Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities

BaP1 is a 22.7-kD P-I-type zinc-dependent metalloproteinase isolated from the venom of the snake Bothrops asper, a medically relevant species in Central America. This enzyme exerts multiple tissue-damaging activities, including hemorrhage, myonecrosis, dermonecrosis, blistering, and edema. BaP1 is a single chain of 202 amino acids that shows highest sequence identity with metalloproteinases isolated front the venoms of snakes of the subfamily Crotalinae. It has six Cys residues involved in three disulfide bridges (Cys 117-Cys 197, Cys 159-Cys 181, Cys 157-Cys 164). It has the consensus sequence H(142)E(143)XXH(146)XXGXXH(152), as well as the sequence C164I165M166, which characterize the metzincin superfamily of metalloproteinases. The active-site cleft separates a major subdomain (residues 1-152), comprising four a-helices and a five-stranded beta-sheet, from the minor subdomain, which is formed by a single a-helix and several loops. The catalytic zinc ion is coordinated by the N-epsilon2 nitrogen atoms of His 142, His 146, and His 152, in addition to a solvent water molecule, which in turn is bound to Glu 143. Several conserved residues contribute to the formation of the hydrophobic pocket, and Met 166 serves as a hydrophobic base for the active-site groups. Sequence and structural comparisons of hemorrhagic and nonhemorrhagic P-I metalloproteinases from snake venoms revealed differences in several regions. In particular, the loop comprising residues 153 to 176 has marked structural differences between metalloproteinases with very different hemorrhagic activities. Because this region lies in close proximity to the active-site microenvironment, it may influence the interaction of these enzymes with physiologically relevant substrates in the extracellular matrix.

Using genetic algorithm to design protein sequence

In this work, genetic algorithms concepts along with a rotamer library for proteins side chains are used to optimize the tertiary structure of the hydrophobic core of Cytochrome b(562) starting from the known PDB structure of its backbone which is kept fixed while the side chains of the hydrophobic core are allowed to adopt the conformations present in the rotamer library. The atoms of the side chains forming the core interact via van der Waals energy. Besides the prediction of the native core structure, it is also suggested a set of different amino acid sequences for this core. Comparison between these new cores and the native are made in terms of their volumes, van der Waals energies values and the numbers of contacts made by the side chains forming the cores. This paper proves that genetic algorithms area efficient to design new sequence for the protein core. (C) 2007 Elsevier B.V. All rights reserved.

Preliminary functional characterization, cloning and primary sequence of Fastuosain, a cysteine peptidase isolated from fruits of Bromelia fastuosa

The present work reports the characterization of Fastuosain, a novel cysteine protease of 25kDa, purified from the unripe fruits of Bromelia fastuosa, a wild South American Bromeliaceae. Proteolytic activity, measured using casein and synthetic substrates, was dependent on the presence of thiol reagents, having maximum activity at pH 7.0. The present work reports cDNA cloning of Fastuosain; cDNA was amplified by PCR using specific primers. The product was 1096pb long. Mature fastuosain has 217 residues, and with the proregion has a total length of 324 residues. Its primary sequence showed high homology with ananain(74%), stem bromelain (66%) and papain (44%).

Completion of the Nucleotide Sequence of a Brazilian Isolate of Southern bean mosaic virus

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

CP trajectory diagram - a tool for a pictorial representation of CP and matter effects in neutrino oscillations

We introduce a CP trajectory diagram in bi-probability space as a powerful tool for a pictorial representation of the genuine CP and the matter effects in neutrino oscillations. The existence of correlated ambiguity in the B is uncovered. The principles of tuning the beam energy for a determination of CP-violating phase delta and the sign of Deltam(13)(2) given baseline distance are proposed to resolve the ambiguity and to maximize the CP-odd effect. We finally point out, quite contrary to what is usually believed, that the ambiguity may be resolved with similar to 50% chance in the super-JHF experiment despite its relatively short baseline of 300 km. (C) 2003 Elsevier B.V. B.V. All rights reserved.

Superfluid Fermi-Fermi mixture: Phase diagram, stability, and soliton formation

We study the phase diagram for a dilute Bardeen-Cooper-Schrieffer superfluid Fermi-Fermi mixture (of distinct mass) at zero temperature using energy densities for the superfluid fermions in one (1D), two (2D), and three (3D) dimensions. We also derive the dynamical time-dependent nonlinear Euler-Lagrange equation satisfied by the mixture in one dimension using this energy density. We obtain the linear stability conditions for the mixture in terms of fermion densities of the components and the interspecies Fermi-Fermi interaction. In equilibrium there are two possibilities. The first is that of a uniform mixture of the two components, the second is that of two pure phases of two components without any overlap between them. In addition, a mixed and a pure phase, impossible in 1D and 2D, can be created in 3D. We also obtain the conditions under which the uniform mixture is stable from an energetic consideration. The same conditions are obtained from a modulational instability analysis of the dynamical equations in 1D. Finally, the 1D dynamical equations for the system are solved numerically and by variational approximation (VA) to study the bright solitons of the system for attractive interspecies Fermi-Fermi interaction in 1D. The VA is found to yield good agreement to the numerical result for the density profile and chemical potential of the bright solitons. The bright solitons are demonstrated to be dynamically stable. The experimental realization of these Fermi-Fermi bright solitons seems possible with present setups.

