Three-dimensional structure of ribonuclease T-1 complexed with an isosteric phosphonate substrate analogue of GpU: Alternate substrate binding modes and catalysis

The X-ray crystal structure of a complex between ribonuclease T-1 and guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2.0 Angstrom resolution. This Ligand is an isosteric analogue of the minimal RNA substrate, guanylyl(3'-5')uridine (GpU), where a methylene is substituted for the uridine 5'-oxygen atom. Two protein molecules are part of the asymmetric unit and both have a GpcU bound at the active site in the same manner. The protein-protein interface reveals an extended aromatic stack involving both guanines and three enzyme phenolic groups. A third GpcU has its guanine moiety stacked on His92 at the active site on enzyme molecule A and interacts with GpcU on molecule B in a neighboring unit via hydrogen bonding between uridine ribose 2'- and 3'-OH groups. None of the uridine moieties of the three GpcU molecules in the asymmetric unit interacts directly with the protein. GpcU-active-site interactions involve extensive hydrogen bonding of the guanine moiety at the primary recognition site and of the guanosine 2'-hydroxyl group with His40 and Glu58. on the other hand, the phosphonate group is weakly bound only by a single hydrogen bond with Tyr38, unlike ligand phosphate groups of other substrate analogues and 3'-GMP, which hydrogen-bonded with three additional active-site residues. Hydrogen bonding of the guanylyl 2'-OH group and the phosphonate moiety is essentially the same as that recently observed for a novel structure of a RNase T-1-3'-GMP complex obtained immediately after in situ hydrolysis of exo-(S-p)-guanosine 2',3'-cyclophosphorothioate [Zegers et al. (1998) Nature Struct. Biol. 5, 280-283]. It is likely that GpcU at the active site represents a nonproductive binding mode for GpU [:Steyaert, J., and Engleborghs (1995) fur. J. Biochem. 233, 140-144]. The results suggest that the active site of ribonuclease T-1 is adapted for optimal tight binding of both the guanylyl 2'-OH and phosphate groups (of GpU) only in the transition state for catalytic transesterification, which is stabilized by adjacent binding of the leaving nucleoside (U) group.

Using a one-dimensional lattice applied to the thermodynamic study of DNA

In this work it is analyzed a one-dimensional lattice which is composed by mass-spring systems with one additional Rosen-Morse potential on site. This kind of lattice is used to study thermodynamic properties of DNA, especially its thermal denaturation. on the context of this work, the Rosen-Morse potential simulates hydrogen bonds between double strands of the molecule. From the graphic of the average stretching of base pairs versus temperature it is possible to observe the thermal denaturation of the system. This result shows that it is possible to obtain phase transition with an asymmetric potential without an infinite barrier.

Statistics and kinetics of single-molecule electron transfer dynamics in complex environments: A simulation model study

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Effect of antioxidant agents on bond strength of composite to bleached enamel with 38% hydrogen peroxide

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Influence of chemical activation of a 35% hydrogen peroxide bleaching gel on its penetration and efficacy-In vitro study

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Low-energy muon-transfer reaction from hydrogen isotopes to helium isotopes

Direct muon transfer in low-energy collisions of the muonic hydrogen H-mu and helium (He++) is considered in a three-body quantum-mechanical framework of coordinate-space integro-differential Faddeev-Hahn-type equations within two- and six-state close coupling approximations. The final-state Coulomb interaction is treated without any approximation employing appropriate Coulomb waves in the final state. This procedure of treating Coulomb interaction leads to much improved results for low-energy transfer rates. The present results agree reasonably well with previous semiclassical calculations. (C) 2002 Elsevier B.V. B.V. All rights reserved.

Positronium-hydrogen atom elastic scattering at medium energies

We study the elastic scattering of positronium atoms by hydrogen atoms at medium energies using partial-wave Born-Oppenheimer (BO) exchange amplitudes and report accurate BO cross sections in the energy range 0 to 60 eV. The present BO results agree with a 22-state R-matrix and a five-state coupled-channel model potential calculation, but disagree strongly with a conventional close-coupling calculation as well as its input BO amplitudes at medium energies.

Positronium-hydrogen-atom scattering in a five-state model

The scattering of orthopositronium (Ps) by hydrogen atoms has been investigated in a five-state coupled-channel model allowing for Ps(1s)H(2s,2p) and Ps(2s,2p)H(1s) excitations using a recently proposed electron-exchange model potential. The higher (n greater than or equal to 3) excitations and ionization of the Ps atom are calculated using the first Born approximation. Calculations are reported of scattering lengths, phase shifts. elastic, Ps and H excitation, and total cross sections. Remarkable correlations are observed between the S-wave Ps-H binding energy and the singlet scattering length, effective range, and resonance energy obtained in various model calculations. These correlations suggest that if a Ps-H dynamical model yields the correct result for one of these four observables, it is expected to lead to the correct result for the other three. The present model, which is constructed so as to reproduce the Ps-H resonance at 4.01 eV, automatically yields a Ps-H bound state at - 1.05 eV that compares well with the accurate value of - 1.067 eV. The model leads to a singlet scattering length of 3.72a(0) and effective range of 1.67a(0), whereas the correlations suggest the precise values of 3.50a(0) and 1.65a(0) for these observables, respectively. [S1050-2947(99)07703-3].

