Molecular determinants of improved cathepsin B inhibition by new cystatins obtained by DNA shuffling

Background: Cystatins are inhibitors of cysteine proteases. The majority are only weak inhibitors of human cathepsin B, which has been associated with cancer, Alzheimer's disease and arthritis. Results: Starting from the sequences of oryzacystatin-1 and canecystatin-1, a shuffling library was designed and a hybrid clone obtained, which presented higher inhibitory activity towards cathepsin B. This clone presented two unanticipated point mutations as well as an N-terminal deletion. Reversing each point mutation independently or both simultaneously abolishes the inhibitory activity towards cathepsin B. Homology modeling together with experimental studies of the reverse mutants revealed the likely molecular determinants of the improved inhibitory activity to be related to decreased protein stability. Conclusion: A combination of experimental approaches including gene shuffling, enzyme assays and reverse mutation allied to molecular modeling has shed light upon the unexpected inhibitory properties of certain cystatin mutants against Cathepsin B. We conclude that mutations disrupting the hydrophobic core of phytocystatins increase the flexibility of the N-terminus, leading to an increase in inhibitory activity. Such mutations need not affect the inhibitory site directly but may be observed distant from it and manifest their effects via an uncoupling of its three components as a result of increased protein flexibility.

Structural and magnetic properties of the oxyborate Co(5)Ti(O(2)BO(3))(2)

We present an extensive study of the oxyborate material Co(5)Ti(O(2)BO(3))(2) using x-ray, magnetic, and thermodynamic measurements. This material belongs to a family of oxyborates known as ludwigites which presents low-dimensional subunits in the form of three leg ladders in its structure. Differently from previously investigated ludwigites the present material does not show long-range magnetic order although it goes into a spin-glass state at low temperatures. The different techniques employed in this paper allow for a characterization of the structure, the nature of the low-energy excitations and the magnetic anisotropy of this system. Its unique magnetic behavior is discussed and compared with those of other magnetic ludwigites.

Adenosine binding to low-molecular-weight purine nucleoside phosphorylase: the structural basis for recognition based on its complex with the enzyme from Schistosoma mansoni

Schistosomes are unable to synthesize purines de novo and depend exclusively on the salvage pathway for their purine requirements. It has been suggested that blockage of this pathway could lead to parasite death. The enzyme purine nucleoside phosphorylase (PNP) is one of its key components and molecules designed to inhibit the low-molecular-weight (LMW) PNPs, which include both the human and schistosome enzymes, are typically analogues of the natural substrates inosine and guanosine. Here, it is shown that adenosine both binds to Schistosoma mansoni PNP and behaves as a weak micromolar inhibitor of inosine phosphorolysis. Furthermore, the first crystal structures of complexes of an LMW PNP with adenosine and adenine are reported, together with those with inosine and hypoxanthine. These are used to propose a structural explanation for the selective binding of adenosine to some LMW PNPs but not to others. The results indicate that transition-state analogues based on adenosine or other 6-amino nucleosides should not be discounted as potential starting points for alternative inhibitors.

Density-functional description of superconducting and magnetic proximity effects across a tunneling barrier

A density-functional formalism for superconductivity and magnetism is presented. The resulting relations unify previously derived Kohn-Sham equations for superconductors and for noncollinear magnetism. The formalism, which discriminates Cooper-pair singlets from triplets, is applied to two quantum liquids coupled by tunneling through a barrier. An exact expression is derived, relating the eigenstates and eigenvalues of the Kohn-Sham equations, unperturbed by tunneling, on one side of the barrier to the proximity-induced ordering potential on the other.

Polarity-Dependent Transcranial Direct Current Stimulation Effects on Central Auditory Processing

Given the polarity dependent effects of transcranial direct current stimulation (tDCS) in facilitating or inhibiting neuronal processing, and tDCS effects on pitch perception, we tested the effects of tDCS on temporal aspects of auditory processing. We aimed to change baseline activity of the auditory cortex using tDCS as to modulate temporal aspects of auditory processing in healthy subjects without hearing impairment. Eleven subjects received 2mA bilateral anodal, cathodal and sham tDCS over auditory cortex in a randomized and counterbalanced order. Subjects were evaluated by the Random Gap Detection Test (RGDT), a test measuring temporal processing abilities in the auditory domain, before and during the stimulation. Statistical analysis revealed a significant interaction effect of time vs. tDCS condition for 4000 Hz and for clicks. Post-hoc tests showed significant differences according to stimulation polarity on RGDT performance: anodal improved 22.5% and cathodal decreased 54.5% subjects' performance, as compared to baseline. For clicks, anodal also increased performance in 29.4% when compared to baseline. tDCS presented polarity-dependent effects on the activity of the auditory cortex, which results in a positive or negative impact in a temporal resolution task performance. These results encourage further studies exploring tDCS in central auditory processing disorders.

