Aproximación in silico al mecanismo de reacción del complejo lacasa POXA1b – ABTS de Pleurotus ostreatus
Figuras
- Autores:
- Tipo de recurso:
- Fecha de publicación:
- 2025
- Institución:
- Universidad de Caldas
- Repositorio:
- Repositorio Institucional U. Caldas
- Idioma:
- spa
- OAI Identifier:
- oai:repositorio.ucaldas.edu.co:ucaldas/26181
- Acceso en línea:
- https://repositorio.ucaldas.edu.co/handle/ucaldas/26181
- Palabra clave:
- 570 - Biología
1. Ciencias Naturales
ABTS
Biorremediación
Dinámica molecular
Lacasa
POXA1b
Transferencia electrónica
Docking
Biología
- Rights
- License
- https://creativecommons.org/licenses/by-nc-nd/4.0/
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Aproximación in silico al mecanismo de reacción del complejo lacasa POXA1b – ABTS de Pleurotus ostreatus |
| title |
Aproximación in silico al mecanismo de reacción del complejo lacasa POXA1b – ABTS de Pleurotus ostreatus |
| spellingShingle |
Aproximación in silico al mecanismo de reacción del complejo lacasa POXA1b – ABTS de Pleurotus ostreatus 570 - Biología 1. Ciencias Naturales ABTS Biorremediación Dinámica molecular Lacasa POXA1b Transferencia electrónica Docking Biología |
| title_short |
Aproximación in silico al mecanismo de reacción del complejo lacasa POXA1b – ABTS de Pleurotus ostreatus |
| title_full |
Aproximación in silico al mecanismo de reacción del complejo lacasa POXA1b – ABTS de Pleurotus ostreatus |
| title_fullStr |
Aproximación in silico al mecanismo de reacción del complejo lacasa POXA1b – ABTS de Pleurotus ostreatus |
| title_full_unstemmed |
Aproximación in silico al mecanismo de reacción del complejo lacasa POXA1b – ABTS de Pleurotus ostreatus |
| title_sort |
Aproximación in silico al mecanismo de reacción del complejo lacasa POXA1b – ABTS de Pleurotus ostreatus |
| dc.contributor.none.fl_str_mv |
Morales-Álvarez, Edwin David Rodas Rodríguez, José Mauricio Grupo de Química Teórica y Bioinformática - QTB (Categoría B) |
| dc.subject.none.fl_str_mv |
570 - Biología 1. Ciencias Naturales ABTS Biorremediación Dinámica molecular Lacasa POXA1b Transferencia electrónica Docking Biología |
| topic |
570 - Biología 1. Ciencias Naturales ABTS Biorremediación Dinámica molecular Lacasa POXA1b Transferencia electrónica Docking Biología |
| description |
Figuras |
| publishDate |
2025 |
| dc.date.none.fl_str_mv |
2025-11-14T19:36:19Z 2025-11-14T19:36:19Z 2025-11-14 |
| dc.type.none.fl_str_mv |
Trabajo de grado - Pregrado http://purl.org/coar/resource_type/c_7a1f Text info:eu-repo/semantics/bachelorThesis |
| dc.identifier.none.fl_str_mv |
https://repositorio.ucaldas.edu.co/handle/ucaldas/26181 Universidad de Caldas Repositorio Institucional Universidad de Caldas repositorio.ucaldas.edu.co |
| url |
https://repositorio.ucaldas.edu.co/handle/ucaldas/26181 |
| identifier_str_mv |
Universidad de Caldas Repositorio Institucional Universidad de Caldas repositorio.ucaldas.edu.co |
| dc.language.none.fl_str_mv |
spa |
| language |
spa |
| dc.relation.none.fl_str_mv |
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Journal of pharmaceutical sciences, 108(4), https://doi.org/10.1016/j.xphs.2018.11.029 1366-1377 |
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https://creativecommons.org/licenses/by-nc-nd/4.0/ Atribución-NoComercial-SinDerivadas 4.0 Internacional (CC BY-NC-ND 4.0) |
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46 páginas application/pdf application/pdf application/pdf application/pdf |
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Universidad de Caldas Facultad de Ciencias Exactas y Naturales Manizales, Caldas. Colombia Biología |
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Universidad de Caldas Facultad de Ciencias Exactas y Naturales Manizales, Caldas. Colombia Biología |
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Universidad de Caldas |
