Combining structure and dynamics: non-denaturing high-pressure effect on lysozyme in solution

Small-angle X-ray scattering (SAXS) and elastic and quasi-elastic neutron scattering techniques were used to investigate the high-pressure-induced changes on interactions, the low-resolution structure and the dynamics of lysozyme in solution. SAXS data, analysed using a global-fit procedure based on a new approach for hydrated protein form factor description, indicate that lysozyme completely maintains its globular structure up to 1500 bar, but significant modi. cations in the protein-protein interaction potential occur at approximately 600-1000 bar. Moreover, the mass density of the protein hydration water shows a clear discontinuity within this pressure range. Neutron scattering experiments indicate that the global and the local lysozyme dynamics change at a similar threshold pressure. A clear evolution of the internal protein dynamics from diffusing to more localized motions has also been probed. Protein structure and dynamics results have then been discussed in the context of protein-water interface and hydration water dynamics. According to SAXS results, the new configuration of water in the first hydration layer induced by pressure is suggested to be at the origin of the observed local mobility changes.

Comparison of the interactomic networks of different species in terms of accessibility

Protein-protein interaction networks were investigated in terms of outward accessibility, which quantifies the effectiveness of each protein in accessing other proteins and is related to the internality of nodes. By comparing the accessibility between 144 ortholog proteins in yeast and the fruit fly, we found that the accessibility tends to be higher among proteins in the fly than in yeast. In addition, z-scores of the accessibility calculated for different species revealed that the protein networks of less evolved species tend to be more random than those of more evolved species. The accessibility was also used to identify the border of the yeast protein interaction network, which was found to be mainly composed of viable proteins.

Seeking for simplicity in complex networks

Complex networks can be understood as graphs whose connectivity properties deviate from those of regular or near-regular graphs, which are understood as being ""simple"". While a great deal of the attention so far dedicated to complex networks has been duly driven by the ""complex"" nature of these structures, in this work we address the identification of their simplicity. The basic idea is to seek for subgraphs whose nodes exhibit similar measurements. This approach paves the way for complementing the characterization of networks, including results suggesting that the protein-protein interaction networks, and to a lesser extent also the Internet, may be getting simpler over time. Copyright (C) EPLA, 2009

Structural stability and reversible unfolding of recombinant porcine S100A12

Porcine S100A12 is a member of the S100 proteins, family of small acidic calcium-binding proteins characterized by the presence of two EF-hand motifs. These proteins are involved in many cellular events such as the regulation of protein phosphorylation, enzymatic activity, protein-protein interaction, Ca(2+) homeostasis, inflammatory processes and intermediate filament polymerization. In addition, members of this family bind Zn(2+) or Ca(2+) with cooperative effect on binding. In this study, the gene sequence encoding porcine S100A12 was obtained by the synthetic gene approach using E. coli codon bias. Additionally, we report a thermodynamic study of the recombinant S100A12 using circular dichroism, fluorescence and isothermal titration calorimetry. The results of urea and temperature induced unfolding and refolding processes indicated a reversible two-state process. Also, the ANS fluorescence studies showed that in presence of divalent ions the protein exposes hydrophobic sites which could facilitate the interaction with other proteins and trigger the physiological responses. (c) 2008 Elsevier B.V. All rights reserved.

Transcriptomics and systems biology analysis in identification of specific pathways involved in cacao resistance and susceptibility to witches' broom disease

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo das interações polifenol-proteína e das reações de escurecimento não-enzimático para o processamento de cajuína

The cashew, a fruit from Brazilian Northeast is used to produce juice due to its flavor and vitamin C richness. However, its acceptance is limited due to its astringency. Cajuína is a derivate product appreciated by its characteristic flavor, freshness and lack of astringency, due to tannin removal. Cajuína is a light yellow beverage made from clarified cashew juice and sterilized after bottling. It differs from the integral and concentrated juice by the clarification and thermal treatment steps. Many problems such as haze and excessive browning could appear if these steps are not controlled. The objective of this work was divided into two stages with the aim to supply process information in order to obtain a good quality product with uniform characteristics (sensory and nutritional). Polyphenol-protein interaction was studied at the clarification step, which is an empirical process, to provide values on the amount of clarifying solution (gelatin) that must be added to achieve a complete juice clarification. Clarification essays were performed with juice dilutions of 1:2 and 1:10 and the effect of metabissulfite and tannic acid addition was evaluated. It was not possible to establish a clarification point. Metabissulfite did not influenced the clarification process however tannic acid addition displaced the clarification point, showing the difficulty visual monitoring of the process. Thermal treatment of clarified juice was studied at 88, 100, 111 e 121 °C. To evaluate the non-enzymatic browning, vitamin C, 5-hidroximetilfurfural (5-HMF) and sugar variation were correlated with color parameters (reflectance spectra, color difference and CIELAB). Kinetic models were obtained for reflectance spectra, ascorbic acid and 5-HMF. It was observed that 5-HMF introduction followed a first order kinetic rate at the beginning of the thermal treatment and a zero order kinetic at later process stages. An inverse correlation was observed between absorbance at 420 nm and ascorbic acid degradation, which indicates that ascorbic acid might be the principal factor on cajuína non-enzymatic browning. Constant sugar concentration showed that this parameter did not contribute directly to the nonenzymatic browning. Optimization techniques showed showed that to obtain a high vitamin C and a low 5-HMF content, the process must be done at 120 ºC. With the water-bath thermal treatment, the 90 °C temperature promoted a lower ascorbic acid degradation at the expense of a higher 5-HMF level

