The influence of the loop between residues 223-235 in beetle luciferase bioluminescence spectra: A solvent gate for the active site of pH-sensitive luciferases

Beetle luciferases emit a wide range of bioluminescence colors, ranging from green to red. Firefly luciferases can shift the spectrum to red in response to pH and temperature changes, whereas click beetle and railroadworm luciferases do not. Despite many studies on firefly luciferases, the origin of pH-sensitivity is far from being understood. Through comparative site-directed mutagenesis and modeling studies, using the pH-sensitive luciferases (Macrolampis and Cratomorphus distinctus fireflies) and the pH-insensitive luciferases (Pyrearinus termitilluminans, Phrixotrix viviani and Phrixotrix hirtus) cloned by our group, here we show that substitutions dramatically affecting bioluminescence colors in both groups of luciferases are clustered in the loop between residues 223-235 (Photinus pyralis sequence). The substitutions at positions 227, 228 and 229 (P. pyralis sequence) cause dramatic redshift and temporal shift in both groups of luciferases, indicating their involvement in labile interactions. Modeling studies showed that the residues Y227 and N229 are buried in the protein core, fixing the loop to other structural elements participating at the bottom of the luciferin binding site. Changes in pH and temperature (in firefly luciferases), as well as point mutations in this loop, may disrupt the interactions of these structural elements exposing the active site and modulating bioluminescence colors. © 2007 The Authors.

The structural origin and biological function of pH-sensitivity in firefly luciferases

Firefly luciferases are called pH-sensitive because their bioluminescence spectra display a typical red-shift at acidic pH, higher temperatures, and in the presence of heavy metal cations, whereas other beetle luciferases (click beetles and railroadworms) do not, and for this reason they are called pH-insensitive. Despite many studies on firefly luciferases, the origin of pH-sensitivity is far from being understood. This subject is revised in view of recent results. Some substitutions of amino-acid residues influencing pH-sensitivity in firefly luciferases have been identified. Sequence comparison, site-directed mutagenesis and modeling studies have shown a set of residues differing between pH-sensitive and pH-insensitive luciferases which affect bioluminescence colors. Some substitutions dramatically affecting bioluminescence colors in both groups of luciferases are clustered in the loop between residues 223-235 (Photinus pyralis sequence). A network of hydrogen bonds and salt bridges involving the residues N229-S284-E311-R337 was found to be important for affecting bioluminescence colors. It is suggested that these structural elements may affect the benzothiazolyl side of the luciferin-binding site affecting bioluminescence colors. Experimental evidence suggest that the residual red light emission in pH-sensitive luciferases could be a vestige that may have biological importance in some firefly species. Furthermore, the potential utility of pH-sensitivity for intracellular biosensing applications is considered. © The Royal Society of Chemistry and Owner Societies.

Structural studies of Helicase NS3 variants from Hepatitis C virus genotype 3 in virological sustained responder and non-responder patients

Background. About 130 million people are infected with the hepatitis C virus (HCV) worldwide, but effective treatment options are not yet available. One of the most promising targets for antiviral therapy is nonstructural protein 3 (NS3). To identify possible changes in the structure of NS3 associated with virological sustained response or non-response of patients, a model was constructed for each helicase NS3 protein coding sequence. From this, the goal was to verify the interaction between helicases variants and their ligands. Findings. Evidence was found that the NS3 helicase portion of non-responder patients contained substitutions in its ATP and RNA binding sites. K210E substitution can cause an imbalance in the distribution of loads, leading to a decrease in the number of ligations between the essential amino acids required for the hydrolysis of ATP. W501R substitution causes an imbalance in the distribution of loads, leading and forcing the RNA to interact with the amino acid Thr269, but not preventing binding of ribavirin inhibitor. Conclusions. Useful information is provided on the genetic profiling of the HCV genotype 3, specifically the coding region of the NS3 protein, improving our understanding of the viral genome and the regions of its protein catalytic site. © 2010 Rahal et al; licensee BioMed Central Ltd.

Tilings induced by a class of cubic Rauzy fractals

We study aperiodic and periodic tilings induced by the Rauzy fractal and its subtiles associated with beta-substitutions related to the polynomial x3-ax2-bx-1 for a≥b≥1. In particular, we compute the corresponding boundary graphs, describing the adjacencies in the tilings. These graphs are a valuable tool for more advanced studies of the topological properties of the Rauzy fractals. As an example, we show that the Rauzy fractals are not homeomorphic to a closed disc as soon as a≤2b-4. The methods presented in this paper may be used to obtain similar results for other classes of substitutions.© 2012 Elsevier B.V. All rights reserved.

