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<p dir="ltr">Photosynthesis is the basis of primary productivity on Earth. Oxygenic photosynthesis utilizes the nearly inexhaustible energy of radiant solar light to fix atmospheric carbon dioxide into usable forms of chemical energy and produces dioxygen as a product. Central to this process are several large hetero-oligomeric protein complexes that comprise the photosynthetic electron transport chain. Photosystem II (PSII) initiates electron transport through the light-driven oxidation of water, in-turn relinquishing protons and oxygen. Through this reaction, electrons are used to form the reductant NADPH, while protons form a proton-motive gradient that is used to drive synthesis of ATP. As a result of this highly energetic reaction, PSII is often subject to oxidative photodamage due to the production of reactive oxygen species. Inevitably, accumulation of oxidative photodamage disrupts the catalytic activity of PSII, resulting in a loss of photosynthetic activity. To deal with the nearly constant incurred photodamage to PSII, oxygenic photoautotrophs undergo a disassembly and repair cycle that results in the complete turnover of the damaged D1 subunit of PSII. Due to its high tendency for damage, the D1 subunit has a half-life of under one hour in high light intensity. Despite our current understanding of photoinhibition and PSII repair, it is still unclear how D1 is replaced so rapidly in response to damaging conditions. Previous research has indicated a role for phosphorylation of PSII in D1 turnover, however the mechanism has not been totally resolved. In the first chapter of this thesis, our current understanding of PSII phosphorylation and oxidative damage is reviewed in the context of PSII repair. In the second chapter, the role of protein phosphorylation in the PSII repair cycle is investigated in the model organism <i>Arabidopsis</i>. Using several PSII phosphorylation mutants, we demonstrate that phosphorylation seems to mediate disassembly of large PSII supercomplexes and dimers into smaller subcomplexes. In the third chapter, the role of oxidative photodamage is investigated in mediating PSII disassembly. Here, we use several <i>in vitro</i> assays to demonstrate that photodamage is sufficient to induce the disassembly of smaller PSII subcomplexes. In the fourth chapter, a technique for determining the stoichiometry of photosynthetic complexes is examined, with implications for understanding PSII repair. Finally, in the fifth chapter, several conclusions and unanswered questions from this thesis are discussed.</p>

