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The light-harvesting complex of photosystem II (LHC-II) is the major antenna complex in plant photosynthesis. It accounts for roughly 30% of the total protein in plant chloroplasts, which makes it arguably the most abundant membrane protein on Earth, and binds about half of plant chlorophyll (Chl). The complex assembles as a trimer in the thylakoid membrane and binds a total of 54 pigment molecules, including 24 Chl a, 18 Chl b, 6 lutein (Lut), 3 neoxanthin (Neo) and 3 violaxanthin (Vio). LHC-II has five key roles in plant photosynthesis. It: (1) harvests sunlight and transmits excitation energy to the reaction centres of photosystems II and I, (2) regulates the amount of excitation energy reaching each of the two photosystems, (3) has a structural role in the architecture of the photosynthetic supercomplexes, (4) contributes to the tight appression of thylakoid membranes in chloroplast grana, and (5) protects the photosynthetic apparatus from photo damage by non photochemical quenching (NPQ). A major fraction of NPQ is accounted for its energy-dependent component qE. Despite being critical for plant survival and having been studied for decades, the exact details of how excess absorbed light energy is dissipated under qE conditions remain enigmatic. Today it is accepted that qE is regulated by the magnitude of the pH gradient (ΔpH) across the thylakoid membrane. It is also well documented that the drop in pH in the thylakoid lumen during high-light conditions activates the enzyme violaxanthin de-epoxidase (VDE), which converts the carotenoid Vio into zeaxanthin (Zea) as part of the xanthophyll cycle. Additionally, studies with Arabidopsis mutants revealed that the photosystem II subunit PsbS is necessary for qE. How these physiological responses switch LHC-II from the active, energy transmitting to the quenched, energy-dissipating state, in which the solar energy is not transmitted to the photosystems but instead dissipated as heat, remains unclear and is the subject of this thesis. From the results obtained during this doctoral work, five main conclusions can be drawn concerning the mechanism of qE: 1. Substitution of Vio by Zea in LHC-II is not sufficient for efficient dissipation of excess excitation energy. 2. Aggregation quenching of LHC-II does not require Vio, Neo nor a specific Chl pair. 3. With one exception, the pigment structure in LHC-II is rigid. 4. The two X-ray structures of LHC-II show the same energy transmitting state of the complex. 5. Crystalline LHC-II resembles the complex in the thylakoid membrane. Models of the aggregation quenching mechanism in vitro and the qE mechanism in vivo are presented as a corollary of this doctoral work. LHC-II aggregation quenching in vitro is attributed to the formation of energy sinks on the periphery of LHC-II through random interaction with other trimers, free pigments or impurities. A similar but unrelated process is proposed to occur in the thylakoid membrane, by which excess excitation energy is dissipated upon specific interaction between LHC-II and a PsbS monomer carrying Zea. At the end of this thesis, an innovative experimental model for the analysis of all key aspects of qE is proposed in order to finally solve the qE enigma, one of the last unresolved problems in photosynthesis research.