Circulation of Different Lineages of Dengue Virus 2, Genotype American/Asian in Brazil: Dynamics and Molecular and Phylogenetic Characterization

The American/Asian genotype of Dengue virus type 2 (DENV-2) was introduced into the Americas in the 80′s. Although there is no data showing when this genotype was first introduced into Brazil, it was first detected in Brazil in 1990. After which the virus spread throughout the country and major epidemics occurred in 1998, 2007/08 and 2010. In this study we sequenced 12 DENV-2 genomes obtained from serum samples of patients with dengue fever residing in São José do Rio Preto, São Paulo (SJRP/SP), Brazil, in 2008. The whole open reading frame or envelope sequences were used to perform phylogenetic, phylogeographic and evolutionary analyses. Isolates from SJRP/SP were grouped within one lineage (BR3) close to isolates from Rio de Janeiro, Brazil. Isolates from SJRP were probably introduced there at least in 2007, prior to its detection in the 2008 outbreak. DENV-2 circulation in Brazil is characterized by the introduction, displacement and circulation of three well-defined lineages in different times, most probably from the Caribbean. Thirty-seven unique amino acid substitutions were observed among the lineages, including seven amino acid differences in domains I to III of the envelope protein. Moreover, we dated here, for the first time, the introduction of American/Asian genotype into Brazil (lineage BR1) to 1988/89, followed by the introduction of lineages BR2 (1998-2000) and BR3 (2003-05). Our results show a delay between the introduction and detection of DENV-2 lineages in Brazil, reinforcing the importance and need for surveillance programs to detect and trace the evolution of these viruses. Additionally, Brazilian DENV-2 differed in genetic diversity, date of introduction and geographic origin and distribution in Brazil, and these are important factors for the evolution, dynamics and control of dengue. © 2013 Drumond et al.

Sonochemical synthesis and magnetism in co-doped ZnO nanoparticles

The understanding and control of ferromagnetism in diluted magnetic semiconducting oxides (DMO) is a special challenge in solid-state physics and materials science due to its impact in magneto-optical devices and spintronics. Several studies and mechanisms have been proposed to explain intrinsic ferromagnetism in DMO compounds since the theoretical prediction of room-temperature ferromagnetism. However, genuine and intrinsic ferromagnetism in 3d-transition metal-doped n-type ZnO semiconductors is still a controversial issue. Furthermore, for DMO nanoparticles, some special physical and chemical effects may also play a role. In this contribution, structural and magnetic properties of sonochemically prepared cobalt-doped ZnO nanoparticles were investigated. A set of ZnO samples was prepared varying cobalt molar concentration and time of ultrasonic exposure. The obtained results showed that single phase samples can be obtained by the sonochemical method. However, cobalt nanoclusters can be detected depending on synthesis conditions. Magnetic measurements indicated a possible ferromagnetic response, associated to defects and cobalt substitutions at the zinc site by cobalt. However, ferromagnetism is depleted at higher magnetic fields. Also, an antiferromagnetic response is detected due to cobalt oxide cluster at high cobalt molar concentrations. © 2012 Springer Science+Business Media, LLC.

Dielectric and structural characterization of Pb1-xAxZr0.40Ti0.60O3 (A = Sr, Ca) ferroelectric ceramics

This paper reports the influence of Sr- and Ca-substitution on the structural and ferroelectric properties of Pb1-xSrxZr0.40Ti0.60O3 (PSZT) and Pb1-xCaxZr0.40Ti0.60O3 (PCZT) ceramic systems. The dielectric measurements show that these substitutions cause a diffuse behavior in the dielectric permittivity curves for all samples. According to the X-ray absorption near-edge structure (XANES) spectra collected at Ti K- and LIII-edge, when Pb was replaced by Sr or Ca, a decrease in the local distortion around Ti atoms in the TiO6 octahedron could be observed. The O K-edge XANES spectra also revealed that the hybridization between O 2p and Pb 6sp states decreased as the amount of Sr or Ca atoms increased. Based on these results, it was possible to ascertain that the ferroelectric behavior in PSZT and PCZT samples bears a close correlation to the hybridization weakening between O 2p and Pb 6 sp states. © 2013 by American Scientific Publishers.

Caracterização molecular do arco da alça V3 da gp 120 do HIV-1

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

Sociedade em rede: faces virtuais da ideologia capitalista do século XXI

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Identificação de Single Nucleotilde Polymorphisms (SMPs) no gene Nove-cis-epoxicaroteníde dioxigenase (NCED) em Eucalyptus

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Perfil eletroforético e cromatográfico das hemoglobinas S-like

Pós-graduação em Genética - IBILCE

Análise comparativa da variação entre quasiespecies do Vírus da Hepatite C genótipo 1 em amostras prétratamento de pacientes tratados com Peginterferon

Pós-graduação em Genética - IBILCE

Polimorfismos no gene JY-1 e suas associações com probabilidade de prenhez precoce e características de crescimento em novilhas da raça Nelore

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

Seleção e caracterização de novos genes vip3A: genes inseticidas de segunda geração de Bacillus thuringiensis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Propriedades topológicas e aritméticas dos fractais de Rauzy

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)