Cross-Talk Between Mitochondria and NADPH Oxidase: Effects of Mild Mitochondrial Dysfunction on Angiotensin II-Mediated Increase in Nox Isoform Expression and Activity in Vascular Smooth Muscle Cells

Mitochondria and NADPH oxidase activation are concomitantly involved in pathogenesis of many vascular diseases. However, possible cross-talk between those ROS-generating systems is unclear. We induced mild mitochondrial dysfunction due to mitochondrial DNA damage after 24 h incubation of rabbit aortic smooth muscle (VSMC) with 250 ng/mL ethidium bromide (EtBr). VSMC remained viable and had 29% less oxygen consumption, 16% greater baseline hydrogen peroxide, and unchanged glutathione levels. Serum-stimulated proliferation was unaltered at 24 h. Although PCR amplification of several mtDNA sequences was preserved, D-Loop mtDNA region showed distinct amplification of shorter products after EtBr. Such evidence for DNA damage was further enhanced after angiotensin-II (AngII) incubation. Remarkably, the normally observed increase in VSMC membrane fraction NADPH oxidase activity after AngII was completely abrogated after EtBr, together with failure to upregulate Nox1 mRNA expression. Conversely, basal Nox4 mRNA expression increased 1.6-fold, while being unresponsive to AngII. Similar loss in AngII redox response occurred after 24 h antimycin-A incubation. Enhanced Nox4 expression was unassociated with endoplasmic reticulum stress markers. Protein disulfide isomerase, an NADPH oxidase regulator, exhibited increased expression and inverted pattern of migration to membrane fraction after EtBr. These results unravel functionally relevant cross-talk between mitochondria and NADPH oxidase, which markedly affects redox responses to AngII. Antioxid Redox Signal 11, 1265-1278.

LATENT RANK CHANGE DETECTION FOR ANALYSIS OF SPLICE-JUNCTION MICROARRAYS WITH NONLINEAR EFFECTS

Alternative splicing of gene transcripts greatly expands the functional capacity of the genome, and certain splice isoforms may indicate specific disease states such as cancer. Splice junction microarrays interrogate thousands of splice junctions, but data analysis is difficult and error prone because of the increased complexity compared to differential gene expression analysis. We present Rank Change Detection (RCD) as a method to identify differential splicing events based upon a straightforward probabilistic model comparing the over-or underrepresentation of two or more competing isoforms. RCD has advantages over commonly used methods because it is robust to false positive errors due to nonlinear trends in microarray measurements. Further, RCD does not depend on prior knowledge of splice isoforms, yet it takes advantage of the inherent structure of mutually exclusive junctions, and it is conceptually generalizable to other types of splicing arrays or RNA-Seq. RCD specifically identifies the biologically important cases when a splice junction becomes more or less prevalent compared to other mutually exclusive junctions. The example data is from different cell lines of glioblastoma tumors assayed with Agilent microarrays.

Hybrid layer-by-layer assembly based on animal and vegetable structural materials: multilayered films of collagen and cellulose nanowhiskers

Layer-by-layer (LBL) assembly was used to combine crystalline rod-like nanoparticles obtained from a vegetable source, cellulose nanowhiskers (CNWs), with collagen, the main component of skin and connective tissue found exclusively in animals. The film growth of the multilayered collagen/CNW was monitored by UV-Vis spectroscopy and ellipsometry measurements, whereas the film morphology and surface roughness were characterized by SEM and AFM. UV-Vis spectra showed the deposition of the same amount of collagen, 5 mg m(-2), in each dipping cycle. Ellipsometry data showed an increment in thickness with the number of layers, and the average thickness of each bilayer was found to be 8.6 nm. The multilayered bio-based nanocomposites were formed by single layers of densely packed CNWs adsorbed on top of each thin collagen layer where the hydrogen bonding between collagen amide groups and OH groups of the CNWs plays a mandatory role in the build-up of the thin films. The approach used in this work represents a potential strategy to mimic the characteristics of natural extracellular matrix (ECM) which can be used for applications in the biomedical field.

