No description available.

No description available.

Numerous pigment protein complexes exist in natural systems to harvest light energy such as photosystem II and Nanosalina xenorhodopsin. However, the mechanisms of these lipid embedded photo-active complexes have yet to be fully understood. Photosystem II is of interest due to being a compact complex which can perform the three initial key steps of photosynthesis: absorb light, transfer the excitation from the antennae to reaction center, and perform efficient charge separation. Despite considerable theoretical and experimental effort the exact mechanism of this process remains uncertain. Nanosalina xenorhodopsin is a more recently discovered inwards proton pump with minimal studies into the inwards proton pumping mechanism. Nanosalina xenorhodopsin is of interest as it contrasts with other known and well studied rhodopsins which serve as outwards proton pumps, moving H+ ions out of a cell. In this work, we use the Hamiltonian ensemble method to construct the first fully ab initio computational models of these systems which will be used to determine the mechanisms of these systems. To construct these models we first investigated the effect of the modeled surrounding membrane and simulated temperature. The effect of the extended modeled environment on calculated results is often overlooked but important for the construction of an accurate ab initio model. Our models showed that both membrane composition and temperature result in significant changes in the behavior of the extended membrane system, relative excitation energies of chromophores, and energy dynamics of a pigment protein complex. The absolute excitation energies of chromophores, absorption spectra, and linear dichroism spectra were comparatively insensitive to changes in the modeled environment. With the effect of the environment established, we present a preliminary method to extend our photosystem II model to include charge transfer states, and a preliminary model of Nanosalina xenorhodopsin which can determine the photocycle states through validation of calculated spectra against experimental results.

Die Multiexzitonen-Theorie des Anregungsenergie-Transfers in Farbstoff-Protein-Komplexen und biologischen Antennensystemen wird um den Prozess der Exziton-Exziton-Vernichtung erweitert. Um eine mikroskopische Beschreibung zu erzielen, wird eine Herangehensweise benutzt, die auf der Internen Konversion der Anregungsenergie innerhalb der Farbstoffmoleküle basiert. Diese Interne Konversion führt zu nicht strahlenden Übergängen von höheren zu niedrigeren Exziton-Mannigfaltigkeiten. Neben der Einbeziehung der Exziton-Exziton-Vernichtung beinhaltet die hier verwendete Multiexziton-Dichtematrixtheorie auch die Kopplung zu niedrig-energetischen Schwingungs-Freiheitsgraden und dem elektrischen Feld. Für den Übergang von der Zwei- zu der Einexzitonen -Mannigfaltigkeit werden exakte und genäherte Ausdrücke hergeleitet. Die erste Anwendung der erweiterten Multiexziton-Dichtematrixtheorie ist die Berechnung von ultra-schnellen differentiellen Absoptionsspektren. Um den Prozess der Exziton-Exziton-Vernichtung in intensitätsabhängigen differenziellen Absorptionsspektren näher zu untersuchen, wird diese Herangehensweise auf den B850 Ring des LH2 von rhodobacter sphaeroides angewendet. Die Bedeutung der Exziton-Exziton-Vernichtung und der Einfluss von statischer Unordnung werden detailiert diskutiert. Die Simulationen der differentiellen Absorptionsspektren mit statischer Unordnung und Orientierungsmittelung zeigen gute Übereinstimmung mit experimentellen Beobachtngen. Durch die Veröffentlichung der Strukturdaten des Photosystem I (PS1) von Synechococcus elongatus wurde es zum ersten Mal möglich, ein Exziton-Modell für die 96 Chorophyllmoleküle einzuführen, die in die Proteinmatrix dieses Antennensystems eingebettet sind. Das Ziel dabei ist, sowohl die linearen Spektren in einem weiten Temperaturbereich, als auch die zeitaufgelöste Fluoreszenz zu reproduzieren. Die Kopplungen und die Dipolmomente der Chlorophyllmoleküle wurden den Strukturdaten entnommen. Da die Energien der einzelnen Farbstoffe stark von deren unmittelbarer Umgebung abhängt, werden diese bestimmt, indem simulierte Absorption, Lineardichroismus und Zirkulardichroismus bei niedrigen Temperaturen den experimentellen Spektren angepasst werden. Nachdem einige Chlorophyllmoleküle den Zuständen mit den niedrigsten Energien zugeordnet wurden, werden die Energien mit Hilfe eines evolutionären Algorithmus angepasst. Die Qualität des PS1 Modells wird durch die