Structure, Dynamics, and RNA Interaction Analysis of the Human SBDS Protein

Shwachman-Bodian-Diamond syndrome is an autosomal recessive genetic syndrome with pleiotropic phenotypes, including pancreatic deficiencies, bone marrow dysfunctions with increased risk of myelodysplasia or leukemia, and skeletal abnormalities. This syndrome has been associated with mutations in the SBDS gene, which encodes a conserved protein showing orthologs in Archaea and eukaryotes. The Shwachman-Bodian-Diamond syndrome pleiotropic phenotypes may be an indication of different cell type requirements for a fully functional SBDS protein. RNA-binding activity has been predicted for archaeal and yeast SBDS orthologs, with the latter also being implicated in ribosome biogenesis. However, full-length SBDS orthologs function in a species-specific manner, indicating that the knowledge obtained from model systems may be of limited use in understanding major unresolved issues regarding SBDS function, namely, the effect of mutations in human SBDS on its biochemical function and the specificity of RNA interaction. We determined the solution structure and backbone dynamics of the human SBDS protein and describe its RNA binding site using NMR spectroscopy. Similarly to the crystal structures of Archaea, the overall structure of human SBDS comprises three well-folded domains. However, significant conformational exchange was observed in NMR dynamics experiments for the flexible linker between the N-terminal domain and the central domain, and these experiments also reflect the relative motions of the domains. RNA titrations monitored by heteronuclear correlation experiments and chemical shift mapping analysis identified a classic RNA binding site at the N-terminal FYSH (fungal, Yhr087wp, Shwachman) domain that concentrates most of the mutations described for the human SBDS. (C) 2010 Elsevier Ltd. All rights reserved.

On the interaction of bovine serum albumin with ionic surfactants: Temperature induced EPR changes of a maleimide nitroxide reflect local protein dynamics and probe solvent accessibility

The interaction of bovine serum albumin (BSA) with the ionic surfactants sodium dodecylsulfate (SDS, anionic), cetyltrimethylammonium chloride (CTAC, cationic) and N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (HPS, zwitterionic) was studied by electron paramagnetic resonance (EPR) spectroscopy of spin label covalently bound to the single free thiol group of the protein. EPR spectra simulation allows to monitor the protein dynamics at the labeling site and to estimate the changes in standard Gibbs free energy, enthalpy and entropy for transferring the nitroxide side chain from the more motionally restricted to the less restricted component. Whereas SDS and CTAC showed similar increases in the dynamics of the protein backbone for all measured concentrations. HPS presented a smaller effect at concentrations above 1.5 mM. At 10 mM of surfactants and 0.15 mM BSA, the standard Gibbs free energy change was consistent with protein backbone conformations more expanded and exposed to the solvent as compared to the native protein, but with a less pronounced effect for HPS. In the presence of the surfactants, the enthalpy change, related to the energy required to dissociate the nitroxide side chain from the protein, was greater, suggesting a lower water activity. The nitroxide side chain also detected a higher viscosity environment in the vicinity of the paramagnetic probe induced by the addition of the surfactants. The results suggest that the surfactant-BSA interaction, at higher surfactant concentration, is affected by the affinities of the surfactant to its own micelles and micelle-like aggregates. Complementary DLS data suggests that the temperature induced changes monitored by the nitroxide probe reflects local changes in the vicinity of the single thiol group of Cys-34 BSA residue. (C) 2011 Elsevier B.V. All rights reserved.

Stoichiometry and thermodynamics of the interaction between the C-terminus of human 90 kDa heat shock protein Hsp90 and the mitochondrial translocase of outer membrane Tom70

A large majority of the 1000-1500 proteins in the mitochondria are encoded by the nuclear genome, and therefore, they are translated in the cytosol in the form and contain signals to enable the import of proteins into the organelle. The TOM complex is the major translocase of the outer membrane responsible for preprotein translocation. It consists of a general import pore complex and two membrane import receptors, Tom20 and Tom70. Tom70 contains a characteristic TPR domain, which is a docking site for the Hsp70 and Hsp90 chaperones. These chaperones are involved in protecting cytosolic preproteins from aggregation and then in delivering them to the TOM complex. Although highly significant, many aspects of the interaction between Tom70 and Hsp90 are still uncertain. Thus, we used biophysical tools to study the interaction between the C-terminal domain of Hsp90 (C-Hsp90), which contains the EEVD motif that binds to TPR domains, and the cytosolic fragment of Tom70. The results indicate a stoichiometry of binding of one monomer of Tom70 per dimer of C-Hsp90 with a K(D) of 360 30 nM, and the stoichiometry and thermodynamic parameters obtained suggested that Tom70 presents a different mechanism of interaction with Hsp90 when compared with other TPR proteins investigated. (C) 2011 Elsevier Inc. All rights reserved.

