Disruption of Saccharomyces cerevisiae by Plantaricin 149 and investigation of its mechanism of action with biomembrane model systems

The action of a synthetic antimicrobial peptide analog of Plantaricin 149 (Pln149a) against Saccharomyces cerevisiae and its interaction with biomembrane model systems were investigated. Pln149a was shown to inhibit S. cerevisiae growth by more than 80% in YPD medium, causing morphological changes in the yeast wall and remaining active and resistant to the yeast proteases even after 24 h of incubation. Different membrane model systems and carbohydrates were employed to better describe the Pln149a interaction with cellular components using circular dichroism and fluorescence spectroscopies, adsorption kinetics and surface elasticity in Langmuir monolayers. These assays showed that Pln149a does not interact with either mono/polysaccharides or zwitterionic LUVs, but is strongly adsorbed to and incorporated into negatively charged surfaces, causing a conformational change in its secondary structure from random-coil to helix upon adsorption. From the concurrent analysis of Pln149a adsorption kinetics and dilatational surface elasticity data, we determined that 2.5 mu M is the critical concentration at which Pln149a will disrupt a negative DPPG monolayer. Furthermore, Pln149a exhibited a carpet-like mechanism of action, in which the peptide initially binds to the membrane, covering its surface and acquiring a helical structure that remains associated to the negatively charged phospholipids. After this electrostatic interaction, another peptide region causes a strain in the membrane, promoting its disruption. (C) 2009 Elsevier B.V. All rights reserved.

Flexibility and inhibitor binding in Cdc25 phosphatases

Cdc25 phosphatases involved in cell cycle checkpoints are now active targets for the development of anti-cancer therapies. Rational drug design would certainly benefit from detailed structural information for Cdc25s. However, only apo- or sulfate-bound crystal structures of the Cdc25 catalytic domain have been described so far. Together with previously available crystalographic data, results from molecular dynamics simulations, bioinformatic analysis, and computer-generated conformational ensembles shown here indicate that the last 30-40 residues in the C-terminus of Cdc25B are partially unfolded or disordered in solution. The effect of C-terminal flexibility upon binding of two potent small molecule inhibitors to Cdc25B is then analyzed by using three structural models with variable levels of flexibility, including an equilibrium distributed ensemble of Cdc25B backbone conformations. The three Cdc25B structural models are used in combination with flexible docking, clustering, and calculation of binding free energies by the linear interaction energy approximation to construct and validate Cdc25B-inhibitor complexes. Two binding sites are identified on top and beside the Cdc25B active site. The diversity of interaction modes found increases with receptor flexibility. Backbone flexibility allows the formation of transient cavities or compact hydrophobic units on the surface of the stable, folded protein core that are unexposed or unavailable for ligand binding in rigid and densely packed crystal structures. The present results may help to speculate on the mechanisms of small molecule complexation to partially unfolded or locally disordered proteins.

A theoretical analysis on the intramolecular proton transfer of alpha-alanine in an aqueous medium

Intramolecular proton transfer from oxygen to nitrogen atoms in the alpha-alanine amino acid has been studied by ab initio methods at the HF/6-31G*, HF/6-31 ++ G** and MP2/6-31 ++ G** levels of calculation including the solvent effects by means of self-consistent reaction field theory. An analysis of the results based on the natural bond orbital charges shows that the transition structure presents an imbalance in the sense that the charge shift lags behind the proton transfer and that the bond formation is always in advance with respect to the bond cleavage. All calculation levels show that the barrier height associated with the conformational change on alpha-alanine is larger than the proton transfer process. (C) 1998 Elsevier B.V. B.V. All rights reserved.

Hydrogen/deuterium exchange mass spectrometry for characterizing phosphoenolpyruvate-induced structural transitions in Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.1)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Phosphate closes the solution structure of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Mycobacterium tuberculosis

The 5-enolpyruvylshikimate-3-phosphate synthase catalyses the sixth step of the shikimate pathway that is responsible for synthesizing aromatic compounds and is absent in mammals, which makes it a potential target for drugs development against microbial diseases. Here, we report the phosphate binding effects at the structure of the 5-enolpyruvyl shikimate-3-phosphate synthase from Mycobacterium tuberculosis. This enzyme is formed by two similar domains that close on each other induced by ligand binding, showing the occurrence of a large conformation change. We have monitored the phosphate binding effects using analytical ultracentrifugation, small angle X-ray scattering and, circular dichroism techniques. The low resolution results showed that the enzyme in the presence of phosphate clearly presented a more compact structure. Thermal-induced unfolding experiments followed by circular dichroism suggested that phosphate rigidified the enzyme. Summarizing, these data suggested that the phosphate itself is able to induce conformational change resulting in the closure movement in the M. tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase. (c) 2006 Elsevier B.V. All rights reserved.