Berechnung der zeitabhängigen Fluoreszenz untermauert (mit zusätzlicher inhomogener Linienbreite), die Simulationen stimmen gut mit aktuellen experimentellen Resultaten überein. Die oben erwähnten Exziton-Modelle beschreiben die jeweiligen Experimente erfolgreich. Der nächste Schritt ist, diese Modelle zu nutzen, um einen neuen Typ von Experiment vorzuschlagen, das Exciton-Steuerungs-Experiment. Auf dem Exciton-Modell des FMO Komplexes von Prosthecochloris aestuarii und dem oben erwähnten PS1 Modell von Synechococcus elongatus aufbauend wird die Bildung von exzitonischen Wellenpaketen durch Laser-Anregung studiert. Diese stellen eine kohärente Überlagerung exzitonischer Zustände dar, ähnlich der bei Schwingungs-Wellenpaketen. Um die spezielle Form des Femtosekunden-Laserpulses zu bestimmen, der zu einer räumlichen Lokalisierung der Anregungsenergie führt, wird die Theorie der optimalen Steuerung verwendet. Die Möglichkeit, solch einen lokalisierten Zielzustand zu erreichen, wird aufgezeigt, auch unter dem Einfluss von energetischer Unordnung und Exziton-Exziton Vernichtung. Ferner wird gezeigt, dass die Effizienz der Lokalisierung und die Länge des optimalen Pulses stark von der Temperatur abhängen. / The multi-exciton description of excitation energy transfer in chromophore complexes and biological light harvesting antenna systems is extended to include the exciton-exciton annihilation processes. To achieve a complete microscopic description the approach is based on intra--chromophore internal conversion processes which leads to non-radiative transitions from higher to lower lying exciton manifolds. Besides an inclusion of exciton-exciton annihilation the used multi-exciton density matrix theory also accounts for a coupling to low-frequency vibrational modes and the radiation field. Concentrating on transitions from the two- to the single-exciton manifold exact and approximate expressions for the annihilation rate are derived. A first application of the introduced extended multi-exciton density matrix theory is given by the computation of ultrafast transient absorption spectra. To elucidate the process of exciton-exciton annihilation in intensity dependent transient absorption data the approach is applied to the B850 ring of the LH2 found in rhodobacter sphaeroides. The signatures of exciton-exciton annihilation as well as the influence of static disorder are discussed in detail. The simulations of transient absorption including static disorder and orientational averaging are in good agreement with experimental data. The recently published structure of the Photosystem I (PS1) of Synechococcus elongatus made it for the first time possible to introduce an excitonic model for the 96 chlorophylls embedded in the protein matrix of that core-antenna system, as presented in this work. The challenge has been to reproduce linear frequency domain spectra in a wide temperature range as well as the time resolved fluorescence. The couplings and the dipole-moments of the chlorophylls are extracted from the x-ray crystal structure. Since the position of the energetic levels of the chlorophylls depend on the respective surrounding their determination is achieved by fitting low temperature absorption, linear dichroism and circular dichroism at the same time. After assigning some chromophores to the red-most states, an evolutionary algorithm is used to get the best fit. The quality of the resulting PS1 model (additionally accounting for inhomogeneous line broadening) is confirmed in calculating time dependent fluorescence spectra which show a good agreement with recent experimental results. The outlined method is also applicable to other photosynthetic antenna systems. The above described exciton models successfully explain the respective measurements. In a second step, they will be used to propose a new type of experiment, the exciton control experiment. Based on an exciton model for the FMO complex of Prosthecochloris aestuarii and the proposed PS1 model of Synechococcus elongatus one studies the laser pulse formation of excitonic wavepackets, i.e. a coherent superposition of excitonic states similar to vibrational wavepackets. Optimal Control theory is used to calculate the shape of femtosecond laser pulses that leads to a spatial localization of excitation energy. The possibility to populate such a localized target state is demonstrated, even in the presence of disorder or exciton-exciton annihilation, and it is shown that the efficiency of localization as well as the length the most suited pulses strongly depend on temperature.

