The mechanisms of ATP - biomacromolecule interactions

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buir.advisorOkur, Halil Ibrahim
dc.contributor.authorAyvaz, Cansın
dc.date.accessioned2023-12-26T11:28:22Z
dc.date.available2023-12-26T11:28:22Z
dc.date.copyright2023-12
dc.date.issued2023-12
dc.date.submitted2023-12-25
dc.departmentDepartment of Chemistry
dc.descriptionCataloged from PDF version of article.
dc.descriptionThesis (Master's): Bilkent University, Department of Chemistry, İhsan Doğramacı Bilkent University, 2023.
dc.descriptionIncludes bibliographical references. (leaves 83-103).
dc.description.abstractAdenosine triphosphate (ATP), one of the most important biomolecules of life, plays a vital role as the primary energy source within cells for essential biological functions. It has recently been discovered that ATP can also serve as a biological hydrotrope to destabilize protein aggregates and fibers. This thesis aims to investigate the recently discovered hydrotropic behavior of ATP and its interaction mechanisms with biomacromolecules, particularly poly(N-isopropylacrylamide) (PNIPAM), using a multi-experimental approach combined with molecular dynamics (MD) simulations. Adapting the bottom-up approach, the phase behavior of macromolecules is examined through phase transition and ATR-FTIR measurements. Additionally, site-specific interactions are identified with quantitative 1H-NMR spectroscopic studies, and the hydration shell structure and cluster morphologies of ATP molecules are explored through Multivariate Curve Resolution (MCR) Raman experiments. It is demonstrated that adenine and adenosine subgroups show negligible effect on the solubility of macromolecules, whereas ATP, AMP, and triphosphate exhibited purely salting-out behavior, and induced the aggregation of macromolecules. In stark contrast to the recently discovered hydrotropic behavior of ATP, no specific interactions between the macromolecule and ATP were observed in spectroscopic ATR-FTIR and 1H-NMR measurements, as well as MD simulations. Surprisingly, at elevated concentrations, self-association of ATP was observed leading to partial destabilization of larger PNIPAM aggregates to smaller ones. In the absence of ATP binding sites, interactions with random-coil-like structured macromolecules do not lead to effective hydrotropic action of ATP. Instead, they function more as stabilizers rather than solubilizing the macromolecules.
dc.description.degreeM.S.
dc.description.degreeby Cansın Ayvaz
dc.embargo.release2024-06-01
dc.format.extent103 leaves : color illustrations, charts ; 30 cm.
dc.identifier.itemidB090968
dc.identifier.urihttps://hdl.handle.net/11693/114018
dc.language.isoEnglish
dc.publisherBilkent University
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectAdenosine triphosphate
dc.subjectAdenosine monophosphate
dc.subjectTripolyphosphate
dc.subjectAdenine
dc.subjectAdenosine
dc.subjectHydrotropes
dc.subjectThermoresponsive polymers
dc.subjectPNIPAM
dc.subjectPDEA
dc.titleThe mechanisms of ATP - biomacromolecule interactions
dc.title.alternativeATP-biyomakromolekül etkileşimlerinin mekanizmaları
dc.typeThesis
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