Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilization
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/j.bpj.2021.06.003 http://hdl.handle.net/11449/229128 |
Resumo: | The nucleocapsid (N) protein of betacoronaviruses is responsible for nucleocapsid assembly and other essential regulatory functions. The N protein N-terminal domain (N-NTD) interacts and melts the double-stranded transcriptional regulatory sequences (dsTRSs), regulating the discontinuous subgenome transcription process. Here, we used molecular dynamics (MD) simulations to study the binding of the severe acute respiratory syndrome coronavirus 2 N-NTD to nonspecific (NS) and TRS dsRNAs. We probed dsRNAs’ Watson-Crick basepairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, triggering melting initiation. dsRNA destabilization driven by N-NTD was more efficient for dsTRSs than dsNS. N-NTD dynamics, especially a tweezer-like motion of β2-β3 and Δ2-β5 loops, seems to play a key role in Watson-Crick basepairing destabilization. Based on experimental information available in the literature, we constructed kinetics models for N-NTD-mediated dsRNA melting. Our results support a 1:1 stoichiometry (N-NTD/dsRNA), matching MD simulations and raising different possibilities for N-NTD action: 1) two N-NTD arms of dimeric N would bind to two different RNA sites, either closely or spatially spaced in the viral genome, in a cooperative manner; and 2) monomeric N-NTD would be active, opening up the possibility of a regulatory dissociation event. |
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Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilizationThe nucleocapsid (N) protein of betacoronaviruses is responsible for nucleocapsid assembly and other essential regulatory functions. The N protein N-terminal domain (N-NTD) interacts and melts the double-stranded transcriptional regulatory sequences (dsTRSs), regulating the discontinuous subgenome transcription process. Here, we used molecular dynamics (MD) simulations to study the binding of the severe acute respiratory syndrome coronavirus 2 N-NTD to nonspecific (NS) and TRS dsRNAs. We probed dsRNAs’ Watson-Crick basepairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, triggering melting initiation. dsRNA destabilization driven by N-NTD was more efficient for dsTRSs than dsNS. N-NTD dynamics, especially a tweezer-like motion of β2-β3 and Δ2-β5 loops, seems to play a key role in Watson-Crick basepairing destabilization. Based on experimental information available in the literature, we constructed kinetics models for N-NTD-mediated dsRNA melting. Our results support a 1:1 stoichiometry (N-NTD/dsRNA), matching MD simulations and raising different possibilities for N-NTD action: 1) two N-NTD arms of dimeric N would bind to two different RNA sites, either closely or spatially spaced in the viral genome, in a cooperative manner; and 2) monomeric N-NTD would be active, opening up the possibility of a regulatory dissociation event.Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)Multiuser Center for Biomolecular Innovation and Department of Physics Institute of Biosciences Letters and Exact Sciences São Paulo State University (UNESP), São José do Rio PretoInstitute of Medical Biochemistry Leopoldo de Meis and National Center for Structural Biology and BioimagingDepartment of Biochemistry Institute of Chemistry Federal University of Rio de JaneiroMultiuser Center for Biomolecular Innovation and Department of Physics Institute of Biosciences Letters and Exact Sciences São Paulo State University (UNESP), São José do Rio PretoFAPERJ: 202.279/2018FAPERJ: 204.432/2014FAPERJ: 210.361/2015FAPERJ: 239.229/2018FAPERJ: 255.940/2020Universidade Estadual Paulista (UNESP)Institute of Medical Biochemistry Leopoldo de Meis and National Center for Structural Biology and BioimagingFederal University of Rio de JaneiroCaruso, Ícaro P. [UNESP]Sanches, Karoline [UNESP]Da Poian, Andrea T.Pinheiro, Anderson S.Almeida, Fabio C.L.2022-04-29T08:30:39Z2022-04-29T08:30:39Z2021-07-20info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article2814-2827http://dx.doi.org/10.1016/j.bpj.2021.06.003Biophysical Journal, v. 120, n. 14, p. 2814-2827, 2021.1542-00860006-3495http://hdl.handle.net/11449/22912810.1016/j.bpj.2021.06.0032-s2.0-85109774342Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBiophysical Journalinfo:eu-repo/semantics/openAccess2022-04-29T08:30:39Zoai:repositorio.unesp.br:11449/229128Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T15:15:14.913219Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilization |
title |
Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilization |
spellingShingle |
Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilization Caruso, Ícaro P. [UNESP] |
title_short |
Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilization |
title_full |
Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilization |
title_fullStr |
Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilization |
title_full_unstemmed |
Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilization |
title_sort |
Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilization |
author |
Caruso, Ícaro P. [UNESP] |
author_facet |
Caruso, Ícaro P. [UNESP] Sanches, Karoline [UNESP] Da Poian, Andrea T. Pinheiro, Anderson S. Almeida, Fabio C.L. |
author_role |
author |
author2 |
Sanches, Karoline [UNESP] Da Poian, Andrea T. Pinheiro, Anderson S. Almeida, Fabio C.L. |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) Institute of Medical Biochemistry Leopoldo de Meis and National Center for Structural Biology and Bioimaging Federal University of Rio de Janeiro |
dc.contributor.author.fl_str_mv |
Caruso, Ícaro P. [UNESP] Sanches, Karoline [UNESP] Da Poian, Andrea T. Pinheiro, Anderson S. Almeida, Fabio C.L. |
description |
The nucleocapsid (N) protein of betacoronaviruses is responsible for nucleocapsid assembly and other essential regulatory functions. The N protein N-terminal domain (N-NTD) interacts and melts the double-stranded transcriptional regulatory sequences (dsTRSs), regulating the discontinuous subgenome transcription process. Here, we used molecular dynamics (MD) simulations to study the binding of the severe acute respiratory syndrome coronavirus 2 N-NTD to nonspecific (NS) and TRS dsRNAs. We probed dsRNAs’ Watson-Crick basepairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, triggering melting initiation. dsRNA destabilization driven by N-NTD was more efficient for dsTRSs than dsNS. N-NTD dynamics, especially a tweezer-like motion of β2-β3 and Δ2-β5 loops, seems to play a key role in Watson-Crick basepairing destabilization. Based on experimental information available in the literature, we constructed kinetics models for N-NTD-mediated dsRNA melting. Our results support a 1:1 stoichiometry (N-NTD/dsRNA), matching MD simulations and raising different possibilities for N-NTD action: 1) two N-NTD arms of dimeric N would bind to two different RNA sites, either closely or spatially spaced in the viral genome, in a cooperative manner; and 2) monomeric N-NTD would be active, opening up the possibility of a regulatory dissociation event. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-07-20 2022-04-29T08:30:39Z 2022-04-29T08:30:39Z |
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://dx.doi.org/10.1016/j.bpj.2021.06.003 Biophysical Journal, v. 120, n. 14, p. 2814-2827, 2021. 1542-0086 0006-3495 http://hdl.handle.net/11449/229128 10.1016/j.bpj.2021.06.003 2-s2.0-85109774342 |
url |
http://dx.doi.org/10.1016/j.bpj.2021.06.003 http://hdl.handle.net/11449/229128 |
identifier_str_mv |
Biophysical Journal, v. 120, n. 14, p. 2814-2827, 2021. 1542-0086 0006-3495 10.1016/j.bpj.2021.06.003 2-s2.0-85109774342 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Biophysical Journal |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
2814-2827 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
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1808128488490663936 |