Modulación estructural del homotetrámero CNGC1 de Arabidopsis thaliana por calmodulina-2: un análisis in silico mediante dinámica molecular de grano grueso (coarse-grain) y All-atom
Figuras, estadísticas, tablas
- 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/26258
- Acceso en línea:
- https://repositorio.ucaldas.edu.co/handle/ucaldas/26258
- Palabra clave:
- 570 - Biología
1. Ciencias Naturales
Calmodulina
Dinámica molecular
Interacción proteína-proteína
All-atom
Coarse-Grained
AtCNGC1
Biología
- Rights
- License
- https://creativecommons.org/licenses/by-nc-nd/4.0/
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Repositorio Institucional U. Caldas |
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| dc.title.none.fl_str_mv |
Modulación estructural del homotetrámero CNGC1 de Arabidopsis thaliana por calmodulina-2: un análisis in silico mediante dinámica molecular de grano grueso (coarse-grain) y All-atom |
| title |
Modulación estructural del homotetrámero CNGC1 de Arabidopsis thaliana por calmodulina-2: un análisis in silico mediante dinámica molecular de grano grueso (coarse-grain) y All-atom |
| spellingShingle |
Modulación estructural del homotetrámero CNGC1 de Arabidopsis thaliana por calmodulina-2: un análisis in silico mediante dinámica molecular de grano grueso (coarse-grain) y All-atom 570 - Biología 1. Ciencias Naturales Calmodulina Dinámica molecular Interacción proteína-proteína All-atom Coarse-Grained AtCNGC1 Biología |
| title_short |
Modulación estructural del homotetrámero CNGC1 de Arabidopsis thaliana por calmodulina-2: un análisis in silico mediante dinámica molecular de grano grueso (coarse-grain) y All-atom |
| title_full |
Modulación estructural del homotetrámero CNGC1 de Arabidopsis thaliana por calmodulina-2: un análisis in silico mediante dinámica molecular de grano grueso (coarse-grain) y All-atom |
| title_fullStr |
Modulación estructural del homotetrámero CNGC1 de Arabidopsis thaliana por calmodulina-2: un análisis in silico mediante dinámica molecular de grano grueso (coarse-grain) y All-atom |
| title_full_unstemmed |
Modulación estructural del homotetrámero CNGC1 de Arabidopsis thaliana por calmodulina-2: un análisis in silico mediante dinámica molecular de grano grueso (coarse-grain) y All-atom |
| title_sort |
Modulación estructural del homotetrámero CNGC1 de Arabidopsis thaliana por calmodulina-2: un análisis in silico mediante dinámica molecular de grano grueso (coarse-grain) y All-atom |
| dc.contributor.none.fl_str_mv |
Nieto Giraldo, Diego Fernando Tayac Giraldo, Juan Camilo Grupo de Química Teórica y Bioinformática - QTB (Categoría B) |
| dc.subject.none.fl_str_mv |
570 - Biología 1. Ciencias Naturales Calmodulina Dinámica molecular Interacción proteína-proteína All-atom Coarse-Grained AtCNGC1 Biología |
| topic |
570 - Biología 1. Ciencias Naturales Calmodulina Dinámica molecular Interacción proteína-proteína All-atom Coarse-Grained AtCNGC1 Biología |
| description |
Figuras, estadísticas, tablas |
| publishDate |
2025 |
| dc.date.none.fl_str_mv |
2025-11-20T15:17:01Z 2025-11-20T15:17:01Z 2025-11-20 |
| 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/26258 Universidad de Caldas Repositorio Institucional Universidad de Caldas repositorio.ucaldas.edu.co |
| url |
https://repositorio.ucaldas.edu.co/handle/ucaldas/26258 |
| 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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Nature Plants, 11(3), 632-642. https://doi.org/10.1038/s41477-025-01923-z Zeng, H., Xu, L., Singh, A., Wang, H., Du, L., & Poovaiah, B. W. (2015). Involvement of calmodulin and calmodulin-like proteins in plant responses to abiotic stresses. Frontiers in Plant Science, 6, 600. https://doi.org/10.3389/fpls.2015.00600 Zhang, X., Tian, J., Li, S., Liu, Y., Feng, T., Wang, Y., Li, Y., Huang, X., & Li, D. (2022). Characterization of the Calmodulin/Calmodulin-like Protein (CAM/CML) Family in Ginkgo biloba, and the Influence of an Ectopically Expressed GbCML Gene (Gb_30819) on Seedling and Fruit Development of Transgenic Arabidopsis. Plants, 11(11), 1506. https://doi.org/10.3390/plants11111506 Zhang, Z., Hou, C., Tian, W., Li, L., & Zhu, H. (2019). Electrophysiological Studies Revealed CaM1-Mediated Regulation of the Arabidopsis Calcium Channel CNGC12. Frontiers in Plant Science, 10. https://doi.org/10.3389/fpls.2019.01090 |
