Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD Simulations

Trigger Factor (TF) is a primary ATP-independent molecular chaperone in bacteria that engages nascent polypeptide chains emerging from the ribosomal exit tunnel to assist their folding. However, the real-time behavior of TF during active translation under near-physiological conditions remains elusiv...

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Autores: Núñez, Eider, Saha, Prithwidip, García Ibarluzea, Markel, Muguruza-Montero, Arantza, Alicante Martínez, Sara, Ramis, Rafael, Leonardo, Aritz, Bergara, Aitor, Villarroel, Álvaro, Rico, Felix
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/413077
Acceso en línea:http://hdl.handle.net/10261/413077
https://api.elsevier.com/content/abstract/scopus_id/105025699578
Access Level:acceso abierto
Palabra clave:Trigger factor (chaperone)
Atomic force microscopy imaging
Molecular dynamics simulations
Protein folding
ribosome
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spelling Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD SimulationsNúñez, EiderSaha, PrithwidipGarcía Ibarluzea, MarkelMuguruza-Montero, ArantzaAlicante Martínez, SaraRamis, RafaelLeonardo, AritzBergara, AitorVillarroel, ÁlvaroRico, FelixTrigger factor (chaperone)Atomic force microscopy imagingMolecular dynamics simulationsProtein foldingribosomeTrigger Factor (TF) is a primary ATP-independent molecular chaperone in bacteria that engages nascent polypeptide chains emerging from the ribosomal exit tunnel to assist their folding. However, the real-time behavior of TF during active translation under near-physiological conditions remains elusive. Here, we employ high-speed atomic force microscopy (HS-AFM) imaging to visualize TF dynamics on intact Escherichia coli ribosomes in real time. We observe that TF transitions between compact and extended conformations and forms stable and transient contacts near ribosomal proteins uL23 and bL17, respectively. Interestingly, TFs engage distinct regions of the same ribosome–nascent chain complex, with one TF binding near the nascent chain and another near bL17, revealing multivalent interactions on the ribosome surface. Complementary all-atom molecular dynamics simulations reproduced the observed TF conformations and interaction dynamics, validating the experimentally observed structural transitions and dual-site engagement. This integrative approach uncovers previously inaccessible dynamics of ribosome-associated chaperones and offers a broadly applicable platform to probe cotranslational folding under near-physiological conditions.We gratefully acknowledge the Basque Government for its funding and support through the postdoctoral grant awarded to E. Nuñez (POS_2021_1_0017) and the project Grupos Consolidados (IT-1707-22), as well as the technical and human support provided by the DIPC Supercomputing Center. We also thank the Spanish Ministry of Science and Innovation for the project Generación del Conocimiento (PID2022-139230NB-I00). This work has also received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 772257).Peer reviewedACS PublicationsEusko JaurlaritzaMinisterio de Ciencia e Innovación (España)Agencia Estatal de Investigación (España)European CommissionNúñez, Eider [0000-0001-8075-9815]Saha, Prithwidip [0000-0003-2600-0415]Muguruza-Montero, Arantza [0000-0001-8713-4949]Alicante Martínez, Sara [0000-0002-3960-8836]Leonardo, Aritz [0000-0002-5942-2270]Bergara, Aitor [0000-0003-2707-1856]Villarroel, Álvaro [0000-0003-1096-7824]Rico, Felix [0000-0002-7757-8340]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202620262025info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/413077https://api.elsevier.com/content/abstract/scopus_id/105025699578reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2022-139230NB-I00info:eu-repo/grantAgreement/EC/H2020/772257The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.1021/acsnano.5c13500https://doi.org/10.1021/acsnano.5c13500Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/4130772026-05-22T06:33:51Z
dc.title.none.fl_str_mv Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD Simulations
title Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD Simulations
spellingShingle Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD Simulations
Núñez, Eider
Trigger factor (chaperone)
Atomic force microscopy imaging
Molecular dynamics simulations
Protein folding
ribosome
title_short Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD Simulations
title_full Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD Simulations
title_fullStr Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD Simulations
title_full_unstemmed Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD Simulations
title_sort Multivalent Interactions between Chaperone and Ribosome-Nascent Chain Complex Revealed by High-Speed AFM and MD Simulations
dc.creator.none.fl_str_mv Núñez, Eider
Saha, Prithwidip
García Ibarluzea, Markel
Muguruza-Montero, Arantza
Alicante Martínez, Sara
Ramis, Rafael
Leonardo, Aritz
Bergara, Aitor
Villarroel, Álvaro
Rico, Felix
author Núñez, Eider
author_facet Núñez, Eider
Saha, Prithwidip
García Ibarluzea, Markel
Muguruza-Montero, Arantza
Alicante Martínez, Sara
Ramis, Rafael
Leonardo, Aritz
Bergara, Aitor
Villarroel, Álvaro
Rico, Felix
author_role author
author2 Saha, Prithwidip
García Ibarluzea, Markel
Muguruza-Montero, Arantza
Alicante Martínez, Sara
Ramis, Rafael
Leonardo, Aritz
Bergara, Aitor
Villarroel, Álvaro
Rico, Felix
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Eusko Jaurlaritza
Ministerio de Ciencia e Innovación (España)
Agencia Estatal de Investigación (España)
European Commission
Núñez, Eider [0000-0001-8075-9815]
Saha, Prithwidip [0000-0003-2600-0415]
Muguruza-Montero, Arantza [0000-0001-8713-4949]
Alicante Martínez, Sara [0000-0002-3960-8836]
Leonardo, Aritz [0000-0002-5942-2270]
Bergara, Aitor [0000-0003-2707-1856]
Villarroel, Álvaro [0000-0003-1096-7824]
Rico, Felix [0000-0002-7757-8340]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Trigger factor (chaperone)
Atomic force microscopy imaging
Molecular dynamics simulations
Protein folding
ribosome
topic Trigger factor (chaperone)
Atomic force microscopy imaging
Molecular dynamics simulations
Protein folding
ribosome
description Trigger Factor (TF) is a primary ATP-independent molecular chaperone in bacteria that engages nascent polypeptide chains emerging from the ribosomal exit tunnel to assist their folding. However, the real-time behavior of TF during active translation under near-physiological conditions remains elusive. Here, we employ high-speed atomic force microscopy (HS-AFM) imaging to visualize TF dynamics on intact Escherichia coli ribosomes in real time. We observe that TF transitions between compact and extended conformations and forms stable and transient contacts near ribosomal proteins uL23 and bL17, respectively. Interestingly, TFs engage distinct regions of the same ribosome–nascent chain complex, with one TF binding near the nascent chain and another near bL17, revealing multivalent interactions on the ribosome surface. Complementary all-atom molecular dynamics simulations reproduced the observed TF conformations and interaction dynamics, validating the experimentally observed structural transitions and dual-site engagement. This integrative approach uncovers previously inaccessible dynamics of ribosome-associated chaperones and offers a broadly applicable platform to probe cotranslational folding under near-physiological conditions.
publishDate 2025
dc.date.none.fl_str_mv 2025
2026
2026
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/413077
https://api.elsevier.com/content/abstract/scopus_id/105025699578
url http://hdl.handle.net/10261/413077
https://api.elsevier.com/content/abstract/scopus_id/105025699578
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2022-139230NB-I00
info:eu-repo/grantAgreement/EC/H2020/772257
The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.1021/acsnano.5c13500
https://doi.org/10.1021/acsnano.5c13500
Sí
dc.rights.none.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 ACS Publications
publisher.none.fl_str_mv ACS Publications
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
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