In this thesis the first fully integrated Boltzmann+hydrodynamics approach to relativistic heavy ion reactions has been developed. After a short introduction that motivates the study of heavy ion reactions as the tool to get insights about the QCD phase diagram, the most important theoretical approaches to describe the system are reviewed. To model the dynamical evolution of the collective system assuming local thermal equilibrium ideal hydrodynamics seems to be a good tool. Nowadays, the development of either viscous hydrodynamic codes or hybrid approaches is favoured. For the microscopic description of the hadronic as well as the partonic stage of the evolution transport approaches have beeen successfully applied, since they generate the full phse-space dynamics of all the particles. The hadron-string transport approach that this work is based on is the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) approach. It constitutes an effective solution of the relativistic Boltzmann equation and is restricted to binary collisions of the propagated hadrons. Therefore, the Boltzmann equation and the basic assumptions of this model are introduced. Furthermore, predictions for the charged particle multiplicities at LHC energies are made. The next step is the development of a new framework to calculate the baryon number density in a transport approach. Time evolutions of the net baryon number and the quark density have been calculated at AGS, SPS and RHIC energies and the new approach leads to reasonable results over the whole energy range. Studies of phase diagram trajectories using hydrodynamics are performed as a first move into the direction of the development of the hybrid approach. The hybrid approach that has been developed as the main part of this thesis is based on the UrQMD transport approach with an intermediate hydrodynamical evolution for the hot and dense stage of the collision. The initial energy and baryon number density distributions are not smooth and not symmetric in any direction and the initial velocity profiles are non-trivial since they are generated by the non-equilibrium transport approach. The fulll (3+1) dimensional ideal relativistic one fluid dynamics evolution is solved using the SHASTA algorithm. For the present work, three different equations of state have been used, namely a hadron gas equation of state without a QGP phase transition, a chiral EoS and a bag model EoS including a strong first order phase transition. For the freeze-out transition from hydrodynamics to the cascade calculation two different set-ups are employed. Either an in the computational frame isochronous freeze-out or an gradual freeze-out that mimics an iso-eigentime criterion. The particle vectors are generated by Monte Carlo methods according to the Cooper-Frye formula and UrQMD takes care of the final decoupling procedure of the particles. The parameter dependences of the model are investigated and the time evolution of different quantities is explored. The final pion and proton multiplicities are lower in the hybrid model calculation due to the isentropic hydrodynamic expansion while the yields for strange particles are enhanced due to the local equilibrium in the hydrodynamic evolution. The elliptic flow values at SPS energies are shown to be in line with an ideal hydrodynamic evolution if a proper initial state is used and the final freeze-out proceeds gradually. The hybrid model calculation is able to reproduce the experimentally measured integrated as well as transverse momentum dependent $v_2$ values for charged particles. The multiplicity and mean transverse mass excitation function is calculated for pions, protons and kaons in the energy range from $E_{\rm lab}=2-160A~$GeV. It is observed that the different freeze-out procedures have almost as much influence on the mean transverse mass excitation function as the equation of state. The experimentally observed step-like behaviour of the mean transverse mass excitation function is only reproduced, if a first order phase transition with a large latent heat is applied or the EoS is effectively softened due to non-equilibrium effects in the hadronic transport calculation. The HBT correlation of the negatively charged pion source created in central Pb+Pb collisions at SPS energies are investigated with the hybrid model. It has been found that the latent heat influences the emission of particles visibly and hence the HBT radii of the pion source. The final hadronic interactions after the hydrodynamic freeze-out are very important for the HBT correlation since a large amount of collisions and decays still takes place during this period.
If we want to develop a semantic analysis for explicit performatives such as I promise you to free Willy, we are faced with the following puzzle: In order to account for the speech act expressed by the performative verb, one can assume that the so-called performative clause is purely performative and provides the illocutionary force of the speech act whose content is given by the semantic object denoted by the complement clause. Yet under this perspective, the performative clause that is, next to the performative verb, the indexicals I and you that refer to the speaker and to the addressee of the utterance context is semantically invisible and does not contribute compositionally its meaning to the meaning of the entire explicit performative sentence. Conversely, if we account for the truth conditional contribution of the performative clause and deny that the meaning of the performative verb is purely performative, then we have to find a way to account for the speech act expressed by the performative verb. Of course, there is already the widely accepted and very appealing indirectness account for explicit performative utterances developed by Bach & Harnish (1979). Roughly, Bach and Harnish solve this