Expression, purification and structural analysis of the Pyrococcus abyssi RNA binding protein PAB1135

Abstract Background The gene coding for the uncharacterized protein PAB1135 in the archaeon Pyrococcus abyssi is in the same operon as the ribonuclease P (RNase P) subunit Rpp30. Findings Here we report the expression, purification and structural analysis of PAB1135. We analyzed the interaction of PAB1135 with RNA and show that it binds efficiently double-stranded RNAs in a non-sequence specific manner. We also performed molecular modeling of the PAB1135 structure using the crystal structure of the protein Af2318 from Archaeoglobus fulgidus (2OGK) as the template. Conclusions Comparison of this model has lead to the identification of a region in PAB1135 that could be involved in recognizing double-stranded RNA.

Theoretical and experimental study of the excitonic binding energy in GaAs/AlGaAs single and coupled double quantum wells

This paper discusses the theoretical and experimental results obtained for the excitonic binding energy (Eb) in a set of single and coupled double quantum wells (SQWs and CDQWs) of GaAs/AlGaAs with different Al concentrations (Al%) and inter-well barrier thicknesses. To obtain the theoretical Eb the method proposed by Mathieu, Lefebvre and Christol (MLC) was used, which is based on the idea of fractional-dimension space, together with the approach proposed by Zhao et al., which extends the MLC method for application in CDQWs. Through magnetophotoluminescence (MPL) measurements performed at 4 K with magnetic fields ranging from 0 T to 12 T, the diamagnetic shift curves were plotted and adjusted using two expressions: one appropriate to fit the curve in the range of low intensity fields and another for the range of high intensity fields, providing the experimental Eb values. The effects of increasing the Al% and the inter-well barrier thickness on Eb are discussed. The Eb reduction when going from the SQW to the CDQW with 5 Å inter-well barrier is clearly observed experimentally for 35% Al concentration and this trend can be noticed even for concentrations as low as 25% and 15%, although the Eb variations in these latter cases are within the error bars. As the Zhao's approach is unable to describe this effect, the wave functions and the probability densities for electrons and holes were calculated, allowing us to explain this effect as being due to a decrease in the spatial superposition of the wave functions caused by the thin inter-well barrier.

Bias and learning in temporal binding: intervals between actions and outcomes are compressed by prior bias

It has consistently been shown that agents judge the intervals between their actions and outcomes as compressed in time, an effect named intentional binding. In the present work, we investigated whether this effect is result of prior bias volunteers have about the timing of the consequences of their actions, or if it is due to learning that occurs during the experimental session. Volunteers made temporal estimates of the interval between their action and target onset (Action conditions), or between two events (No-Action conditions). Our results show that temporal estimates become shorter throughout each experimental block in both conditions. Moreover, we found that observers judged intervals between action and outcomes as shorter even in very early trials of each block. To quantify the decrease of temporal judgments in experimental blocks, exponential functions were fitted to participants’ temporal judgments. The fitted parameters suggest that observers had different prior biases as to intervals between events in which action was involved. These findings suggest that prior bias might play a more important role in this effect than calibration-type learning processes.

Expression and accumulation of the two-domain odorant-binding protein AaegOBP45 in the ovaries of blood-fed Aedes aegypti

BACKGROUND: Aedes aegypti mosquitoes are the main vectors of dengue viruses. Despite global efforts to reduce the prevalence of dengue using integrated vector management strategies, innovative alternatives are necessary to help prevent virus transmission. Detailed characterizations of Ae. aegypti genes and their products provide information about the biology of mosquitoes and may serve as foundations for the design of new vector control methods. FINDINGS: We studied the Ae. aegypti gene, AAEL010714, that encodes a two-domain odorant-binding protein, AaegOBP45. The predicted gene structure and sequence were validated, although single nucleotide polymorphisms were observed. Transcriptional and translational products accumulate in the ovaries of blood fed females and are not detected or are at low abundance in other tissues. CONCLUSIONS: We validated the Ae. aegypti AAEL010714 gene sequence and characterized the expression profile of a two-domain OBP expressed in ovaries. We propose that AaegOBP45 function as a component of the mosquito eggshell.