Structural control of gold nanoparticles self-assemblies by layer-by-layer process

This work presents a novel way to introduce gold nanoparticles (Au NPs) in a multilayer polymer produced by the layer-by-layer (LbL) assembling technique. The technique chosen shows that, depending on the pH used, different morphological structures can be obtained from monolayer or bilayer Au NPs. The MEIS and RBS techniques allowed for the modelling of the interface polymer-NPs, as well as the understanding of the interaction of LbL system, when adjusting the pH in weak polyelectrolytes. The process reveals that the optical properties of multilayer systems could be fine-tuned by controlling the addition of metallic nanoparticles, which could also modify specific polarization responses.

Surface effects in the magnetic properties of crystalline 3 nm ferrite nanoparticles chemically synthesized

We have systematically studied the magnetic properties of ferrite nanoparticles with 3, 7, and 11 nm of diameter with very narrow grain size distributions. Samples were prepared by the thermal decomposition of Fe (acac)(3) in the presence of surfactants giving nanoparticles covered by oleic acid. High resolution transmission electron microscopy (HRTEM) images and XRD diffraction patterns confirms that all samples are composed by crystalline nanoparticles with the spinel structure expected for the iron ferrite. ac and dc magnetization measurements, as well in-field Mossbauer spectroscopy, indicate that the magnetic properties of nanoparticles with 11 and 7 nm are close to those expected for a monodomain, presenting large M(S) (close to the magnetite bulk). Despite the crystalline structure observed in HRTEM images, the nanoparticles with 3 nm are composed by a magnetically ordered region (core) and a surface region that presents a different magnetic order and it contains about 66% of Fe atoms. The high saturation and irreversibility fields in the M(H) loops of the particles with 3 nm together with the misalignment at 120 kOe in the in-field Mossbauer spectrum of surface component indicate a high surface anisotropy for the surface atoms, which is not observed for the core. For T < 10 K, we observe an increase in the susceptibility and of the magnetization for former sample, indicating that surface moments tend to align with applied field increasing the magnetic core size. (C) 2010 American Institute of Physics. [doi:10.1063/1.3514585]

Spectroscopic, structural, and functional characterization of the alternative low-spin state of horse heart cytochrome c

The alternative low-spin states of Fe3+ and Fe2+ cytochrome c induced by SDS or AOT/hexane reverse micelles exhibited the heme group in a less rhombic symmetry and were characterized by electron paramagnetic resonance, UV-visible, CD, magnetic CD, fluorescence, and Raman resonance. Consistent with the replacement of Met 80 by another strong field ligand at the sixth heme iron coordination position, Fe3+ ALSScytc exhibited 1-nm Soret band blue shift and e enhancement accompanied by disappearance of the 695-nm charge transfer band. The Raman resonance, CD, and magnetic CD spectra of Fe3+ and Fe2+ ALSScytc exhibited significant changes suggestive of alterations in the heme iron microenvironment and conformation and should not be assigned to unfold because the Trp(59) fluorescence remained quenched by the neighboring heme group. ALSScytc was obtained with His(33) and His(26) carboxyethoxylated horse cytochrome c and with tuna cytochrome c (His(33) replaced by Asn) pointing out Lys(79) as the probable heme iron ligand. Fe3+ ALSScytc retained the capacity to cleave tert-butylhydroperoxide and to be reduced by dithiothreitol and diphenylacetaldehyde but not by ascorbate. Compatible with a more open heme crevice, ALSScytc exhibited a redox potential similar to 200 mV lower than the wild-type protein (1220 mV) and was more susceptible to the attack of free radicals.

