The three-dimensional structure of bothropasin, the main hemorrhagic factor from Bothrops jararaca venom: Insights for a new classification of snake venom metalloprotease subgroups

Bothropasin is a 48 kDa hemorrhagic PIII snake venom metalloprotease (SVMP) isolated from Bothrops jararaca, containing disintegrin/cysteine-rich adhesive domains. Here we present the crystal structure of bothropasin complexed with the inhibitor POL647. The catalytic domain consists of a scaffold of two subdomains organized similarly to those described for other SVMPs, including the zinc and calcium-binding sites. The free cysteine residue Cys(189) is located within a hydrophobic core and it is not available for disulfide bonding or other interactions. There is no identifiable secondary structure for the disintegrin domain, but instead it is composed mostly of loops stabilized by seven disulfide bonds and by two calcium ions. The ECD region is in a loop and is structurally related to the RGD region of RGD disintegrins, which are derived from I`ll SVMPs. The ECD motif is stabilized by the Cys(117)_Cys(310) disulfide bond (between the disintegrin and cysteine-rich domains) and by one calcium ion. The side chain of Glu(276) of the ECD motif is exposed to solvent and free to make interactions. In bothropasin, the HVR (hyper-variable region) described for other Pill SVMPs in the cysteine-rich domain, presents a well-conserved sequence with respect to several other Pill members from different species. We propose that this subset be referred to as PIII-HCR (highly conserved region) SVMPs. The differences in the disintegrin-like, cysteine-rich or disintegrin-like cysteine-rich domains may be involved in selecting target binding, which in turn could generate substrate diversity or specificity for the catalytic domain. (C) 2008 Elsevier Ltd. All rights reserved.

Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations

Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 angstrom resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis, for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting beta-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge-charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.

Structure and Calcium-Binding Activity of LipL32, the Major Surface Antigen of Pathogenic Leptospira sp.

Leptospixosis, a spirochaetal zoonotic disease caused by Leptospira, has been recognized as an important emerging infectious disease. LipL32 is the major exposed outer membrane protein found exclusively in pathogenic leptospires, where it accounts for up to 75% of the total outer membrane proteins. It is highly immunogenic, and recent studies have implicated LipL32 as an extracellular matrix binding protein, interacting with collagens, fibronectin, and laminin. In order to better understand the biological role and the structural requirements for the function of this important lipoprotein, we have determined the 2.25-angstrom-resolution structure of recombinant LipL32 protein corresponding to residues 21-272 of the wild-type protein (LipL32(21-272)). The LipL32(21-272) monomer is made of a jelly-roll fold core from which several peripheral secondary structures protrude. LipL32(21-272) is structurally similar to several other jelly-roll proteins, some of which bind calcium ions and extracellular matrix proteins. Indeed, spectroscopic data (circular dichroism, intrinsic tryptophan fluorescence, and extrinsic 1-amino-2-naphthol-4-sulfonic acid fluorescence) confirmed the calcium-binding properties of LipL32(21-272). Ca(2+) binding resulted in a significant increase in the thermal stability of the protein, and binding was specific for Ca(2+) as no structural or stability perturbations were observed for Mg(2+), Zn(2+), or Cu(2+). Careful examination of the crystal lographic structure suggests the locations of putative regions that could mediate Ca(2+) binding as well as binding to other interacting host proteins, such as collagens, fibronectin, and lamixidn. (C) 2009 Elsevier Ltd. All rights reserved.

