Room for improvement in the initial martini 3 parameterization of peptide interactions

Detalhes bibliográficos
Autor(a) principal: Spinti, J. Karl
Data de Publicação: 2023
Outros Autores: Neiva Nunes, Fernando, Melo, Manuel N.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/158652
Resumo: Funding Information: We thank T. Cordeiro for bringing to our attention the coiled coil system that motivated part of this study. J.K.S. acknowledges an internship sponsored by Fundação Luso-Americana para o Desenvolvimento through its Study in Portugal Network. M.N.M. thanks Fundação para a Ciência e a Tecnologia, Portugal for fellowship CEECIND/04124/2017 , and for funding project MOSTMICRO-ITQB with references UIDB/04612/2020 and UIDP/04612/2020 . Publisher Copyright: © 2023 The Authors
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spelling Room for improvement in the initial martini 3 parameterization of peptide interactionsCoarse-grainCoiled coilMartiniMolecular dynamicsPeptidesTransmembranePhysics and Astronomy(all)Physical and Theoretical ChemistryFunding Information: We thank T. Cordeiro for bringing to our attention the coiled coil system that motivated part of this study. J.K.S. acknowledges an internship sponsored by Fundação Luso-Americana para o Desenvolvimento through its Study in Portugal Network. M.N.M. thanks Fundação para a Ciência e a Tecnologia, Portugal for fellowship CEECIND/04124/2017 , and for funding project MOSTMICRO-ITQB with references UIDB/04612/2020 and UIDP/04612/2020 . Publisher Copyright: © 2023 The AuthorsThe Martini 3 coarse-grain force field has greatly improved upon its predecessor, having already been successfully employed in several applications. Here, we gauge the accuracy of Martini 2 and 3 protein interactions in two types of systems: coiled coil peptide dimers in water and transmembrane peptides. Coiled coil dimers form incorrectly under Martini 2 and not at all under Martini 3. With transmembrane peptides, Martini 3 represents better the membrane thickness–peptide tilt relationship, but shorter peptides do not remain transmembranar. We discuss related observations, and describe mitigation strategies involving either scaling interactions or restraining the system.Instituto de Tecnologia Química e Biológica António Xavier (ITQB)RUNSpinti, J. KarlNeiva Nunes, FernandoMelo, Manuel N.2023-10-03T22:19:00Z2023-05-162023-05-16T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10362/158652eng0009-2614PURE: 72619539https://doi.org/10.1016/j.cplett.2023.140436info: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:RCAAP2024-03-11T05:41:11Zoai:run.unl.pt:10362/158652Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:57:15.096794Repositório 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 Room for improvement in the initial martini 3 parameterization of peptide interactions
title Room for improvement in the initial martini 3 parameterization of peptide interactions
spellingShingle Room for improvement in the initial martini 3 parameterization of peptide interactions
Spinti, J. Karl
Coarse-grain
Coiled coil
Martini
Molecular dynamics
Peptides
Transmembrane
Physics and Astronomy(all)
Physical and Theoretical Chemistry
title_short Room for improvement in the initial martini 3 parameterization of peptide interactions
title_full Room for improvement in the initial martini 3 parameterization of peptide interactions
title_fullStr Room for improvement in the initial martini 3 parameterization of peptide interactions
title_full_unstemmed Room for improvement in the initial martini 3 parameterization of peptide interactions
title_sort Room for improvement in the initial martini 3 parameterization of peptide interactions
author Spinti, J. Karl
author_facet Spinti, J. Karl
Neiva Nunes, Fernando
Melo, Manuel N.
author_role author
author2 Neiva Nunes, Fernando
Melo, Manuel N.
author2_role author
author
dc.contributor.none.fl_str_mv Instituto de Tecnologia Química e Biológica António Xavier (ITQB)
RUN
dc.contributor.author.fl_str_mv Spinti, J. Karl
Neiva Nunes, Fernando
Melo, Manuel N.
dc.subject.por.fl_str_mv Coarse-grain
Coiled coil
Martini
Molecular dynamics
Peptides
Transmembrane
Physics and Astronomy(all)
Physical and Theoretical Chemistry
topic Coarse-grain
Coiled coil
Martini
Molecular dynamics
Peptides
Transmembrane
Physics and Astronomy(all)
Physical and Theoretical Chemistry
description Funding Information: We thank T. Cordeiro for bringing to our attention the coiled coil system that motivated part of this study. J.K.S. acknowledges an internship sponsored by Fundação Luso-Americana para o Desenvolvimento through its Study in Portugal Network. M.N.M. thanks Fundação para a Ciência e a Tecnologia, Portugal for fellowship CEECIND/04124/2017 , and for funding project MOSTMICRO-ITQB with references UIDB/04612/2020 and UIDP/04612/2020 . Publisher Copyright: © 2023 The Authors
publishDate 2023
dc.date.none.fl_str_mv 2023-10-03T22:19:00Z
2023-05-16
2023-05-16T00:00:00Z
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/10362/158652
url http://hdl.handle.net/10362/158652
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 0009-2614
PURE: 72619539
https://doi.org/10.1016/j.cplett.2023.140436
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.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
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instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
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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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