Docking and small angle X-ray scattering studies of purine nucleoside phosphorylase

Docking simulations have been used to assess protein complexes with some success. Small angle X-ray scattering (SAXS) is a well-established technique to investigate protein spatial configuration. This work describes the integration of geometric docking with SAXS to investigate the quaternary structure of recombinant human purine nucleoside phosphorylase (PNP). This enzyme catalyzes the reversible phosphorolysis of N-ribosidic bonds of purine nucleosides and deoxynucleosides. A genetic deficiency due to mutations in the gene encoding for PNP causes gradual decrease in T-cell immunity. Inappropriate activation of T-cells has been implicated in several clinically relevant human conditions such as transplant rejection, rheumatoid arthritis, lupus, and T-cell lymphomas. PNP is therefore a target for inhibitor development aiming at T-cell immune response modulation and has been submitted to extensive structure-based drug design. The present analysis confirms the trimeric structure observed in the crystal. The potential application of the present procedure to other systems is discussed. (C) 2003 Elsevier B.V. All rights reserved.

A Decomposition and Noise Removal Method Combining Diffusion Equation and Wave Atoms for Textured Images

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

Extruded vesicles of dioctadecyldimethylammonium bromide and chloride investigated by light scattering and cryogenic transmission electron microscopy

Combined dynamic and static light scattering (DLS, SLS) and cryogenic transmission electron microscopy (cryo-TEM) were used to investigate extruded cationic vesicles of dioctadecyldimethylammonium chloride and bromide (DODAX, X being Cl- or Br-). In salt-free dispersions the mean hydrodynamic diameter, D-h, and the weight average molecular weight, M-w, are larger for DODAB than for DODAC vesicles, and both D-h and M-w increase with the diameter (phi) of the extrusion filter. NaCl (NaBr) decreases (increases) the DODAB (DODAC) vesicle size, reflecting the general trend of DODAB to assemble as larger vesicles than DODAC. The polydispersity index is lower than 0.25, indicating the dispersions are rather polydisperse. Cryo-TEM micrographs show that the smaller vesicles are spherical while the larger ones are oblong or faceted, and the vesicle samples are fairly polydisperse in size and morphology. They also indicate that the vesicle size increases with phi and DODAB assembles as larger vesicles than DODAC. Lens-shaped vesicles were observed in the extruded preparations. Both light scattering and cryo-TEM indicate that the vesicle size is larger or smaller than phi when phi is smaller or larger than the optimal phi* approximate to 200 nm. (C) 2008 Elsevier B.V. All rights reserved.

Photoacoustic spectroscopy of aromatic amino acids in proteins

This paper concerns the use of photoacoustic spectroscopy (PAS) to study the presence of aromatic amino acid in proteins. We examined the aromatic amino acids in six proteins with well-known structures using absorption spectra of near ultraviolet PAS over the wavelength range 240-320 nm. The fundamental understanding of the physical and chemical properties that govern the absorption of light and a subsequent release of heat to generate a transient pressure wave was used to test the concept of monitoring aromatic amino acids with this method. Second derivative spectroscopy in the ultraviolet region of proteins was also used to study the regions surrounding the aromatics and the percentage area in each band was related in order to determine the contribution in function of the respective molar extinction coefficients for each residue. Further investigation was conducted into the interaction between sodium dodecyl sulphate (SDS) and bothropstoxin-I (BthTx-I), with the purpose of identifying the aromatics that participate in the interaction. The clear changes in the second derivative and curve-fitting procedures suggest that initial SDS binding to the tryptophan located in the dimer interface and above 10 SDS an increased intensity between 260 and 320 nm, demonstrating that the more widespread tyrosine and phenylalanine residues contribute to the SDS/BthTx-I interactions. These results demonstrate the potential of near UV-PAS for the investigation of membrane proteins/detergent complexes in which light scattering is significant.

Thermal and Structural Behavior of Dioctadecyldimethylammonium Bromide Dispersions Studied by Differential Scanning Calorimetry and X-Ray Scattering

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

On exact boundary controllability for linearly coupled wave equations

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Scattering of positronium by H, He, Ne, and Ar

The low-energy scattering of the ortho-positronium (Ps) by H, He, Ne, and Ar atoms has been investigated in the coupled-channel framework by using a recently proposed time-reversal symmetric non-local electron-exchange model potential with a single parameter C. For H and He, we use a three-Ps-state coupled-channel model and, for Ar and Ne, we use a static-exchange model. The sensitivity of the results is studied with respect to the parameter C. Present low-energy cross-sections for He, Ne and Ar are in good agreement with experiment. (C) 2000 Elsevier B.V. B.V. All rights reserved.