Le premier volet de ce travail portera sur l’expérience acquise lors d’un stage d’étude à Tokyo, au Japon, dans le groupe de recherche du Pr. Makoto Fujita, une sommité d’envergure internationale dans le domaine de l’auto-assemblage. En continuité avec les plus récents travaux du Pr. Fujita, des systèmes poreux auto-assemblés présentant des cavités fonctionnalisées ont été développés dans le but d’encapsuler des acides gras afin d’en déterminer la structure cristalline. Ces éponges ont été caractérisées par des techniques courantes telles que la spectroscopie à résonance magnétique nucléaire 1H, 13C{1H} et Cosy, la spectrométrie de masse, l’analyse élémentaire, la microscopie optique infrarouge ainsi que la diffraction des rayons X. Une autre approche employée pour obtenir de meilleures propriétés spectroscopiques fut la synthèse de dendrimères métalliques de génération 0. Un nouveau ligand de type 1,3,5-triazine a été synthétisé par une réaction typique de cyclisation de nitrile en présence catalytique d’hydrure de sodium. Des espèces mono-, bis- et trinucléaire de Ru(II) furent synthétisés ainsi que deux espèces hétérométalliques de Ru(II)/Pt(II) et de Ru(II)/Os(II). Tous les complexes obtenus furent caractérisés par spectroscopie à résonance magnétique nucléaire (1H, 13C{1H} et Cosy) à l’état liquide, par spectroscopie de masse à haute résolution et par analyse élémentaire. La génération de dihydrogène à partir de l’espèce hétérométallique a été étudiée. Les propriétés optiques et électroniques ont été analysées par spectroscopie UV-Vis, par analyse de la luminescence, du temps de vie de luminescence, par des analyses de rendement quantique ainsi que par des analyses de voltampérométrie cyclique à balayage. Finalement, dans le but d’améliorer les propriétés spectroscopiques d’absorption de complexes métalliques, nous avons synthétisé une série de polymères homo- et hétérométalliques, intégrant des ligands de type bis(2,2’:6,2’’-terpyridine). Les complexes générés furent caractérisés par diverses techniques tel que la spectroscopie à résonance magnétique nucléaire (1H, 13C{1H} et Cosy) à l’état liquide, par spectroscopie de masse à haute résolution ainsi que par analyse élémentaire. Les propriétés optiques et électroniques ont été analysées par spectroscopie UV-Vis, par analyse de la luminescence, du temps de vie de luminescence, par des analyses de rendement quantique ainsi que par des analyses de voltampérométrie cyclique à balayage. / It is well known that the self-assembly of small molecules into macromolecular species gives rise to an amplification and amelioration of their general properties. A first section on self-assembly will emphasize the acquired experience during an internship in Tokyo, Japan, in Pr. Makoto Fujita’s research group, a worldwide Figure in the area of self-assembly. Concomitant with the latest results obtained in Pr. Fujita research group on the self-assembly of molecular sponges, studies on molecular sponges with functionalized cavities will be presented. Such sponges were used to encapsulate fatty acids in order to determine their crystal structure. The sponges were characterized in different ways, such as 1H and 13C NMR, mass spectrometry, elemental analysis, optical microscopy coupled with infrared detection as well as X-ray diffraction. Another path of investigation to gain good spectroscopic properties is to synthesize metallodendrimers. A new 1,3,5-triazine ligand was synthesized by a typical nitrile cyclization in the presence of sodium hydride. Mono-, bis- and trimetallic Ru(II) species as well as heterometallic Ru(II)/Pt(II) and Ru(II)/Os(II) complexes were synthesized. All the complexes were characterized by nuclear magnetic resonance spectroscopy (1H, 13C{1H} and Cosy NMR) in the liquid state, high-resolution mass spectrometry, elemental analysis as well as X-ray diffraction in some cases. Attempts to generate H2 with the heterometallic species as catalysts have been investigated. The optical and electronic properties were also investigated by UV-Vis spectroscopy, luminescence analysis, excited state lifetimes, quantum yield efficiency and cyclic voltammetry.Finally, with the goal of having enhance light absorption, we synthesized a series of homo- and heterometallic coordination polymers with a ligand of the “back-to-back” terpyridine type. The complexes obtained were characterized by various techniques, such as nuclear magnetic resonance spectroscopy, high-resolution mass spectrometry as well as elementary analysis. The optical as well as the electronic properties were also investigated, using luminescence spectroscopy, excited state lifetime analysis, quantum yield determination and by cyclic voltammetry.

The work presented in this thesis was aimed to investigate the structure-function relationship of several photosynthetic Light-Harvesting Complexes (LHCs) including Chlorophyll Protein 29 (CP29) and Light-Harvesting Complex II (LHCII) of green plants, and Fenna-Matthews-Olson (FMO) complex of green sulfur bacterium Chlorobium tepidum. Based on the exciton calculations, a model was proposed to the electronic excited states (EES) of both CP29 and LHCII complexes by incorporating a considerable part of the current information offered by structure determination, mutagenesis analysis and spectroscopy in the modeling. The essential parameters for characterizing the excited states, Qy dipole orientations and site energies were assigned by suggesting a model that can explain both the key features of the linear (polarized) absorption spectra and the time scales of the energy transfer processes in CP29 and LHCII. The idea of offering structural information through setting connection between the spectroscopy and the spectral simulations were supported by the presented results on CP29 and LHCII. New spectroscopic measurements (absorption, linear dichroism (LD) and circular dichroism), carried out at 4 K on the FMO complex were presented, and also the LD spectrum was corrected for the degree of orientation of the sample, in order to provide comparison of not only the shape but also the size of the simulated and experimental spectra. The EES structure of the FMO complex was studied by simulating the measured optical spectra with more realistic model than the previously applied models. Simulations have been carried out with a computer program based on exciton model, which includes inhomogeneous, homogeneous and lifetime broadenings explicitly.