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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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http://purl.org/coar/access_right/c_abf2 |
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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) http://purl.org/coar/access_right/c_abf2 |
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53 páginas application/pdf application/pdf application/pdf application/pdf |
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Universidad de Caldas Facultad de Ciencias Exactas y Naturales Manizales Biología |
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Universidad de Caldas Facultad de Ciencias Exactas y Naturales Manizales Biología |
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Universidad de Caldas |
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Modulación estructural del homotetrámero CNGC1 de Arabidopsis thaliana por calmodulina-2: un análisis in silico mediante dinámica molecular de grano grueso (coarse-grain) y All-atom570 - Biología1. Ciencias NaturalesCalmodulinaDinámica molecularInteracción proteína-proteínaAll-atomCoarse-GrainedAtCNGC1BiologíaFiguras, estadísticas, tablasLa señalización mediada por el ion calcio Ca²⁺ es un mecanismo fundamental y universal, esencial para la adaptación de las plantas a su entorno. Los canales iónicos activados por nucleótidos cíclicos (CNGC) actúan como componentes centrales de este sistema, facilitando el flujo de Ca²⁺ a través de la membrana plasmática. Este flujo es vital para gobernar procesos críticos que aseguran la supervivencia del organismo completo, participando en el desarrollo, la nutrición mineral, la inmunidad y la respuesta al estrés fisiológico, incluyendo el estrés salino y patogénico. Por lo tanto, la importancia de analizar la modulación de estos canales radica en que la Calmodulina (CaM) opera como un sensor primario de Ca²⁺, decodificando la "firma de calcio" para activar las respuestas celulares y adaptativas correspondientes. Unos de los mecanismos de regulación de los CNGC es su interacción con la proteína calmodulina (CaM), mediante un sistema de retroalimentación dual. Este sistema previene la toxicidad iónica causada por una sobrecarga de Ca²⁺: a bajas concentraciones de Ca²⁺ , la forma libre de calcio (Apo-CaM) se une al canal y promueve su apertura, pero cuando el influjo eleva el Ca²⁺ citosólico a altos niveles, la CaM saturada (Ca²⁺−CaM o Holo-CaM) sufre un cambio conformacional que provoca la inhibición y el cierre del canal. A pesar de este conocimiento sobre los componentes y la lógica regulatoria general, y a pesar de la conocida afinidad de AtCaM2 por el AtCNGC1, los detalles atómicos de cómo una isoforma específica como CaM2 modula la estructura y dinámica de un canal homotetramérico como AtCNGC1 no han sido resueltos. Estudios recientes de crio-microscopía electrónica (cryo-EM) de CNGC1 han confirmado su estructura tetramérica y mecanismos de gating, pero las regiones de unión a CaM (los dominios N y C-terminales) son altamente flexibles y permanecen invisibles, confirmando este como el principal vacío de conocimiento. El proyecto propuesto se centra en abordar esta brecha, utilizando simulaciones in silico avanzadas (dinámica molecular de grano grueso y All-atom) para determinar si la unión de la AtCaM2 induce cambios conformacionales en el canal AtCNGC1 y para evaluar en detalle la naturaleza, la estabilidad y la dinámica de la interacción entre ambas proteínas.Calcium ion (Ca²⁺) signaling is a fundamental and universal mechanism essential for plant adaptation to the environment. Cyclic nucleotide-gated ion channels (CNGCs) act as central components of this system, facilitating Ca²⁺ flux across the plasma membrane. This flux is vital for governing critical processes that ensure whole-organism survival, participating in development, mineral nutrition, immunity, and