Diss. (sammanfattning) Linköping : Linköpings universitet, 2008. / Härtill 4 uppsatser. Includes bibliographical references.

Diss. (sammanfattning) Linköping : Linköpings universitet, 2008. / Härtill 4 uppsatser.

In der vorliegenden Arbeit sind unterschiedliche Kopplungsstrategien des natürlichen Photosystems I (PSI) aus Cyanobakterium Thermosynechococcus elongatus mit verschiedenen Elektrodenoberflächen sowie Interaktion mit Nanomaterialien und Enzymen bearbeitet worden. Zum einen wurde gezeigt, dass die Immobilisierung des PSI auf modifizierten mehr-wandigen Kohlenstoffnanoröhrchen zur funktionalen Photobiohybridelektrode führt. Dabei wurde das PSI mit der Elektrode elektrisch mit Hilfe eines Redoxproteins, Cytochrom c (cyt c), verknüpft. Das System (PSI-cyt c) wurde auch auf eine dreidimensionale Elektrodenoberfläche des Metaloxids Indiumzinnoxid (eng. ITO) übertragen. Hierbei wurde zusätzlich die TransparenzEigenschaft solcher Oberflächen ausgenutzt. Die Präparation solcher transparenter Elektroden wurde optimiert, um höhere Photoströme zu generieren. Weiterhin wurde eine neue Methode der elektrischen Kontaktierung des PSI mit der Elektrode etabliert. Hierfür wurden Fullerene eingesetzt. Durch erhöhte molekulare Effizienz wurde gezeigt, dass Fullerene effektivere Elektronvermittler zwischen PSI und der Elektrode sind als das cyt c. Zusätzlich wurden im Rahmen dieser Doktorarbeit die photokatalytischen Eigenschaften von PSI mit den biokatalytischen Eigenschaften des Enzyms humane Sulphit Oxidase (hSOx) kombiniert. Hierbei wurde das Enzym als ein alternativer und effizienter Elektronzulieferer für PSI eingesetzt. Ein drittes Protein, das cyt c, fungierte als elektrisches Bindeglied und sicherte die elektrische Kommunikation zwischen den katalytischen Proteinen im System und der Elektrode. Die Komplexität des PSI sowie seine Kommunikation mit anorganischen Nanomaterialien und anderen komplexen Biomolekülen, wie z.B. Enzymen, zeigt ein großes Potential des Einsatzes von PSI-basierter Biohybriden in den Biotechnologien der Zukunft. / In this thesis, different strategies for coupling of the natural complex photosystem I from the cyanobacterium Thermosynechococcus elongatus with different electrode surfaces, and the interaction of PSI with nanomaterials and enzymes has been investigated. First, it was shown that immobilization of PSI on modified multi-walled carbon nanotubes (MWNT) leads to a functional photobiohybrid electrode. Here, PSI has been electrically wired to the electrode via a redox-active protein, cytochrome c (cyt c). The system (PSI-cyt c) has been scaled up to the three-dimensional surface of a metal-oxide, indium tin oxide (ITO). Here, additionally the high transparency property of this material has been exploited. The new preparation procedure of such transparent electrodes has been optimized in order to achieve high pohotocurrents. Furthermore, a new method of electric wiring of the PSI with the electrode has been established. Here, fullerenes have been employed. The high molecular efficiency of such a system proves that fullerenes are more effective wiring agents between the PSI and the electrode as compared to the cyt c. Additionally, in this thesis the photocatalytic property of the PSI has been combined with the biocatalytic property of the enzyme human sulphite oxidase, hSOx. Here, the enzyme has been employed as an alternative electron supplier for PSI. The third protein, cyt c, acted as an electric wiring agent and ensured electric communication between both catalytic proteins of the system and the electrode. The versatility of the PSI as well as its communication with anorganic nanomaterials and biological molecules, e.g. such as enzymes, shows a great potential for use of PSI-based biohybrids in the future biotechnological applications.