Impacto da emissão dual-class na estrutura de capital

A tese propõe que empresas que emitem apenas ações com direitos de voto utilizam mais capitais de terceiros do que empresas que emitem tanto ações votantes quanto não votantes. No desenvolvimento do trabalho, foi demonstrada a relevância de relacionar endividamento ao fato de uma empresa emitir ou não ações sem direito a voto, considerando as principais teorias de estrutura de capital e a realidade brasileira. Como os modelos teóricos que explicam o nível de endividamento das empresas ainda carecem de capacidade explicativa, a busca por novos determinantes está presente na literatura de estrutura de capital. A ocorrência da emissão de ações em classes diferenciadas (dual-class) como fator impactante no nível de endividamento foi analisada sob três prismas: de mercado, dos setores e das empresas que unificaram suas ações. Pelas três investigações ficou evidenciada a perspectiva de que o endividamento seja menor nos casos de emissão de ações preferenciais, considerando o ambiente de negociação e regulamentação do Brasil. A aceitação da tese tem reflexos teóricos na identificação de um fator que deve ser levado em consideração nos modelos de estrutura de capital, bem como suscita a importância de gestores, investidores e credores reconhecerem que o fato de uma empresa ser dual-class impacta não apenas na sua estrutura de controle, mas principalmente em sua estrutura de capital. Entre as considerações da aceitação da tese, estaria o reconhecimento de que empresas que ingressam no Novo Mercado na prática estão, no longo prazo, trocando o uso de ações preferenciais como forma de financiamento pela emissão de dívida.

KittyCat: a cognitive model of structure-form discovery

Cognition is a core subject to understand how humans think and behave. In that sense, it is clear that Cognition is a great ally to Management, as the later deals with people and is very interested in how they behave, think, and make decisions. However, even though Cognition shows great promise as a field, there are still many topics to be explored and learned in this fairly new area. Kemp & Tenembaum (2008) tried to a model graph-structure problem in which, given a dataset, the best underlying structure and form would emerge from said dataset by using bayesian probabilistic inferences. This work is very interesting because it addresses a key cognition problem: learning. According to the authors, analogous insights and discoveries, understanding the relationships of elements and how they are organized, play a very important part in cognitive development. That is, this are very basic phenomena that allow learning. Human beings minds do not function as computer that uses bayesian probabilistic inferences. People seem to think differently. Thus, we present a cognitively inspired method, KittyCat, based on FARG computer models (like Copycat and Numbo), to solve the proposed problem of discovery the underlying structural-form of a dataset.

Population structure, habitat use and conservation of short-finned pilot whales Globicephala macrorhynchus in the Archipelago of Madeira

This thesis provides information on the grouping structure, survival, abundance, dive characteristics and habitat preferences of short-finned pilot whales occurring in the oceanic archipelago of Madeira (Portugal, NE Atlantic), based on data collected between 2001-2011, and contributes for its conservation. Photo-identification methods and genetic analyses demonstrated that there is a large degree of variability in site fidelity, including resident, regular visitor and transient whales, and that they may not be genetically isolated. It is proposed that the pilot whales encountered in Madeira belong to a single population encompassing several clans, possibly three clans of island-associated (i.e. resident and regular visitor) whales and others of transients, each containing two to three matrilineal pods. Mark-recapture methods estimated that the island-associated community is composed of less than 150 individuals and that their survival rate is within the range of other long-lived cetacean species, and that around 300 whales of different residency patterns uses the southern area of the island of Madeira from mid-summer to mid-autumn. No significant trend was observed between years. Time-depth recorders deployed in adult whales during daytime revealed that they spend over ¾ of their time at the surface, that they have a low diving rate, and that transient whales also forage during their passage. The analyses of visual data collected from nautical and aerial line-transect surveys indicate a core/preferred habitat area in the south-east of the island of Madeira. That area is used for resting, socializing, foraging, breeding, calving and birthing. Thus, that area should be considered as an important habitat for this species, at least seasonally (during autumn) when the species is more abundant, and included in conservation plans. No direct threat needing urgent measures was identified, although the impact of some activities like whale-watching or marine traffic should be assessed.

Gross and microscopic observations on the lingual structure of the franciscana (Pontoporia blainvillei-gervais and d'orbigny, 1844)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Controlador em modo dual adaptativo robusto - DMARC

The so-called Dual Mode Adaptive Robust Control (DMARC) is proposed. The DMARC is a control strategy which interpolates the Model Reference Adaptive Control (MRAC) and the Variable Structure Model Reference Adaptive Control (VS-MRAC). The main idea is to incorporate the transient performance advantages of the VS-MRAC controller with the smoothness control signal in steady-state of the MRAC controller. Two basic algorithms are developed for the DMARC controller. In the first algorithm the controller's adjustment is made, in real time, through the variation of a parameter in the adaptation law. In the second algorithm the control law is generated, using fuzzy logic with Takagi-Sugeno s model, to obtain a combination of the MRAC and VS-MRAC control laws. In both cases, the combined control structure is shown to be robust to the parametric uncertainties and external disturbances, with a fast transient performance, practically without oscillations, and a smoothness steady-state control signal