Binding of the wheat germ lectin to Cryptococcus neoformans chitooligomers affects multiple mechanisms required for fungal pathogenesis

The principal capsular component of Cryptococcus neoformans, glucuronoxylomannan (GXM), interacts with surface glycans, including chitin-like oligomers. Although the role of GXM in cryptococcal infection has been well explored, there is no information on how chitooligomers affect fungal pathogenesis. In this study, surface chitooligomers of C. neoformans were blocked through the use of the wheat germ lectin (WGA) and the effects on animal pathogenesis, interaction with host cells, fungal growth and capsule formation were analyzed. Treatment of C. neoformans cells with WGA followed by infection of mice delayed mortality relative to animals infected with untreated fungal cells. This observation was associated with reduced brain colonization by lectin-treated cryptococci. Blocking chitooligomers also rendered yeast cells less efficient in their ability to associate with phagocytes. WGA did not affect fungal viability, but inhibited GXM release to the extracellular space and capsule formation. In WGA-treated yeast cells, genes that are involved in capsule formation and GXM traffic had their transcription levels decreased in comparison with untreated cells. Our results suggest that cellular pathways required for capsule formation and pathogenic mechanisms are affected by blocking chitin-derived structures at the cell surface of C. neoformans. Targeting chitooligomers with specific ligands may reveal new therapeutic alternatives to control cryptococcosis.

Probing the interaction of brain fatty acid binding protein (B-FABP) with model membranes

Brain fatty acid-binding protein (B-FABP) interacts with biological membranes and delivers polyunsaturated fatty acids (FAs) via a collisional mechanism. The binding of FAs in the protein and the interaction with membranes involve a motif called "portal region", formed by two small α-helices, A1 and A2, connected by a loop. We used a combination of site-directed mutagenesis and electron spin resonance to probe the changes in the protein and in the membrane model induced by their interaction. Spin labeled B-FABP mutants and lipidic spin probes incorporated into a membrane model confirmed that BFABP interacts with micelles through the portal region and led to structural changes in the protein as well in the micelles. These changes were greater in the presence of LPG when compared to the LPC models. ESR spectra of B-FABP labeled mutants showed the presence of two groups of residues that responded to the presence of micelles in opposite ways. In the presence of lysophospholipids, group I of residues, whose side chains point outwards from the contact region between the helices, had their mobility decreased in an environment of lower polarity when compared to the same residues in solution. The second group, composed by residues with side chains situated at the interface between the α-helices, experienced an increase in mobility in the presence of the model membranes. These modifications in the ESR spectra of B-FABP mutants are compatible with a less ordered structure of the portal region inner residues (group II) that is likely to facilitate the delivery of FAs to target membranes. On the other hand, residues in group I and micelle components have their mobilities decreased probably as a result of the formation of a collisional complex. Our results bring new insights for the understanding of the gating and delivery mechanisms of FABPs.

Interactions between calcium and heavy metals in Norway spruce : Accumulation and binding of metals in wood and bark

