The effects of macromolecular and serum supplements and oxygen tension during bovine in vitro procedures on kinetics of oocyte maturation and embryo development

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

Intermolecular interactions and characterization of the novel factor Xa exosite involved in macromolecular recognition and inhibition: Crystal structure of human Gla-domainless factor Xa complexed with the anticoagulant protein NAPc2 from the hematophagous nematode Ancylostoma caninum

NAPc2, an anticoagulant protein from the hematophagous nematode Ancylostoma caninum evaluated in phase-II/IIa clinical trials, inhibits the extrinsic blood coagulation pathway by a two step mechanism, initially interacting with the hitherto uncharacterized factor Xa exosite involved in macromolecular recognition and subsequently inhibiting factor VIIa (K-i = 8.4 pM) of the factor VIIa/tissue factor complex. NAPc2 is highly flexible, becoming partially ordered and undergoing significant structural changes in the C terminus upon binding to the factor Xa exosite. In the crystal structure of the ternary factor Xa/NAPc2/selectide complex, the binding interface consists of an intermolecular antiparallel beta-sheet formed by the segment of the polypeptide chain consisting of residues 74-80 of NAPc2 with the residues 86-93 of factor Xa that is additional maintained by contacts between the short helical segment (residues 67-73) and a turn (residues 26-29) of NAPc2 with the short C-terminal helix of factor Xa (residues 233-243). This exosite is physiologically highly relevant for the recognition and inhibition of factor X/Xa by macromolecular substrates and provides a structural motif for the development of a new class of inhibitors for the treatment of deep vein thrombosis and angioplasty. (c) 2006 Elsevier Ltd. All rights reserved.

Protein-Ion Binding Process on Finite Macromolecular Concentration. A Poisson-Boltzmann and Monte Carlo Study

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Macromolecular properties of cepacian in water and in dimethylsulfoxide

Cepacian is the exopolysaccharide produced by the majority of the so far investigated clinical strains of the Burkholderia cepacia complex. This is a group of nine closely related bacterial species that might cause serious lung infections in cystic fibrosis patients, in some cases leading to death. In this paper the aggregation ability and the conformational properties of cepacian chain were investigated to understand its role in biofilm formation. Viscosity and atomic force microscopy studies in water and in mixed (dimethylsulfoxide/water) solvent indicated the formation of double stranded molecular structures in aqueous solutions. Inter-residue short distances along cepacian chain were investigated by NOE NMR, which showed that two side chains of cepacian were not conformation ally free due to strong interactions with the polymer backbone. These interactions were attributed to hydrogen bonding and contributed to structure rigidity. (c) 2007 Elsevier Ltd. All rights reserved.

Periodic waves and solitons in a nonlinear fibre with resonant impurities

We shall consider a coupled nonlinear Schrodinger equation- Bloch system of equations describing the propagation of a single pulse through a nonlinear dispersive waveguide in the presence of resonances; this could be, for example, a doped optical fibre. By making use of the integrability of the dynamic equations, we shall apply the finite-gap integration method to obtain periodic solutions for this system. Next, we consider the problem of the formation of solitons at a sharp front pulse and, by means of the Whitham modulational theory, we derive the amplitude and velocity of the largest soliton.

Asymmetric exclusion model with impurities

An integrable asymmetric exclusion process with impurities is formulated. The model displays the full spectrum of the stochastic asymmetric XXZ chain plus new levels. We derive the Bethe equations and calculate the spectral gap for the totally asymmetric diffusion at half filling. While the standard asymmetric exclusion process without impurities belongs to the KPZ universality class with an exponent 3/2, our model has a scaling exponent 5/3.

Effect of interstitial impurities on internal friction measurements in niobium

Measurements of internal friction as a function of temperature were carried out in samples of mobium containing different amounts of interstitial solutes (oxygen and nitrogen) and one sample of mobium containing initially only nitrogen as interstitial solute. The experimental spectra of internal friction as a function of temperature were obtained with a torsion pendulum of the inverted Ke-type and resolved, using the method of successive subtraction, into a series of constituent Debye peaks corresponding to different interactions. For each relaxation process it was possible to obtain the height (Q(max)(-1)) and temperature (T-p) of the peak, the activation energy (E) and the relaxation time (t(o)). The height, shape and temperature of these peaks depend on the concentration of interstitial elements. The observed peaks were associated with matrix-interstitial (Nb-O, Nb-N) and interstitial-interstitial (O-N) interaction processes. (C) 2003 Elsevier B.V. All rights reserved.

Monte Carlo and modified Tanford-Kirkwood results for macromolecular electrostatics calculations

The understanding of electrostatic interactions is an essential aspect of the complex correlation between structure and function of biological macromolecules. It is also important in protein engineering and design. Theoretical studies of such interactions are predominantly done within the framework of Debye-Huckel theory. A classical example is the Tanford-Kirkwood (TK) model. Besides other limitations, this model assumes an infinitesimally small macromolecule concentration. By comparison to Monte Carlo (MC) simulations, it is shown that TK predictions for the shifts in ion binding constants upon addition of salt become less reliable even at moderately macromolecular concentrations. A simple modification based on colloidal literature is suggested to the TK scheme. The modified TK models suggested here satisfactorily predict MC and experimental shifts in the calcium binding constant as a function of protein concentration for the calbindin D-9k mutant and calmodulin.

Magnetic behavior of interstitial Fe impurities in divalent Ca, Sr, and Yb hosts

We have used a first-principles real-space approach to investigate the electronic structure and the magnetic behavior of interstitial Fe impurities in divalent Ca, Sr, and Yb hosts. The dependence of the local moment as a function of lattice relaxation around the impurity is obtained and contrasted with that of interstitial Fe in trivalent and tetravalent Zr, Y, Ti, and Sc hosts. The trends obtained for local moment formation at the impurity site an in agreement with experimental time-differential perturbed gamma-ray angular distribution technique observations.

