concluded that compound I of PVC contains an oxoferryl Por*+-FeIV=O species with partial protonation of the distal histidine and compound I of HPC contains a hydroxoferryl Por-FeIV-OH with the second oxidation equivalent delocalized as a protein radical. The findings support the idea that there is a relation between radical migration to the protein and protonation of the oxoferryl bond in catalase.     

X-ray characterization of precipitates in cerium-doped PbTe and SnTe crystals

The homogeneity, solid solubility, and chemical bonds in the new materials PbTe, SnTe doped with Ce were investigated. Scanning electron microscope observation and electron probe microanalysis carried out on PbTe crystals doped with Ce, revealed three types of Ce-rich precipitates with following compositions: CeTe₂, Ce₃Te₇, Ce₂Te₅ and small admixture of PbTe in precipitates. The solubility of Ce in PbTe matrix was estimated as 0.5±0.1 at. %. The solubility of PbTe in CeTe₂ and Ce₃Te₇ was found to be 3±0.5 at. %, but 7±0.5 at. % in the case of Ce₂Te₅. In SnTe crystal doped with Ce only one kind of precipitate with composition Ce₂SnTe₅ was found. Cerium solubility in SnTe matrix was estimated to be 1±0.25 at. %. According to our knowledge this is the first report of the identification of Ce₂SnTe₅ compound. The similar compounds Ce₂SnS₅ and Ce₂SnSe₅ are known. Received: 9 December 1998 / Accepted: 9 February 1999 / Published online: 28 April 1999     

Chemistry, photophysics, and ultrafast kinetics of two structurally related Schiff bases containing the naphthalene or quinoline ring

The two structurally related Schiff bases, 2-hydroxynaphthylidene-(8-aminoquinoline) (HNAQ) and 2-hydroxynaphthylidene-1(')-naphthylamine (HNAN), were studied by means of steady-state and time resolved optical spectroscopies as well as time-dependent density functional theory (TDDFT) calculations. The first one, HNAQ, is stable as a keto tautomer in the ground state and in the excited state in solutions, therefore it was used as a model of a keto tautomer of HNAN which exists mainly in its enol form in the ground state at room temperature. Excited state intramolecular proton transfer in the HNAN molecule leads to a very weak (quantum yield of the order of 10(-4)) strongly Stokes-shifted fluorescence. The characteristic time of the proton transfer (about 30 fs) was estimated from femtosecond transient absorption data supported by global analysis and deconvolution techniques. Approximately 35% of excited molecules create a photochromic form whose lifetime was beyond the time window of the experiment (2 ns). The remaining ones reach the relaxed S(1) state (of a lifetime of approximately 4 ps), whose emission is present in the decay associated difference spectra. Some evidence for the back proton transfer from the ground state of the keto form with the characteristic time of approximately 13 ps was also found. The energies and orbital characteristics of main electronic transitions in both molecules calculated by TDDFT method are also discussed.     

Pressure-induced superconductivity in tetragonal NdBa2Cu3O6+x

The appearance of superconductivity and relaxation of the transition temperature to its equilibrium value T _c≈30 K over the course of five days have been observed in a tetragonal sample of NdBa₂Cu₃O_6.67 under 1 GPa pressure. The time dependence T _c(t) correlates with a decrease of the room-temperature electrical resistance R(t). The superconducting phase disappears 1.3 h after the pressure is removed. This behavior is explained by a redistribution of charge as a result of pressure-induced oxygen reordering in the CuO_x planes. A large effect of oxygen ordering on the transition temperature under pressure has been observed near the metal-insulator transition (the largest of all those measured in the 1-2-3 system), along with a nonlinear temperature dependence of T _c. Fiz. Tverd. Tela (St. Petersburg) 39, 1328–1334 (August 1997)