Uma abordagem indireta para o Controlador em Modo Dual Adaptativo Robusto

In this work is proposed an indirect approach to the DualMode Adaptive Robust Controller (DMARC), combining the typicals transient and robustness properties of Variable Structure Systems, more specifically of Variable Structure Model Reference Adaptive Controller (VS-MRAC), with a smooth control signal in steady-state, typical of conventional Adaptive Controllers, as Model Reference Adaptive Controller (MRAC). The goal is to provide a more intuitive controller design, based on physical plant parameters, as resistances, inertia moments, capacitances, etc. Furthermore, with the objective to follow the evolutionary line of direct controllers, it will be proposed an indirect version for the Binary Model Reference Adaptive Controller (B-MRAC), that was the first controller attemptting to act as MRAC as well as VS-MRAC, depending on a pre-defined fixed parameter

On the performance of a dual-mode non-linear vibration energy harvesting device

The research trend for harvesting energy from the ambient vibration sources has moved from using a linear resonant generator to a non-linear generator in order to improve on the performance of a linear generator; for example, the relatively small bandwidth, intolerance to mistune and the suitability of the device for low-frequency applications. This article presents experimental results to illustrate the dynamic behaviour of a dual-mode non-linear energy-harvesting device operating in hardening and bi-stable modes under harmonic excitation. The device is able to change from one mode to another by altering the negative magnetic stiffness by adjusting the separation gap between the magnets and the iron core. Results for the device operating in both modes are presented. They show that there is a larger bandwidth for the device operating in the hardening mode compared to the equivalent linear device. However, the maximum power transfer theory is less applicable for the hardening mode due to occurrence of the maximum power at different frequencies, which depends on the non-linearity and the damping in the system. The results for the bi-stable mode show that the device is insensitive to a range of excitation frequencies depending upon the input level, damping and non-linearity.

Structure of chorismate synthase from Mycobacterium tuberculosis

In bacteria, fungi, plants, and apicomplexan parasites, the aromatics compounds, such as aromatics amino acids, are synthesized through seven enzymes from the shikimate pathway, which are absent in mammals. The absence of this pathway in mammals make them potential targets for development of new therapy against infectious diseases, such as tuberculosis, which is the world's second commonest cause of death from infectious disease. The last enzyme of shikimate pathway is the chorismate synthase (CS), which is responsible for conversion of the 5-enolpyruvylshikimate-3-phosphate to chorismate. Here, we report the crystallographic structure of CS from Mycobacterium tuberculosis (MtCS) at 2.65 angstrom resolution. The MtCS structure is similar to other CS structures, presenting beta-alpha-beta sandwich structural topology, in which each monomer of MtCS consists of a central helical core. The MtCS can be described as a tetramer formed by a dimer of dimers. However, analytical ultracentrifugation studies suggest the MtCS is a dimer with a more asymmetric shape than observed on the crystallographic dimer and the existence of a low equilibrium between dimer and tetramer. Our results suggest that the MtCS oligomerization is concentration dependent and some conformational changes must be involved on that event. (c) 2005 Elsevier B.V. All rights reserved.

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)

Structure of large two-neutron halos in light exotic nuclei

The structure of three-body halo nuclei formed by two neutrons and a core (nnc) is studied using zero-range interactions. The halo wave function can be completely parameterized only by the s-wave scattering lengths and two-neutron separation energy. The sizes and the neutron-neutron correlation function of Li-11 and Be-14 are calculated and compared to experimental data. A general classification scheme for three-body halos with two identical particles is discussed as well as the critical conditions to allow excited Efimov states.

Structure of exotic three-body systems

The classification of large halos formed by two identical particles and a core is systematically addressed according to interparticle distances. The root-mean-square distances between the constituents are described by universal scaling functions obtained from a renormalized zero-range model. Applications for halo nuclei, Li-11 and Be-14, and for atomicn He-4(3) are briefly discussed. The generalization to four-body systems is proposed.

Preparation of hierarchically structured porous aluminas by a dual soft template method

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)