Molecular models of NS3 protease variants of the Hepatitis C virus

Background: Hepatitis C virus (HCV) currently infects approximately three percent of the world population. In view of the lack of vaccines against HCV, there is an urgent need for an efficient treatment of the disease by an effective antiviral drug. Rational drug design has not been the primary way for discovering major therapeutics. Nevertheless, there are reports of success in the development of inhibitor using a structure-based approach. One of the possible targets for drug development against HCV is the NS3 protease variants. Based on the three-dimensional structure of these variants we expect to identify new NS3 protease inhibitors. In order to speed up the modeling process all NS3 protease variant models were generated in a Beowulf cluster. The potential of the structural bioinformatics for development of new antiviral drugs is discussed.Results: the atomic coordinates of crystallographic structure 1CU1 and 1DY9 were used as starting model for modeling of the NS3 protease variant structures. The NS3 protease variant structures are composed of six subdomains, which occur in sequence along the polypeptide chain. The protease domain exhibits the dual beta-barrel fold that is common among members of the chymotrypsin serine protease family. The helicase domain contains two structurally related beta-alpha-beta subdomains and a third subdomain of seven helices and three short beta strands. The latter domain is usually referred to as the helicase alpha-helical subdomain. The rmsd value of bond lengths and bond angles, the average G-factor and Verify 3D values are presented for NS3 protease variant structures.Conclusions: This project increases the certainty that homology modeling is an useful tool in structural biology and that it can be very valuable in annotating genome sequence information and contributing to structural and functional genomics from virus. The structural models will be used to guide future efforts in the structure-based drug design of a new generation of NS3 protease variants inhibitors. All models in the database are publicly accessible via our interactive website, providing us with large amount of structural models for use in protein-ligand docking analysis.

A micelle nucleation model for the interaction of dodecyl sulphate with Lys49-phospholipases A(2)

Bothropstoxin-I (BthTx-I) is a Lys49-PLA(2) from the venom of Bothrops jararacussu that lacks detectable catalytic activity, yet causes rapid Ca2+-independent membrane damage. With the aim of understanding the interaction between BthTx-I and amphiphilic molecules, we have studied the interaction of sodium dodecyl sulphate (SDS) with the protein. Circular dichroism and attenuated total reflection Fourier-transform infrared spectra of BthTx-I reveal changes in the alpha-helical organization of the protein at an SDS/BthTx-I molar ratio of 20-25. At SDS/BthTx-I ratios of 40-45 the alpha-helices return to a native-like conformation, although fluorescence emission anisotropy measurements of 2-amino-N-hexadecyl-benzamide (AHBA) demonstrate that the total SDS is below the critical micelle concentration when this transition occurs. These results may be interpreted as the result of SDS accumulation by the BthTx-I homodimer and the formation of a pre-micelle SDS/BthTx-I complex, which may subsequently be released from the protein surface as a free micelle. Similar changes in the alpha-helical organization of BthTx-I were observed in the presence of dipalmitoylphosphatidylcholine liposomes, suggesting that protein structure transitions coupled to organization changes of bound amphiphiles may play a role in the Ca2+-independent membrane damage by Lys49-PLA(2)s. (c) 2006 Elsevier B.V. All rights reserved.

SU(5)circle times Z(13) grand unification model

We propose an SU(5) grand unified model with an invisible axion and the unification of the three coupling constants which is in agreement with the values, at M(Z), of alpha, alpha(s), and sin(2)theta(W). A discrete, anomalous, Z(13) symmetry implies that the Peccei-Quinn symmetry is an automatic symmetry of the classical Lagrangian protecting, at the same time, the invisible axion against possible semiclassical gravity effects. Although the unification scale is of the order of the Peccei-Quinn scale the proton is stabilized by the fact that in this model the standard model fields form the SU(5) multiplets completed by new exotic fields and, also, because it is protected by the Z(13) symmetry.

Dynamic critical behavior of percolation observables in the 2d Ising model

We present preliminary results of our numerical study of the critical dynamics of percolation observables for the two-dimensional Ising model. We consider the (Monte-Carlo) short-time evolution of the system obtained with a local heat-bath method and with the global Swendsen-Wang algorithm. In both cases, we find qualitatively different dynamic behaviors for the magnetization and Omega, the order parameter of the percolation transition. This may have implications for the recent attempts to describe the dynamics of the QCD phase transition using cluster observables.

The signature of dark energy perturbations in galaxy cluster surveys

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

A Markovian model market-Akerlof's lemons and the asymmetry of information

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Non-uniform drag force on the Fermi accelerator model

Some dynamical properties of a particle suffering the action of a generic drag force are obtained for a dissipative Fermi Acceleration model. The dissipation is introduced via a viscous drag force, like a gas, and is assumed to be proportional to a power of the velocity: F alpha -nu(gamma). The dynamics is described by a two-dimensional nonlinear area-contracting mapping obtained via the solution of Newton's second law of motion. We prove analytically that the decay of high energy is given by a continued fraction which recovers the following expressions: (i) linear for gamma = 1; (ii) exponential for gamma = 2; and (iii) second-degree polynomial type for gamma = 1.5. Our results are discussed for both the complete version and the simplified version. The procedure used in the present paper can be extended to many different kinds of system, including a class of billiards problems.

