Easy Bioinformatics Analysis (EBiAn): a package for manipulating and analysis of short biological sequences

The work of biochemists and molecular biologists often is dependent or extremely favored by a preliminary computer analysis. Thus, the development of an efficient and friendly computational tool is very important. In this work, we developed a package of programs in Javascript language which can be used online or locally. The programs depend exclusively of Web browsers and are compatible with Internet Explorer, Opera, Mozilla Firefox and Google Chrome. With the EBiAn package it is can perform the main analysis and manipulation of DNA, RNA, proteins and peptides sequences. The programs can be freely accessed and adapted or modified to generate new programs

A WEB-BASED RESOURCE FOR STRUCTURAL INFORMATION ON eIF5A AND ITS RELATED PROTEINS: NEW POTENTIAL THERAPEUTIC TARGETS IN MANY HUMAN DISORDERS

Objective: There is a considerable therapeutic interest in eIF5A as a potential target for drug development through inhibition of hypusination. In this regards, protein structural information is fundamental. Herein, we reported the developing of a web-based system, called eIF5ADB, which compiles all protein structural data on eIF5A and its related proteins.Methods: The eIF5ADB database was implemented as a MySQL relational database, using PHP scripting language. Web interfaces were developed using HTML, CSS and JavaScript. The data were collected from PDB, UniProt and Entrez databases. These data were filtered appropriately using specialized literature.Results: The database provides three modules that allow to search, acquisition of contents and access to statistical data, besides direct links to matching to external databases.Conclusion: The platform developed here is very useful for researchers interested in this content and can be accessed at http: //www. gurupi. uft. edu. br/btoxdb/eif5adb.Â

DETERMINAÇÃO DA CONCENTRAÇÃO ÓTIMA DE MEIO DE CULTURA PARA A MICROALGA SPIROGYRA SP. E DE POSSÍVEIS CRIOPROTETORES PARA SUA CONSERVAÇÃO

Os estudos relacionados ao emprego de microalgas para a síntese de biocombustíveis vêm ganhando espaço nos últimos anos, sendo estes motivados especialmente pelas várias problemáticas encontradas na utilização de culturas agrícolas convencionais para o mesmo fim. Nesse sentido, em função da grande capacidade de armazenar açúcares, a microalga Spirogyra sp. tem se destacado como possível matéria-prima para a produção de bioetanol. Com o intuito de otimizar o seu cultivo, o presente trabalho teve como objetivos a determinação da concentração de meio de cultura ideal para o seu desenvolvimento e de possíveis crioprotetores para a sua conservação por congelamento. Dentre as três concentrações analisadas do meio Bold’s Basal Medium (20, 60 e 100%), o meio a 60% foi o que possibilitou o maior crescimento microalgal. Com relação aos criopreservantes testados, o glicerol se mostrou ineficiente como crioprotetor. Já para o dimetilsulfóxido (DMSO) e metanol, os meios com 5%, 10% e 15% dos reagentes possibilitaram a reativação do metabolismo celular da microalga após um período de 21 dias de congelamento a -20° C. Pesquisas que busquem a potencialização do desenvolvimento da microalga Spirogyra sp. são essenciais para viabilizar o processo de produção de bioetanol em larga escala utilizando-a como matéria-prima. Contudo, apesar do enorme potencial e benefícios que ela apresenta quando empregada com esse propósito, estudos com esse objetivo ainda são limitados

Peptídeos derivados da toxina bacteriana ParE: síntese, estrutura e ação inibitória sobre a atividade de topoisomerases

O sistema ParE-ParD é um sistema toxina-antitoxina bacteriano, sendo ParE a toxina e ParD a antitoxina. ParD é capaz de neutralizar a ação de ParE formando um complexo com o mesmo, o qual é eficaz na autorregulação do operon parDE. Estudos têm mostrado que a atividade tóxica de ParE ocorre inibindo a atividade da DNA girase, mas nenhum efeito desta proteína sobre a atividade da topoisomerase IV foi observado até hoje. Baseando-se na estrutura primária da toxina ParE de Escherichia coli, bem como nos escassos dados em relação a esta toxina, a meta deste trabalho foi a obtenção de peptídeos sintéticos baseados nesta proteína a fim de avaliar as sequências de aminoácidos responsáveis pela interação com as diferentes topoisomerases bacterianas, além de tentar isolar uma sequência polipeptídica com potencial atividade inibitória sobre essas enzimas. Utilizando modelagem molecular por homologia, um modelo tridimensional para toxina ParE de E. coli foi obtido e validado. Com base nos dados estruturais inferidos a partir do modelo da estrutura tridimensional de ParE, 12 peptídeos foram racionalmente desenhados e sintetizados pela metodologia da fase sólida. Ensaios de inibição in vitro da atividade de superenovelamento de DNA pela girase e de relaxamento de DNA pela topoisomerase IV foram realizados e indicaram que os peptídeos ParE3 (ParE 80-100), ParE8 (ParE 61-105), ParE10 (ParE 61-87) e ParE12 (ParE 61-79) atuam como bons inibidores de ambas enzimas. Ensaios de fluorescência intrínseca e anisotropia de fluorescência, empregando peptídeos sintéticos derivados de ParE, evidenciaram que o processo de inibição da atividade da DNA girase pela toxina ParE deve ocorrer por interação com a proteína GyrA da enzima. Foi iniciado neste trabalho os primeiros testes usando lipossomas como veículos...The operon parDE encode a toxin-antitoxin system formed by ParE toxin and its antitoxin ParD. ParD is able to neutralize ParE action and is effective in autoregulation of the operon. Studies have shown that the toxic activity of the ParE occurs by inhibiting the activity of DNA gyrase, but no effect of this protein on the activity of topoisomerase IV has been observed yet. Based on the primary structure of the Escherichia coli ParE toxin, as well as the scarce data of this toxin, the aim of this work was to obtain synthetic peptides based on this protein in order to assess the amino acid sequences responsible for interaction with the bacterial topoisomerases, besides trying to isolate a polypeptide sequence with potential inhibitory activity against these enzymes. Using molecular homology modeling, a three-dimensional model for E. coli ParE toxin was obtained and validated. Based on structural data inferred from ParE threedimensional model, 12 peptides were rationally designed and synthesized by solid-phase method. Tests of inhibition of the supercoiling reaction of the DNA gyrase and inhibition of DNA relaxation by topoisomerase IV were performed and indicated that the peptides ParE3 (ParE 80-100), ParE8 (ParE 61-105), ParE10 (ParE 61 -87) and ParE12 (ParE 61-79) act as good inhibitors of both enzymes. Intrinsic fluorescence and fluorescence anisotropy assays, using synthetic peptides derived from ParE showed that inhibition process of activity of the DNA gyrase by ParE toxin must occur by interaction with the GyrA protein. In this work was started the first tests using liposomes as carrier vehicles for bioactive peptides derived from ParE. The peptides were efficiently encapsulated in soybean phosphatidyl choline liposomes. It was observed, although reduced, inhibition of bacterial growth when peptides encapsulated in liposomes were... (Complete abstract click electronic access below)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