Waste products from the forest industry are to be spread in forests in Sweden to counteract nutrient depletion due to whole tree harvesting. This may increase the bioavailability of calcium (Ca) and heavy metals, such as cadmium (Cd), copper (Cu) and zinc (Zn) in forest soils. Heavy metals, like Cd, have already been enriched in forest soils in Sweden, due to deposition of air pollutions, and acidification of forest soils has increased the bioavailability of toxic metals for plant uptake. Changes in the bioavailability of metals may be reflected in altered accumulation of Ca and heavy metals in forest trees, changes in tree growth, including wood formation, and altered tree species composition. This thesis aims at examining: A) if inter- or intra- specific differences in sensitivity to Cd occur in the most common tree species of Sweden, and if so, to study if these can be explained by the uptake and distribution of Cd within the plant: B) how elevated levels of Ca, Cd, Cu and Zn affect the accumulation and attachment of metals in bark and wood, and growth of young Norway spruce (Picea abies): C) how waste products from the forest industry, such as wood ash, influence the contents of Ca, Cd, Cu and Zn in wood and bark of young Norway spruce. Sensitivity to Cd, and its uptake and distribution, in seedlings of Picea abies, Pinus sylvestris and Betula pendula from three regions (southern, central and northern parts) of Sweden, treated with varying concentrations of Cd, were compared. Differences in root sensitivity to Cd both among and within woody species were found and the differences could to some extent be explained by differences in uptake and translocation of Cd. The root sensitivity assays revealed that birch was the least, and spruce the most, sensitive species, both to the external and to tissue levels of Cd. The central ecotype of the species tested tended to be most Cd resistant. The radial distribution, accumulation and attachment of, and interactions between Ca and heavy metals in stems of two-year-old Norway spruce trees treated with elevated levels of Cd, Cu, Zn and/or Ca, were investigated. Further, the influence of these metals on growth, and on root metal content, was examined. Accumulation of the metals was enhanced in wood, bark and/or roots at elevated levels of the metal in question. Even at low levels of the metals, similar to after application of wood ash, an enhanced accumulation was apparent in wood and/or bark, except for Cd. The increased accumulation of Zn and Cu in the stem did not affect the growth. However, Cu decreased the accumulation of Ca in wood. Higher levels of Cu and Cd reduced the stem diameter and the toxic effect was associated with a reduced Ca content in wood. Copper and Cd also decreased the accumulation of Zn in the stem. On the other hand, elevated levels of Ca increased the stem diameter and reduced the accumulation of Cd, Cu, Zn and Mn in wood and/or bark. When metals interacted with each other the firmly bound fraction of the metal reduced was in almost all cases not affected. As an exception, Cd decreased the firmly bound fraction of Zn in the stem. The influence of pellets of wood ash (ash) or a mixture of wood ash and green liquor dregs (ash+GLD), in the amount of 3000 kg ha-1, on the contents of Ca, Cd, Cu and Zn in wood and bark of young Norway spruce in the field was examined. The effect of the treatments on the metal content of bark and wood was larger after 3 years than after 6 years. Treatment with ash+GLD had less effect on the heavy metal content of bark and wood than treatment with ash alone. The ash treatment increased the Cu and Zn content in bark and wood, respectively, after 3 years, and decreased the Ca content of the wood after 6 years. The ash+GLD treatment increased the Ca content of the bark and decreased the Zn content of bark and wood after 3 years. Both treatments reduced, or tended to decrease, the Cd content in wood and bark at both times. To conclude, small changes in the bioavailability of Ca, Cu, Cd and Zn in forest soils, such as after spreading pellets of wood ash or a mixture of wood ash and green liquor dregs from the forest industry, will be reflected in an altered accumulation of metals in wood and bark of Norway spruce. It will not only be reflected in changed accumulation of those metals in which bioavailability in the soil has been enhanced, but also of other metals, probably partly due to interactions between metals. When metals interact the exchangeable bound fraction of the metal reduced is suggested to be the main fraction affected. The small alterations in accumulation of metals should not affect the growth of Norway spruce, especially since the changes in accumulation of metals are low, and further since these decrease over time. However, as an exception, one positive and maybe persistent effect of the waste products is that these may decrease the accumulation of Cd in Norway spruce, which partly may be explained by competition with Ca for uptake, translocation and binding. A decreased accumulation of Cd in Norway spruce will probably affect the trees positively, since Norway spruce is one of the most sensitive species to Cd of the forest trees in Sweden. Thus, spreading of waste products from the forest industry may be a solution to decrease the accumulation of Cd in Norway spruce. In a longer perspective, this will decrease the risk of Cd altering the tree species composition of the forest ecosystem. An elevated bioavailability of Ca in forest soils will, in addition to Cd, probably also decrease the accumulation of other less competitive heavy metals, like Zn and Mn, in the stem.

Isolation and functional characterization of Hrp65-binding proteins in Chironomus tentans

It is well-established that the organization of nuclear components influences gene expression processes, yet little is known about the mechanisms that contribute to the spatial co-ordination of nuclear activities. The salivary gland cells of Chironomus tentans provide a suitable model system for studying gene expression in situ, as they allow for direct visualization of the synthesis, processing and export of a specific protein-coding transcript, the Balbiani ring (BR) pre-mRNA, in a nuclear environment in which chromatin and non-chromatin structures can easily be distinguished. The RNAbinding protein Hrp65 has been identified in this model system as a protein associated with non-chromatin nucleoplasmic fibers, referred to as connecting fibers (CFs). The CFs associate with BR RNP particles in the nucleoplasm, suggesting that Hrp65 is involved in mRNA biogenesis at the post-transcriptional level. However, the function of Hrp65 is not known, nor is the function or the composition of CFs. In the work described in this thesis, we have identified by yeast two-hybrid screening and characterized different proteins that bind to Hrp65. These proteins include a novel hnRNP protein in C. tentans named Hrp59, various isoforms of Hrp65, the splicing- and mRNA export factor HEL/UAP56, and a RING-domain protein of unknown function. Immuno-electron microscopy experiments showed that Hrp59 and HEL are present in CFs, and in larger structures in the nucleoplasm of C. tentans salivary gland cells. Hrp59 is a C. tentans homologue of human hnRNP M, and it associates cotranscriptionally with a subset of pre-mRNAs, including its own transcript, in a manner that does not depend quantitatively on the amount of synthesized RNA. Hrp59 accompanies the BR pre-mRNA from the gene to the nuclear envelope, and is released from the BR mRNA at the nuclear pore complex. We have identified the preferred RNA targets of Hrp59 in Drosophila cells, and we have shown that Hrp59 binds preferentially to exonic splicing enhancer sequences. Hrp65 self-associates through an evolutionarily conserved domain that can also mediate heterodimerization of Hrp65 homologues. Different isoforms of Hrp65 interact with each other in all possible combinations, and Hrp65 can oligomerize into complexes of at least six molecules. The interaction between different Hrp65 isoforms is crucial for their intracellular localization, and we have discovered a mechanism by which Hrp65-2 is imported into the nucleus through binding to Hrp65-1. Hrp65 binds to HEL/UAP56 in C. tentans cells. We have analyzed the distribution of the two proteins on polytene chromosomes and in the nucleoplasm of salivary gland cells, and our results suggest that Hrp65 and HEL become associated during posttranscriptional gene expression events. HEL binds to the BR pre-mRNP cotranscriptionally, and incorporation of HEL into the pre-mRNP does not depend on the location of introns along the BR pre-mRNA. HEL accompanies the BR mRNP to the nuclear pore and is released from the BR mRNP during translocation into the cytoplasm.

