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Authors
Abstract(s)
Introdução: As proteínas são moléculas essenciais ao funcionamento do organismo,
apresentam inúmeras funções e estão envolvidas na regulação da maioria dos processos
celulares. A interação proteína-proteína é um dos mecanismos utilizado na cavidade oral
para a relação microrganismo-hospedeiro. Apesar da reconhecida importância dos
microrganismos, o conhecimento específico das interações estabelecidas entre estes e o
Homem é atualmente um tópico relevante de investigação, que visa compreender do
ponto de vista molecular a colonização do corpo humano pelos microrganismos. Muitos
resultados da proteómica têm sido publicados sobre proteínas microbianas e proteínas
do hospedeiro, hoje é preciso pensar em formas de analisar e interligar os
conhecimentos produzidos pelo trabalho laboratorial de forma rápida e eficaz. Com este
propósito surgiram métodos computacionais para a previsão da interação proteínaproteína.
A análise e interpretação crítica dos dados gerados pelas ciências Ómicas para
novas propostas de interação com significado biológico só é possível com os métodos
computacionais através de ferramentas bioinformáticas.
Objetivos: Analisar e discutir os resultados obtidos pelo OralInt v2.0 à luz dos
conhecimentos biológicos. Gerar informação que possibilite melhorar o desempenho do
OralInt v2.0.
Materiais e métodos: Dos resultados obtidos do OralInt v2.0 foram selecionadas as
200000 interações com maior nível de confiança, que foram analisadas através de
diversas ferramentas informáticas.
Resultados e Discussão: O OralInt v2.0 analisou 21086 proteínas das quais obteve um
elevado número de previsão de interações. Com as 200000 interações apresentando um
score entre 1 e 0,925 foi construído o interactoma da cavidade oral, em que constam
apenas 10768 proteínas. No entanto 47% das interações são estabelecidas entre
proteínas do hospedeiro e proteínas microbianas. Este resultado melhora o desempenho
do OralInt v2.0 do que o registado na versão anterior (12%). A análise topológica da
rede do interactoma da cavidade oral apresenta uma distribuição de interações
compatíveis com outras redes de PPIs estudadas, em que a maioria das proteínas (74%)
apresentam um número de previsão de interação baixo ([1-25]). O OralInt v2.0 prevê algumas interações interessantes para Porphyromonas gingivalis e para Streptococcus
mutans dois microrganismos importantes na cavidade oral.
Conclusão: Este trabalho mostra que a atual versão do OralInt v2.0 já consegue uma
previsão próxima do que se pensa ser o ambiente oral (há mais interações
microbioma/hospedeiro previstas). No entanto são, necessários ajustes adicionais ao
mesmo para que possam figurar interações entre proteínas já descritas na literatura. É
ainda necessário olhar para os parâmetros analisados pelo OralInt v2.0 para que os
parâmetros biológicos das proteínas tenham um maior peso nas previsões obtidas.
Introduction: Proteins are essential to the organism, and many are involved in the regulation of relevant cellular processes. Protein-protein interaction is one of the mechanisms used in the oral cavity for the establishment of microorganism-host interaction. Despite the recognized importance of microorganisms, the specific knowledge of the interactions established between them and the Human is currently an important topic of research that aims to understand, from the molecular point of view, the colonization of the human body by microorganisms. Many proteomics results have been published on microbial and host proteins, now we must think of ways to analyze and interlink the knowledge produced by laboratory work. For this purpose several computational methods emerged for predicting protein-protein interactions. The analysis and critical interpretation of data generated by the Omics sciences for new proposals of interactions with biological significance is only possible with computational methods using bioinformatics tools. Objectives: To analyze and discuss the results obtained by OralInt v2.0 in the light of biological knowledge. To generate information that will allow the improvement of the performance of OralInt v2.0. Methods: From the results of OralInt v2.0, 200,000 interactions were selected with the highest confidence level and analyzed with various software tools. Results and Discussion: The OralInt v2.0 analyzed 21086 proteins, and produced a large number of predicted interactions. Only the interactions with a significance level between 1 and 0,925 were analyzed. The interactome of the oral cavity, was constructed with 10,768 proteins. However, 47% of the interactions are established between the host and microbial proteins. The topological analysis of the interactome of the oral cavity presents a distribution network compatible with interactions of other PPIs networks studied, in which most proteins (74%) have a low number of prediction interaction ([1- 25]). New interactions not previously described are proposed for Porphyromonas gingivalis and Streptococcus mutans. Conclusion: Although the current version of OralInt v2.0 can make a close prediction of what is thought to be the oral environment (there are more microbiome interactions / host predicted), further adjustments are required to include interactions between proteins described in the literature. Furthermore, it is necessary to look at the parameters analyzed by OralInt v2.0 to ensure that biological parameters of proteins are given more weight in the obtained predictions
Introduction: Proteins are essential to the organism, and many are involved in the regulation of relevant cellular processes. Protein-protein interaction is one of the mechanisms used in the oral cavity for the establishment of microorganism-host interaction. Despite the recognized importance of microorganisms, the specific knowledge of the interactions established between them and the Human is currently an important topic of research that aims to understand, from the molecular point of view, the colonization of the human body by microorganisms. Many proteomics results have been published on microbial and host proteins, now we must think of ways to analyze and interlink the knowledge produced by laboratory work. For this purpose several computational methods emerged for predicting protein-protein interactions. The analysis and critical interpretation of data generated by the Omics sciences for new proposals of interactions with biological significance is only possible with computational methods using bioinformatics tools. Objectives: To analyze and discuss the results obtained by OralInt v2.0 in the light of biological knowledge. To generate information that will allow the improvement of the performance of OralInt v2.0. Methods: From the results of OralInt v2.0, 200,000 interactions were selected with the highest confidence level and analyzed with various software tools. Results and Discussion: The OralInt v2.0 analyzed 21086 proteins, and produced a large number of predicted interactions. Only the interactions with a significance level between 1 and 0,925 were analyzed. The interactome of the oral cavity, was constructed with 10,768 proteins. However, 47% of the interactions are established between the host and microbial proteins. The topological analysis of the interactome of the oral cavity presents a distribution network compatible with interactions of other PPIs networks studied, in which most proteins (74%) have a low number of prediction interaction ([1- 25]). New interactions not previously described are proposed for Porphyromonas gingivalis and Streptococcus mutans. Conclusion: Although the current version of OralInt v2.0 can make a close prediction of what is thought to be the oral environment (there are more microbiome interactions / host predicted), further adjustments are required to include interactions between proteins described in the literature. Furthermore, it is necessary to look at the parameters analyzed by OralInt v2.0 to ensure that biological parameters of proteins are given more weight in the obtained predictions
Description
Keywords
Interatómica Interação proteína-proteína Biofilme oral OralInt Cytoscape Interatomic Protein-protein interaction Oral biofilm