Antiparticle Contribution in the Cross Ladder Diagram for Bethe-Salpeter Equation in the Light-Front

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

Two-Point Function at Two Loops via Triangle Diagram Insertion

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Podzolization as a deferralitization process: dynamics and chemistry of ground and surface waters in an Acrisol-Podzol sequence of the upper Amazon Basin

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

Nucleotide sequence, genomic organization and chromosome localization of 5S rDNA in two species of Curimatidae (Teleostei, Characiformes)

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

Comparative analysis of differentially expressed sequence tags of sweet orange and mandarin infected with Xylella fastidiosa

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Phase diagram for freeze-dried persimmon

Phase transitions of freeze-dried persimmon in a large range of moisture content were determined by differential scanning calorimetry (DSC). In order to study this transitions at low and intermediate moisture content domains, samples were conditioned by adsorption at various water activities (a(w) = 0.11-0.90) at 25 degreesC. For the high moisture content region, samples were obtained by water addition. At a(w) less than or equal to 0.75 two glass transitions were visible, with T(g) decreasing with increasing water activity due to water plasticizing effect. The first T(g) is due to the matrix formed by sugars and water, the second one, less visible and less plasticized by water, is probably due to macromolecules of the fruit pulp. At a(w) between 0.80 and 0.90 a devitrification peak appeared after T(g) and before T(m). At this moisture content range, the Gordon-Taylor model represented satisfactorily the matrix glass transition curve. At the higher moisture content range (a(w) > 0.90), the more visible phenomenon was the ice melting. T(g) appeared less visible because the enthalpy change involved in glass transition is practically negligible in comparison with the latent heat of melting. In the high moisture content domain T(g) remained practically constant around T(g)' (-56.6 degreesC). (C) 2001 Elsevier B.V. B.V. All rights reserved.

Glass transitions and state diagram for freeze-dried pineapple

Glass transition temperature of freeze-dried pineapple conditioned by adsorption at various water activities at 25 degreesC was determined by differential scanning calorimetry (DSC). High moisture content samples corresponding to water activities higher than 0.9, obtained by liquid water addition, were also analysed. The DSC traces showed a well-visible shift in baseline at the glass transition temperature (T(g)). Besides, no ice formation was observed until water activity was equal to 0.75. For water activities lower than 0.88, the glass transition curve showed that T(g) decreased with increasing moisture content and the experimental data could be well-correlated by the Gordon-Taylor equation. For higher water activities, this curve exhibited a discontinuity, with suddenly increasing glass transition temperatures approaching a constant value that corresponds to the T(g) of the maximally freeze-concentrated amorphous matrix. The unfreezable water content was determined through melting enthalpy dependence on the sample moisture content.

Podzolization as a deferralitization process: a study of an Acrisol-Podzol sequence derived from Palaeozoic sandstones in the northern upper Amazon Basin

Morphological, geochemical and mineralogical studies were carried out in a representative soil catena of the low-elevation plateaux of the upper Amazon Basin to interpret the steps and mechanisms involved in the podzolization of low-activity clay soils. The soils are derived from Palaeozoic sandstones. They consist of Hydromorphic Podzols under tree savannah in the depressions of the plateaux and predominantly of Acrisols covered by evergreen forest elsewhere.Incipient podzolization in the uppermost Acrisols is related to the formation of organic-rich A and Bhs horizons slightly depleted in fine-size particles by both mechanical particle transfer and weathering. Weathering of secondary minerals by organic acids and formation of organo-metallic complexes act simultaneously over short distances. Their vertical transfer is limited. Selective dissolution of aluminous goethite, then gibbsite and finally kaolinite favour the preferential cheluviation of first Fe and secondly Al. The relatively small amount of organo-metallic complexes produced is related to the quartzitic parent materials, and the predominance of Al over Fe in the spodic horizons is due to the importance of gibbsite in these low-activity clay soils.Morphologically well-expressed podzols occur in strongly iron-depleted topsoils of the depression. Mechanical transfer and weathering of gibbsite and kaolinite by organic acids is enhanced and leads to residual accumulation of sands. Organo-metallic complexes are translocated in strongly permeable sandy horizons and impregnate at depth the macro-voids of embedded soil and saprolite materials to form the spodic Bs and 2BCs horizons. Mechanical transfer of black particulate organic compounds devoid of metals has occurred later within the sandy horizons of the podzols. Their vertical transfer has formed well-differentiated A and Bh horizons. Their lateral removal by groundwater favours the development of an albic E horizon. In an open and waterlogged environment, the general trend is therefore towards the removal of all the metals that have initially accumulated as a response to the ferralitization process and have temporarily been sequestrated in organic complexes in previous stages of soil podzolization.