Desarrollo de un protocolo metodológico in sílico para comprender las posibles interacciones entre la proteína YlbF de Staphylococcus aureus con ARN

La proteína YlbF, que forma parte de la familia de proteínas con dominio com_ylbF estudiadas principalmente en Bacillus subtilis, está involucrada en la regulación de la formación de biofilm, competencia y esporulación. Dado que este dominio es conservado, se postula que proteínas homólogas en otras...

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Autores:
Ruiz Castellanos, Julian Santiago
Tipo de recurso:
https://purl.org/coar/resource_type/c_7a1f
Fecha de publicación:
2024
Institución:
Universidad El Bosque
Repositorio:
Repositorio U. El Bosque
Idioma:
spa
OAI Identifier:
oai:repositorio.unbosque.edu.co:20.500.12495/13493
Acceso en línea:
https://hdl.handle.net/20.500.12495/13493
https://repositorio.unbosque.edu.co
Palabra clave:
Staphylococcus aureus
YlbF
Dinámica molecular
in sílico
Simulación
Energías intermoleculares
610.28
Staphylococcus aureus
YlbF
Molecular dynamics
in silico
Simulation
Intermolecular Energies
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License
Acceso cerrado
id UNBOSQUE2_435b1a44f325f30c19487d4a90471532
oai_identifier_str oai:repositorio.unbosque.edu.co:20.500.12495/13493
network_acronym_str UNBOSQUE2
network_name_str Repositorio U. El Bosque
repository_id_str
dc.title.none.fl_str_mv Desarrollo de un protocolo metodológico in sílico para comprender las posibles interacciones entre la proteína YlbF de Staphylococcus aureus con ARN
dc.title.translated.none.fl_str_mv Development of an in silico methodological protocol to understand the possible interactions between the Staphylococcus aureus YlbF protein with RNA
title Desarrollo de un protocolo metodológico in sílico para comprender las posibles interacciones entre la proteína YlbF de Staphylococcus aureus con ARN
spellingShingle Desarrollo de un protocolo metodológico in sílico para comprender las posibles interacciones entre la proteína YlbF de Staphylococcus aureus con ARN
Staphylococcus aureus
YlbF
Dinámica molecular
in sílico
Simulación
Energías intermoleculares
610.28
Staphylococcus aureus
YlbF
Molecular dynamics
in silico
Simulation
Intermolecular Energies
title_short Desarrollo de un protocolo metodológico in sílico para comprender las posibles interacciones entre la proteína YlbF de Staphylococcus aureus con ARN
title_full Desarrollo de un protocolo metodológico in sílico para comprender las posibles interacciones entre la proteína YlbF de Staphylococcus aureus con ARN
title_fullStr Desarrollo de un protocolo metodológico in sílico para comprender las posibles interacciones entre la proteína YlbF de Staphylococcus aureus con ARN
title_full_unstemmed Desarrollo de un protocolo metodológico in sílico para comprender las posibles interacciones entre la proteína YlbF de Staphylococcus aureus con ARN
title_sort Desarrollo de un protocolo metodológico in sílico para comprender las posibles interacciones entre la proteína YlbF de Staphylococcus aureus con ARN
dc.creator.fl_str_mv Ruiz Castellanos, Julian Santiago
dc.contributor.advisor.none.fl_str_mv Guillem Gloria, Pedro Manuel
Corredor Rozo, Zayda Lorena
dc.contributor.author.none.fl_str_mv Ruiz Castellanos, Julian Santiago
dc.subject.none.fl_str_mv Staphylococcus aureus
YlbF
Dinámica molecular
in sílico
Simulación
Energías intermoleculares
topic Staphylococcus aureus
YlbF
Dinámica molecular
in sílico
Simulación
Energías intermoleculares
610.28
Staphylococcus aureus
YlbF
Molecular dynamics
in silico
Simulation
Intermolecular Energies
dc.subject.ddc.none.fl_str_mv 610.28
dc.subject.keywords.none.fl_str_mv Staphylococcus aureus
YlbF
Molecular dynamics
in silico
Simulation
Intermolecular Energies