Photosystem I (PSI) aus dem thermophilen Cyanobakterium Thermosynechococcus elongatus ist ein transmembraner Protein-Pigment-Superkomplex der photosynthetischen Elektronentransportkette. Er wandelt die Energie des Lichts in elektrische Energie mit einer Quanteneffizienz von nahezu 100 % um. Dazu uberträgt PSI Elektronen von Plastocyanin bzw. Cytochrom c6 (Cyt c6) auf Ferredoxin. Die Struktur des PSI wurde bereits 2001 mit einer Auflösung von 2,5 Å beschrieben (Jordan et al. 2001). Es lässt sich zur Generierung von Photoströmen auf Elektrodenoberflächen assemblieren und zur Produktion von Biokraftstoffen mit Enzymen koppeln. Die elektrische Kontaktierung des PSI mit Elektrodenoberflächen kann durch Komplexierung mit dem mitochondrialem Cytochrom c aus Pferdeherz (Cyt cHH) erhöht werden. Aufgrund der Nutzbarkeit dieses Proteinkomplexes sollte geklärt werden, wie PSI und Cyt cHH wechselwirken und wie sich die Interaktion von der des nativen PSI-Cyt c6-Komplexes unterscheidet. Deshalb lag der Fokus meiner Arbeit darauf, die Bindung des Cyt c6 und seines Analogons Cyt cHH an PSI mit kinetischen, kalorimetrischen, theoretischen und strukturellen Methoden zu untersuchen. Das Cyt c6 bindet im reduzierten Zustand an PSI und verringert nach erfolgtem Elektronentransfer seine Affinität. Das Cyt cHH bindet dagegen sowohl im reduzierten als auch im oxidierten Zustand an PSI. Mit Hilfe der kinetischen Messungen habe ich Bedingungen identifiziert, unter denen PSI mit dem jeweiligen Cytochrom c einen stabilen Komplex eingeht. Mit Hilfe eines rigid-body dockings wurden potenzielle Bindungsstellen der beiden Cytochrome berechnet. Fur Cyt c6 ergab sich eine spezifische Bindungsstelle, die eine gute Übereinstimmung mit den von mir gemessenen Kinetiken sowie mit weiteren Literaturdaten zeigt. Diese Bindungsstelle korreliert mit der veröffentlichten Kostruktur des bakteriellen Reaktionszentrums mit Cyt c2 aus Rhodobacter sphaeroides. Demgegenüber sind mehrere Cyt cHH-Bindungsstellen ... / Photosystem I (PSI) from the thermophilic cyanobacterium Thermosynechococcus elongatus is a membrane-bound, multipigment protein supercomplex. It converts light to electrochemical energy with a quantum efficiency of almost 100 %. It reduces the luminal proteins plastocyanin and cytochrome c6 (Cyt c6) to oxidize the stromal protein Ferredoxin. The structure of PSI has been solved in 2001 at a resolution of 2,5 Å (Jordan et al. 2001). PSI can be assembled on an electrode surface to produce photocurrents and the generated electrons can be used for the production of biofuels. The mitochondrial cytochrome c from horse heart (Cyt cHH) binds strongly to both, PSI and the electrode surface, and can therefore be applied to improve the electrical coupling. Due to the practical use of the PSI-Cyt c complex, the aim of my thesis is to characterize the interaction of PSI with Cyt c6 and the analog Cyt cHH. To this end, the binding of both cytochromes to PSI was analyzed by kinetic, calorimetric, theory-based and structural methods. Cyt c6 binds to PSI while being reduced and decreases its affinity after transferring its electron. In contrast, Cyt cHH binds to PSI in both oxidation states, reduced and oxidized, with identical affinity. By means of kinetic measurements, I identified conditions in which PSI forms a stable complex with either of the two cytochromes. The positions of the cytochrome binding sites at PSI were calculated by a rigid-body docking. For the calculation with Cyt c6, the majority of the potential binding sites are located at the luminal side of PSI, close to P700. The theoretic properties of one of these binding sites are in good agreement with my own kinetic measurements and literature data. The position and orientation of Cyt c6 in this theoretic binding site is almost identical to the localization of Cyt c2 in cocrystals with the bacterial reaction center from Rhodobacter sphaeroides. The potential Cyt cHH binding sites are uniformly distributed over ...