puzzle in deriving the performativity by means of a pragmatic inference process. According to them, the important speech act performed by means of the utterance of the explicit performative sentence is a kind of the conventionalized indirect speech act. However, the boundary between semantics and pragmatics can be drawn in many various ways. Therefore, I think there could be other perspectives regarding the interface between the truth-functional treatment of the declarative explicit performative sentences and the speech acts performed with their utterances and which are expressed by the performative verbs. Hence, this thesis consists in the experiment to develop a further analysis and to check out its consequences with respect to the semantics and pragmatics of explicit performative utterances and the new interface emerged. Briefly, the experiment runs as follows: First, I develop an analysis for explicit performative sentences framed by parenthetical structures such as in (1)(a). In a second step, this parenthetical analysis is applied to the proper Austinian explicit performative sentences in (1)(b). (1) a. Tomorrow, I promise you this, I will teach them Tyrolean songs. b. I promise you that I will teach them Tyrolean songs. To analyze at first explicit performatives framed by parenthetical structures bears the convenience that we are faced with two utterances of two main clauses. In (1)(a) there is the utterance of the host sentence Tomorrow I will teach them Tyrolean songs, and the utterance of the explicit parenthetical I promise you this, where the demonstrative this refers to the utterance of Tomorrow I will teach them Tyrolean songs. Since speakers perform speech acts with utterances of main clauses, I assume that the meaning of the explicit parenthetical I promise you this specifies that the actual illocutionary force of the utterance of Tomorrow I will teach them Tyrolean songs is the illocutionary force of a promise. Hence, instead of deriving an indirect illocutionary force by means of a pragmatic inference schema, we can deal with an ordinary direct speech act that is performed with the utterance of the host sentence. This kind of analysis stresses the particular discourse function of explicit performative utterances. Performative verbs are used whenever the contextual information is not sufficient to determine the illocutionary force of the corresponding implicit speech act. The resulting consequences of the parenthetical analysis are interesting since they cast a different light on performative verbs. Surprisingly, the performative verbs are not performative at all. They do not constitute the execution of a speech act, but are execution supporting. Instead of constituting the particular illocutionary force, they merely specify the illocutionary force of the utterance of the host sentence. For instance, the speaker utters the explicit parenthetical I promise you this for specifying what he is simultaneously doing. Hence the speaker does not succeed in performing the promise simply because he is uttering I promise you this. Rather, by means of the information conveyed by the utterance of I promise you this, the potential illocutionary forces of the utterance of the host sentence are disambiguated. Thus, it is not the case that explicit parentheticals are trivially true when uttered. Their function is more complex. Their self-verifying property (‘saying so makes it so’) is explained by means of disambiguation. Furthermore, according to the parenthetical analysis, instead of being purely performative, the performative verbs contribute compositionally their meanings to the truth conditions of the entire explicit performative sentence. Together with its consequences, this analysis is applied to the proper Austinian performatives, which display subordination. I assume that regardless of their structure, explicit performatives always semantically and pragmatically behave as the parenthetical analysis predicts.
This study addresses the structure-function relationships of three essential membrane proteins: Porin from Paracoccus denitrificans, Porin OmpG from Eschericia coli and BetP from Corynobacterium glutamicum using Fourier transform infrared (FT-IR) spectroscopy and Attenuated Total Reflection (ATR) techniques. The structure of porin from P. denitrificans is known for more than a decade; however, the mechanism for loss of functionality together with the monomerization was not clear. In this study we have addressed the role of lipids for the functionality of porin using FT-IR. OmpF porin was found to interact with the lipid molecules via the aromatic girdles surrounding the protein for functionality. In this study, molecular bonds and groups of the lipids were established as reporter groups probing at different depths of the bilayer in order to understand the interaction partner of the aromatic girdles of porins. Monomerization of the trimeric assembly of OmpF porin reconstituted in lipids is induced by increasing the temperature. Porin (OmpF) was found to be extremely stable: The secondary structure of the protein was unaltered up to the temperature-induced main transition, around 80-90 °C, above which it is denatured. However, the interaction of the aromatic girdle with the lipid molecules exhibited distinct changes at much lower temperature values (40 - 50°) where, according to the previous functional studies, monomerization and the loss of function occurs. The results are compared with OmpG porin from E.coli, for which the functional unit is a monomer. The aromatic girdle-lipid interaction was monitored by the tyrosine aromatic ring C=C vibrational mode, a universal marker for the protein stability and interaction. We have also found that the aromatic girdles of porins are interacting with the interfacial region of the lipid bilayer instead of lipid headgroups. Lipid-protein