Effect of lentil tannins on albumin hydrolysis by trypsin

Os taninos da casca da semente de lentilha foram extraídos e purificados, levados à interação com albumina isolada de lentilha e com caseína; e estudados por turbidimetria. As interações da albumina e caseína com taninos purificados, a várias relações tanino-proteína, mostraram ser independente e dependente do pH, respectivamente. Hidrólise in vitro com tripsina das proteínas sem taninos indicou que o aquecimento a 99°C/15 min reduzia a susceptibilidade da albumina e aumentava a da caseína à tripsina. A influência de diferentes relações tanino:proteína (1:40; 1:20; 1:5; 1:2,5) na hidrólise mostrou maior inibição para caseína que para albumina de lentilha, independente de aquecimento. Após aquecimento ambas proteínas foram mais hidrolizadas para qualquer das relações tanino proteínas estudadas. A eletroforese em gel de poliacrilamida-dodecilsulfato de sódio do transcurso da hidrólise da interação tanino-albumina nativa mostra a dependência da relação tanino:proteína.

Contribuição ao estudo de redes complexas: modelo de afinidade com métrica

Currently the interest in large-scale systems with a high degree of complexity has been much discussed in the scientific community in various areas of knowledge. As an example, the Internet, protein interaction, collaboration of film actors, among others. To better understand the behavior of interconnected systems, several models in the area of complex networks have been proposed. Barabási and Albert proposed a model in which the connection between the constituents of the system could dynamically and which favors older sites, reproducing a characteristic behavior in some real systems: connectivity distribution of scale invariant. However, this model neglects two factors, among others, observed in real systems: homophily and metrics. Given the importance of these two terms in the global behavior of networks, we propose in this dissertation study a dynamic model of preferential binding to three essential factors that are responsible for competition for links: (i) connectivity (the more connected sites are privileged in the choice of links) (ii) homophily (similar connections between sites are more attractive), (iii) metric (the link is favored by the proximity of the sites). Within this proposal, we analyze the behavior of the distribution of connectivity and dynamic evolution of the network are affected by the metric by A parameter that controls the importance of distance in the preferential binding) and homophily by (characteristic intrinsic site). We realized that the increased importance as the distance in the preferred connection, the connections between sites and become local connectivity distribution is characterized by a typical range. In parallel, we adjust the curves of connectivity distribution, for different values of A, the equation P(k) = P0e

Restriction endonuclease banding and digestion resistant heterochromatin in triatomines, genus Panstrongylus

The present work realized a comparative study in meiosis of two triatomines, Panstrongylus herreri and P. megistus, by cytogenetic techniques involving the restriction endonucleases Hae III and Alu I and C-banding. The system of sex chromosomes in Panstrongylus is of the X1X2Y type, and experiments corroborated the common origin hypothesis of the X chromosomes by fragmentation of single X. In both species the restriction endonucleases (RE) presented banding patterns in part similar to C-banding. However, in some early meiotic phases it was possible to verify differentiation of the heterochromatic pattern. This work suggests that other elements besides presence of recognition sites, such as chromatin packing degree and DNA-protein interaction, act in RE results, since digestion patterns occur in early spermatogenesis. However, metaphase chromosomes were practically inaccessible to the endonucleases.

Papel das proteínas Yops de Yersinia pseudotuberculosis na ativação dos linfócitos B

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Mapping eIF5A binding sites for Dys1 and Lia1: In vivo evidence for regulation of eIF5A hypusination

The evolutionarily conserved factor eIF5A is the only protein known to undergo hypusination, a unique posttranslational modification triggered by deoxyhypusine synthase (Dys1). Although eIF5A is essential for cell viability, the function of this putative translation initiation factor is still obscure. To identify eIF5A-binding proteins that could clarify its function, we screened a two-hybrid library and identified two eIF-5A partners in S. cerevisiae: Dys1 and the protein encoded by the gene YJR070C, named Lia1 (Ligand of eIF5A). The interactions were confirmed by GST pulldown. Mapping binding sites for these proteins revealed that both eIF5A domains can bind to Dys1, whereas the C-terminal domain is sufficient to bind Lia1. We demonstrate for the first time in vivo that the N-terminal α-helix of Dys1 can modulate enzyme activity by inhibiting eIF5A interaction. We suggest that this inhibition be abrogated in the cell when hypusinated and functional eIF5A is required. © 2003 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.