Kinetic model of poly(3-hydroxybutyrate) thermal degradation from experimental non-isothermal data

The non-isothermal data given by TG curves for poly(3-hydroxybutyrate) (PHB) were studied in order to obtain a consistent kinetic model that better represents the PHB thermal decomposition. Thus, data obtained from the dynamic TG curves were suitably managed in order to obtain the Arrhenius kinetic parameter E according to the isoconversional F-W-O method. Once the E parameters is found, a suitable logA and kinetic model (f(alpha)) could be calculated. Hence, the kinetic triplet (E +/- SD, logA +/- SD and f(alpha)) obtained for the thermal decomposition of PHB under non-isothermal conditions was E=152 +/- 4 kJ mol(-1), logA=14.1 +/- 0.2 s(-1) for the kinetic model, and the autocatalytic model function was: f(alpha)=alpha(m)(1-alpha)(n)=alpha(0.42)(1-alpha)(0.56).

Ashcroft model potential study of lattice dynamics of α-iron and barium

Ashcroft model potential has been used to compute phonon dispersion relations along the three principal symmetry directions, i.e. [k00], [kk0] and [kkk] for alpha-iron and barium. The computed phonons gave a reasonable agreement with the experimental ones in all the three principal summetry directions expect for the T-2 branch in [KK0] direction where the present study failed to reproduce the experimental findings.

Chloroquine is therapeutic in murine experimental model of paracoccidioidomycosis

Chloroquine, due to its basic properties, has been shown to prevent the release of iron from holotransferrin, thereby interfering with normal iron metabolism in a variety of cell types. We have studied the effects of chloroquine on the evolution of experimental paracoccidioidomycosis by evaluating the viable fungal recovery from lung, liver and spleen from infected mice and H2O2, NO production, tumor necrosis factor-alpha (TNF-alpha), interleukin (IL)-6, IL-10 levels and transferrin receptor (TfR) expression from uninfected and infected peritoneal macrophages. Chloroquine caused a significant decrease in the viable fungal recovery from all organs tested, during all periods of evaluation. Peritoneal macrophages from chloroquine-treated infected mice showed higher H2O2 production and TfR expression, and decreased levels of NO, endogenous and stimulated-TNF-alpha, IL-6 and IL-10 during the three evaluated periods. However, despite its suppressor effects on the macrophage function, the chloroquine therapeutic effect upon murine paracoccidioidomycosis was probably due to its effect on iron metabolism, blocking iron uptake by cells, and consequently restricting iron to fungus growth and survival.

MODEL FOR ASYMPTOTIC D-STATE PARAMETERS OF LIGHT-NUCLEI - APPLICATION TO HE-4

A simple method for calculating the asymptotic D-state observables for light nuclei is suggested. The method exploits the dominant clusters of the light nuclei. The method is applied to calculate the He-4 asymptotic D to S normalization ratio rho(alpha) and the closely related D-state parameter D2alpha. The study predicts a correlation between D2alpha and B(alpha), and between rho(alpha) and B(alpha), where B(alpha) is the binding energy of He-4. The present study yields rho(alpha) congruent-to -0.14 and D2alpha congruent-to -0.12 fm2 consistent with the correct experimental eta(d) and the binding energies of the deuteron, triton, and the alpha particle, where eta(d) is the deuteron D-state to S-state normalization ratio.

Esterase patterns and phylogenetic relationships of species and strains included in the Drosophila buzzatii cluster

Ten strains of two species in the Drosophila buzzatii cluster (D. serido and D. seriema) were examined as to esterase patterns using polyacrylamide gel electrophoresis. The migration rate of esterases, and their substrate specificity to alpha and beta naphthyl acetates, were analysed. Other esterase features such as inhibition behaviour, presence in males and females and location in the head, thorax or abdomen of flies, were also examined. The present data,together with results obtained by others for eight strains of D. koepferae, D. serido, D. seriema and D. buzzatii, show that 69 bands have been detected in the eighteen strains studied. This total number of bands was used for comparison of strains and species by similarity index, analysis of dependence and cluster analysis. The comparisons confirmed the existence of a high degree of similarity among D. seriema strains and among D. koepferae strains, but indicated differentiation among the D. serido strains. Two strains (D69R2 and D69R5) which differed from the others of the latter species, showed closer affinities with D. buzzatii, which indicates the need for further work on those strains classified as D. serido.