On the interaction of bovine serum albumin with ionic surfactants: Temperature induced EPR changes of a maleimide nitroxide reflect local protein dynamics and probe solvent accessibility

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Interaction between brain L-type calcium channels and alpha(2)-adrenoceptors in the inhibition of sodium appetite

Calcium channels mediate the actions of many drugs. The present work investigated whether diltiazem, an L-type calcium channel blocker, alters the inhibition of sodium appetite induced by noradrenaline and the alpha(2)-adrenoceptor agonist clonidine. Adult male Holtzman rats (N=4-8) with cannula implanted into the third cerebral ventricle were submitted to sodium depletion {furosemide sc+24-h removal of ambiente sodium). Sodium depleted control animals that received 0.9% NaCl as vehicle injected intracerebroventricularly (i.c.v) ingested 13.0+/-1.5 ml/120 min of 1.8% NaCl. Intracerebroventricular injection of either noradrenaline (80 nmol) or clonidine (20 nmol) inhibited 1.8% NaCl intake from 70 to 90%. Prior i.c.v. injection of diltiazem (6-48 nmol) inhibited from 50 to 100% the effect of noradrenaline and clonidine in a dose-response manner. Diltiazem alone at 100 nmol inhibited, but at 50 nmol had no effect on, sodium appetite. The results suggest: (1) common ionic mechanisms involving calcium channels for the inhibition that noradrenaline and clonidine exert on sodium appetite and (2) a dual role for the benzothiazepine site of L-type calcium channels in the control of sodium appetite. (C) 2002 Elsevier B.V. B V. All rights reserved.

Experimental paracoccidioidomycosis in hamster: transmission electron microscopy of inoculation site lesion

Estudou-se sequencialmente, à microscopia eletrônica de transmissão, a interação entre Paracoccidioides brasiliensis (Pb) e células inflamatórias em hamsters inoculados por via intratesticular. Seis horas após inoculações havia predominância de neutrófilos, estando presentes algumas células mononucleares e eosinófilos. Os neutrófilos foram progressivamente substituídos por células mononucleares. Fungos viáveis apresentavam-se fagocitados ou circunscritos por células inflamatórias, geralmente com ampla interface hospedeiro-parasita. Fungos mortos ou degenerados eram acompanhados de interfase estreita. A camada externa da parede do Pb era às vezes quebrada quando em contacto com neutrófilos, em vários pontos, sendo os fragmentos dessa parede descamados e fagocitados. Células fúngicas pequenas com um único núcleo se relacionavam com ampla interfase enquanto as células maiores e multinucleadas apresentavam paredes irregulares, por vezes, contendo lomasoma e/ou estrutura semelhante à mielina. Diferentes padrões de interação do Pb com células do hospedeiro podem ser decorrentes do a fluxo de células inflamatórias funcionalmente diferentes ao local de inoculação ou à idade dos fungos ou ambos os fatores.

Active and exo-site inhibition of human factor Xa: Structure of des-Gla factor Xa inhibited by NAP5, a potent nematode anticoagulant protein from Ancylostoma caninum

Hookworms are hematophagous nematodes capable of growth, development and subsistence in living host systems such as humans and other mammals. Approximately one billion, or one in six, people worldwide are infected by hookworms causing gastrointestinal blood loss and iron deficiency anemia. The hematophagous hookworm Ancylostoma caninum produces a family of small, disulfide-linked protein anticoagulants (75-84 amino acid residues). One of these nematode anticoagulant proteins, NAP5, inhibits the amidolytic activity of factor Xa (fXa) with K-i = 43 pM, and is the most potent natural fXa inhibitor identified thus far. The crystal structure of NAP5 bound at the active site of gamma-carboxyglutamic acid domainless factor Xa (des-fXa) has been determined at 3.1 angstrom resolution, which indicates that Asp189 (fXa, S1 subsite) binds to Arg40 (NAP5, P1 site) in a mode similar to that of the BPTI/trypsin interaction. However, the hydroxyl group of Ser39 of NAP5 additionally forms a hydrogen bond (2.5 angstrom) with His57 NE2 of the catalytic triad, replacing the hydrogen bond of Ser195 OG to the latter in the native structure, resulting in an interaction that has not been observed before. Furthermore, the C-terminal extension of NAP5 surprisingly interacts with the fXa exosite of a symmetry-equivalent molecule forming a short intermolecular beta-strand as observed in the structure of the NAPc2/fXa complex. This indicates that NAP5 can bind to fXa at the active site, or the exosite, and to fX at the exosite. However, unlike NAPc2, NAP5 does not inhibit fVIIa of the fVIIa/TF complex. (c) 2007 Elsevier Ltd. All rights reserved.

