Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods

Autores
Khanum, Sofia; Carbone, Vincenzo; Gupta, Sandeep K.; Yeung, Juliana; Shu, Dairu; Wilson, Tania; Parlane, Natalie A.; Altermann, Eric; Estein, Silvia Marcela; Janssen, Peter H.; Wedlock, D. Neil; Heiser, Axel
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
In silico prediction of epitopes is a potentially time-saving alternative to experimental epitopeidentifcation but is often subject to misidentifcation of epitopes and may not be useful for proteinsfrom archaeal microorganisms. In this study, we mapped B- and T-cell epitopes of a model antigefrom the methanogen Methanobrevibacter ruminantium M1, the Big_1 domain (AdLP-D1, amino acids 19–198) of an adhesin-like protein. A series of 17 overlapping 20-mer peptides was selected to cove the Big_1 domain. Peptide-specifc antibodies were produced in mice and measured by ELISA, while an in vitro splenocyte re-stimulation assay determined specifc T-cell responses. Overall, fve peptide of the 17 peptides were shown to be major immunogenic epitopes of AdLP-D1. These immunogenic regions were examined for their localization in a homology-based model of AdLP-D1. Validate epitopes were found in the outside region of the protein, with loop like secondary structures refecting their fexibility. The empirical data were compared with epitope predictions made by programmes based on a range of algorithms. In general, the epitopes identifed by in silico predictions were not comparable to those determined empirically.
Fil: Khanum, Sofia. Agresearch; Nueva Zelanda
Fil: Carbone, Vincenzo. Agresearch; Nueva Zelanda
Fil: Gupta, Sandeep K.. Agresearch; Nueva Zelanda
Fil: Yeung, Juliana. Agresearch; Nueva Zelanda
Fil: Shu, Dairu. Agresearch; Nueva Zelanda
Fil: Wilson, Tania. Agresearch; Nueva Zelanda
Fil: Parlane, Natalie A.. Agresearch; Nueva Zelanda
Fil: Altermann, Eric. Agresearch; Nueva Zelanda. Massey University; Nueva Zelanda
Fil: Estein, Silvia Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; Argentina
Fil: Janssen, Peter H.. Agresearch; Nueva Zelanda
Fil: Wedlock, D. Neil. Agresearch; Nueva Zelanda
Fil: Heiser, Axel. Agresearch; Nueva Zelanda
Materia
EPITOPES
SILICA GEL PREDICTION
METANOGENIC BACTERIA
ADHESIN
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/257310
Acceder
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network_acronym_str CONICETDig
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network_name_str CONICET Digital (CONICET)
spelling Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methodsKhanum, SofiaCarbone, VincenzoGupta, Sandeep K.Yeung, JulianaShu, DairuWilson, TaniaParlane, Natalie A.Altermann, EricEstein, Silvia MarcelaJanssen, Peter H.Wedlock, D. NeilHeiser, AxelEPITOPESSILICA GEL PREDICTIONMETANOGENIC BACTERIAADHESINhttps://purl.org/becyt/ford/4.3https://purl.org/becyt/ford/4In silico prediction of epitopes is a potentially time-saving alternative to experimental epitopeidentifcation but is often subject to misidentifcation of epitopes and may not be useful for proteinsfrom archaeal microorganisms. In this study, we mapped B- and T-cell epitopes of a model antigefrom the methanogen Methanobrevibacter ruminantium M1, the Big_1 domain (AdLP-D1, amino acids 19–198) of an adhesin-like protein. A series of 17 overlapping 20-mer peptides was selected to cove the Big_1 domain. Peptide-specifc antibodies were produced in mice and measured by ELISA, while an in vitro splenocyte re-stimulation assay determined specifc T-cell responses. Overall, fve peptide of the 17 peptides were shown to be major immunogenic epitopes of AdLP-D1. These immunogenic regions were examined for their localization in a homology-based model of AdLP-D1. Validate epitopes were found in the outside region of the protein, with loop like secondary structures refecting their fexibility. The empirical data were compared with epitope predictions made by programmes based on a range of algorithms. In general, the epitopes identifed by in silico predictions were not comparable to those determined empirically.Fil: Khanum, Sofia. Agresearch; Nueva ZelandaFil: Carbone, Vincenzo. Agresearch; Nueva ZelandaFil: Gupta, Sandeep K.. Agresearch; Nueva ZelandaFil: Yeung, Juliana. Agresearch; Nueva ZelandaFil: Shu, Dairu. Agresearch; Nueva ZelandaFil: Wilson, Tania. Agresearch; Nueva ZelandaFil: Parlane, Natalie A.. Agresearch; Nueva ZelandaFil: Altermann, Eric. Agresearch; Nueva Zelanda. Massey University; Nueva ZelandaFil: Estein, Silvia Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; ArgentinaFil: Janssen, Peter H.. Agresearch; Nueva ZelandaFil: Wedlock, D. Neil. Agresearch; Nueva ZelandaFil: Heiser, Axel. Agresearch; Nueva ZelandaNature2022-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/257310Khanum, Sofia; Carbone, Vincenzo; Gupta, Sandeep K.; Yeung, Juliana; Shu, Dairu; et al.; Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods; Nature; Scientific Reports; 12; 1; 6-2022; 1-132045-2322CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41598-022-14545-8info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-022-14545-8info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:44:19Zoai:ri.conicet.gov.ar:11336/257310instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-22 11:44:19.711CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods
title Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods
spellingShingle Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods
Khanum, Sofia
EPITOPES
SILICA GEL PREDICTION
METANOGENIC BACTERIA
ADHESIN
title_short Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods
title_full Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods
title_fullStr Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods
title_full_unstemmed Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods
title_sort Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods
dc.creator.none.fl_str_mv Khanum, Sofia
Carbone, Vincenzo
Gupta, Sandeep K.