Almost all life on Earth depends on the products of photosynthesis - the biochemical process whereby solar energy is stored as chemical-rich compounds. The energy of captured photons is transferred through a network of pigment-protein complexes towards the reaction center. The reaction center is responsible for trans-membrane charge separation, which generates a proton motive force which drives all subsequent biochemical reactions. The ultrafast (femtosecond) nature of the primary processes in photosynthesis is the main reason for its astonishing efficiency. On this timescale, quantum effects start to play a role and can appear in measured spectra as oscillations. It has been hypothesized that these are evidence of wave-like energy transfer. To unveil the fundamental principals of ultrafast excitation energy transfer in both natural and artificial light-harvesting systems, advanced spectroscopy techniques have been utilized. Coherent two- dimensional electronic spectroscopy is a state of the art technique which allows the most complete spectroscopic and temporal information to be extracted from the system under study. This technique has allowed us to identify a new photophysical process where the coherence of the initially excited state is shifted to the ground state upon an energy transfer step. Coherence...

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This Ph.D. thesis is an exploration of carotenoids by ultrafast, time-resolved absorption spectroscopy to investigate their complicated relaxation processes, means of energy transfer, and dependence on structure. The introduction begins with an overview of carotenoids, intended for the reader to appreciate their importance and their complexity as revealed by decades of research in carotenoid photophysics. To understand the primary concerns of this research field, the reader is guided through basic theory of energetic processes, the experimental method, and methods of analysis. The main body of the text is the Research Chapter, containing four sections, each describing research using varied ultrafast transient absorption spectroscopies on carotenoids in solution and when bound to a host protein. Section 2.1 concerns an equilibration phenomenon in the lowest excited state of the carotenoid fucoxanthin in various solutions and temperatures by a multi-pulse transient absorption method. The same method is applied to fucoxanthin in a host antennae protein of the pennate diatom Phaeodactylum tricornutum to investigate the function of the equilibration in energy transfer to Chlorophyll a in Section 2.2. The next two sections regard the effect of carotenoid structure on its relaxation dynamics. Section 2.3 investigates the effect of the non-conjugated acyloxy group of two fucoxanthin derivatives in various solvents. Here, one of the energetic states involved in the equilibrium mentioned above is seen drastically affected. Lastly, Section 2.4 investigates alloxanthin, a carotenoid with an unusual pair of carbon-carbon triple bonds. Their effect on the conjugation is evaluated based upon the molecules' decay dynamics. A general summary and conclusion is provided at the end.

La pollution de l'environnement, sa remédiation et l'obtention de sources d'énergie plus propres et plus efficaces sont des problématiques difficiles auxquels les humains sont confrontés. Parmi les nombreux matériaux développés par les scientifiques, les polymères de coordination cristallins type MOFs sont de plus en plus développés dans plusieurs domaines, du fait de la facilité et la versatilité de leur synthèse. La recherche sur ces matériaux est récente, mais les possibilités qu’offrent ces matériaux pour différentes applications sont énormes.C'est dans ce cadre que nous avons travaillé sur la conception et la synthèse de différents MOF pour la récupération, le recyclage et/ou la dégradation de certains polluants. En utilisant différentes approches de synthèse, nous avons obtenu des matériaux efficaces pour les diffèrent applications ciblées de ces matériaux. Nous pensons que les MOF ont le potentiel pour solutionner certains problèmes cruciaux comme la décontamination de l'environnement. / The pollution of the environment, its remediation and to obtain a cleaner and more efficient energy sources are some of the most challenging topics that humans are now facing. Among the several materials that scientists have developed, Metal Organic Frameworks (MOFs) are gaining a lot of attention on several fields due to the easiness and the versatility in which these materials can be designed, synthesized and used. Even when research on these materials is still young, the possibilities that they offer are enormous.It is on this frame that our work group has worked on the design and the synthesis of different MOFs for the recovery, the recycling and/or the degradation of some pollutants of interest. By using different synthesis approaches we have tested the versatility in the synthesis and the possible applications of these materials. We believe that MOFs hold the potential to solve some crucial issues in the recovery of the environment.