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Aproximación in silico al mecanismo de reacción del complejo lacasa POXA1b – ABTS de Pleurotus ostreatus570 - Biología1. Ciencias NaturalesABTSBiorremediaciónDinámica molecularLacasaPOXA1bTransferencia electrónicaDockingBiologíaFigurasLas lacasas fúngicas de alto potencial, como POXA1b de Pleurotus ostreatus, son biocatalizadores versátiles para oxidar sustratos aromáticos y mediar procesos de biorremediación. Este trabajo caracteriza in silico el complejo POXA1b–ABTS y propone una ruta de transferencia electrónica (ET) compatible con la reducción de O₂ a H₂O. Se construyó un modelo estructural de POXA1b con glicosilaciones y el centro multicobre completo y estados de protonación a pH 4.5. El reconocimiento de sustratos se estudió mediante docking por lotes (AutoDock Vina 1.2) de ABTS-2 y 99 colorantes industriales. Posteriormente, el complejo ABTS–POXA1b se sometió a dinámica molecular (MD) de 200 ns con el software AMBER24; se verificó estabilidad termodinámica y se realizó clústering por RMSD de proteína y ligando. El docking mostró una distribución de afinidades centrada en −8.59 kcal/mol, con un subconjunto reducido de ligandos de alta afinidad (mínimo ~−11.6 kcal/mol; Direct Blue 71). Un mapa de contactos identificó “hotspots” en PRO393, ASN207, PHE238, ASN263 y SER426 (ocupancias ≥75%). En MD, ABTS-2 permaneció anclado cerca de CuT1 mediante un enlace de hidrógeno persistente HIS456–N(azino) (≈2.14±0.21 Å; 158.7±11.4° ≥50 ns) y una red de interacciones π con PHE238, PHE331, PHE338, PRO393 e ILE453; además, el grupo sulfonato estableció múltiples enlaces de hidrógeno con el backbone de ALA329 y vecinos. El clústering del ligando estuvo dominado por tres poses que explicaron ~66% de la trayectoria, con variabilidad localizada en bucles que rodean el bolsillo. Integrando estos hallazgos, se propone una ET desde ABTS a CuT1 (coordinado por HIS394/CYS451/HIS456), seguida de transferencia intraproteica hacia el TNC y reducción de O₂, coherente con lacasas fúngicas de alto potencial. En conjunto, el “ancla” HIS456–azino y la red π emergen como determinantes de orientación y estabilidad del sustrato, con implicaciones para ingeniería de sitio activo y selección de mediadores en la decoloración de colorantes y remoción de contaminantes aromáticos.High-potential fungal laccases, such as POXA1b from Pleurotus ostreatus, are versatile biocatalysts for oxidizing aromatic substrates and mediating bioremediation processes. This work characterizes the POXA1b–ABTS complex in silico and proposes an electron transfer (ET) pathway compatible with the reduction of O2 to H2O. A structural model of POXA1b was constructed with glycosylations and the complete multi-copper center and protonation states at pH 4.5. Substrate recognition was studied by batch docking (AutoDock Vina 1.2) of ABTS-2 and 99 industrial dyes. Subsequently, the ABTS–POXA1b complex underwent 200 ns molecular dynamics (MD) with AMBER24 software; thermodynamic stability was verified, and clustering was performed by protein and ligand RMSD. Docking showed an affinity distribution centered at −8.59 kcal/mol, with a small subset of high-affinity ligands (minimum ~−11.6 kcal/mol; Direct Blue 71). A contact map identified hotspots at PRO393, ASN207, PHE238, ASN263, and SER426 (occupancies ≥75%). In MD, ABTS-2 remained anchored near CuT1 via a persistent HIS456–N(azino) hydrogen bond (≈2.14±0.21 Å; 158.7±11.4° ≥50 ns) and a network of π interactions with PHE238, PHE331, PHE338, PRO393, and ILE453; in addition, the sulfonate group established multiple hydrogen bonds with the backbone of ALA329 and neighbors. Ligand clustering was dominated by three poses that explained ~66% of the trajectory, with variability localized in loops surrounding the pocket. Integrating these findings, an ET from ABTS to CuT1 (coordinated by HIS394/CYS451/HIS456) is proposed, followed by intraprotein transfer to TNC and O2 reduction, consistent with high-potential fungal laccases. Together, the HIS456–azino “anchor” and the π network emerge as determinants of substrate orientation and stability, with implications for active site engineering and mediator selection in dye decolorization and aromatic contaminant removal.Resumen -- Introducción -- Objetivos -- Objetivo General -- Objetivos Específicos -- Materiales y métodos -- Modelado computacional -- Estudio de acoplamiento -- Simulación de dinámica molecular -- Análisis de resultados -- Resultados -- Modelado computacional -- Estudio de acoplamiento -- Simulación de dinámica molecular -- Discusión -- Conclusiones -- ReferenciasPregradoBiólogo(a)Universidad de CaldasFacultad de Ciencias Exactas y NaturalesManizales, Caldas. 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