Effects of nitric oxide and arginine vasopressin on sodium intake induced by central angiotensin II. Part 2

We study the effects of angiotensin receptors antagonists, arginine vasopressin receptor antagonist, L-arginine and L-NAME, injected into supraoptic nucleus of the hypothalamus (SON) on sodium intake induced by the injection of angiotensin II (ANGII). Holtzman rats weighing 200-250 g with canulae implanted into the SON were used. The drugs were injected in 0.5 μL over 30-60 sec. Sodium intake after injection of saline SAL+SAL 0.15 M NaCl was 0.10±00.1 mL 2 h -1; SAL+ANGII injected into SON increased sodium intake. Losartan injected prior to ANGII into SON decreased sodium intake induced by ANGII. PD123319 injected prior to ANGII produced no changes in sodium intake induced by ANGII. AVPA receptor V 1 antagonist injected prior to ANGII reduced sodium intake with a less intensity than losartan. L-arginine injected prior to ANGII decreases sodium intake at a same intensity than losartan. L-NAME injected prior to ANGII potentiated sodium intake induced by ANGII. Losartan injected simultaneously with L-arginine prior to ANGII blocked the natriorexigenic effect of ANGII. These results confirm the importance of SON in the control of sodium intake. Also suggest that both AT 1 and arginine vasopressin V 1 receptors interact with nitrergic pathways within the SON influencing the sodium metabolism by changing sodium appetite induced by ANGII. © 2007 Asian Network for Scientific Information.

Orphan nuclear receptor NGFI-B forms dimers with nonclassical interface

The orphan receptor nerve growth factor-induced B (NGFI-B) is a member of the nuclear receptor's subfamily 4A (Nr4a). NGFI-B was shown to be capable of binding both as a monomer to an extended half-site containing a single AAAGGTCA motif and also as a homodimer to a widely separated everted repeat, as opposed to a large number of nuclear receptors that recognize and bind specific DNA sequences predominantly as homo- and/or heterodimers. To unveil the structural organization of NGFI-B in solution, we determined the quaternary structure of the NGFI-B LBD by a combination of ab initio procedures from small-angle X-ray scattering (SAXS) data and hydrogen-deuterium exchange followed by mass spectrometry. Here we report that the protein forms dimers in solution with a radius of gyration of 2.9 nm and maximum dimension of 9.0 nm. We also show that the NGFI-B LBD dimer is V-shaped, with the opening angle significantly larger than that of classical dimer's exemplified by estrogen receptor (ER) or retinoid X receptor (RXR). Surprisingly, NGFI-B dimers formation does not occur via the classical nuclear receptor dimerization interface exemplified by ER and RXR, but instead, involves an extended surface area composed of the loop between helices 3 and 4 and C-terminal fraction of the helix 3. Remarkably, the NGFI-B dimer interface is similar to the dimerization interface earlier revealed for glucocorticoid nuclear receptor (GR), which might be relevant to the recognition of cognate DNA response elements by NGFI-B and to antagonism of NGFI-B-dependent transcription exercised by GR in cells. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society.

Developing new radiotherapy techniques using linac based gamma radiation sources

A major challenge in cancer radiotherapy is to deliver a lethal dose of radiation to the target volume while minimizing damage to the surrounding normal tissue. We have proposed a model on how treatment efficacy might be improved by interfering with biological responses to DNA damage using exogenous electric fields as a strategy to drastically reduce radiation doses in cancer therapy. This approach is demonstrated at this Laboratory through case studies with prokaryotes (bacteria) and eukaryotes (yeast) cells, in which cellkilling rates induced by both gamma radiation and exogenous electric fields were measured. It was found that when cells exposed to gamma radiation are immediately submitted to a weak electric field, cell death increases more than an order of magnitude compared to the effect of radiation alone. This finding suggests, although does not prove, that DNA damage sites are reached and recognized by means of long-range electric DNA-protein interaction, and that exogenous electric fields could destructively interfere with this process. As a consequence, DNA repair is avoided leading to massive cell death. Here we are proposing the use this new technique for the design and construction of novel radiotherapy facilities associated with linac generated gamma beams under controlled conditions of dose and beam intensity.