Temperature effects on the oscillatory electro-oxidation of methanol on platinum

We report in this paper the effect of temperature on the oscillatory electro-oxidation of methanol on polycrystalline platinum in aqueous sulfuric acid media. Potential oscillations were studied under galvanostatic control and at four temperatures ranging from 5 to 35 degrees C. For a given temperature, the departure from thermodynamic equilibrium does not affect the oscillation period and results in a slight increase of the oscillation amplitude. Apparent activation energies were also evaluated in voltammetric and chronoamperometric experiments and were compared to those obtained under oscillatory conditions. In any case, the apparent activation energies values fell into the region between 50 and 70 kJ mol(-1). Specifically under oscillatory conditions an apparent activation energy of 60 +/- 3 kJ mol(-1) and a temperature coefficient q(10) of about 2.3 were observed. The present findings extend our recently published report (J. Phys. Chem. A, 2008, 112, 4617) on the temperature effect on the oscillatory electro-oxidation of formic acid. We found that, despite the fact that both studies were carried out under similar conditions, unlike the case of formic acid, only conventional, Arrhenius, dynamics was observed for methanol.

Surface structure effects on the electrochemical oxidation of ethanol on platinum single crystal electrodes

Ethanol oxidation has been studied on Pt(111), Pt(100) and Pt(110) electrodes in order to investigate the effect of the surface structure and adsorbing anions using electrochemical and FTIR techniques. The results indicate that the surface structure and anion adsorption affect significantly the reactivity of the electrode. Thus, the main product of the oxidation of ethanol on the Pt(111) electrode is acetic acid, and acetaldehyde is formed as secondary product. Moreover, the amount of CO formed is very small, and probably associated with the defects present on the electrode surface. For that reason, the amount of CO(2) is also small. This electrode has the highest catalytic activity for the formation of acetic acid in perchloric acid. However, the formation of acetic acid is inhibited by the presence of specifically adsorbed anions, such as (bi) sulfate or acetate, which is the result of the formation of acetic acid. On the other hand, CO is readily formed at low potentials on the Pt(100) electrode, blocking completely the surface. Between 0.65 and 0.80 V, the CO layer is oxidized and the production of acetaldehyde and acetic acid is detected. The Pt(110) electrode displays the highest catalytic activity for the splitting of the C-C bond. Reactions giving rise to CO formation, from either ethanol or acetaldehyde, occur at high rate at any potential. On the other hand, the oxidation of acetaldehyde to acetic acid has probably the lower reaction rate of the three basal planes.

Effects of drill cuttings discharge on meiofauna communities of a shelf break site in the southwest Atlantic

The present study investigates the effects of drill cutting discharges on the structure of meiofauna communities in an area of the shelf break at Campos Basin, Southeast Brazil. Drilling activities were operated, in a first phase, with water-based fluid and, in a second phase, with synthetic fluid paraffin-based (NAF-III). A total of 135 samples taken at a pre-drilling situation (MS1) and two post-drilling moments (MS2 and MS3-3 and 22 months post-drilling, respectively) were analyzed. Effects on meiofauna were dependent on two main factors: 1-the impact received during drilling operation, if water-based or synthetic/water-based drilling fluid and 2-the background state, if it already presented signs of previous drilling activities or not. Based on univariate and multivariate analysis, there were evidences that the most affected area after drilling was those under the influence of synthetic-based fluid and that already had signs of previous drillings activities. The region impacted only by water-based fluid was less affected and the only one that completely recovered after 22 months. Nematodes and copepods had different responses to the impact. While copepods flourish in the impacted area and recovered 22 months after drilling, nematodes were adversely affected shortly after drilling and the community structure only recovered where hydrocarbons had been depleted.

Effects of land cover on chemical characteristics of streams in the Cerrado region of Brazil

The Cerrado is the second largest Brazilian biome and contains the headwaters of three major hydrological basins in Brazil. In spite of the biological and ecological relevance of this biome, there is little information about how land use changes affect the chemistry of low-order streams in the Cerrado. To evaluate these effects streams that drain areas under natural, rural, and urban land cover were sampled near Brasilia, Brazil. Water samples were collected between September 2004 and December 2006. Chemical concentrations generally followed the pattern of Urban > Rural > Natural. Median conductivity of stream water of 21.6 (interquartile: 22.7) mu S/cm in urban streams was three and five-fold greater relative to rural and natural areas, respectively. In the wet season, despite of increasing discharge, concentration of many solutes were higher, particularly in rural and natural streams. Streams also presented higher total dissolved N (TDN) loads from natural to rural and urban although DIN:DON ratios did not differ significantly. In natural and urban streams TDN was 80 and 77% dissolved organic N, respectively. These results indicate that alterations in land cover from natural to rural and urban are changing stream water chemistry in the Cerrado with increasing solute concentrations, in addition to increased TDN output in areas under urban cover, with potential effects on ecosystem function.