Les complexes collecteurs de lumière des bactéries photosynthétiques absorbent l'énergie solaire, et transfèrent l'énergie avec grande efficacité aux centres réactionnels, siùge où elle est captée pour l'utilisation par la cellule. Nous savons peu des détails du transfert d'énergie entre les différents complexes collecteurs de lumière. Dans cette thèse, j'ai isolé différents complexes collecteurs de lumière à partir de plusieurs souches de bactéries pourpres. J'ai construit de modèles 3D par homologie et les structures possibles de dimères ont également été examinés. Les sites de pontage dans ces protéines montrent la possibilité de construire des dimères avec des structures biologiquement pertinentes. J'ai développé un protocole pour construire de dimères de protéines collectrices de lumière fortement oligomériques. Le protocole que j'ai mis en place contient trois grandes étapes : d'abord la réaction de lysines dans les complexes à un très faible degré de réaction, et la purification des protéines marquées. Ensuite, les groupes réactifs de dibenzocyclooctyne (DBCO) ou de l'azoture sont introduits au complexe. Finalement, la réaction sans cuivre de cycloaddition azoture-alcyne promue par distorsion a pour conséquence la synthèse de dimères. / The light harvesting apparatus of photosynthetic bacteria absorb the energy from sunlight and transfer the energy with high efficiency to the reaction center, where it is captured for use by the cell. We know little about the details of energy transfer between different light-harvesting complexes. In this thesis I isolated several different types of light-harvesting complex from various stains of purple bacteria. 3D models were built, based on homology modeling, and possible dimer structures were examined. The cross linking sites in these protein shown the possiblity of forming biologically relevant dimer structures. I have developed a protocol to make dimers, from highly oligomeric light harvesting proteins. The protocol developed contains three main steps: first reaction of lysines in the complex at a very low degrees of reaction and purifying the labelled protein. Then coupling the reactive groups of dibenzylcyclootyne (DBCO) or of azide separately to the different complexes. Finally, the copper free strain promoted azide-alkyne cycloaddition reaction occurred to synthesize the dimer.

Title: Artificial light-harvesting antenna based on an aggregation of bacteriochlorophyll c with selected pigments Author: Tomáš Malina Department: Department of Chemical Physics and Optics Supervisor of the master thesis: doc. RNDr. Jakub Pšenčík, Ph.D., KCHFO MFF UK Abstract: Solar energy is one of the most important energy sources for all living organisms. The light harvesting takes place in specialised photosynthetic complexes called antennas; they typically contain pigments held by a protein scaffold. Antennas of green bacteria, chlorosomes, are unique in this respect, for they do not need proteins to organise the pigments. The pigments contained in chlorosomes, bacteriochlorophyll (BChl) c, d or e, aggregate spontaneously. This self-aggregation can be used to form an artificial light-harvesting antenna the absorption spectrum of which can be extended by addition of other pigments. Antennas based on aggregation of BChl c with β-carotene and BChl a were prepared by a fast and slow method. The excitation energy transfer efficiency between these pigments was studied. The efficiency of energy transfer from BChl c to BChl a reached up to 95 %, the efficiency of energy transfer from β-carotene to BChl c was lower. An important role of β- carotene in artificial aggregates as well as in chlorosomes is its...