Computational prediction of protein-protein interactions in Leishmania predicted proteomes

Detalhes bibliográficos
Autor(a) principal: Rezende, Antônio Mauro de
Data de Publicação: 2012
Outros Autores: Folador, Edson Luiz, Resende, Daniela de Melo, Ruiz, Jerônimo Conceição
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/7839
Resumo: Fundação Oswaldo Cruz. Centro de Pesquisa René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, Brazil/Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Bioquímica e Imunologia. Belo Horizonte, MG, Brazil
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spelling Rezende, Antônio Mauro deFolador, Edson LuizResende, Daniela de MeloRuiz, Jerônimo Conceição2014-06-26T12:02:30Z2014-06-26T12:02:30Z2012REZENDE, Antonio Mauro e al. Computational prediction of protein-protein interactions in Leishmania predicted proteomes. Plos One. 2012, vol.7, pp. e513041932-6203https://www.arca.fiocruz.br/handle/icict/7839engPublic Library of ScienceComputational prediction of protein-protein interactions in Leishmania predicted proteomesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Centro de Pesquisa René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, Brazil/Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Bioquímica e Imunologia. Belo Horizonte, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisa René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, Brazil/Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, BrazilFundação Oswaldo Cruz. Centro de Pesquisa René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, Brazil/Universidade Federal de Ouro Preto. Laboratório de Pesquisas Clínicas. Ouro Preto, MG, BrazilFundação Oswaldo Cruz. Centro de Pesquisa René Rachou. Laboratório de Parasitologia Celular e MolecularThe Trypanosomatids parasites Leishmania braziliensis, Leishmania major and Leishmania infantum are important human pathogens. Despite of years of study and genome availability, effective vaccine has not been developed yet, and the chemotherapy is highly toxic. Therefore, it is clear just interdisciplinary integrated studies will have success in trying to search new targets for developing of vaccines and drugs. An essential part of this rationale is related to protein-protein interaction network (PPI) study which can provide a better understanding of complex protein interactions in biological system. Thus, we modeled PPIs for Trypanosomatids through computational methods using sequence comparison against public database of protein or domain interaction for interaction prediction (Interolog Mapping) and developed a dedicated combined system score to address the predictions robustness. The confidence evaluation of network prediction approach was addressed using gold standard positive and negative datasets and the AUC value obtained was 0.94. As result, 39,420, 43,531 and 45,235 interactions were predicted for L. braziliensis, L. major and L. infantum respectively. For each predicted network the top 20 proteins were ranked by MCC topological index. In addition, information related with immunological potential, degree of protein sequence conservation among orthologs and degree of identity compared to proteins of potential parasite hosts was integrated. This information integration provides a better understanding and usefulness of the predicted networks that can be valuable to select new potential biological targets for drug and vaccine development. Network modularity which is a key when one is interested in destabilizing the PPIs for drug or vaccine purposes along with multiple alignments of the predicted PPIs were performed revealing patterns associated with protein turnover. In addition, around 50% of hypothetical protein present in the networks received some degree of functional annotation which represents an important contribution since approximately 60% of Leishmania predicted proteomes has no predicted function.Drug interactionsLeishmania majorNetwork analysisProtein interaction networksProteomesSequence databasesinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZORIGINALComputational prediction of protein-protein interactions in Leishmania predicted proteomes.pdfComputational prediction of protein-protein interactions in Leishmania predicted proteomes.pdfapplication/pdf1144181https://www.arca.fiocruz.br/bitstream/icict/7839/1/Computational%20prediction%20of%20protein-protein%20interactions%20in%20Leishmania%20predicted%20proteomes.pdf8031f5a087f544239fbb4964d3259fb1MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81914https://www.arca.fiocruz.br/bitstream/icict/7839/2/license.txt7d48279ffeed55da8dfe2f8e81f3b81fMD52TEXTComputational prediction of protein-protein interactions in Leishmania predicted proteomes.pdf.txtComputational prediction of protein-protein interactions in Leishmania predicted proteomes.pdf.txtExtracted texttext/plain65211https://www.arca.fiocruz.br/bitstream/icict/7839/5/Computational%20prediction%20of%20protein-protein%20interactions%20in%20Leishmania%20predicted%20proteomes.pdf.txt199957e5bfd5ad7003dab1973566bdb4MD55THUMBNAILComputational prediction of protein-protein interactions in Leishmania predicted proteomes.pdf.jpgComputational prediction of protein-protein interactions in Leishmania predicted proteomes.pdf.jpgGenerated Thumbnailimage/jpeg2137https://www.arca.fiocruz.br/bitstream/icict/7839/4/Computational%20prediction%20of%20protein-protein%20interactions%20in%20Leishmania%20predicted%20proteomes.pdf.jpg489d3335bb34254b7ca1d66afe72c28dMD54icict/78392018-04-05 23:45:50.635oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352018-04-06T02:45:50Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.pt_BR.fl_str_mv Computational prediction of protein-protein interactions in Leishmania predicted proteomes
title Computational prediction of protein-protein interactions in Leishmania predicted proteomes
spellingShingle Computational prediction of protein-protein interactions in Leishmania predicted proteomes
Rezende, Antônio Mauro de
Drug interactions
Leishmania major
Network analysis
Protein interaction networks
Proteomes
Sequence databases
title_short Computational prediction of protein-protein interactions in Leishmania predicted proteomes
title_full Computational prediction of protein-protein interactions in Leishmania predicted proteomes
title_fullStr Computational prediction of protein-protein interactions in Leishmania predicted proteomes
title_full_unstemmed Computational prediction of protein-protein interactions in Leishmania predicted proteomes
title_sort Computational prediction of protein-protein interactions in Leishmania predicted proteomes
author Rezende, Antônio Mauro de
author_facet Rezende, Antônio Mauro de
Folador, Edson Luiz
Resende, Daniela de Melo
Ruiz, Jerônimo Conceição
author_role author
author2 Folador, Edson Luiz
Resende, Daniela de Melo
Ruiz, Jerônimo Conceição
author2_role author
author
author
dc.contributor.author.fl_str_mv Rezende, Antônio Mauro de
Folador, Edson Luiz
Resende, Daniela de Melo
Ruiz, Jerônimo Conceição
dc.subject.en.pt_BR.fl_str_mv Drug interactions
Leishmania major
Network analysis
Protein interaction networks
Proteomes
Sequence databases
topic Drug interactions
Leishmania major
Network analysis
Protein interaction networks
Proteomes
Sequence databases
description Fundação Oswaldo Cruz. Centro de Pesquisa René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, Brazil/Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Bioquímica e Imunologia. Belo Horizonte, MG, Brazil
publishDate 2012
dc.date.issued.fl_str_mv 2012
dc.date.accessioned.fl_str_mv 2014-06-26T12:02:30Z
dc.date.available.fl_str_mv 2014-06-26T12:02:30Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv REZENDE, Antonio Mauro e al. Computational prediction of protein-protein interactions in Leishmania predicted proteomes. Plos One. 2012, vol.7, pp. e51304
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/7839
dc.identifier.issn.none.fl_str_mv 1932-6203
identifier_str_mv REZENDE, Antonio Mauro e al. Computational prediction of protein-protein interactions in Leishmania predicted proteomes. Plos One. 2012, vol.7, pp. e51304
1932-6203
url https://www.arca.fiocruz.br/handle/icict/7839
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
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