Labaditin, a cyclic peptide with rich biotechnological potential: preliminary toxicological studies and structural changes in water and lipid membrane environment

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Fluorescence study of the interaction between metal ions and methyl methacrylate methacrylic acid copolymers in aqueous solutions: thallium(I), calcium(II), and terbium(III)

The binding of the cations thallium(I), calcium(II) and terbium(III) to methyl methacrylate-methacrylic acid copolymers with different fractions of acid groups (x) has been studied in aqueous solution at, various pH values using the fluorescence of covalently bonded 9-vinyl anthracene as a probe. In all cases, the extent of binding increases as a function of the charge of the polymer with either increasing fraction of carboxylic acids or of pH. However, differences are observed in the behavior of the three cations, With Tl(I), quenching of the anthracene group fluorescence is observed. indicating that the thallium(I) approaches the probe and suggesting that the alkylanthracene is probably in a relatively polar region. Binding constants have been determined from anthracene quenching data and from studies with the fluorescent-probe sodium pyrenetetrasulfonate, Good agreement is obtained between the two methods, and values for the binding constants increase from 250 to 950 M-1 as x increases from 0.39 to 1. It is suggested that the cation is held in the polyelectrolyte domain, partly by Debye-Huckel effects and partly by more specific interactions. Stronger binding is found with calcium(II) and terbium(III), and in this case increases in fluorescence intensity are observed on complexation due to the anthracene group being in a more hydrophobic region, probably as a result of conformational changes in the polymer chain. In the former case the stoichiometry of the interaction was determined from the fluorescence data to involve two carboxylate groups bound per calcium. Association constants were found using murexide as an indicator of free calcium to vary from 8400 to 37 000 M-1 as x increases from 0.39 to 1. It is suggested that in this case specific calcium(II)-carboxylate interactions contribute to the binding. With terbium(III), a greater increase in the probe fluorescence intensity was observed than with calcium, and it is suggested that the interaction with the polymer is even stronger, leading to a more pronounced conformational change in the polymer. It is proposed that the terbium(III) interacts with sis carboxylic groups on the polymer chain, with three being coordinated and three attracted by electrostatic interactions.

Modulation of the Pharmacological Activities of Secretory Phospholipase A2 from Crotalus durissus cascavella Induced by Naringin

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

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.

Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human PPACK-thrombin

Both human and bovine prothrombin fragment 2 (the second kringle) have been cocrystallized separately with human PPACK (D-Phe-Pro-Arg)-thrombin, and the structures of these noncovalent complexes have been determined and refined (R = 0.155 and 0.157, respectively) at 3.3-Å resolution using X-ray crystallographic methods. The kringles interact with thrombin at a site that has previously been proposed to be the heparin binding region. The latter is a highly electropositive surface near the C-terminal helix of thrombin abundant in arginine and lysine residues. These form salt bridges with acidic side chains of kringle 2. Somewhat unexpectedly, the negative groups of the kringle correspond to an enlarged anionic center of the lysine binding site of lysine binding kringles such as plasminogens K1 and K4 and TPA K2. The anionic motif is DGDEE in prothrombin kringle 2. The corresponding cationic center of the lysine binding site region has an unfavorable Arg70Asp substitution, but Lys35 is conserved. However, the folding of fragment 2 is different from that of prothrombin kringle 1 and other kringles: the second outer loop possesses a distorted two-turn helix, and the hairpin β-turn of the second inner loop pivots at Val64 and Asp70 by 60°. Lys35 is located on a turn of the helix, which causes it to project into solvent space in the fragment 2-thrombin complex, thereby devastating any vestige of the cationic center of the lysine binding site. Since fragment 2 has not been reported to bind lysine, it most likely has a different inherent folding conformation for the second outer loop, as has also been observed to be the case with TPA K2 and the urokinase kringle. The movement of the Val64-Asp70 β-turn is most likely a conformational change accompanying complexation, which reveals a new heretofore unsuspected flexibility in kringles. The fragment 2-thrombin complex is only the second cassette module-catalytic domain structure to be determined for a multidomain blood protein and only the third domain-domain interaction to be described among such proteins, the others being factor Xa without a Gla domain and Ca2+ prothrombin fragment 1 with a Gla domain and a kringle. © 1993 American Chemical Society.

