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Im ersten Teil dieser Arbeit sind Protein-Protein Docking-Studien dokumentiert. Bis heute konnten die meisten Protein-Komplex-Strukturen nicht experimentell aufgeklärt werden, so auch die beiden oben genannten Elektrontransfer-Komplexe. Nach einem erfolgreichen Test wurden verschiedene Cytochrom c Oxidase:Cytochrom c Paare mit der gleichen Methode gedockt: COX aus Paracoccus denitrificans mit Pferdeherz Cytochrom c und COX mit dem löslichen Fragment des membrangebundenen Cytochrom C552 (beide aus P. denitrificans). Im zweiten Teil dieser Arbeit wurde die diffusive Annäherung des Cytochrom c an die Cytochrom c Qxidase mit der Brownschen Dynamik Methode simuliert. Die Diffusionsbewegung eines Brownschen Teilchens in wässriger Lösung wird durch die Langevin-Gleichung bestimmt. Der auf dieser Gleichung fußende Ermak-McCammon-Algorithmus ist Grundlage der Simulationsmethode. Die so ermittelten Raten für COX und Pferdeherz, sowie für COX und Cytochrom C552, wurden dann mit experimentell gewonnenen Raten verglichen. Da die Elektrostatik für den Annäherungsprozeß dieser Proteine eine so gewichtige Rolle spielt, wirken sich Mutationen, die mit einer Ladungsänderung einhergehen, merklich aus. Dies ist vor allem dann der Fall, wenn sich die Mutation in der Nähe der Bindungsstelle befindet. Aus dem gleichen Grund ist die Assoziationsrate auch stark von der Ionenstärke der umgebenden Lösung abhängig. Steigt die Ionenkonzentration wird die elektrostatische Komplementarität der Bindingsstellen der beiden Makromoleküle stärker abgeschirmt, und die Rate sinkt. Diese beiden relativen Trends konnten durch die Simulationen gut reproduziert und bestätigt werden. Allerdings liegen die absoluten Resultate merklich über den experimentell gemessenen Raten. Es ist sehr gut möglich, daß post-diffusive Effekte, die nicht in einer Brownschen Dynamik Simulation von starren Körpern berücksichtigt werden können, die Raten erniedrigen. Um den Einfluß der Membranumgebung auf die Wechselwirkung des Elektrontransportsystems zu untersuchen. wurde eine DPPC Doppelschicht um die Oxidase modelliert und energieminimiert. Mit Poisson-Boltzmann Rechnungen wurde das elektrostatische Potential dieses Nanosystems untersucht und mit dem der einzelnen Oxidase verglichen. Durch einen modifizierten Set-up konnten dann auch für dieses Membransystem Brownsche Dynamik Simulationen durchgeführt werden. Der Vergleich mit den vorhergehenden Simulationen ohne Membran erbrachte bemerkenswerte Ergebnisse. Während die Assoziationsraten für Pferdeherz Cytochrom c durch den Membraneinfluß erniedrigt wurden, stiegen sie im Fall des physiologischen Transferpartners c552. Pferdeherz Cytochrom c weist eine positive Nettoladung und einen ausgeprägten bipolaren Charakter auf. Eine große Zahl positiv geladener Seitenketten befindet sich auf der gleichen Hemisphäre wie die Bindungsstelle. Obwohl die DPPC Lipidmoleküle neutral sind, zeigten die Elektrostatikrechnungen, daß die Membranoberfläche abstoßend auf positive Ladungen wirkt. Da sich nun die Bindungsstelle der Oxidase für Cytochrom c nur etwa 10 Å oberhalb der Membran befindet, verringert sich die Wahrscheinlichkeit der Assoziation.
