Publicação
Study of the monomer-dimer equilibrium of the pH-sensing protein PsbS using molecular dynamics simulations
| Resumo: | "Photosystem II subunit S (PsbS) plays a central role in non-photochemical quenching (NPQ), a key photoprotective mechanism that allows plants to dissipate excess absorbed energy under fluctuating light. Acting as a pH sensor, PsbS undergoes protonation-dependent conformational changes triggered by lumen acidification, but the molecular determinants of its activation and dimerization remain still not fully understood. In this study, we employ constant pH molecular dynamics (CpHMD) simulations to investigate the protonation behaviour, conformational dynamics, and pH-dependent dimerization free energies of PsbS. Protonation states of titratable residues were sampled across a range of pH values (3-8), allowing to construct titration curves and estimate residue pa shifts. These revealed positively shifted pa values for several lumen-exposed glutamates, which can act as pH sensors in the physiological window of pH 5–6. Protonation correlation analysis further indicated the presence of complex networks encompassing both lumenal and stromal residues, suggesting long-range communication across the membrane in both monomeric and dimeric states.(...)" |
|---|---|
| Autores principais: | Vitória, Sara Moreno Jorge |
| Assunto: | PsbS NPQ dimerization pH-sensitive behaviour constant pH molecular dynamics |
| Ano: | 2025 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade Nova de Lisboa |
| Idioma: | inglês |
| Origem: | Repositório Institucional da UNL |
| _version_ | 1868984257137868800 |
|---|---|
| author | Vitória, Sara Moreno Jorge |
| author_facet | Vitória, Sara Moreno Jorge |
| author_role | author |
| contributor_name_str_mv | Baptista, António RUN |
| country_str | PT |
| creators_json_txt | [{\"Person.name\":\"Vitória, Sara Moreno Jorge\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | Baptista, António RUN |
| datacite.creators.creator.creatorName.fl_str_mv | Vitória, Sara Moreno Jorge |
| datacite.date.Accepted.fl_str_mv | 2025-12-09T00:00:00Z |
| datacite.date.available.fl_str_mv | 2026-04-13T16:41:20Z |
| datacite.date.embargoed.fl_str_mv | 2026-04-13T16:41:20Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| datacite.subjects.subject.fl_str_mv | PsbS NPQ dimerization pH-sensitive behaviour constant pH molecular dynamics |
| datacite.titles.title.fl_str_mv | Study of the monomer-dimer equilibrium of the pH-sensing protein PsbS using molecular dynamics simulations |
| dc.contributor.none.fl_str_mv | Baptista, António RUN |
| dc.creator.none.fl_str_mv | Vitória, Sara Moreno Jorge |
| dc.date.Accepted.fl_str_mv | 2025-12-09T00:00:00Z |
| dc.date.available.fl_str_mv | 2026-04-13T16:41:20Z |
| dc.date.embargoed.fl_str_mv | 2026-04-13T16:41:20Z |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | http://hdl.handle.net/10362/202201 |
| dc.language.none.fl_str_mv | eng |
| dc.rights.cclincense.fl_str_mv | http://creativecommons.org/licenses/by/4.0/ |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_abf2 |
| dc.subject.none.fl_str_mv | PsbS NPQ dimerization pH-sensitive behaviour constant pH molecular dynamics |
| dc.title.fl_str_mv | Study of the monomer-dimer equilibrium of the pH-sensing protein PsbS using molecular dynamics simulations |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_bdcc |
| description | "Photosystem II subunit S (PsbS) plays a central role in non-photochemical quenching (NPQ), a key photoprotective mechanism that allows plants to dissipate excess absorbed energy under fluctuating light. Acting as a pH sensor, PsbS undergoes protonation-dependent conformational changes triggered by lumen acidification, but the molecular determinants of its activation and dimerization remain still not fully understood. In this study, we employ constant pH molecular dynamics (CpHMD) simulations to investigate the protonation behaviour, conformational dynamics, and pH-dependent dimerization free energies of PsbS. Protonation states of titratable residues were sampled across a range of pH values (3-8), allowing to construct titration curves and estimate residue pa shifts. These revealed positively shifted pa values for several lumen-exposed glutamates, which can act as pH sensors in the physiological window of pH 5–6. Protonation correlation analysis further indicated the presence of complex networks encompassing both lumenal and stromal residues, suggesting long-range communication across the membrane in both monomeric and dimeric states.(...)" |