interaction was found to be not only essential for the structural stability, but also for the functionality of OmpF porin. We have also studied the structural properties of OmpG from E.coli. The structure of OmpG at two pH values has been resolved using X-ray crystallography and the channel has been proposed to attain different states at different pH values as closed (pH < 5.5) and open (pH >7.5). This study, using IR spectroscopy, revealed that the pH-induced opening and closing of the channel is reflected by the frequency shifts of the ? sheet structure. OmpG has more rigid ? barrel properties upon opening of the channel. IR spectral analysis revealed multiple ? sheet signals with different hydrogen bond strengths. This enabled us to monitor the formation of hydrogen bridges between the extracellular loops upon opening of the channel. The conclusion that OmpG porin having two states at different pH values was also confirmed by the three mutants where the role of the histidine pair (H231 & H261) and loop 6 has been addressed. Temperature-profiling of the wild type (WT) protein and the mutants did not show pH dependent structural stability differences in detergent solution. However, the WT protein was found to be more stable in the open form in 2D crystals than the closed form. Reconstitution into lipids has increased the transition temperature value by ~20 °C in the closed state and ~25 °C in the open state. Therefore we conclude that the open and closed state of OmpG has structural stability differences that are only revealed in the lipid environment. A comparison of the transition temperature values of OmpG WT and the mutants suggested that the hydrogen bond network among S218-H231-H261-D267, together with the formation of 12 residue-long ?-sheet contributes to the structural stability of the open channel. In the process of closing and opening of the channel, the globular structure of the protein remains mainly unchanged, while there are changes in the side chain moieties. In addition to the role of the histidine pair and the loop L6, in situ opening/closing experiments showed that the negatively charged amino acids, i.e. Asp and Glu, and Arg residues also play an active role; possibly by interacting with each other inside the pore lumen. Therefore it could be concluded that the closure of the channel at acidic pH values is not only via closing the channel entrance by loop 6, but also via changing the electric potential inside the lumen due to the different states of charged amino acids in order to effectively block the gateway. BetP from C.glutamicum attains an active and inactive state in order to adjust its glycine betaine uptake rate to the osmotic conditions that the cell encounters. The structure of BetP is not yet available. The WT protein exhibited structural differences in the presence of excess K+, which is one of the activation conditions. In 2D crystals, increasing the ionic strength to 700 mM K+ was shown to induce changes in the ?-helical moiety with contributions from the ester groups and one Tyr residue using ATR-FTIR. An increase in ionic strength to 220 mM K+ was found to be the threshold value of potassium concentration ([K+]) where the protein exhibits structural alterations in detergent solution. The determined [K+] values are in good agreement with the previous functional studies. However, there are differences in the activation profile of BetP in 2D crystals and in detergent solution, which points out that the lipids are involved in the conformational transition from the inactive to the active state and their absence can lead to different structural properties. BetP WT was found to have ~65% alpha-helix, ~25% random coil and ~10% turn structure in detergent solution. In the presence of excess K+, the WT protein is found to adapt more unordered structure. Secondary structure analysis of the mutants revealed that both the N- and C-terminus are in ?-helical conformation. Reconstitution of WT protein in 2D crystals increased the main transition (denaturation) temperature value from ~62 °C to ~85 °C, a clear indication that the protein is more stable in lipid environment. Temperature-profiling of the two forms of the WT protein revealed that the structural breakdown is preceeded by monomerization of the trimeric assembly. Comparing the two forms of the WT protein and the mutant BetA, we conclude that the oligomeric status is stabilized via the interactions among hydrophilic regions involving the N terminus. H/D exchange and activation with excess K+ in D2O-buffer revealed that activation of the protein involves the interaction of Arg and Asp/Glu residues in the cytoplasmic region of the protein. BetP WT and the two mutants tested, i.e. BetA and BetP?C45, showed differences in protein packing upon activation. The WT protein and BetP?C45 mutant also show changes in the hydrogen bonding properties of turns. Since BetA does not show such a property in activation, we conclude that the N-terminus interacts with the loops in the inactive state via the interaction of charged amino acids for the WT protein and that this interaction is altered during the activation. It could be argued that the protein packing is affected via the changes in turns upon activation. We also have found experimental evidence that one Tyr residue has different orientations in the active and inactive state of BetP. Based on the previous functional studies, it could be one of the five Tyr residues in the cytoplasmic region of the protein (in loop 3, 6, 7 or C-terminus). The mutant BetP?C45, on the other hand, showed fewer differences between the active and inactive state conditions and based on the H/D exchange rates, the mutant shows the properties of an active WT protein, proving that the C-terminal truncation impairs the conformational transition between the active and inactive states.