Mitogen activated protein kinases (MAPKs) are found in all eukaryotic cells and represent crucial elements in the signal transduction from the plasma membrane to the nucleus. Although a broad variety of extracellular stimuli activate MAPKs, they evoke very distinct cellular responses. The amplitude and duration of MAPK activation determine signal identity and ultimately cell fate. A tight and finely tuned regulation is therefore critical for a specific cellular response. The role and the regulation of extracellular signal-regulated kinase 5 (ERK5), a MAPK with a large and unique C-terminal tail, were studied in different cellular systems. The study highlights two aspects of ERK5 regulation: control of the phosphorylation state and regulated protein stability. In analogy to other MAPKs ERK5 is activated by dual phosphorylation of threonine and tyrosine residues in its activation motif. A first part of the study concentrates on whether and how the protein tyrosine phosphatase PTP-SL is involved in the downregulation of the ERK5 signal. The direct interaction of both proteins is shown to result in mutual modulation of their enzymatic activities. PTP-SL is a substrate of ERK5 and, independent of its phosphorylation, binding to the kinase enhances its catalytic phosphatase activity. On the other hand, interaction with PTP-SL does not only downregulate enzymatic ERK5 activity but also effectively impedes its translocation to the nucleus. The second part of this study focuses on the interaction of ERK5 with c-Abl and its oncogenic variants Bcr/Abl and v-Abl. In this study these tyrosine kinases are demonstrated to regulate ERK5 by two mechanisms: first, by induction of kinase activity and secondly, by stabilisation of the ERK5 protein. Stabilisation involves the direct interaction of unique ERK5 domains with Abl kinases and is independent of MAPK cascade activation. The level of ERK5 and its intrinsic basal activity – rather than its activation – are essential for v-Abl-induced transformation as well as for survival of Bcr/Abl-positive leukaemia cells. Stabilisation of ERK5 thus contributes to cell survival and should therefore be considered as an additional aspect in therapy of chronic myeloid leukaemia. Taken together, the results obtained in this study demonstrate that diverse pathways regulate ERK5 signalling by affecting kinase activity, localisation and protein stability. While the phosphatase PTP-SL is involved in negative regulation of ERK5, Abl kinases potently activate ERK5 and increase its half-life. Protein stabilisation thus is presented as a novel mechanism in the regulation of MAPKs.
Gegenstand dieser Arbeit sind Eigenschaften angeregter hadronischer Materie sowie physikalische Systeme, in denen diese Materie auftritt bzw. produziert wird. Die Beschreibung der stark wechselwirkenden Materie erfolgt in einem hadronischen, chiral-symmetrischen SU(3)L x SU(3)R Modell, welches die Saturierungseigenschaften von Kernmaterie und die Eigenschaften von Atomkernen reproduziert. Die Untersuchung heißer und dichter unendlicher hadronischor Materie zeigt, dass das vom Modell vorhergesagte Phasendiagramm stark von den Kopplungen der Baryonenresonanzen abhängt. Für kalte hadronische Materie ergibt die Einbeziehung des Baryonendekupletts und die Freiheit in deren Vektorkopplungen eine sehr große Bandbreite an verschiedenen Zustandsgleichungen. Für heiße hadronische Materie mit verschwindendem baryochemischen Potential zeigt sich ebenfalls eine starke Abhängigkeit der Eigenschaften hadronischer Materie von der Ankopplung der baryonischen Resonanzen. Es werden drei verschiedene Parametrisierungen betrachtet. Das resultierende Phasenübergangsverhalten variiert von einem "Crossover" über einen schwachen, zu einem doppelten Phasenübergang erster Ordnung. Es zeigt sich jedoch, dass die beobachteten Eigenschaften von Neutronensternen die Unbestimmtheit bzgl. der Vektorkopplung dieser Freiheitsgrade und damit der Zustandsgleichung deutlich verringern. Das Raum-Zeit Verhalten relativistischer Schwerionenkollisionen bei SPS- und RHIC-Energien wird mittels einer hydrodynamischen Simulation unter Benutzung der chiralen Zustandsgleichungen untersucht. Dabei spiegelt sich das unterschiedliche Phasenübergangsverhalten deutlich im Ausfrierverhalten der hadronischen Materie wider. Die im chiralen Modell berechneten Teilchenzahlverhältnisse werden mit den aus Schwerionenkollisionen von AGS- bis RHIC-Energien erhaltenen experimentellen Daten verglichen. Dabei zeigt sich, dass die verschiedenen Parametersätze des chiralen Modells und die Rechnungen für ein nichtwechselwirkendes, ideales Hadronengas eine ähnlich gute Beschreibung der gemessenen Weite liefern. Die deduzierten Ausfrierwerte für die Temperatur sind sensitiv auf das Phasenübergangsverhalten und liegen unterhalb der jeweiligen kritischen Temperatur. Die vorhergesagten Ausfriermassen sind in allen Parametrisierungen sehr ähnlich mit Abweichungen bis zu 15% von den entsprechenden Vakuumwerten. Die Untersuchung der Eigenschaften von Vektormesonen in dichter Materie erfolgt in der Mittleren-Feld- und in der HartreeNäherung. Hierbei zeigt sich eine signifikante Reduzierung der Teilchenmassen durch Vakuumpolarisationseffekte.
