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

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dc.contributor.advisorGuillem Gloria, Pedro Manuel
dc.contributor.advisorCorredor Rozo, Zayda Lorena
dc.contributor.authorRuiz Castellanos, Julian Santiago
dc.date.accessioned2024-11-30T06:43:02Z
dc.date.available2024-11-30T06:43:02Z
dc.date.issued2024-11
dc.description.abstractLa 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.
dc.description.abstractenglishThe 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.
dc.description.degreelevelPregradospa
dc.description.degreenameBioingenierospa
dc.description.sponsorshipLaboratorio de genética molecular bacteriana
dc.format.mimetypeapplication/pdf
dc.identifier.instnameinstname:Universidad El Bosquespa
dc.identifier.reponamereponame:Repositorio Institucional Universidad El Bosquespa
dc.identifier.repourlhttps://repositorio.unbosque.edu.co
dc.identifier.urihttps://hdl.handle.net/20.500.12495/13493
dc.language.isoes
dc.publisher.facultyFacultad de Ingenieríaspa
dc.publisher.grantorUniversidad El Bosquespa
dc.publisher.programBioingenieríaspa
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dc.rights.accessrightsinfo:eu-repo/semantics/closedAccess
dc.rights.accessrightsrl.org/coar/access_right/c_14cbhttp://pu
dc.rights.localAcceso cerradospa
dc.subjectStaphylococcus aureus
dc.subjectYlbF
dc.subjectDinámica molecular
dc.subjectin sílico
dc.subjectSimulación
dc.subjectEnergías intermoleculares
dc.subject.ddc610.28
dc.subject.keywordsStaphylococcus aureus
dc.subject.keywordsYlbF
dc.subject.keywordsMolecular dynamics
dc.subject.keywordsin silico
dc.subject.keywordsSimulation
dc.subject.keywordsIntermolecular Energies
dc.titleDesarrollo de un protocolo metodológico in sílico para comprender las posibles interacciones entre la proteína YlbF de Staphylococcus aureus con ARN
dc.title.translatedDevelopment of an in silico methodological protocol to understand the possible interactions between the Staphylococcus aureus YlbF protein with RNA
dc.type.coarhttps://purl.org/coar/resource_type/c_7a1f
dc.type.coarversionhttps://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.driverinfo:eu-repo/semantics/bachelorThesis
dc.type.hasversioninfo:eu-repo/semantics/acceptedVersion
dc.type.localTesis/Trabajo de grado - Monografía - Pregradospa

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