The characterization of microscopic properties in correlated low-dimensional materials is a challenging problem due to the effects of dimensionality and the interplay between the many different lattice and electronic degrees of freedom. Competition between these factors gives rise to interesting and exotic magnetic phenomena. An understanding of how these phenomena are driven by these degrees of freedom can be used for rational design of new materials, to control and manipulate these degrees of freedom in order to obtain desired properties. In this work, we study these effects in materials with small exchange interaction between the magnetic ions such as metal-organic and inorganic dilute compounds. We overcome the dfficulties in studying these kind of materials by combining classical and quantum mechanical ab initio methods and many-body theory methods in an effective theoretical approach. To treat metal-organic compounds we elaborate a novel two-step methodology which allows one to include quantum effects while reducing the computational cost. We show that our approach is an effective procedure, leading at each step, to additional insights into the essential features of the phenomena and materials under study. Our investigation is divided into two parts, the first one concerning the exploration of the fundamental physical properties of novel Cu(II) hydroquinone-based compounds. We have studied two representatives of this family, a polymeric system Cu(II)-2,5-bis(pyrazol-1-yl)-1,4-dihydroxybenzene (CuCCP) and a coupled system Cu2S2F6N8O12 (TK91). The second part concerns the study of magnetic phenomena associated with the interplay between different energy scales and dimensionality in zero-, one- and two-dimensional compounds. In the zero-dimensional case, we have performed a comprehensive study of Cu4OCl6L4 with L=diallylcyanamide=NC-N-(CH2-CH=CH2)2 (Cu4OCl6daca4). Interpretations of the magnetic properties for this tetrameric compound have been controversial and inconsistent. From our studies, we conclude that the common models usually applied to this and other representatives in the same family of cluster systems fail to provide a consistent description of their low temperature magnetic properties and we thus postulate that in such systems it is necessary to take into account quantum fluctuations due to possible frustrated behavior. In the one-dimensional case, we studied polymeric Fe(II)-triazole compounds, which are of special relevance due to the possibility of inducing a spin transition between low and high spin state by applying a external perturbation. A long standing problem has been a satisfactory microscopic explanation of this large cooperative phenomenon. A lack of X-ray data has been one mitigating reason for the absence of microscopic studies. In this work, we present a novel approach to the understanding of the microscopic mechanism of spin crossover in such systems and show that in these kind of compounds magnetic exchange between high spin Fe(II) centers plays an important role. The correct description of the underlying physics in many materials is often hindered by the presence of anisotropies. To illustrate this difficulty, we have studied a two dimensional dilute compound K2V3O8 which exhibits an unusual spin reorientation effect when applying magnetic fields. While this effect can be understood when considering anisotropies in the system, it is not sufficient to reproduce experimental observations. Based on our studies of the electronic and magnetic properties in this system, we predict an extra exchange interaction and the presence of an additional magnetic moment at the non-magnetic V site. This sheds a new light into the controversial recent experimental data for the magnetic properties of this material.
This thesis contributes to the field of soft matter research and studies the importance of hydrodynamic interactions during free-solution electrophoresis of linear polyelectrolytes by means of coarse-grained molecular dynamics simulations including full electro-hydrodynamic interactions. The center of attention is the specific role of hydrodynamic interactions on the electrophoretic behaviour of charged macromolecules. Points of interest are the dependence of hydrodynamic interactions on the chain length, the chain flexibility and the surrounding counterions, and their combined influence on important observables such as the static chain conformations and the dynamic transport coefficients, i.e., the diffusion and the electrophoretic mobility. These problems are addressed by extensive computer simulations that are quantitatively matched with experimental results. Existing theoretical predictions are carefully examined and are augmented by the observations in this thesis.