Characterization of L-type Calcium Channel Binding-Site of a new class of Calcium modulators by a Multidisciplinary approach

Many potential diltiazem related L-VDCC blockers were developed using a multidisciplinary approach. This current study was to investigate and compare diltiazem with to the newly developed compounds by mouse Langendorff-perfused heart, Ca2+-transient and on recombinant L-VDCC. Twenty particular compounds were selected by the ligand-based virtual screening procedure (LBVS). From these compounds, five of them (5b, M2, M7, M8 and P1) showed a potent and selective inotropic activity on guinea-pig left atria driven 1 Hz. Further assays displayed an interesting negative inotropic effect of M2, M8, P1 and M7 on guinea pig isolated left papillary muscle driven at 1 Hz, a relevant vasorelaxant activity of 5b, M2, M7, M8 and P1 on K+-depolarized guinea-pig ileum longitudinal smooth muscle and a significant inhibition of contraction of 5b, M2, M8 and P1 on carbachol stimulated ileum longitudinal smooth muscle. Wild-type human heart and rabbit lung α1 subunits were expressed (combined with the regulatory α2δ and β3 subunits) in Xenopus Leavis oocytes using a two-electrode voltage clamp technique. Diltiazem is a benzothiazepine Ca2+ channel blocker used clinically for its antihypertensive and antiarrhythmic effects. Previous radioligand binding assays revealed a complex interaction with the benzothiazepine binding site for M2, M7 and M8. (Carosati E. et al. J. Med Chem. 2006, 49; 5206). In agreement with this findings, the relative order of increased rates of contraction and relaxation at lower concentrations s(≤10-6M) in unpaced hearts was M7>M2>M8>P1. Similar increases in Ca2+ transient were observed in cardiomyocytes. Diltiazem showed negative inotropic effects whereas 5b had no significant effect. Diltiazem blocks Ca2+current in a use-dependent manner and facilitates the channel by accelerating the inactivation and decelerating the recovery from inactivation. In contrast to diltiazem, the new analogs had no pronounced use-dependence. Application of 100 μM M8, M2 showed ~ 10% tonic block; in addition, M8, M2 and P1 shifted the steady state inactivation in hyperpolarized direction and the current inactivation time was significantly decreased compared with control (219.6 ± 11.5 ms, 226 ± 14.5 vs. 269 ± 12.9 vs. 199.28 ± 8.19 ms). Contrary to diltiazem, the recovery from the block by M8 and M2 was comparable to control. Only P1 showed a significantly decrease of the time for the recovery from inactivation. All of the compounds displayed the same sensitivity on the Ca2+ channel rabbit lung α1 except P1. Taken together, these findings suggest that M8, M2 and P1 might directly decrease the binding affinity or allow rapid dissociation from the benzothiazepine binding site.

Molecular architecture of fur binding to iron-induced and - repressed genes in Helicobacter pylori