Determination of site-site distance and site concentration within polymer beads: A combined swelling-electron paramagnetic resonance study

[GRAPHICS]This work proposes a combined swelling-electron paramagnetic resonance (EPR) approach aiming at determining some unusual polymer solvation parameters relevant for chemical processes occurring inside beads. Batches of benzhydrylamine-resin (BHAR), a copolymer of styrene-1% divinylbenzene containing phenylmethylamine groups were, labeled with the paramagnetic amino acid 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amine-4-carboxylic acid (TOAC), and their swelling properties and EPR spectra were examined in DCM and DMF. By taking into account the BHARs labeling degrees, the corresponding swelling values, and some polymer structural characteristics, it was possible to calculate polymer swelling parameters, among them, the volume and the number of sites per bead, site-site distances and site concentration. The latter values ranged from 17 to 170 angstrom and from 0.4 to 550 mM, respectively. EPR spectroscopy was applied to validate the multistep calculation strategy of these swelling parameters. Spin-spin interaction was detected in the labeled resins at site-site distances less than approximately 60 A or probe concentrations higher than approximately 1 x 10(-2) M, in close agreement with the values obtained for the spin probe free in solution. Complementarily, the yield of coupling reactions in different resins indicated that the greater the inter-site distance or the lower the site concentration, the faster the reaction. The results suggested that the model and the experimental measurements developed for the determination of solvation parameters represent a relevant step forward for the deeper understanding and improvement of polymer-related processes.

A new biophysics approach using photoacoustic spectroscopy to study the DNA-ethidium bromide interaction

We have examined the binding processes of ethidium bromide interacting with calf thymus DNA using photoacoustic spectroscopy. These binding processes are generally investigated by a combination of absorption or fluorescence spectroscopies with hydrodynamic techniques. The employment of photoacoustic spectroscopy for the DNA-ethidium bromide system identified two binding manners for the dye. The presence of two isosbestic points (522 and 498 nm) during DNA titration was evidence of these binding modes. Analysis of the photoacoustic amplitude signal data was performed using the McGhee-von Hippel excluded site model. The binding constant obtained was 3.4 x 10(8) M(bp)(-1), and the number of base pairs excluded to another dye molecule by each bound dye molecule (n) was 2. A DNA drug dissociation process was applied using sodium dodecyl sulfate to elucidate the existence of a second and weaker binding mode. The dissociation constant determined was 0.43 mM, whose inverse value was less than the previously obtained binding constant, demonstrating the existence of the weaker binding mode. The calculated binding constant was adjusted by considering the dissociation constant and its new value was 1.2 x 10(9) M(bp)(-1) and the number of excluded sites was 2.6. Using the photoacoustic technique it is also possible to obtain results regarding the dependence of the quantum yield of the dye on its binding mode. While intercalated between two adjacent base pairs the quantum yield found was 0.87 and when associated with an external site it was 0.04. These results reinforce the presence of these two binding processes and show that photoacoustic spectroscopy is more extensive than commonly applied spectroscopies.

On the interaction of small molecules with hemoproteins: Sperm whale myoglobin

The spin label TEMPO does not show a binding to myoglobin molecule in solution. This is probably due to the fact that this protein does not have a hydrophobic pocket large enough to accommodate the TEMPO molecule. In the crystal the spin label is bound and two kinds of spectra are observed: one isotropic and the other anisotropic. The anisotropic site is probably an intermolecular one. The correlation time for the label in the crystal is very sensitive to temperature showing a transition near 30 °C. This change can be explained as a result of the conformational change observed for myoglobin near this temperature: the motion of the spin label becomes more restricted below this temperature. Change in hydration is the probable cause of this structural change. The changes in the EPR spectra of the anisotropic label suggest that it is bound near the first layers of protein in the crystal. © 1985 Societá Italiana di Fisica.

Study of water and dimethylformamide interaction by computer simulation

Monte Carlo simulations of water-dimethylformamide (DMF) mixtures were performed in the isothermal and isobaric ensemble at 298.15 K and 1 atm. The intermolecular interaction energy was calculated using the classical 6-12 Lennard-Jones pairwise potential plus a Coulomb term. The TIP4P model was used for simulating water molecules, and a six-site model previously optimised by us was used to represent DMF. The potential energy for the water-DMF interaction was obtained via standard geometric combining rules using the original potential parameters for the pure liquids. The radial distribution functions calculated for water-DMF mixtures show well characterised hydrogen bonds between the oxygen site of DMF and hydrogen of water. A structureless correlation curve was observed for the interaction between the hydrogen site of the carbonyl group and the oxygen site of water. Hydration effects on the stabilisation of the DMF molecule in aqueous solution have been investigated using statistical perturbation theory. The results show that energetic changes involved in the hydration process are not strong enough to stabilise another configuration of DMF than the planar one.

Biotic interaction between spionid polychaetes and bouchardiid brachiopods: Paleoecological, taphonomic and evolutionary implications

Shells of Bouchardia rosea (Brachiopoda, Rhynchonelliformea) are abundant in Late Holocene death assemblages of the Ubatuba Bight, Brazil, SW Atlantic. This genus is also known from multiple localities in the Cenozoic fossil record of South America. A total of 1211 valves of B. rosea, 2086 shells of sympatric bivalve mollusks (14 nearshore localities ranging in depth from 0 to 30 m), 80 shells of Bouchardia zitteli, San Julián Formation, Paleogene, Argentina, and 135 shells of Bouchardia transplatina, Camacho Formation, Neogene, Uruguay were examined for bioerosion traces. All examined bouchardiid shells represent shallow-water, subtropical marine settings. Out of 1211 brachiopod shells of B. rosea, 1201 represent dead individuals. A total of 149 dead specimens displayed polychaete traces (Caulostrepsis). Live polychaetes were found inside Caulostrepsis borings in 10 life-collected brachiopods, indicating a syn-vivo interaction (Caulostrepsis traces in dead shells of B. rosea were always empty). The long and coiled peristomial palps, large chaetae on both sides of the 5th segment, and flanged pygidium found in the polychaetes are characteristic of the polychaete genus Polydora (Spionidae). The fact that 100% of the Caulostrepsis found in living brachiopods were still inhabited by the trace-making spionids, whereas none was found in dead hosts, implies active biotic interaction between the two living organisms rather than colonization of dead brachiopod shells. The absence of blisters, the lack of valve/site stereotypy, and the fact that tubes open only externally are all suggestive of a commensal relationship. These data document a new host group (bouchardiid rhynchonelliform brachiopods) with which spionids can interact (interestingly, spionid-infested sympatric bivalves have not been found in the study area despite extensive sampling). The syn-vivo interaction indicates that substantial bioerosion may occur when the host is alive. Thus, the presence of such bioerosion traces on fossil shells need not imply a prolonged post-mortem exposure of shells on the sea floor. Also, none of the Paleogene and Neogene Bouchardia species included any ichnological evidence for spionid infestation. This indicates that the Spionidae/ Bouchardia association may be geologically young, although the lack of older records may also reflect limited sampling and/or taphonomic biases.

Interaction of Bacillus thuringiensis Cry1 and Vip3A proteins with Spodoptera frugiperda midgut binding sites

Vip3Aa, Vip3Af, Cry1Ab, and Cry1Fa were tested for their toxicities and binding interactions. Vip3A proteins were more toxic than Cry1 proteins. Binding assays showed independent specific binding sites for Cry1 and Vip3A proteins. Cry1Ab and Cry1Fa competed for the same binding sites, whereas Vip3Aa competed for those of Vip3Af. Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Evaluating interaction with websites: Case study of a government website of the Brazilian Ministry of labor and employment

This paper presents a usability evaluation of the MTE (Ministry of Labor e Employment) website in order to measure the effectiveness, efficiency and user satisfaction regarding the website. The participants were 12 users (07 users were female and 05 male). The results indicate that although the education level of all participants and computing experience, many of them have had difficulty in finding information and do not recommend the site. © 2013 Springer-Verlag Berlin Heidelberg.

Uma análise sobre a avaliação emocional de web site por similaridade e por contiguidade

Pós-graduação em Design - FAAC