description La proteína YlbF, que forma parte de la familia de proteínas con dominio com_ylbF estudiadas principalmente en Bacillus subtilis, está involucrada en la regulación de la formación de biofilm, competencia y esporulación. Dado que este dominio es conservado, se postula que proteínas homólogas en otras bacterias Gram positivas podrían cumplir funciones similares. En Staphylococcus aureus, un microorganismo oportunista que causa infecciones intrahospitalarias en pacientes de alto riesgo se sospecha que YlbF está relacionada con la regulación de factores de virulencia, especialmente a nivel transcripcional, como sugiere la presencia de un dominio putativo de unión a ácidos nucleicos y estudios en mutantes nulos. En este proyecto de grado elaboró un protocolo bioinformático centrado en el desarrollo de un pipeline para obtener parámetros y llevar a cabo una dinámica molecular de la proteína YlbF de S. aureus en complejo con ARN, con el objetivo de evaluar posibles sitios de interacción (hotspots) en términos de energías, distancias y empaquetamiento hidrofóbico y su validación mediante metodologías in silico de análisis termodinámico. El flujo de trabajo incluyó la preparación de datos biológicos, obtención de estructuras proteicas y de ARN, definición de parámetros de simulación, construcción de los sistemas a simular, así como la ejecución de la dinámica molecular, su análisis y validación al realizar sustituciones clave por alanina para evaluar los cambios en las interacciones llevando a cabo un análisis comparativo de energías por aminoácido el fin de identificar aquellos residuos que presentan las energías más favorables entre las variantes mutantes y no mutantes. Hecho esto, se observó la participación de diferentes aminoácidos durante la simulación, destacando Arg193, Lys194, Arg207 y Arg209. Estos residuos mostraron una fuerte interacción con el ARN, lo que sugiere una unión potencialmente estable. La naturaleza de esta interacción parece estar relacionada con la carga positiva de estos aminoácidos, que facilita su unión a los grupos fosfato de la cadena de ARN.
publishDate 2024
dc.date.accessioned.none.fl_str_mv 2024-11-30T06:43:02Z
dc.date.available.none.fl_str_mv 2024-11-30T06:43:02Z
dc.date.issued.none.fl_str_mv 2024-11
dc.type.coar.fl_str_mv http://purl.org/coar/resource_type/c_7a1f
dc.type.local.spa.fl_str_mv Tesis/Trabajo de grado - Monografía - Pregrado
dc.type.coar.none.fl_str_mv https://purl.org/coar/resource_type/c_7a1f
dc.type.driver.none.fl_str_mv info:eu-repo/semantics/bachelorThesis
dc.type.coarversion.none.fl_str_mv https://purl.org/coar/version/c_970fb48d4fbd8a85
format https://purl.org/coar/resource_type/c_7a1f
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12495/13493
dc.identifier.instname.spa.fl_str_mv instname:Universidad El Bosque
dc.identifier.reponame.spa.fl_str_mv reponame:Repositorio Institucional Universidad El Bosque
dc.identifier.repourl.none.fl_str_mv https://repositorio.unbosque.edu.co
url https://hdl.handle.net/20.500.12495/13493
https://repositorio.unbosque.edu.co
identifier_str_mv instname:Universidad El Bosque
reponame:Repositorio Institucional Universidad El Bosque
dc.language.iso.fl_str_mv spa
language spa
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spelling Guillem Gloria, Pedro ManuelCorredor Rozo, Zayda LorenaRuiz Castellanos, Julian Santiago2024-11-30T06:43:02Z2024-11-30T06:43:02Z2024-11https://hdl.handle.net/20.500.12495/13493instname:Universidad El Bosquereponame:Repositorio Institucional Universidad El Bosquehttps://repositorio.unbosque.edu.coLa proteína YlbF, que forma parte de la familia de proteínas con dominio com_ylbF estudiadas principalmente en Bacillus subtilis, está involucrada en la regulación de la formación de biofilm, competencia y esporulación. Dado que este dominio es conservado, se postula que proteínas homólogas en otras bacterias Gram positivas podrían cumplir funciones similares. En Staphylococcus aureus, un microorganismo oportunista que causa infecciones intrahospitalarias en pacientes de alto riesgo se sospecha que YlbF está relacionada con la regulación de factores de virulencia, especialmente a nivel transcripcional, como sugiere la presencia de un dominio putativo de unión a ácidos nucleicos y estudios en mutantes nulos. En este proyecto de grado elaboró un protocolo bioinformático centrado en el desarrollo