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Si us plau utilitzeu sempre aquest identificador per citar o enllaçar aquest document: https://hdl.handle.net/2445/223690
Characterization of protein conformational ensembles from Förster resonance energy transfer simulations
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[eng] This thesis focuses on the study of partially disordered proteins (IDPs), using calmodulin (CaM) as the system under study. Calmodulin is a crucial protein involved in numerous physiological processes, and its well-documented structure and function make it an ideal candidate for this research. The primary aim is to explore the conformational ensembles of calmodulin through molecular dynamics (MD) simulations, using two distinct force fields: Amber ff14SB, widely used for proteins, and a99SB-disp, specifically refined for disordered proteins like CaM. By generating and analyzing FRET observables, the study evaluates which force field better reflects the dynamic behavior of calmodulin. A central component of this work is the application of Förster Resonance Energy Transfer (FRET) to gain insights into protein conformational dynamics. Advanced computational methods, including TrESP-MMPol and QM/MMPol, are employed to model the energy transfer process and assess how environmental factors affect FRET observables. A particular emphasis is placed on environmental screening, which describes how interactions between the chromophores and their surroundings such as solvent molecules or protein structures modify energy transfer. This screening effect addresses limitations in traditional models, offering a more accurate representation of real-world systems. In addition to environmental screening, this thesis explores key factors influencing FRET, such as Coulombic dipole interactions and orientational anisotropy between the chromophores. A novel screening function is also introduced to study how environmental effects depend on distance, enhancing our understanding of energy transfer in complex biological systems. By connecting theoretical models with experimental data, this research deepens our understanding of calmodulin's confirmational and functional behavior. Through the integration of computational simulations and FRET methodologies, this work advances our ability to study partially disordered proteins and contributes valuable insights to the broader field of protein dynamics and energy transfer.
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GONZALO PALAO, Daniel. Characterization of protein conformational ensembles from Förster resonance energy transfer simulations. [consulta: 26 de novembre de 2025]. [Disponible a: https://hdl.handle.net/2445/223690]