Convergent variational calculation of positronium-hydrogen-atom scattering lengths

We present a convergent variational basis-set calculational scheme for elastic scattering of the positronium atom by the hydrogen atom in S wave. Highly correlated trial functions with appropriate symmetry are needed to achieve convergence. We report convergent results for scattering lengths in atomic units for both singlet (= 3.49 +/-0.20) and triplet (= 2.46 +/-0.10) states.

Effect of electron exchange in positronium-hydrogen scattering

The elastic and inelastic scattering of ortho-positronium (Ps) by the hydrogen atom have been investigated using a three-Ps-state close-coupling approximation. The higher (n greater than or equal to 3) excitations and ionization of the Ps atom are treated within the framework of the Born approximation. In both cases the effect of electron exchange has been included by a parameter-free nonlocal model potential derived from an antisymmetrization of the wavefunction followed by the removal of nonorthogonality. Calculations are reported of scattering lengths,phase shifts, and of elastic, Ps excitation, and total cross sections. The trend of present target elastic total cross section agrees qualitatively with available experimental results on Ps-impact scattering.

Prediction of a weakly bound excited state in the He-4(2)-Li-7 molecule

A scale-independent approach, valid for weakly bound three-body systems, is used to analyze the existence of excited Thomas-Efimov states in molecular systems with three atoms: a helium dimer together with isotopes of lithium (Li-6 and Li-7) and sodium (Na-23). With the present study and the available data, we can clearly predict that the He-4(2)-Li-7 system supports an excited state with binding energy close to 2.31 mK. (C) 2000 American Institute of Physics. [S0021-9606(00)30442-1].

A theoretical study of the A(2)Sigma(+)-X-2 Pi system of the SiP molecule

The A (2)Sigma(+) and X(2)Pi electronic states of the SiP species have been investigated theoretically at a very high level of correlation treatment (CASSCF/MRSDCI). Very accurate potential energy curves are presented for both states, as well as the associated spectroscopic constants as derived from the vib-rotational energy levels determined by means of the numerical solution of the radial Schrodinger equation. Electronic transition moment function, oscillator strengths, Einstein coefficients for spontaneous emission, and Franck-Condon factors for the A(2)Sigma(+)-X(2)Pi system have been calculated. Dipole moment functions and radiative lifetimes for both states have also been determined. Spin-orbit coupling constants are also reported. The radiative lifetimes for the A(2)Sigma(+) state, taking into account the spin-orbit diagonal correction to the X(2)Pi state, decrease from a value of 138 ms at v' = 0 to 0.48 ms at v' = 8, and, for the X(2)Pi state, from 2.32 s at v = 1 to 0.59 s at v = 5. Vibrational and rotational transitions are expected to be relatively strong.

Influence of support on catalytic behavior of nickel catalysts in the steam reforming of ethanol for hydrogen production

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effect of hydrogen charging on the stability of SAE 10B22 steel surface in alkaline solutions

The influence of hydrogen charging into a quenched and tempered boron steel membrane electrode (SAE 10B22) was studied using borate buffer (pH 8.4) and NaOH solutions (pH 12.7), with or without the addition of 0.01 M EDTA. At the hydrogen input side, hydrogen charging influenced cyclic voltammograms increasing the anodic charge of iron(II) hydroxide formation, and decreasing the donor density of passive films. These results suggest that the hydrogen ingress caused instability of metallic surface, increasing the surface area activity. (C) 2005 Elsevier Ltd. All rights reserved.

Flow-injection spectrophotometric determination of azithromycin in pharmaceutical formulations using p-chloranil in the presence of hydrogen peroxide

A flow-injection (FI) spectrophotometric procedure exploiting merging zones is proposed for the determination of azithromycin in pharmaceutical formulations. The method is based on the reaction of azithromycin with tetrachloro-phenzoquinone (p-chloranil) accelerated by hydrogen peroxide and conducted in a methanol medium, producing a purple-red color compound (lambda(max) = 540 nm). The FI system and the experimental conditions were optimized using a multivariate method. Beer's law is obeyed in a concentration range of 50 - 1600 mu g mL(-1) with an excellent correlation coefficient (r = 0.9998). The detection limit and the quantification limit were 6.6 and 22.1 mu g mL(-1), respectively. No interference was observed from the common excipients, and the recoveries were within 98.6 to 100.4%. The procedure was applied to the determination of azithromycin in pharmaceuticals with a high sampling rate (65 samples h(-1)). The results obtained by the proposed method were in good agreement with those obtained by the comparative method at 95% confidence level.