BtoxDB: a comprehensive database of protein structural data on toxin-antitoxin systems

Purpose: Toxin-antitoxin (TA) systems are diverse and abundant genetic modules in prokaryotic cells that are typically formed by two genes encoding a stable toxin and a labile antitoxin. Because TA systems are able to repress growth or kill cells and are considered to be important actors in cell persistence (multidrug resistance without genetic change), these modules are considered potential targets for alternative drug design. In this scenario, structural information for the proteins in these systems is highly valuable. In this report, we describe the development of a web-based system, named BtoxDB, that stores all protein structural data on TA systems.Methods: The BtoxDB database was implemented as a MySQL relational database using PHP scripting language. Web interfaces were developed using HTML, CSS and JavaScript. The data were collected from the PDB, UniProt and Entrez databases. These data were appropriately filtered using specialized literature and our previous knowledge about toxin-antitoxin systems.Results: The database provides three modules ("Search", "Browse" and "Statistics") that enable searches, acquisition of contents and access to statistical data. Direct links to matching external databases are also available.Conclusions: The compilation of all protein structural data on TA systems in one platform is highly useful for researchers interested in this content. BtoxDB is publicly available at http://www.gurupi.uftedu.br/ btoxdb. (C) 2015 Elsevier Ltd. All rights reserved.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Function inferences from a molecular structural model of bacterial ParE toxin

Toxin-antitoxin (TA) systems contribute to plasmid stability by a mechanism that relies on the differential stabilities of the toxin and antitoxin proteins and leads to the killing of daughter bacteria that did not receive a plasmid copy at the cell division. ParE is the toxic component of a TA system that constitutes along with RelE an important class of bacterial toxin called RelE/ParE superfamily. For ParE toxin, no crystallographic structure is available so far and rare in vitro studies demonstrated that the target of toxin activity is E. coli DNA gyrase. Here, a 3D Model for E. coli ParE toxin by molecular homology modeling was built using MODELLER, a program for comparative modeling. The Model was energy minimized by CHARMM and validated using PROCHECK and VERIFY3D programs. Resulting Ramachandran plot analysis it was found that the portion residues failing into the most favored and allowed regions was 96.8%. Structural similarity search employing DALI server showed as the best matches RelE and YoeB families. The Model also showed similarities with other microbial ribonucleases but in a small score. A possible homologous deep cleft active site was identified in the Model using CASTp program. Additional studies to investigate the nuclease activity in members of ParE family as well as to confirm the inhibitory replication activity are needed. The predicted Model allows initial inferences about the unexplored 3D structure of the ParE toxin and may be further used in rational design of molecules for structure­function studies.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Toxin-antitoxin systems and its biotechnological applications

Toxin-antitoxin (TA) systems are important genetic modules composed by two elements: a toxin, that is always a protein, and an antitoxin, that can be a RNA or a protein and neutralizes the toxic effect of toxin. These systems are widespread in bacteria and archaea, found on plasmids and chromosomes. According to the nature of the antitoxin and its mode of interaction with the toxin, TA systems are grouped into five types. In general, the antitoxin is less stable than the toxin and is rapidly degraded in special conditions, leaving the toxin free to act on its cellular targets. TA modules are important in several events in cell physiology such as plasmid maintenance, formation of persister cells, stress resistance, protection from bacteriophages and regulation of biofilm formation, acting on crucial cellular processes including translation, replication, cytoskeleton formation and membrane integrity. TA systems components have proven to be very useful in biotechnology, being used to enhance cloning selection and protein expression in living bacterial cells. Furthermore, they are also considered as promising targets for the development of antibacterial drugs and can be used in gene therapy. Here, we reported current aspects and the application of TA modules in biotechnology research.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES