Characterization of the phenolate-keto oxyluciferin/luciferase interactions in the S1 state by QM/MM energy decomposition analysis

Unraveling the nature of the interaction on the complex formed by the oxyluciferin chromophore in the first electronically excited state and the luciferase enzyme can lead to a more profound understanding of fireflies’ bioluminescence, which is a natural process with a large amount of applications i...

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Detalles Bibliográficos
Autores: Mateo de la Fuente, Henar, Anguita Ortiz, Nuria, Mandado, Marcos, Nogueira Pérez, Juan José
Tipo de recurso: artículo
Fecha de publicación:2026
País:España
Institución:Universidad Autónoma de Madrid
Repositorio:Biblos-e Archivo. Repositorio Institucional de la UAM
Idioma:inglés
OAI Identifier:oai:dnet:biblosearchi::2d6dd366d184a039bf09115e0357bb13
Acceso en línea:https://hdl.handle.net/10486/775001
https://dx.doi.org/10.1016/j.compbiolchem.2026.109148
Access Level:acceso abierto
Palabra clave:Bioluminescence
Luciferin
Energy-decomposition analysis
QM/MM
Molecular dynamics
Química
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spelling Characterization of the phenolate-keto oxyluciferin/luciferase interactions in the S1 state by QM/MM energy decomposition analysisMateo de la Fuente, HenarAnguita Ortiz, NuriaMandado, MarcosNogueira Pérez, Juan JoséBioluminescenceLuciferinEnergy-decomposition analysisQM/MMMolecular dynamicsQuímicaUnraveling the nature of the interaction on the complex formed by the oxyluciferin chromophore in the first electronically excited state and the luciferase enzyme can lead to a more profound understanding of fireflies’ bioluminescence, which is a natural process with a large amount of applications in medicine. In this work, we have studied the interaction of the phenolate-keto oxyluciferin (OLU) chromophore and the luciferase protein, and we have found that the interaction energy is governed mostly by electrostatic terms. Nonetheless, non-electrostatic contributions are non-negligible due to the high presence of -systemcontaining amino acids within the bioluminescent pocket. Furthermore, we have outlined a methodology for performing energy decomposition analysis in the excited state using a multiscale hybrid electrostaticembedding QM/MM approach, stressing that the OLUFF force field is not suitable for this task from a force field-base approach. Moreover, we have analyzed how the proximity of PHE249 and SER349 affect the different terms of the interaction energy, unraveling that the most relevant terms of their contributions are polarization and electrostatic, respectively. This strategy can be extended to investigate the interactions of the other three potential emitters within the OLU/luciferase complex, as well as complexes with mutated proteins. Such analyses may help clarify the factors governing color modulation in the bioluminescent process and provide valuable insights for tuning the OLU/luciferase complex to enhance its applicabilityThe authors acknowledge the support of the Universidad Autónoma de Madrid through the predoctoral Contract Formación de Personal Investigador (FPI-UAM), the Xunta de Galicia, Spain through the project GRC2024/27 and the Spanish Ministry of Science and Innovation through the projects PID2024-162002NB-I00 and PID2022-138023NBI00 (funded by MCIN/AEI/10.13039/501100011033)ElsevierDepartamento de QuímicaFacultad de CienciasGobierno de España20262026-06-01research articlehttp://purl.org/coar/resource_type/c_2df8fbb1VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/10486/775001https://dx.doi.org/10.1016/j.compbiolchem.2026.109148reponame:Biblos-e Archivo. Repositorio Institucional de la UAMinstname:Universidad Autónoma de MadridInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial 4.0 Internationalhttp://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:dnet:biblosearchi::2d6dd366d184a039bf09115e0357bb132026-06-23T12:46:27Z
dc.title.none.fl_str_mv Characterization of the phenolate-keto oxyluciferin/luciferase interactions in the S1 state by QM/MM energy decomposition analysis
title Characterization of the phenolate-keto oxyluciferin/luciferase interactions in the S1 state by QM/MM energy decomposition analysis
spellingShingle Characterization of the phenolate-keto oxyluciferin/luciferase interactions in the S1 state by QM/MM energy decomposition analysis
Mateo de la Fuente, Henar
Bioluminescence
Luciferin
Energy-decomposition analysis
QM/MM
Molecular dynamics
Química
title_short Characterization of the phenolate-keto oxyluciferin/luciferase interactions in the S1 state by QM/MM energy decomposition analysis
title_full Characterization of the phenolate-keto oxyluciferin/luciferase interactions in the S1 state by QM/MM energy decomposition analysis
title_fullStr Characterization of the phenolate-keto oxyluciferin/luciferase interactions in the S1 state by QM/MM energy decomposition analysis
title_full_unstemmed Characterization of the phenolate-keto oxyluciferin/luciferase interactions in the S1 state by QM/MM energy decomposition analysis
title_sort Characterization of the phenolate-keto oxyluciferin/luciferase interactions in the S1 state by QM/MM energy decomposition analysis
dc.creator.none.fl_str_mv Mateo de la Fuente, Henar
Anguita Ortiz, Nuria
Mandado, Marcos
Nogueira Pérez, Juan José
author Mateo de la Fuente, Henar
author_facet Mateo de la Fuente, Henar
Anguita Ortiz, Nuria
Mandado, Marcos
Nogueira Pérez, Juan José
author_role author
author2 Anguita Ortiz, Nuria
Mandado, Marcos
Nogueira Pérez, Juan José
author2_role author
author
author
dc.contributor.none.fl_str_mv Departamento de Química
Facultad de Ciencias
Gobierno de España
dc.subject.none.fl_str_mv Bioluminescence
Luciferin
Energy-decomposition analysis
QM/MM
Molecular dynamics
Química
topic Bioluminescence
Luciferin
Energy-decomposition analysis
QM/MM
Molecular dynamics
Química
description Unraveling the nature of the interaction on the complex formed by the oxyluciferin chromophore in the first electronically excited state and the luciferase enzyme can lead to a more profound understanding of fireflies’ bioluminescence, which is a natural process with a large amount of applications in medicine. In this work, we have studied the interaction of the phenolate-keto oxyluciferin (OLU) chromophore and the luciferase protein, and we have found that the interaction energy is governed mostly by electrostatic terms. Nonetheless, non-electrostatic contributions are non-negligible due to the high presence of -systemcontaining amino acids within the bioluminescent pocket. Furthermore, we have outlined a methodology for performing energy decomposition analysis in the excited state using a multiscale hybrid electrostaticembedding QM/MM approach, stressing that the OLUFF force field is not suitable for this task from a force field-base approach. Moreover, we have analyzed how the proximity of PHE249 and SER349 affect the different terms of the interaction energy, unraveling that the most relevant terms of their contributions are polarization and electrostatic, respectively. This strategy can be extended to investigate the interactions of the other three potential emitters within the OLU/luciferase complex, as well as complexes with mutated proteins. Such analyses may help clarify the factors governing color modulation in the bioluminescent process and provide valuable insights for tuning the OLU/luciferase complex to enhance its applicability
publishDate 2026
dc.date.none.fl_str_mv 2026
2026-06-01
dc.type.none.fl_str_mv research article
http://purl.org/coar/resource_type/c_2df8fbb1
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/10486/775001
https://dx.doi.org/10.1016/j.compbiolchem.2026.109148
url https://hdl.handle.net/10486/775001
https://dx.doi.org/10.1016/j.compbiolchem.2026.109148
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial 4.0 International
http://creativecommons.org/licenses/by-nc/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial 4.0 International
http://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:Biblos-e Archivo. Repositorio Institucional de la UAM
instname:Universidad Autónoma de Madrid
instname_str Universidad Autónoma de Madrid
reponame_str Biblos-e Archivo. Repositorio Institucional de la UAM
collection Biblos-e Archivo. Repositorio Institucional de la UAM
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812455

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