Actinobacillus actinomycetemcomitans lipopolysaccharide-mediated experimental bone loss model for aggressive periodontitis

Background: Bacterial constituents, such as Gram-negative derived lipopolysaccharide (LPS), can initiate inflammatory bone loss through induction of host-derived inflammatory cytokines. The aim of this study was to establish a model of aggressive inflammatory alveolar bone loss in rats using LPS derived from the periodontal pathogen Actinobacillus actinomycetemcomitans.Methods: Eighteen female Sprague-Dawley rats were divided into LPS test (N = 12) and saline control (N = 6) groups. All artimals received injections to the palatal molar gingiva three times per week for 8 weeks. At 8 weeks, linear and volumetric alveolar bone loss was measured by micro-computed tomography (mu CT). The prevalence of inflammatory infiltrate, proinflammatory cytokines, and osteoclasts was assessed from hematoxylin and eosin, immunohistochemical, or tartrate-resistant acid phosphatase (TRAP)-stained sections. Statistical analysis was performed.Results: A. actinomycetemcomitans LPS induced severe bone loss over 8 weeks, whereas control groups were unchanged. Linear and volumetric analysis of maxillae by mu CT indicated significant loss of bone with LPS, administration. Histologic examination revealed increased inflammatory infiltrate, significantly increased immunostaining for interleukin IL-6 and -1 beta and tumor necrosis factor-alpha, and more TRAP-positive osteoclasts in the LPS group compared to controls.Conclusion: Oral injections of LPS derived from the periodontal pathogen A. actinomycetemcomitans can induce severe alveolar bone loss and proinflammatory cytokine production in rats by 8 weeks.

Model peptides mimic the structure and function of the N-terminus of the pore-forming toxin sticholysin II

To investigate the role of the N-terminal region in the lytic mechanism of the pore-forming toxin sticholysin II (St II), we studied the conformational and functional properties of peptides encompassing the first 30 residues of the protein. Peptides containing residues 1-30 (P1-30) and 11-30 (P11-30) were synthesized and their conformational properties were examined in aqueous solution as a function of peptide concentration, pH, ionic strength, and addition of the secondary structure-inducing solvent trifluoroethanol (TFE). CD spectra showed that increasing concentration, pH, and ionic strength led to aggregation of P1-30; as a consequence, the peptide acquired beta-sheet conformation. In contrast, P11-30 exhibited practically no conformational changes under the same conditions, remaining essentially structureless. Moreover, this peptide did not undergo aggregation. These differences clearly point to the modulating effect of the first 10 hydrophobic residues on the peptides aggregation and conformational properties. In TFE both the first ten hydrophobic peptides acquired alpha-helical conformation, albeit to a different extent, P11-30 displayed lower alpha-helical content. P1-30 presented a larger-fraction of residues in alpha-helical conformation in TFE than that found in St II's crystal structure for that portion of the protein. Since TFE mimics the membrane em,, such increase in helical content could also occur upon toxin binding to membranes and represent a step in the mechanism of pore formation. The peptides conformational properties correlated well with their functional behaviour. Thus, P1-30 exhibited much higher hemolytic activity than P11-30. In addition, P11-30 was able to block the toxin's hemolytic activity. The size of pores formed in red blood cells by P 1-30 was estimated by measuring the permeability PEGs of different molecular mass. The pore radius (0.95 +/- 0.01 nm) was very similar to that of the PEGs of different pore formed by the toxin. The results demonstrate that the synthetic peptide P1-30 is a good model of St 11 conformation and function and emphasize the contribution of the toxin's N-terminal region, and, in particular, the hydrophobic residues 1-10 to pore formation. (c) 2005 Wiley Periodicals, Inc.

Cellular recruitment and cytokine generation in a rat model of allergic lung inflammation are differentially modulated by progesterone and estradiol

We evaluated the role of estradiol and progesterone in allergic lung inflammation. Rats were ovariectomized (Ovx) and, 7 days later, were sensitized with ovalbumin (OA) and challenged after 2 wk with inhaled OA; experiments were performed 1 day thereafter. Ovx-allergic rats showed reduced cell recruitment into the bronchoalveolar lavage (BAL) fluid relative to sham-Ovx allergic rats, as was observed in intact allergic rats treated with ICI-182,780. Estradiol increased the number of cells in the BAL of Ovx-allergic rats, whereas progesterone induced an additional reduction. Cells of BAL and bone marrow (BM) of Ovx-allergic rats released elevated amounts of IL-10 and reduced IL-1 beta and TNF-alpha. BM cells of Ovx-allergic rats released increased amounts of IL-10 and lower amounts of IL-4. Estradiol treatment of Ovx-allergic rats decreased the release of IL-10 but increased that of IL-4 by BM cells. Estradiol also caused an increased release of IL-1 beta and TNF-alpha by BAL cells. Progesterone significantly increased the release of IL-10, IL-1 beta, and TNF-alpha by BAL cells and augmented that of IL-4 by BM cells. Degranulation of bronchial mast cells from Ovx rats was reduced after in vitro challenge, an effect reverted by estradiol but not by progesterone. We suggest that the serum estradiol-to-progesterone ratio might drive cellular recruitment, modulating the pulmonary allergy and profile of release of anti-inflammatory or inflammatory cytokines. The existence of such dual hormonal effects suggests that the hormone therapy of asthmatic postmenopausal women and of those suffering of premenstrual asthma should take into account the possibility of worsening the pulmonary conditions.