Simulations de dynamique moléculaires du complexe collecteur de lumière de type 2 d’une bactérie pourpre dans différents environnements micellaires et membranaire

Abstract : Purple photosynthetic bacteria, such as Rhodopseudomonas acidophila (strain 10050), have a synthetic apparatus which is composed by membrane protein complexes with specialized pigments to harvest the light. This photosynthetic apparatus is composed of 2 types of light harvesting (LH) complex called LH1 and LH2, and a reactional center (RC). The light is mainly absorbed by photosynthetic pigments bounded to LH2 complex and the resulting excitation energy is transferred to LH1 complex, then to RC where it is transformed to chemical energy. The crystallography data allowed to show that the LH2 complex is composed of a perfectly symmetrical 9 sub-unit ensemble, formed by 2 small protein sub-unit α and β associated to 1 carotenoid (rhodopine glucoside) and 3 bacteriochlorophylls-a. The spectroscopy fluorescence experiences carried out as a function of time on unique LH2 complexes shown that the intensity and the position of the electronic transition of complexes can strongly fluctuate with the time. These observations describe a « dynamic disorder » linked with the biological function of the LH2 complex, which reveal the efficiency of the use of light energy. Even if the large number of studies highlight the existence of this « disorder » to interpret experimental data of fluorescence, a few number of studies analyzed at molecular level the local or global fluctuations inside of LH2 complex which govern this disorder. The molecular description of the dynamic disorder of LH2 complex will permit more precise comprehension about the ability to use of solar energy of these complexes with a huge efficiency, and thus, they are very important for setting up the sustainable energy production system.The aim of this project thesis is a better understanding the origin of this « disorder » at atomic scale by using classical molecular dynamics approaches. In order to do this, we modeled the LH2 complex in different biomimetic environments composed of detergents (dimethyldodecylamine-N-oxide (LDAO) and the β octyle glucoside (βOG)) and of POPC membrane. The first part of this study consisted in developing original models for these detergents, as well as for the different components of the LH2 complex, and to analyze the aggregation of detergent molecules around the complex. To validate our models, small angle X-ray scattering (SAXS) experiments have been realized with the LH2-LDAO and LH2-βOG complexes. In the second part, we specifically studied the interactions of peptide-pigment and pigment-pigment depending on the environment. Our results revealed significant differences concerning the dynamic of the complex and the interactions of pigment-pigment and pigment-protein depending on the environment. In the end, in order to relate the variations of interactions between the different components of complex, as described in our simulations, to the variations of absorption of the LH2 complex and to dynamic disorder, ab-initio calculations have been done from the representative atomic structures of our simulations.
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Esra Karakas. Simulations de dynamique moléculaires du complexe collecteur de lumière de type 2 d’une bactérie pourpre dans différents environnements micellaires et membranaire. Biophysique [physics.bio-ph]. Université Paris-Saclay, 2016. Français. ⟨NNT : 2016SACLX012⟩. ⟨tel-01461588⟩

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