Prediction of peptide and protein propensity for amyloid formation

Detalhes bibliográficos
Autor(a) principal: Família, Carlos
Data de Publicação: 2015
Outros Autores: Dennison, Sarah R., Quintas, Alexandre, Phoenix, David A.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10400.26/14872
Resumo: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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spelling Prediction of peptide and protein propensity for amyloid formationPeptideProteinAmyloid formationThis is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited."Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo structural changes, which lead to amyloid formation, are quite diverse and share no obvious sequence or structural homology, despite the structural similarity found in the fibrils. To address these issues, a novel approach based on recursive feature selection and feed-forward neural networks was undertaken to identify key features highly correlated with the self-assembly problem. This approach allowed the identification of seven physicochemical and biochemical properties of the amino acids highly associated with the self-assembly of peptides and proteins into amyloid-like fibrils (normalized frequency of β-sheet, normalized frequency of β-sheet from LG, weights for β-sheet at the window position of 1, isoelectric point, atom-based hydrophobic moment, helix termination parameter at position j+1 and ΔG° values for peptides extrapolated in 0 M urea). Moreover, these features enabled the development of a new predictor (available at http://cran.r-project.org/web/packages/appnn/index.html) capable of accurately and reliably predicting the amyloidogenic propensity from the polypeptide sequence alone with a prediction accuracy of 84.9 % against an external validation dataset of sequences with experimental in vitro, evidence of amyloid formation."PLoSRepositório ComumFamília, CarlosDennison, Sarah R.Quintas, AlexandrePhoenix, David A.2016-09-27T10:53:46Z2015-08-01T00:00:00Z2015-08-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.26/14872engFamília C, Dennison SR, Quintas A, Phoenix DA (2015) Prediction of Peptide and Protein Propensity for Amyloid Formation. PLoS ONE 10(8): e0134679. doi:10.1371/journal.pone.01346791932-620310.1371/journal.pone.0134679info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2022-10-06T14:52:30Zoai:comum.rcaap.pt:10400.26/14872Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T15:08:21.867770Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Prediction of peptide and protein propensity for amyloid formation
title Prediction of peptide and protein propensity for amyloid formation
spellingShingle Prediction of peptide and protein propensity for amyloid formation
Família, Carlos
Peptide
Protein
Amyloid formation
title_short Prediction of peptide and protein propensity for amyloid formation
title_full Prediction of peptide and protein propensity for amyloid formation
title_fullStr Prediction of peptide and protein propensity for amyloid formation
title_full_unstemmed Prediction of peptide and protein propensity for amyloid formation
title_sort Prediction of peptide and protein propensity for amyloid formation
author Família, Carlos
author_facet Família, Carlos
Dennison, Sarah R.
Quintas, Alexandre
Phoenix, David A.
author_role author
author2 Dennison, Sarah R.
Quintas, Alexandre
Phoenix, David A.
author2_role author
author
author
dc.contributor.none.fl_str_mv Repositório Comum
dc.contributor.author.fl_str_mv Família, Carlos
Dennison, Sarah R.
Quintas, Alexandre
Phoenix, David A.
dc.subject.por.fl_str_mv Peptide
Protein
Amyloid formation
topic Peptide
Protein
Amyloid formation
description This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
publishDate 2015
dc.date.none.fl_str_mv 2015-08-01T00:00:00Z
2015-08-01T00:00:00Z
2016-09-27T10:53:46Z
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.uri.fl_str_mv http://hdl.handle.net/10400.26/14872
url http://hdl.handle.net/10400.26/14872
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Família C, Dennison SR, Quintas A, Phoenix DA (2015) Prediction of Peptide and Protein Propensity for Amyloid Formation. PLoS ONE 10(8): e0134679. doi:10.1371/journal.pone.0134679
1932-6203
10.1371/journal.pone.0134679
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv PLoS
publisher.none.fl_str_mv PLoS
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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