Predicting peptides structure with solvation potential and rotamer library dependent of the backbone

In this work, genetic algorithms concepts along with a rotamer library dependent of backbone and implicit solvation potential are used to study the tertiary structure of peptides. We starting from known primary sequence and optimize the structure of the backbone while the side chains allowed adopting the conformations present in a rotamer library. The GA, implemented with two force fields with a growing complexity, was used predict the structure of a polyalanine and a poly-isolueucine. This paper presents good and interesting results about the study of peptides structures and about the development of computational tools to study peptides structures. (C) 2007 Elsevier B.V. All rights reserved.

Structure and composition of the stream ichthyofauna of four tributary rivers of the upper Rio Parana basin, Brazil

The ichthyofauna of 24 stretches of streams, all of 100 m length and of fifth or lower order and most of second and third order, were sampled along four left bank tributaries (Rio do Peixe, Rio Aguapei, Rio Sao Jose dos Dourados, lower Rio Tiete of the main channel of the Rio Parana in the state of São Paulo, southeastern Brazil. Sampling of the fish fauna at each of the six sites in the four basins incorporated a standardized fish collecting methodology and a standardized documentation of environmental data serving as the basis for a comparative analysis of the collecting locations. The 8,189 fish specimens collected represented six orders, 18 families, 42 genera, and 56 species, with a total biomass of 28.8 kg. Approximately 52% of the collected species were characiforms, 28% siluriforms, 9% gymnotiforms, 5% cyprinodontiforms, 4% perciforms, and 2% synbranchiforms. The most abundant of the species were the characiforms Astyanax altiparanae (15% of total) and Knodus moenkhausii (12% of total). The two species with the largest overall biomasses were A. altiparanae (34% of total biomass) and the siluriform Hypostomus sp. (8% of total biomass). Analysis of the trophic structure of the studied ichthyofauna indicated that the 10 numerically dominant species across the 24 sampled streams can be grouped into five guilds that are in decreasing order of numerical importance: omnivores, insectivores, insectivores/invertivores, periphytivores, and algivores. Species richness in the sampled stream stretches varied from six to 20 species with an average richness of 14. The species richness estimated by extrapolation for all 24 sampled stream stretches was 67 species. The Characidae are predominant among the collected specimens with approximately 50% of both individuals and biomass, a fact hypothesized to be a function of several attributes typical of the family. Six of the 56 collected species were new to science and six other species are of indefinite taxonomic status and require further analysis in order to determine their identity.

Effects of physical habitat degradation on the stream fish assemblage structure in a pasture region

We compared the fish assemblage structure from streams with different intensities of physical habitat degradation and chemical water pollution by domestic sewage in southeastern Brazil. Eight streams (R1-R8) showing less disturbed or more disturbed conditions of chemical water quality and of physical habitat quality were selected. Cumulative abundance and biomass, combined in ABC plots, revealed (i) biomass curves above the abundance curves, represented by the streams R1-R2 (water and habitat less disturbed) and R5-R6 (water more disturbed and habitat less disturbed), and (ii) biomass curves below the abundance curves, represented by the streams R3-R4 (water less disturbed and habitat more disturbed) and R7-R8 (water and habitat more disturbed). The quantitative structure of the ichthyofauna showed significant correspondence with physical habitat condition but not with chemical water quality. The most significant species to cause the dissimilarity between less disturbed and more disturbed physical habitats was the exotic Poecilia reticulata. Such results indicate that in the focused region-with little influence of industrial pollution, noncritical domestic sewage discharge, and soil predominantly used for pasture-streams with high physical habitat integrity possess a differently structured ichthyofauna than streams with relatively low physical habitat integrity, reinforcing the importance of the physical habitat quality and riparian conservation along these water courses, warranting the conservation of these systems. Indeed, our results also reinforce the importance of including biotic descriptors, particularly of the ichthyo-fauna, in water-monitoring programs designed to reveal signs of human interference.

Community structure of aquatic insects (Ephemeroptera, Plecoptera, and Trichoptera) in Cerrado streams of Paraguay, Paraná, and São Francisco river basins

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

Bond strengths, degree of conversion of the cement and molecular structure of the adhesive-dentine joint in fibre post restorations

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Pion structure in the instanton liquid model

The covariant quark model of the pion based on the effective nonlocal quark-hadron Lagrangian involving nonlocality induced by instanton fluctuations of the QCD vacuum is reviewed. Explicit gauge invariant formalism allows us to construct the conserved vector and axial currents and to demonstrate their consistency with the Ward-Takahashi identities and low-energy theorems. The spontaneous breaking of chiral symmetry results in the dynamic quark mass and the vertex of the quark-pion interaction, both momentum-dependent. The parameters of the instanton vacuum, the average size of the instantons, and the effective quark mass are expressed in terms of the vacuum expectation values of the lowest dimension quark-gluon operators and low-energy pion observables. The transition pion form factor for the processes gamma*gamma --> pi (0) and gamma*gamma* --> pi (0) is analyzed in detail. The kinematic dependence of the transition form factor at high momentum transfers allows one to determine the relationship between the light-cone amplitude of the quark distribution in the pion and the quark-pion vertex function. Its dynamic dependence implies that the transition form factor gamma*gamma --> pi (0) at high momentum transfers is acutely sensitive to the size of the nonlocality of nonperturbative fluctuations in the QCD vacuum. In the leading twist, the distribution amplitude and the distribution function of the valence quarks in the pion are calculated at a low normalization point of the order of the inverse average instanton size rho (-1)(c). The QCD results are evolved to higher momentum transfers and are in reasonable agreement with available experimental data on the pion structure.