Coil to extended coil transition in polygalacturonic acid: Conductometric titration and monte carlo simulations

The conformational transition from coil to extended coil for polygalacturonic acid has been studied by conductometric titrations and Monte Carlo simulations. The results of conductometric titrations at different polymer concentrations have been analyzed using the model proposed by Manning,1 which describes the conductivity of polyelectrolitic solutions. This experimental approach provides the transport factor and the average distance between charged groups at different degrees of ionization (α). The mean distances between charged groups have been compared with the values obtained by Monte Carlo simulations. In these simulations the polymer chain is modeled as a self-avoiding random walk in a cubic lattice. The monomers interact through the unscreened Coulombic potential. The ratio between the end-to-end distance and the number of ionized beads provides the average distance between charged monomers. The experimental and theoretical values are in good agreement for the whole range of ionization degrees accessed by conductometric titrations. These results suggest that the electrostatic interactions seem to be the major contribution for the coil to extended coil conformational change. The small deviations for α ≤ 0.5 suggests that the stiffness of the chain, associated with local interactions, becomes increasingly significant as the fraction of charged groups is decreased. © 2000 American Chemical Society.

Análise estrutural e funcional da interação física entre eIF5A e suas enzimas modificadoras em Saccharomyces cerevisiae

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Epidemiologia molecular das infecções por rotavírus G2 ao longo de 16 anos (1992 a 2008) na região amazônica, Brasil

No Brasil, estima-se que os rotavírus causem 3.352.053 episódios de diarreia, 655.853 ambulatoriais, 92.453 hospitalizações e 850 mortes envolvendo crianças menores de 5 anos de idade. Os rotavírus pertencem à família Reoviridae, gênero Rotavirus. A partícula viral é constituída por três camadas proteicas concêntricas e pelo genoma viral reunindo 11 segmentos de RNA com dupla fita. Reconhecem-se 23 genótipos G e 31 genótipos P. Dentre os genótipos G detectados até o momento, o G2 atua como um dos mais importantes, estando geralmente associado ao genótipo P[4]. Nos últimos três anos se tem observado em larga escala global a reemergência do genótipo G2, sendo um dos mais detectados nos anos que sucederam a implantação da vacina contra rotavírus, particularmente no Brasil. Este estudo teve como objetivo a caracterização molecular de amostras do tipo G2 obtidas de crianças participantes de estudos em gastroenterites virais na região amazônica, Brasil, no período de 1992 a 2008. Foram selecionadas 53 amostras positivas para rotavírus genótipo G2 que foram sequenciadas para VP7 e 38 para VP4. Inicialmente, as amostras foram genotipadas por RT-PCR e seus produtos purificados, quantificados e sequenciados. As amostras também foram testadas quanto ao perfil de migração dos segmentos de RNA. As sequências obtidas dos genes VP4 e VP7 foram alinhadas e editadas no programa Bioedit (v.6.05) e comparadas a outras sequências de RV registradas no banco de genes utilizando o programa BLAST. A árvore filogenética foi feita utilizando o programa Mega 2.1. Do total de 53 amostras sequenciadas para o gene VP7, a análise filogenética revelou a existência de duas linhagens (II e III) e três sublinhagens (IIa, IIc, IId) que circularam em períodos diferentes na população. Amostras das sub-linhagem IIa e IIc apresentaram mutação na posição no aminoácido da posição 96 (Asp/ Asn) . Essa modificação pode resultar em uma alteração conformacional dos epítopos reconhecidos por anticorpos neutralizantes. As linhagens de G2 que circularam em Belém foram idênticas àquelas de outros Estados da região amazônica envolvidos no estudo. O gene VP[4] foi sequenciado na região da VP8*, sendo 36 pertencentes do genótipo P[4] e 3 ao P[6]. No genótipo P[4] foi identificada a circulação de duas linhagens, P[4]-4 ocorrendo nos anos de 1998-2000, e P[4]-5 que circulou nos períodos de 1993-1994 e 2006-2008. Nossos resultados reforçam dados de ocorrência continental que evidenciam a reemergência do genótipo G2 com a variante gênica IIc, a qual se estabeleceu na população em associação com o genótipo P[4]-5. A grande homologia entre as cepas de G2 que circularam entre os diferentes estados envolvidos no estudo sugere que as mutações registradas ultrapassaram barreiras geográficas e temporais.

Imunossensores à base de filmes nanoestruturados de fibroína da seda - peptídeo antigênico NS5A-1-vanadato de ítrio: európio para detecção de Hepatite C

Pós-graduação em Química - IQ

Avaliação física e radiográfica dos carpos, tarsos e articulações interfalangeanas de touros de raças zebuínas em regime de colheita de sêmen

Pós-graduação em Medicina Veterinária - FCAV