PsbO (manganese-stabilizing protein) is the largest extrinsic protein of photosystem II, located on the lumen side of photosystem. It is present in all known oxyphototrophic organisms. PsbO facilitates photosynthetic water splitting, which takes place in an oxygen evolving center (Mn4CaO5 cluster) of photosystem II. This work is focused on PsbO of higher plants and its isoforms, particularly their evolution and functions. Bioinformatic analyses revealed that majority of higher plants express exactly two psbO isoforms. A phylogenetic tree of PsbO sequences has an unusual topology. The two paralogous isoforms do not diverge at the base of the phylogenetic tree, as anticipated, but rather at the end of particular branches, at the level of family or lower taxonomic unit. In this work we propose and discuss several hypotheses concerning evolution of PsbO isoforms. The work further includes detailed analysis and identification of protein spots assigned to PsbO on 2D IEF-SDS PAGE gels of potato thylakoid proteins. We identified predominant version of PsbO isoform in most of the spots. We did not succeed to find any posttranslational modification. We optimized a method of psbO expression in E. coli and subsequent purification, which yielded relatively big amount of properly folded recombinant protein. Analysis of...

Phytoplankton chlorophyll-a fluorescence, measured in situ, can be applied as a tool to estimate primary production in the ocean over a large range of temporal and spatial scales. This non-invasive technique allows for fast assessments of photo-physiological parameters in contrast to the traditional methodologies (14C uptake and O2 evolution). The main photo-physiological parameters derived by the available instruments are yields, and as such, require careful interpretation. The comprehension of the main sources of variability of the photochemical and the light absorption efficiencies in marine phytoplankton has increased in the past years, largely by studies using monospecific cultures. In natural communities, however, the development of primary production models based on chlorophyll-a fluorescence remain limited as they are simultaneously subjected to a wide range of environmental and biological factors. This study will test the hypothesis that photo-physiological models for primary production estimates can be improved when key phytoplankton features, such as the pigments composition and dominant cell size, are taking into account. The approach was to contrast the photo-physiological parameters derived from measurements in distinct oceanographic regions, as well as those derived in a specific environment with presented different nutrient concentration according to the time of sampling. In addition, we showed for monospecific cultures, how the photo-physiological parameters are quantitatively related to the production of carbon under the interactive effects of taxonomic composition and cell size. The proportions of photosynthetic and photoprotective pigments present in the community were related to the bulk photochemical efficiency and the cross-section of light absorption, but varied among oceanographic regions and the depth of the water column. A parameterization of fluorescence-derived primary production rates, using four dominant size classes, was derived for natural phytoplankton communities under different nutrients conditions in a coastal environment, showing that the parameters differed among size classes above a threshold of nutrient concentration. The direct conversion rates between fluorescence-derived primary production and carbon assimilation rates, computed for two distinct phytoplankton cell sizes grown in controlled laboratorial conditions, showed that cell size strongly influences the efficiency of light absorption and photochemistry, however