Soliton propagation in a medium with Kerr nonlinearity and resonant impurities: A variational approach

The soliton propagation in a medium with Kerr nonlinearity and resonant impurities was studied by a variational approach. The existence of a solitary wave was shown within the framework of a combined nonintegrable system composed of one nonlinear Schrödinger and a pair of Bloch equations. The analytical solution which was obtained, was tested through numerical simulations confirming its solitary wave nature.

Macromolecular array patterns of silk gland secretion in social Hymenoptera larvae

The cocoon, produced by most holometabolous insects, is built with silk that is usually produced by the larval salivary gland. Although this silk has been widely studied in the Lepidoptera, its composition and macromolecular arrangement remains unknown in the Hymenoptera. The macromolecular array patterns of the silk in the larval salivary gland of some meliponids, wasps, and ants were analyzed with polarized-light microscopy, and they were compared with those of Bombyx mori (Lepidoptera). There is a birefringent secretion in the glandular lumen of all larvae, due to filamentous structural proteins that display anisotropy. The silk in the distal, middle and proximal regions of the secretory portion of Formicidae and Vespidae glands presented a lattice optical pattern. We found a different pattern in the middle secretory portion of the Meliponini, with a zigzag rather than a lattice pattern. This indicates that the biopolymer fibers begin their macromolecular reorganization at this glandular region, different from the Formicidae and the Vespidae, in which the zigzag optical pattern was only found at the lateral duct. Probably, the mechanism of silk production in the Hymenoptera is a characteristic inherited from a common ancestor of Vespoidea and Sphecoidea; the alterations in the pattern observed in the Meliponini could be a derived characteristic in the Hymenoptera. We found no similarity in the macromolecular reorganization patterns of the silk between the Hymenoptera species and the silkworm.

Agronomic effectiveness of cationic phosphate impurities present in superphosphate fertilizers as affected by soil pH

The general concept that low-water-soluble phosphorus (P) fertilizers should be more agronomically effective when applied to acidic soils was developed based on sources containing mainly calcium (Ca)-P compounds, but it may not hold true for sources with different chemical composition. To obtain information related to this issue, two important iron (Fe)-potassium (K)-P compounds present in superphosphates [Fe 3 KH 8 (PO 4 ) 6·6H 2 O, H8, and Fe 3 KH 14 (PO 4 ) 8·4H 2 O, H14] were prepared and characterized. These P sources were used to provide 30 and 60 mg P kg -1 as neutral ammonium citrate (NAC)+H 2 O-soluble P. Reagent-grade monocalcium phosphate (MCP) was used as a standard P source with high water solubility with an additional rate of 120 mg P kg -1 included. Also, mixtures of both Fe-K-P compounds and MCP were prepared to provide 0, 25, 50, 75, and 100% of the total P as MCP. All sources were applied to a clayey loamy acid soil (pH 5.3) classified as Rhodic Kanhapludult. The soil was incubated at two rates (0 and 10 g kg -1 ) of lime, which resulted in pH 5.4 and 6.8. Upland rice was cultivated to maturity. The H14 compound confirmed to be a highly effective source of P for the rice plants at both soil pH, as opposed to the H8, which was poorly effective when applied alone. When mixed with water-soluble P (WSP), the H8 was able to provide P to the plants with the maximum yield of upland rice reached with 54.8 and 80.5% of WSP for pH 5.4 and 6.8, respectively. The high agronomic performance of the H14 compound clearly indicates that this low-water-soluble P source cannot be deemed as ineffective at high soil pH. Copyright © Taylor & Francis Group, LLC.

Synergy of DNA-bending nucleoid proteins and macromolecular crowding in condensing DNA

Many prokaryotic nucleoid proteins bend DNA and form extended helical protein-DNA fibers rather than condensed structures. On the other hand, it is known that such proteins (such as bacterial HU) strongly promote DNA condensation by macromolecular crowding. Using theoretical arguments, we show that this synergy is a simple consequence of the larger diameter and lower net charge density of the protein-DNA filaments as compared to naked DNA, and hence, should be quite general. To illustrate this generality, we use light-scattering to show that the 7kDa basic archaeal nucleoid protein Sso7d from Sulfolobus solfataricus (known to sharply bend DNA) likewise does not significantly condense DNA by itself. However, the resulting protein-DNA fibers are again highly susceptible to crowding-induced condensation. Clearly, if DNA-bending nucleoid proteins fail to condense DNA in dilute solution, this does not mean that they do not contribute to DNA condensation in the context of the crowded living cell. © 2007 World Scientific Publishing Company.

Crystal structure of Jararacussin-I: The highly negatively charged catalytic interface contributes to macromolecular selectivity in snake venom thrombin-like enzymes

Snake venom serine proteinases (SVSPs) are hemostatically active toxins that perturb the maintenance and regulation of both the blood coagulation cascade and fibrinolytic feedback system at specific points, and hence, are widely used as tools in pharmacological and clinical diagnosis. The crystal structure of a thrombin-like enzyme (TLE) from Bothrops jararacussu venom (Jararacussin-I) was determined at 2.48 Å resolution. This is the first crystal structure of a TLE and allows structural comparisons with both the Agkistrodon contortrix contortrix Protein C Activator and the Trimeresurus stejnegeri plasminogen activator. Despite the highly conserved overall fold, significant differences in the amino acid compositions and three-dimensional conformations of the loops surrounding the active site significantly alter the molecular topography and charge distribution profile of the catalytic interface. In contrast to other SVSPs, the catalytic interface of Jararacussin-I is highly negatively charged, which contributes to its unique macromolecular selectivity. © 2012 The Protein Society.