| dirty | 0 |
| eu_rights_str_mv | openAccess |
| format | masterThesis |
| fulltext.url.fl_str_mv | https://run.unl.pt/bitstreams/4156f6e6-1890-4884-bf11-0118251ffd46/download |
| id | run_348dd3f4ddbced016ceb2e5b9be57ca5 |
| identifier.url.fl_str_mv | http://hdl.handle.net/10362/202201 |
| inst_facet_str | urn:organizationAcronym:unl{{{_:::_}}}Universidade Nova de Lisboa |
| instacron_str | unl |
| institution | Universidade Nova de Lisboa |
| instname_str | Universidade Nova de Lisboa |
| language | eng |
| network_acronym_str | run |
| network_name_str | Repositório Institucional da UNL |
| oai_identifier_str | oai:run.unl.pt:10362/202201 |
| organization_str_mv | urn:organizationAcronym:unl |
| person_str_mv | Vitória, Sara Moreno Jorge |
| publishDate | 2025 |
| repo_facet_str | urn:repositoryAcronym:run{{{_:::_}}}Repositório Institucional da UNL |
| reponame_str | Repositório Institucional da UNL |
| repository_id_str | urn:repositoryAcronym:run |
| service_str_mv | urn:repositoryAcronym:run |
| spelling | engeng"Photosystem II subunit S (PsbS) plays a central role in non-photochemical quenching (NPQ), a key photoprotective mechanism that allows plants to dissipate excess absorbed energy under fluctuating light. Acting as a pH sensor, PsbS undergoes protonation-dependent conformational changes triggered by lumen acidification, but the molecular determinants of its activation and dimerization remain still not fully understood. In this study, we employ constant pH molecular dynamics (CpHMD) simulations to investigate the protonation behaviour, conformational dynamics, and pH-dependent dimerization free energies of PsbS. Protonation states of titratable residues were sampled across a range of pH values (3-8), allowing to construct titration curves and estimate residue pa shifts. These revealed positively shifted pa values for several lumen-exposed glutamates, which can act as pH sensors in the physiological window of pH 5–6. Protonation correlation analysis further indicated the presence of complex networks encompassing both lumenal and stromal residues, suggesting long-range communication across the membrane in both monomeric and dimeric states.(...)"application/pdfengStudy of the monomer-dimer equilibrium of the pH-sensing protein PsbS using molecular dynamics simulationsVitória, Sara Moreno JorgeBaptista, AntónioHostingInstitutionOrganizationalRUNe-mailmailto:run@unl.ptrun@unl.ptURNurn:tid:2041560682026-04-13T16:41:20Z2025-12-092025-09-272025-12-09T00:00:00ZHandlehttp://hdl.handle.net/10362/202201http://purl.org/coar/access_right/c_abf2open accessPsbSNPQdimerizationpH-sensitive behaviourconstant pH molecular dynamics40452875 bytesliteraturehttp://purl.org/coar/resource_type/c_bdccmaster thesis2025-12-09http://creativecommons.org/licenses/by/4.0/http://purl.org/coar/access_right/c_abf2application/pdffulltexthttps://run.unl.pt/bitstreams/4156f6e6-1890-4884-bf11-0118251ffd46/download |
| spellingShingle | Study of the monomer-dimer equilibrium of the pH-sensing protein PsbS using molecular dynamics simulations Vitória, Sara Moreno Jorge PsbS NPQ dimerization pH-sensitive behaviour constant pH molecular dynamics |
| status | SINGLETON |
| subject.fl_str_mv | PsbS NPQ dimerization pH-sensitive behaviour constant pH molecular dynamics |
| title | Study of the monomer-dimer equilibrium of the pH-sensing protein PsbS using molecular dynamics simulations |
| title_full | Study of the monomer-dimer equilibrium of the pH-sensing protein PsbS using molecular dynamics simulations |
| title_fullStr | Study of the monomer-dimer equilibrium of the pH-sensing protein PsbS using molecular dynamics simulations |
| title_full_unstemmed | Study of the monomer-dimer equilibrium of the pH-sensing protein PsbS using molecular dynamics simulations |
| title_short | Study of the monomer-dimer equilibrium of the pH-sensing protein PsbS using molecular dynamics simulations |
| title_sort | Study of the monomer-dimer equilibrium of the pH-sensing protein PsbS using molecular dynamics simulations |
| topic | PsbS NPQ dimerization pH-sensitive behaviour constant pH molecular dynamics |
| topic_facet | PsbS NPQ dimerization pH-sensitive behaviour constant pH molecular dynamics |
| url | http://hdl.handle.net/10362/202201 |
| visible | 1 |