species-specific responses in photosynthetic energy allocation dominated the differences observed in how absorbed light is utilized to carbon assimilation, i.e., in the electron requirements for carbon assimilation. The results highlighted the importance of the tight coupling of nutrients availability and phytoplankton communities, as well as for measurements of chlorophyll-a fluorescence in the ocean and primary production models. This work presents a novel contribution to the increasing efforts to apply fluorescence-based techniques to understand and parameterize primary production estimates in marine systems, especially at highly dynamic environments. / A fluorescência da clorofila-a do fitoplâncton, medida in situ, pode ser uma ferramenta para estimar produção primária no oceano em grande escala temporal e espacial. Esta técnica não-invasiva permite análises rápidas de parâmetros foto-fisiológicos ao contrário de metodologias tradicionais (assimilação de 14C e produção de O2). Os principais parâmetros foto-fisiológicos de instrumentos disponíveis hoje tratam-se de eficiências, e como tal, requerem cuidados em serem interpretados. A compreensão das principais fontes de variabilidade da eficiência fotoquímica e de absorção de luz no fitoplâncton marinho tem aumentado nos últimos anos, em sua maioria em cultivos monoespecíficos. Em comunidades naturais, entretanto, o desenvolvimento de modelos de produção primária baseados na fluorescência da clorofila-a ainda é limitado uma vez que estão sujeitos à uma ampla gama de fatores ambientais e biológicos. Esse estudo testa a hipótese de que modelos foto-fisiológicos para estimar produção primária podem ser aprimorados considerando-se características fundamentais do fitoplâncton, como a composição de pigmentos e tamanho celular dominante. A estratégia foi contrastar parâmetros foto-fisiológicos derivados de medidas em regiões oceanográficas distintas, assim como medidas em um ambiente específico com diferentes concentrações de nutrientes ao longo do período amostrado. Adicionalmente, apresentamos através de cultivos monoespecíficos, como parâmetros foto-fisiológicos são quantitativamente relacionados à produção de carbono e os efeitos interativos da composição taxonômica e tamanho celular nessa relação. A proporção de pigmentos fotossintéticos e fotoprotetores da comunidade foram relacionados à eficiência fotoquímica e seção transversal de absorção de luz, porém variaram de acordo com a região oceanográfica e profundidade na coluna d\'água. Uma parameterização de taxas de produção primária derivadas da fluorescência, usando quatro classes de tamanho dominantes, foi proposta para comunidades naturais de fitoplâncton sob condições de nutrientes diferentes em um ambiente costeiro, mostrando que os parâmetros diferiram entre as classes de tamanho acima de um limiar de concentração de nutrientes. As taxas de conversão diretas entre produção primária derivada da fluorescência e taxas de assimilação de carbono, computadas para dois tamanhos de fitoplâncton crescidos em condições controladas em laboratório, mostraram que tamanho celular influencia as eficiências de absorção de luz e fotoquímica, porém respostas espécie-específicas na alocação de energia fotossintética dominaram as diferenças observadas em como a luz absorvida é utilizada para assimilação de carbono, ou seja, na razão de elétrons exigidos para assimilação de carbono. Os resultados destacam a importância do acoplamento da disponibilidade de nutrientes com a comunidade fitoplanctônica, assim como das medidas de fluorescência da clorofila-a no oceano e nos modelos de produção primária. Este trabalho apresenta uma contribuição inédita nos esforços crescentes em aplicar técnicas baseadas na fluorescência para entender e parameterizar estimativas de produção primária nos sistemas marinhos, especialmente em ambientes altamente dinâmicos.