physiological stress responses, including salt and pathogenic stress. Therefore, the importance of analyzing the modulation of these channels lies in the fact that Calmodulin (CaM) operates as a primary Ca²⁺ sensor, decoding the "calcium signature" to trigger corresponding cellular and adaptive responses. One of the regulatory mechanisms of CNGCs is their interaction with the calmodulin protein (CaM) through a dual feedback system. This system prevents ionic toxicity caused by Ca²⁺ overload: at low Ca²⁺ concentrations, the calcium-free form (Apo-CaM) binds to the channel and promotes its opening. However, when the influx raises cytosolic Ca²⁺ to high levels, saturated CaM (Ca²⁺−CaM or Holo-CaM) undergoes a conformational change that leads to inhibition and closure of the channel. Despite existing knowledge of the general regulatory logic and the known affinity of AtCaM2 for AtCNGC1, the atomic details of how a specific isoform such as CaM2 modulates the structure and dynamics of a homotetrameric channel like AtCNGC1 have not been resolved. Recent cryo-electron microscopy (cryo-EM) studies of CNGC1 have confirmed its tetrameric structure and gating mechanisms, but the CaM-binding regions (N- and C-terminal domains) are highly flexible and remain invisible, establishing this as the principal knowledge gap. The proposed project focuses on addressing this gap by employing advanced in silico simulations (coarse-grained and all-atom molecular dynamics) to determine whether the binding of AtCaM2 induces conformational changes in the AtCNGC1 channel and to evaluate the nature, stability, and dynamics of the interaction between both proteins in detail. The implemented multiscale in silico approach validated the modulation hypothesis. The results demonstrated that binding of AtCaM2 (in its Apo-CaM state) induces a significant conformational change: the channel in the absence of CaM displays high structural flexibility, with RMSD peaks reaching up to 15 Å, whereas binding to each monomer of the four AtCaM2 subunits drastically reduces this mobility, stabilizing the complex in a markedly more rigid conformation. All-atom simulations of the complex confirmed its high conformational stability, reaching structural equilibrium (RMSD ~4.0 Å). This study proposes an atomic mechanism in which Apo-CaM acts as a molecular "scaffold," restricting channel flexibility, locking it into more rigid conformations over time, and representing its functionally open state.Introducción -- Justificación -- Impacto Científico y Aplicado de la Tesis -- Problemática -- Pregunta de investigación -- Objetivos -- Objetivo General -- Objetivos Específicos -- Marco conceptual -- Lista de Abreviaturas -- Definiciones Conceptuales -- Marco Teórico -- Señalización del Calcio como Eje Central en la Fisiología Vegetal -- Canales Iónicos Activados por Nucleótidos Cíclicos (CNGC) -- Arquitectura Molecular y Dominios Funcionales de los CNGC -- Mecanismos Complejos de Regulación de la Actividad de los CNGC -- Regulación por CaM -- Isoformas de CaM y Especificidad en la Interacción -- AtCNGC1 y las Limitaciones del Conocimiento Estructural -- Metodología -- Modelado Estructural mediante AlphaFold3 -- Análisis Estructural y Selección de Modelos Representativos -- Simulaciones Coarse-Grained (CG) de Dinámica Molecular -- Refinamiento Atómico y Simulaciones All-Atom -- Análisis Cuantitativo de Dinámica e Interacción -- Resultados -- Evaluación de la coherencia estructural entre modelos (RMSD) -- Perfil de flexibilidad estructural por residuo (RMSF) -- Caracterización de la interfaz de interacción CNGC1–CaM -- Dinámica molecular del complejo CNGC1–AtCaM2 -- Estabilidad estructural global: RMSD -- Flexibilidad local: RMSF -- Dinámica molecular del CNGC1 sin CaM -- Inestabilidad estructural global: RMSD -- Implicaciones funcionales -- Discusión -- ConclusionesPregradoEste estudio se fundamenta en un enfoque computacional multiescala orientado a caracterizar los determinantes estructurales y dinámicos que describen la interacción entre el canal iónico CNGC1 de Arabidopsis thaliana y AtCaM2. 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