Theoretical study of the interplay between structure and spectroscopy in biosystems
[eng] The interplay between structure and spectroscopy in biosystems is an important scientific challenge to understand a variety of mechanisms underlying protein function in life sciences, a challenge that requires the smart combination of diverse methodologies, from excited state methods to biomol...
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| Tipo de recurso: | tesis doctoral |
| Estado: | Versión publicada |
| Fecha de publicación: | 2024 |
| País: | España |
| Institución: | Universidad de Barcelona |
| Repositorio: | Dipòsit Digital de la UB |
| OAI Identifier: | oai:diposit.ub.edu:2445/220444 |
| Acceso en línea: | https://hdl.handle.net/2445/220444 http://hdl.handle.net/10803/694249 |
| Access Level: | acceso abierto |
| Palabra clave: | Sistemes biològics Biomolècules Biological systems Biomolecules |
| Sumario: | [eng] The interplay between structure and spectroscopy in biosystems is an important scientific challenge to understand a variety of mechanisms underlying protein function in life sciences, a challenge that requires the smart combination of diverse methodologies, from excited state methods to biomolecular simulation techniques. By employing multiscale approaches combining classical molecular dynamics (MD), enhanced sampling techniques, continuum solvation models and quantum mechanics/molecular mechanics (QM/MM) methods, this doctoral thesis aims at advancing in this field by applying multiscale approaches to characterize the structural and photophysical properties of different systems of interest. The thesis contains a methodological part addressing the parametrization of the linear-scaling ddCOSMO- MST continuum solvation models aimed at tackling large biomolecular systems. A second part applies the MST continuum model and atomistic simulations to characterize the structural and aggregation properties of napthenic acids. Then, the thesis addresses the application of multiscale approaches to study two paradigmatic examples of interrelation between structure and spectroscopy in biosciences, the molecular basis for photoacclimation and light harvesting in cryptophyte photosynthetic complexes (PC577 and PE545) and the development of strategies to study the conformational preferences of intrinsically disordered proteins like Sic1, which can then be assessed by comparison of simulated and observed Förster resonance energy transfer (FRET) spectroscopic data. These applications serve as an example for the challenges faced by current biomolecular theoretical spectroscopy, in photosynthesis related to the complexity of exciton dynamics in pigment-protein complexes, whereas in disordered proteins difficulties are related to the efficient and accurate exploration of the conformational space. |
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