Flexibility and inhibitor binding in Cdc25 phosphatases

Cdc25 phosphatases involved in cell cycle checkpoints are now active targets for the development of anti-cancer therapies. Rational drug design would certainly benefit from detailed structural information for Cdc25s. However, only apo- or sulfate-bound crystal structures of the Cdc25 catalytic domain have been described so far. Together with previously available crystalographic data, results from molecular dynamics simulations, bioinformatic analysis, and computer-generated conformational ensembles shown here indicate that the last 30-40 residues in the C-terminus of Cdc25B are partially unfolded or disordered in solution. The effect of C-terminal flexibility upon binding of two potent small molecule inhibitors to Cdc25B is then analyzed by using three structural models with variable levels of flexibility, including an equilibrium distributed ensemble of Cdc25B backbone conformations. The three Cdc25B structural models are used in combination with flexible docking, clustering, and calculation of binding free energies by the linear interaction energy approximation to construct and validate Cdc25B-inhibitor complexes. Two binding sites are identified on top and beside the Cdc25B active site. The diversity of interaction modes found increases with receptor flexibility. Backbone flexibility allows the formation of transient cavities or compact hydrophobic units on the surface of the stable, folded protein core that are unexposed or unavailable for ligand binding in rigid and densely packed crystal structures. The present results may help to speculate on the mechanisms of small molecule complexation to partially unfolded or locally disordered proteins.

Identification of a gene encoding adaptin-like protein in the Paracoccidioides brasiliensis genome by random amplified polymorphic DNA analysis

Paracoccidioides brasiliensis isolates are not homogeneous in their patterns of pathogenicity in animals and adhesion to epithelial cells. During this investigation, genotypic differences were observed between two samples of P. brasiliensis strain 18 yeast phase (Pbl 8) previously cultured many times, one taken before (Pb18a) and the other after (Pb18b) animal inoculation. Random amplified polymorphic DNA analysis using the primer OPJ4 distinguished Pb18b from Pbl Ba by one 308 bp DNA fragment, which after cloning and sequencing was shown to encode a polypeptide sequence homologous to the protein beta-adaptin. It is suggested, by comparison to other micro-organisms, that this protein might play an important role in the virulence of P. brasiliensis. This result demonstrates the influence of in vitro subculturing on the genotype of this organism.

Encoding mechanisms based on fast oscillations in the retina of the cat and their dependencies on anesthesia

Processing in the visual system starts in the retina. Its complex network of cells with different properties enables for parallel encoding and transmission of visual information to the lateral geniculate nucleus (LGN) and to the cortex. In the retina, it has been shown that responses are often accompanied by fast synchronous oscillations (30 - 90 Hz) in a stimulus-dependent manner. Studies in the frog, rabbit, cat and monkey, have shown strong oscillatory responses to large stimuli which probably encode global stimulus properties, such as size and continuity (Neuenschwander and Singer, 1996; Ishikane et al., 2005). Moreover, simultaneous recordings from different levels in the visual system have demonstrated that the oscillatory patterning of retinal ganglion cell responses are transmitted to the cortex via the LGN (Castelo-Branco et al., 1998). Overall these results suggest that feedforward synchronous oscillations contribute to visual encoding. In the present study on the LGN of the anesthetized cat, we further investigate the role of retinal oscillations in visual processing by applying complex stimuli, such as natural visual scenes, light spots of varying size and contrast, and flickering checkerboards. This is a necessary step for understanding encoding mechanisms in more naturalistic conditions, as currently most data on retinal oscillations have been limited to simple, flashed and stationary stimuli. Correlation analysis of spiking responses confirmed previous results showing that oscillatory responses in the retina (observed here from the LGN responses) largely depend on the size and stationarity of the stimulus. For natural scenes (gray-level and binary movies) oscillations appeared only for brief moments probably when receptive fields were dominated by large continuous, flat-contrast surfaces. Moreover, oscillatory responses to a circle stimulus could be broken with an annular mask indicating that synchronization arises from relatively local interactions among populations of activated cells in the retina. A surprising finding in this study was that retinal oscillations are highly dependent on halothane anesthesia levels. In the absence of halothane, oscillatory activity vanished independent of the characteristics of the stimuli. The same results were obtained for isoflurane, which has similar pharmacological properties. These new and unexpected findings question whether feedfoward oscillations in the early visual system are simply due to an imbalance between excitation and inhibition in the retinal networks generated by the halogenated anesthetics. Further studies in awake behaving animals are necessary to extend these conclusions

Flexibility and Torsional Strength of ProTaper and ProTaper Universal Rotary Instruments Assessed by Mechanical Tests

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The promoter of a gene encoding an isoflavone reductase-like protein in coffee (Coffea arabica) drives a stress-responsive expression in leaves

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

CaPrx, a Coffea arabica gene encoding a putative class III peroxidase induced by root-knot nematode infection

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

Constructions of codes through the semigroup ring B[X; 1/2(2)Z(0)] and encoding

For any finite commutative ring B with an identity there is a strict inclusion B[X; Z(0)] subset of B[X; Z(0)] subset of B[X; 1/2(2)Z(0)] of commutative semigroup rings. This work is a continuation of Shah et al. (2011) [8], in which we extend the study of Andrade and Palazzo (2005) [7] for cyclic codes through the semigroup ring B[X; 1/2; Z(0)] In this study we developed a construction technique of cyclic codes through a semigroup ring B[X; 1/2(2)Z(0)] instead of a polynomial ring. However in the second phase we independently considered BCH, alternant, Goppa, Srivastava codes through a semigroup ring B[X; 1/2(2)Z(0)]. Hence we improved several results of Shah et al. (2011) [8] and Andrade and Palazzo (2005) [7] in a broader sense. Published by Elsevier Ltd

Caste flexibility and variation according to the colony cycle in the swarm-founding wasp, Parachartergus fraternus (Gribodo) (Hymenoptera : Vespidae : Epiponini)

Differences between castes and related aspects in Parachartegus fraternus (Gribodo) have been studied in various stages of the colony cycle. Five colonies from three colony development stages (namely, pre-emergence, worker-producing and male-producing) were analyzed. The main results were: irrespective of colony age, castes were always morphologically indistinguishable; non-inseminated ovary-developed females were found in four colonies; because differences of castes were physiological rather than morphological, castes are evidently post-imaginally determined and this is probably taking place according to the colony conditions. These findings support the occurrence of caste totipotency in Parachartergus fraternus.

SEQUENCE OF A CDNA-ENCODING BOTHROPSTOXIN-I, A MYOTOXIN FROM THE VENOM OF BOTHROPS-JARARACUSSU

With the aim of further understanding the structure/function relationships in the membrane-damaging activity of the Lys(49) phospholipase A(2) (Lys(49)-PLA(2)) sub-family, we used PCR (polymerase chain reaction) on total venom gland cDNAs from Bothrops jararacussu with degenerate oligodeoxyribonucleotides encoding the N- and C-termini of myotoxin II, a Lys(49)-PLA(2) from Bothrops asper. A 350-bp cDNA coding for bothropstoxin I (BtxtxI) was amplified. Sequencing of the amplified fragment shows that BtxtxI has a Lys(49), and comparison with the known structure of myotoxin II showed that the amino acids involved in the formation of a novel dimeric structure in this protein were also conserved.