Protein-DNA dissociation kinetics and chromosome organization in a model bacterial confinement

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buir.advisorErbaş, Aykut
dc.contributor.authorKoşar, Zafer
dc.date.accessioned2021-09-09T08:36:18Z
dc.date.available2021-09-09T08:36:18Z
dc.date.copyright2021-09
dc.date.issued2021-09
dc.date.submitted2021-09-09
dc.departmentGraduate Program in Materials Science and Nanotechnologyen_US
dc.descriptionCataloged from PDF version of article.en_US
dc.descriptionThesis (Master's): Bilkent University, Department of Materials Science and Nanotechnology, İhsan Doğramacı Bilkent University, 2021.en_US
dc.descriptionIncludes bibliographical references (leaves 101-106).en_US
dc.description.abstractTranscriptional initiation and repression require the temporal interactions of transcription factors with DNA. Recent experiments showed that the interaction lifetime is crucial for transcriptional regulation. Relevantly, in vitro single-molecule studies showed that nucleoid-associated proteins (NAPs) dissociate rapidly from DNA through facilitated dissociation (FD) with the increasing phase-solution protein concentration. Nevertheless, it is not clear whether such a concentration-dependent mechanism is functional in bacterial confinement, in which NAP levels and the 3D chromosomal architecture are coupled. Here, we employ extensive coarse-grained molecular simulations, where we model the dissociation of specific and nonspecific dimeric NAPs from a high-molecular-weight circular DNA polymer in a rod-shaped structure constituting the cellular boundaries. Our simulations indicate that the peak cellular protein concentrations result in highly compact chromosomal conformations. Such compactions lead to shorter DNA-residence times but only for NAPs demonstrating sequence-specificity, such as the factor for inversion stimulation (Fis). On the other hand, the dissociation rates of nonspecific NAPs decrease with the increasing protein concentrations, exhibiting an inverse FD behavior. Another set of simulations utilizing restrained chromosome models reveal DNA-segmental fluctuations as the cause of this reversed response, suggesting that moderate chromosomal compaction promotes protein dissociation. Together, our findings suggest that cellular quantities of structural DNA-binding proteins could be highly influential on their residence times and the chromosome architecture.en_US
dc.description.degreeM.S.en_US
dc.description.statementofresponsibilityby Zafer Koşaren_US
dc.format.extentxvi, 107 leaves : color illustrations, color charts ; 30 cm.en_US
dc.identifier.itemidB154113
dc.identifier.urihttp://hdl.handle.net/11693/76507
dc.language.isoEnglishen_US
dc.publisherBilkent Universityen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectFacilitated dissociationen_US
dc.subjectTranscriptional regulationen_US
dc.subjectChromosome organizationen_US
dc.subjectMolecular dynamics simulationsen_US
dc.titleProtein-DNA dissociation kinetics and chromosome organization in a model bacterial confinementen_US
dc.title.alternativeModel bakteri hücre sınırlarında protein-DNA ayrılma kinetikleri ve kromozom organizasyonuen_US
dc.typeThesisen_US
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Graduate Program in Materials Science and Nanotechnology - Master's degree