The ferric uptake regulator protein Fur regulates iron-dependent gene expression in bacteria. In the human pathogen Helicobacter pylori, Fur has been shown to regulate iron-induced and iron-repressed genes. Herein we investigate the molecular mechanisms that control this differential iron-responsive Fur regulation. Hydroxyl radical footprinting showed that Fur has different binding architectures, which characterize distinct operator typologies. On operators recognized with higher affinity by holo-Fur, the protein binds to a continuous AT-rich stretch of about 20 bp, displaying an extended protection pattern. This is indicative of protein wrapping around the DNA helix. DNA binding interference assays with the minor groove binding drug distamycin A, point out that the recognition of the holo-operators occurs through the minor groove of the DNA. By contrast, on the apo-operators, Fur binds primarily to thymine dimers within a newly identified TCATTn10TT consensus element, indicative of Fur binding to one side of the DNA, in the major groove of the double helix. Reconstitution of the TCATTn10TT motif within a holo-operator results in a feature binding swap from an holo-Fur- to an apo-Fur-recognized operator, affecting both affinity and binding architecture of Fur, and conferring apo-Fur repression features in vivo. Size exclusion chromatography indicated that Fur is a dimer in solution. However, in the presence of divalent metal ions the protein is able to multimerize. Accordingly, apo-Fur binds DNA as a dimer in gel shift assays, while in presence of iron, higher order complexes are formed. Stoichiometric Ferguson analysis indicates that these complexes correspond to one or two Fur tetramers, each bound to an operator element. Together these data suggest that the apo- and holo-Fur repression mechanisms apparently rely on two distinctive modes of operator-recognition, involving respectively the readout of a specific nucleotide consensus motif in the major groove for apo-operators, and the recognition of AT-rich stretches in the minor groove for holo-operators, whereas the iron-responsive binding affinity is controlled through metal-dependent shaping of the protein structure in order to match preferentially the major or the minor groove.

The role of the NG2 proteoglycan in migration and characterization of the interaction with the intracellular binding partner, Syntenin

NG2 is a transmembrane proteoglycan with two N-terminal LNS domains and a C-terminal PDZ-binding motif. It is expressed in the developing and adult CNS by oligodendroglial precursor cells and subpopulations of perisynaptic glia and elsewhere by many immature cell types. In order to elucidate the functions of the protein and the heterogenous cell population which expresses it, we undertook to identify and characterise interaction partners of the molecule. The presence of the C-terminal PDZ recognition site in NG2 suggested PDZ-domain proteins as intracellular binding partners. In this work, interaction between the PDZ protein Syntenin and NG2 has been characterised. Syntenin is known to be involved in plasma membrane dynamics, metastasis and adhesion. Syntenin may thus link NG2 to the cytoskeleton, mediating migration of developing oligodendrocytes to axonal tracts prior to myelination, as well as process movement of NG2+ perisynaptic glia. NG2 is involved in cell spreading and polyclonal antibodies against NG2 inhibit the migration of immature glia and cell lines expressing the molecule. In this work we have characterised the segments of the extracellular portion of NG2 that are involved in migration. We found that the extracellular region immediately preceding the transmembrane segment is most important for cell motility. As part of this thesis, biochemical approaches to identify a trans-binding ligand interacting with the extracellular part of NG2 was also explored.

Identification of the N-Linked Glycosylation Sites of the Transcription Factor Rest and Effect of Glycosylation on DNA Binding and Transcriptional Activity

REST is a zinc-finger transcription factor implicated in several processes such as maintenance of embryonic stem cell pluripotency and regulation of mitotic fidelity in non-neuronal cells [Chong et al., 1995]. The gene encodes for a 116-kDa protein that acts as a molecular platform for co-repressors recruitment and promotes modifications of DNA and histones [Ballas, 2005]. REST showed different apparent molecular weights, consistent with the possible presence of post-translational modifications [Lee et al., 2000]. Among these the most common is glycosylation, the covalent attachment of carbohydrates during or after protein synthesis [Apweiler et al., 1999] My thesis has ascertained, for the first time, the presence of glycan chians in the transcription factor REST. Through enzymatic deglycosylation and MS, oligosaccharide composition of glycan chains was evaluated: a complex mixture of glycans, composed of N-acetylgalactosamine, galactose and mannose, was observed thus confirming the presence of O- and N-linked glycan chains. Glycosylation site mapping was done using a 18O-labeling method and MS/MS and twelve potential N-glycosylation sites were identified. The most probable glycosylation target residues were mutated through site-directed mutagenesis and REST mutants were expressed in different cell lines. Variations in the protein molecular weight and mutant REST ability to bind the RE-1 sequence were analyzed. Gene reporter assays showed that, altogether, removal of N-linked glycan chains causes loss of transcriptional repressor function, except for mutant N59 which showed a slight residual repressor activity in presence of IGF-I. Taken togheter these results demonstrate the presence of complex glycan chians in the transcription factor REST: I have depicted their composition, started defining their position on the protein backbone and identified their possible role in the transcription factor functioning. Considering the crucial role of glycosylation and transcription factors activity in the aetiology of many diseases, any further knowledge could find important and interesting pharmacological application.