none

Halorhodospira halophila photoactive yellow protein (PYP) is a promising candidate to act as a photoswitching domain in engineered proteins due to the structural changes that occur during its photocycle. Absorption of a photon of wavelength 446 nm triggers trans to cis isomerization of its 4-hydroxycinnamic acid chromophore leading to large structural perturbations in the protein, particularly in the N-terminus. In the dark, a slower cis to trans reisomerization of the chromophore restores the protein’s native fold. The fusion of proteins to PYP’s N-terminus may therefore enable photomodulation of the activity of the attached protein. To test this hypothesis, this thesis descibes genetically encoded photoswitchable DNA-binding proteins that were developed by fusing the prototypical leucine-zipper type DNA-binding protein GCN4 bZIP to the N-terminus of PYP. Five different fusion constructs of full length or truncated GCN4 bZIP and full length PYP as well as fusion constructs of full length GCN4 bZIP and N-terminally truncated PYP mutants were designed in a structure-based approach to determine if the dimerization and DNA binding activities could be controlled by the PYP photocycle. Extensive biophysical characterization of the fusion constructs in the dark and under blue light irradiation using electronic absorption, circular dichroism and fluorescence spectroscopic techniques were performed. As all the fusion proteins could complete photocycles, the DNA binding abilities of the dark and light-adapted states of the proteins were characterized using spectroscopic techniques as well as by the electrophoretic mobility shift assay. All the fusion constructs maintained DNA-binding abilities, however they each differed in their affinities and the extent to which they were activated by blue light irradiation. The reasons for these differences in DNA-binding abilities and photoactivation are explored. Using the results from the characterization of these constructs, proposals are also made to develop more robust genetically encoded photoactivatable DNA-binding proteins of the same type.

Halorhodospira halophila photoactive yellow protein (PYP) is a promising candidate to act as a photoswitching domain in engineered proteins due to the structural changes that occur during its photocycle. Absorption of a photon of wavelength 446 nm triggers trans to cis isomerization of its 4-hydroxycinnamic acid chromophore leading to large structural perturbations in the protein, particularly in the N-terminus. In the dark, a slower cis to trans reisomerization of the chromophore restores the protein’s native fold. The fusion of proteins to PYP’s N-terminus may therefore enable photomodulation of the activity of the attached protein. To test this hypothesis, this thesis descibes genetically encoded photoswitchable DNA-binding proteins that were developed by fusing the prototypical leucine-zipper type DNA-binding protein GCN4 bZIP to the N-terminus of PYP. Five different fusion constructs of full length or truncated GCN4 bZIP and full length PYP as well as fusion constructs of full length GCN4 bZIP and N-terminally truncated PYP mutants were designed in a structure-based approach to determine if the dimerization and DNA binding activities could be controlled by the PYP photocycle. Extensive biophysical characterization of the fusion constructs in the dark and under blue light irradiation using electronic absorption, circular dichroism and fluorescence spectroscopic techniques were performed. As all the fusion proteins could complete photocycles, the DNA binding abilities of the dark and light-adapted states of the proteins were characterized using spectroscopic techniques as well as by the electrophoretic mobility shift assay. All the fusion constructs maintained DNA-binding abilities, however they each differed in their affinities and the extent to which they were activated by blue light irradiation. The reasons for these differences in DNA-binding abilities and photoactivation are explored. Using the results from the characterization of these constructs, proposals are also made to develop more robust genetically encoded photoactivatable DNA-binding proteins of the same type.

Cette thèse porte sur le développement d'un appareil couplant la spectrométrie de masse avec la spectrométrie de mobilité ionique et la spectroscopie laser, dans le but d'effectuer des analyses conformationnelles sur des édifices biomoléculaires. La construction, la mise au point et l'optimisation de l'appareil font l'objet de la première partie de ce mémoire. En particulier, il s'est agi de déterminer les caractéristiques de l'appareil (résolution, fréquence de fonctionnement…) par une série de tests sur des systèmes modèles. Dans un deuxième temps, nous avons effectué des mesures de spectroscopie d'action sur des conformères sélectionnés en mobilité. Nous avons étudié la relation entre la conformation et les propriétés optiques d'un système en mesurant le photo-détachement d'électron de divers conformères sélectionnés. Dans le cadre de la spectroscopie d'action, nous avons utilisé les possibilités nouvelles offertes par l'appareil pour réaliser des expériences de photo-isomérisation cis-trans sur des complexes non-covalents. Sur cet exemple, nous avons montré l'intérêt de cet appareil pour mesurer des spectres d'action de photo-isomérisation. Et enfin, nous avons montré la possibilité de réaliser des mesures de spectroscopie d'action basée sur le Transfert d'Energie par Résonance de Förster (FRET), en phase gazeuse, résolu en conformation / This thesis deals with the development of a new instrument coupling mass spectrometry, ion mobility spectrometry and laser spectroscopy. The aim is to perform structural analysis on biomolecular systems.The first part of this thesis focuses on the construction, the development and the optimization of the set-up. The main point was to determine the features of the set-up (resolution, working frequency) by series of tests with model systems.In a second phase, we did conformer resolved action spectroscopy. We studied the relation between the conformation and the optical properties of one system by measuring photo- electron detachment on different selected conformers. In the framework of action spectroscopy we used the new capacity of the set-up to perform cis-trans photo-isomerization on non-covalent complexes. We showed with this example interest of the use of this instrument to measure photo-isomerization action spectra. We finally showed the possibility to perform conformer resolved action spectroscopy measurements based on Förster Resonance Energy Transfer (FRET) in the gas phase