Yeung, Juliana
Shu, Dairu
Wilson, Tania
Parlane, Natalie A.
Altermann, Eric
Estein, Silvia Marcela
Janssen, Peter H.
Wedlock, D. Neil
Heiser, Axel
author Khanum, Sofia
author_facet Khanum, Sofia
Carbone, Vincenzo
Gupta, Sandeep K.
Yeung, Juliana
Shu, Dairu
Wilson, Tania
Parlane, Natalie A.
Altermann, Eric
Estein, Silvia Marcela
Janssen, Peter H.
Wedlock, D. Neil
Heiser, Axel
author_role author
author2 Carbone, Vincenzo
Gupta, Sandeep K.
Yeung, Juliana
Shu, Dairu
Wilson, Tania
Parlane, Natalie A.
Altermann, Eric
Estein, Silvia Marcela
Janssen, Peter H.
Wedlock, D. Neil
Heiser, Axel
author2_role author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv EPITOPES
SILICA GEL PREDICTION
METANOGENIC BACTERIA
ADHESIN
topic EPITOPES
SILICA GEL PREDICTION
METANOGENIC BACTERIA
ADHESIN
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.3
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv In silico prediction of epitopes is a potentially time-saving alternative to experimental epitopeidentifcation but is often subject to misidentifcation of epitopes and may not be useful for proteinsfrom archaeal microorganisms. In this study, we mapped B- and T-cell epitopes of a model antigefrom the methanogen Methanobrevibacter ruminantium M1, the Big_1 domain (AdLP-D1, amino acids 19–198) of an adhesin-like protein. A series of 17 overlapping 20-mer peptides was selected to cove the Big_1 domain. Peptide-specifc antibodies were produced in mice and measured by ELISA, while an in vitro splenocyte re-stimulation assay determined specifc T-cell responses. Overall, fve peptide of the 17 peptides were shown to be major immunogenic epitopes of AdLP-D1. These immunogenic regions were examined for their localization in a homology-based model of AdLP-D1. Validate epitopes were found in the outside region of the protein, with loop like secondary structures refecting their fexibility. The empirical data were compared with epitope predictions made by programmes based on a range of algorithms. In general, the epitopes identifed by in silico predictions were not comparable to those determined empirically.
Fil: Khanum, Sofia. Agresearch; Nueva Zelanda
Fil: Carbone, Vincenzo. Agresearch; Nueva Zelanda
Fil: Gupta, Sandeep K.. Agresearch; Nueva Zelanda
Fil: Yeung, Juliana. Agresearch; Nueva Zelanda
Fil: Shu, Dairu. Agresearch; Nueva Zelanda
Fil: Wilson, Tania. Agresearch; Nueva Zelanda
Fil: Parlane, Natalie A.. Agresearch; Nueva Zelanda
Fil: Altermann, Eric. Agresearch; Nueva Zelanda. Massey University; Nueva Zelanda
Fil: Estein, Silvia Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; Argentina
Fil: Janssen, Peter H.. Agresearch; Nueva Zelanda
Fil: Wedlock, D. Neil. Agresearch; Nueva Zelanda
Fil: Heiser, Axel. Agresearch; Nueva Zelanda
description In silico prediction of epitopes is a potentially time-saving alternative to experimental epitopeidentifcation but is often subject to misidentifcation of epitopes and may not be useful for proteinsfrom archaeal microorganisms. In this study, we mapped B- and T-cell epitopes of a model antigefrom the methanogen Methanobrevibacter ruminantium M1, the Big_1 domain (AdLP-D1, amino acids 19–198) of an adhesin-like protein. A series of 17 overlapping 20-mer peptides was selected to cove the Big_1 domain. Peptide-specifc antibodies were produced in mice and measured by ELISA, while an in vitro splenocyte re-stimulation assay determined specifc T-cell responses. Overall, fve peptide of the 17 peptides were shown to be major immunogenic epitopes of AdLP-D1. These immunogenic regions were examined for their localization in a homology-based model of AdLP-D1. Validate epitopes were found in the outside region of the protein, with loop like secondary structures refecting their fexibility. The empirical data were compared with epitope predictions made by programmes based on a range of algorithms. In general, the epitopes identifed by in silico predictions were not comparable to those determined empirically.
publishDate 2022
dc.date.none.fl_str_mv 2022-06
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/257310
Khanum, Sofia; Carbone, Vincenzo; Gupta, Sandeep K.; Yeung, Juliana; Shu, Dairu; et al.; Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods; Nature; Scientific Reports; 12; 1; 6-2022; 1-13
2045-2322
CONICET Digital
CONICET
url http://hdl.handle.net/11336/257310
identifier_str_mv Khanum, Sofia; Carbone, Vincenzo; Gupta, Sandeep K.; Yeung, Juliana; Shu, Dairu; et al.; Mapping immunogenic epitopes of an adhesin-like protein from Methanobrevibacter ruminantium M1 and comparison of empirical data with in silico prediction methods; Nature; Scientific Reports; 12; 1; 6-2022; 1-13
2045-2322
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41598-022-14545-8
info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-022-14545-8
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature
publisher.none.fl_str_mv Nature
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 12.982451

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