Mixing of superconducting d(x2-y2) state with s-wave states for different filling and temperature

We study the order parameter for mixed-symmetry states involving a major d(x2-y2) state and various minor s-wave states (s, s(xy), and Sx2+y2) for different filling and temperature for mixing angles 0 and pi /2. We employ a two-dimensional tight-binding model incorporating second-neighbor hopping for tetragonal and orthorhombic lattice. There is mixing for the symmetric s state both on tetragonal and orthorhombic lattice. The s(xy) state mixes with the d(x2-y2) state only on orthorhombic lattice. The s(x2+y2) state never mixes with the d(x2-y2) state. The temperature dependence of the order parameters is also studied. (C) 2001 Elsevier B.V. B.V. All rights reserved.

Two phase transitions in (s+id)-wave Bardeen-Cooper-Schrieffer superconductivity

We establish universal behaviour in the temperature dependencies of some observables in (s + id)-wave BCS superconductivity in the presence of a weak a wave. We find also a second second-order phase transition. As temperature is lowered-past the usual critical temperature T-c, a less ordered superconducting phase is created in the d wave, which changes to a more ordered phase in a (s + id) wave at T-c1 (

Resonance in Bose-Einstein condensate oscillation from a periodic variation in scattering length

Using the explicit numerical solution of the axially symmetric Gross-Pitaevskii equation, we study the oscillation of the Bose-Einstein condensate (BEC) induced by a periodic variation in the atomic scattering length a. When the frequency of oscillation of a is an even multiple of the radial or axial trap frequency, respectively, the radial or axial oscillation of the condensate exhibits resonance with a novel feature. In this nonlinear problem without damping, at resonance in the steady state the amplitude of oscillation passes through a maximum and minimum. Such a growth and decay cycle of the amplitude may keep on repeating. Similar behaviour is also observed in a rotating BEC.

s-wave approximation for asymmetry in nonmesonic decay of finite hypernuclei

We establish the bridge between the commonly used Nabetani-Ogaito-Sato-Kishimoto (NOSK) formula for the asymmetry parameter a(Lambda) in the Lambda p -> np emission of polarized hypernuclei, and the shell-model (SM) formalism for finite hypernuclei. We demonstrate that the s-wave approximation leads to a SM formula for a(Lambda) that is as simple as the NOSK one and that reproduces the exact results for (5)(Lambda)He and (12)(Lambda)C better than initially expected. The simplicity achieved here is indeed remarkable. The new formalism makes the theoretical evaluation of a(Lambda) more transparent and explains clearly why the one-meson exchange model is unable to account for the experimental data of (5)(Lambda)He.

Positronium scattering by a hydrogen molecule including exchange

We perform a three-positronium (Ps) state [Ps(ls,2s,2p)] coupled-channel calculation of Ps-H-2 scattering including the effect of electron exchange. At medium energies, higher excitations and ionization of Ps are treated within the framework of the first Born approximation. In both cases exchange is included using a recently proposed nonlocal model exchange potential which is free of non-orthogonality problems common in the usual antisymmetrization scheme. The present total cross sections at low and medium energies are in encouraging agreement with experiment.

Resonances in a trapped 3D Bose-Einstein condensate under periodically varying atomic scattering length

Nonlinear oscillations of a 3D radial symmetric Bose-Einstein condensate under periodic variation in time of the atomic scattering length have been studied. The time-dependent variational approach is used for the analysis of the characteristics of nonlinear resonances in the oscillations of the condensate. The bistability in oscillations of the BEC width is investigated. The dependence of the BEC collapse threshold on the drive amplitude and parameters of the condensate and trap is found. Predictions of the theory are confirmed by numerical simulations of the full Gross-Pitaevskii equation.

Entanglement and entropy operator for strings in pp-wave time dependent background

In this Letter new aspects of string theory propagating in a pp-wave time dependent background with a null singularity are explored. It is shown the appearance of a 2d entanglement entropy dynamically generated by the background. For asymptotically flat observers, the vacuum close to the singularity is unitarily inequivalent to the vacuum at tau = -infinity and it is shown that the 2d entanglement entropy diverges close to this point. As a consequence. The positive time region is inaccessible for observers in tau = -infinity. For a stationary measure, the vacuum at finite time is seen by those observers as a thermal state and the information loss is encoded as a heat bath of string states. (c) 2006 Elsevier B.V. All rights reserved.

Positronium scattering by atoms and molecules at low energies

The recent theoretical and experimental activities in positronium (Ps) scattering by atoms and molecules are reviewed with special emphasis at low energies. We critically compare the results of different groups - theoretical and experimental. The theoretical approaches considered include the R-matrix and close-coupling methods applied to Ps-H, Ps-He and Ps-Li scattering, and a coupled-channel approach with a nonlocal model potential for Ps scattering by H, He, H-2, Ne, Ar, Li, Na, K, Rb, Cs and Ps and for pickoff quenching in Ps-He scattering. Results for scattering lengths, partial. total and differential cross-sections as well as resonance and binding energies in different systems are discussed. (C) 2002 Elsevier B.V. B.V. All rights reserved.