de un pipeline para obtener parámetros y llevar a cabo una dinámica molecular de la proteína YlbF de S. aureus en complejo con ARN, con el objetivo de evaluar posibles sitios de interacción (hotspots) en términos de energías, distancias y empaquetamiento hidrofóbico y su validación mediante metodologías in silico de análisis termodinámico. El flujo de trabajo incluyó la preparación de datos biológicos, obtención de estructuras proteicas y de ARN, definición de parámetros de simulación, construcción de los sistemas a simular, así como la ejecución de la dinámica molecular, su análisis y validación al realizar sustituciones clave por alanina para evaluar los cambios en las interacciones llevando a cabo un análisis comparativo de energías por aminoácido el fin de identificar aquellos residuos que presentan las energías más favorables entre las variantes mutantes y no mutantes. Hecho esto, se observó la participación de diferentes aminoácidos durante la simulación, destacando Arg193, Lys194, Arg207 y Arg209. Estos residuos mostraron una fuerte interacción con el ARN, lo que sugiere una unión potencialmente estable. La naturaleza de esta interacción parece estar relacionada con la carga positiva de estos aminoácidos, que facilita su unión a los grupos fosfato de la cadena de ARN.Laboratorio de genética molecular bacterianaBioingenieroPregradoThe YlbF protein, part of the com_ylbF domain family studied mainly in Bacillus subtilis, is involved in the regulation of biofilm formation, competence, and sporulation. Given the conserved nature of this domain, it is hypothesized that homologous proteins in other Gram-positive bacteria might perform similar functions. In Staphylococcus aureus, an opportunistic microorganism responsible for nosocomial infections in high-risk patients, YlbF is suspected to be linked to the regulation of virulence factors, particularly at the transcriptional level, as indicated by the presence of a putative nucleic acid-binding domain and studies in null mutants. In this degree project, a bioinformatics protocol was developed, focusing on creating a pipeline to obtain parameters and conduct molecular dynamics simulations of the S. aureus YlbF protein in complex with RNA. The goal was to evaluate potential interaction sites (hotspots) in terms of energies, distances, and hydrophobic packing, and validate these through in silico thermodynamic analysis methodologies. The workflow included preparing biological data, obtaining protein and RNA structures, defining simulation parameters, constructing the systems to be simulated, executing molecular dynamics, analyzing the results, and validating key substitutions with alanine to assess changes in interactions. This included a comparative analysis of energies per amino acid to identify residues showing the most favorable energies between mutant and non-mutant variants. As a result, different amino acids were highlighted during the simulation, with Arg193, Lys194, Arg207, and Arg209 showing strong interactions with RNA, suggesting a potentially stable binding. This interaction is likely related to the positive charge of these amino acids, which facilitates their binding to the phosphate groups of the RNA chain.application/pdfStaphylococcus aureusYlbFDinámica molecularin sílicoSimulaciónEnergías intermoleculares610.28Staphylococcus aureusYlbFMolecular dynamicsin silicoSimulationIntermolecular EnergiesDesarrollo de un protocolo metodológico in sílico para comprender las posibles interacciones entre la proteína YlbF de Staphylococcus aureus con ARNDevelopment of an in silico methodological protocol to understand the possible interactions between the Staphylococcus aureus YlbF protein with RNABioingenieríaUniversidad El BosqueFacultad de IngenieríaTesis/Trabajo de grado - Monografía - Pregradohttps://purl.org/coar/resource_type/c_7a1fhttp://purl.org/coar/resource_type/c_7a1finfo:eu-repo/semantics/bachelorThesishttps://purl.org/coar/version/c_970fb48d4fbd8a85Abellan Blázquez, A. (2016). 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