Effect of bound nucleon internal structure change on nuclear structure functions

Effect of bound nucleon internal structure change on nuclear structure functions is investigated based on local quark-hadron duality. The bound nucleon structure functions calculated for charged-lepton and (anti)neutrino scattering are all enhanced in symmetric nuclear matter at large Bjorken-x (x greater than or similar to 0.85) relative to those in a free nucleon. This implies that a part of the enhancement observed in the nuclear structure function F-2 (in the resonance region) at large Bjorken-x (the EMC effect) is due to the effect of the bound nucleon internal structure change. However, the x dependence for the charged-lepton and (anti)neutrino scattering is different. The former (latter) is enhanced (quenched) in the region 0.8 less than or similar to x less than or similar to 0.9 (0.7 less than or similar to x less than or similar to 0.85) due to the difference of the contribution from axial vector forrn factor. Because of these differences charge symmetry breaking in parton distributions will be enhanced in nuclei. (c) 2005 Elsevier B.V. All rights reserved.

Temperature Effect on the Structure and Formation Kinetics of Vinyltriethoxysilane-Derived Organic/Silica Hybrids

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

Effects of poly(vinyl alcohol) additions on the structure of silica xerogels

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

Effects of Dimerization on the Structure and Biological Activity of Antimicrobial Peptide Ctx-Ha

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The role of the Eu3+ ions in structure and photoluminescence properties of SrBi2Nb2O9 powders

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Spatial and temporal variation in population structure of Hemigrammus marginatus (Characiformes: Characidae) in streams of the Ivinhema River Basin, Brazil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Purification, sequencing and structural characterization of the phospholipase A(1) from the venom of the social wasp Polybia paulista (Hymenoptera, Vespidae)

The biochemical and functional characterization of wasp venom toxins is an important prerequisite for the development of new tools both for the therapy of the toxic reactions due to envenomation caused by multiple stinging accidents and also for the diagnosis and therapy of allergic reactions caused by this type of venom. PLA(1) was purified from the venom of the neotropical social wasp Polybia paulista by using molecular exclusion and cation exchange chromatographies; its amino acid sequence was determined by using automated Edman degradation and compared to the sequences of other vespid venom PLA(1)'s. The enzyme exists as a 33,961.40 da protein, which was identified as a lipase of the GX class, liprotein lipase superfamily, pancreatic lipases (ab20.3) homologous family and RP2 sub-group of phospholipase. P. paulista PLA(1) is 53-82% identical to the phospholipases from wasp species from Northern Hemisphere. The use restrained-based modeling permitted to describe the 3-D structure of the enzyme, revealing that its molecule presents 23% alpha-helix, 28% beta-sheet and 49% coil. The protein structure has the alpha/beta fold common to many lipases; the core consists of a tightly packed beta-sheet constituted of six-stranded parallel and one anti-parallel beta-strand, surrounded by four alpha-helices. P. paulista PLA(1) exhibits direct hemolytic action against washed red blood cells with activity similar to the Cobra cardiotoxin from Naja naja atra. In addition to this, PLA(1) was immunoreactive to specific IgE from the sera of P. paulista-sensitive patients. (c) 2007 Elsevier Ltd. All rights reserved.

Crystal structure of myotoxin-II: A myotoxic phospholipase A2 - Homologue from Bothrops moojeni venom.

The crystal structure of Myotoxin-II (MjTX-II), a Lys49 PLA(2)-homologue from Bothrops moojeni venom has been determined and refined at 2.0 Angstrom to a crystallographic residual of 19.7% (R-free = 28.1%). MjTX-II is a dimer in the crystal, with the monomers in the asymmetric unit related by a two-fold symmetry axis running through the dimer interface. The dimers of MjTX-II and the Lys49 PLA(2) from B. asper venom are similar, however the relative orientations of the monomers suggests a flexible dimer interface, which serves as a hinge between the two molecules.

Dynamical scaling properties of nanoporous undoped and Sb-doped SnO2 supported thin films during tri- and bidimensional structure coarsening

The coarsening of the nanoporous structure developed in undoped and 3% Sb-doped SnO2 sol-gel dip-coated films deposited on a mica substrate was studied by time-resolved small-angle x-ray scattering (SAXS) during in situ isothermal treatments at 450 and 650 degrees C. The time dependence of the structure function derived from the experimental SAXS data is in reasonable agreement with the predictions of the statistical theory of dynamical scaling, thus suggesting that the coarsening process in the studied nanoporous structures exhibits dynamical self-similar properties. The kinetic exponents of the power time dependence of the characteristic scaling length of undoped SnO2 and 3% Sb-doped SnO2 films are similar (alpha approximate to 0.09), this value being invariant with respect to the firing temperature. In the case of undoped SnO2 films, another kinetic exponent, alpha('), corresponding to the maximum of the structure function was determined to be approximately equal to three times the value of the exponent alpha, as expected for the random tridimensional coarsening process in the dynamical scaling regime. Instead, for 3% Sb-doped SnO2 films fired at 650 degrees C, we have determined that alpha(')approximate to 2 alpha, thus suggesting a bidimensional coarsening of the porous structure. The analyses of the dynamical scaling functions and their asymptotic behavior at high q (q being the modulus of the scattering vector) provided additional evidence for the two-dimensional features of the pore structure of 3% Sb-doped SnO2 films. The presented experimental results support the hypotheses of the validity of the dynamic scaling concept to describe the coarsening process in anisotropic nanoporous systems.