We consider the long-time behaviour of spatially extended random populations with locally dependent branching. We treat two classes of models: 1) Systems of continuous-time random walks on the d-dimensional grid with state dependent branching rate. While there are k particles at a given site, a branching event occurs there at rate s(k), and one of the particles is replaced by a random number of offspring (according to a fixed distribution with mean 1 and finite variance). 2) Discrete-time systems of branching random walks in random environment. Given a space-time i.i.d. field of random offspring distributions, all particles act independently, the offspring law of a given particle depending on its position and generation. The mean number of children per individual, averaged over the random environment, equals one The long-time behaviour is determined by the interplay of the motion and the branching mechanism: In the case of recurrent symmetrised individual motion, systems of the second type become locally extinct. We prove a comparison theorem for convex functionals of systems of type one which implies that these systems also become locally extinct in this case, provided that the branching rate function grows at least linearly. Furthermore, the analysis of a caricature model leads to the conjecture that local extinction prevails generically in this case. In the case of transient symmetrised individual motion the picture is more complex: Branching random walks with state dependent branching rate converge towards a non-trivial equilibrium, which preserves the initial intensity, whenever the branching rate function grows subquadratically. Systems of type 1) and systems of type 2) with quadratic branching rate function show very similar behaviour. They converge towards a non-trivial equilibrium if a conditional exponential moment of the collision time of two random walks of an order that reflects the variability in the branching mechanism is finite almost surely. The equilibrium population has finite variance of the local particle number if the corresponding unconditional exponential moment is finite. These results are proved by means of genealogical representations of the locally size-biased population. Furthermore, we compute the threshold values for existence of conditional exponential moments of the collision time of two random walks in terms of the entropy of the transition functions, using tools from large deviations theory. Our results prove in particular that - in contrast to the classical case of independent branching - there is a regime of equilibria with variance of the local number of particles.
One of the known apoptotic pathways in mammalian cells involves release of mitochondrial Cytochrome c into the cytosol. Cyt c then together with ATP or dATP induces a conformational change in the adaptator protein Apaf-1 (a homologue of the C. elegans CED4 protein) (Zou, Henzel et al. 1997), leading to its oligomerization and the recruitment of several pro-Casp-9 molecules. This protein complex assembly called "apoptosome" leads to the activation of Casp-9 which then initiates or amplifies the caspase cascade. The cell death program can be stalled at several points and we were interested in identifying new proteins inhibiting cell death downstream of Cyt c release. This thesis describes how I have screened a cDNA library derived from a pool of human breast carcinomas in a yeast-based survival screen, using the S. pombe yeast strain HC4 containing an inducible CED4 construct(James, Gschmeissner et al. 1997). The screen resulted in the identification of six proteins displaying cell death-inhibiting activity in S. pombe as well as anti-apoptotic potential in mammalian cells. Those six molecules were RoRet (Ruddy, Kronmal et al. 1997), Aven (Chau, Cheng et al. 2000), Fte-1/S3a (Kho, Wang et al. 1996), PGC2 (Padilla, Kaur et al. 2000; Goetze, Eilers et al. 2002), SAA1-2ß (Moriguchi, Terai et al. 2001) and FBP (Brockstedt, Rickers et al. 1998) of which I selected RoRet, Aven and Fte-1/S3a for further analysis. RoRet is a new anti-apoptotic molecule that can inhibit the mitochondrial pathway via its PRY-SPRY domain. RoRet does not seem to bind to Apaf-1, and does not co-localize with the activated Apaf-1/Caspase-9 complex. Aven was published to act as an anti-apoptotic protein and suggested to function via the recruitment of Bcl-XL to Apaf-1. This work shows that its C-terminal domain can bind to Apaf-1 and has a strong anti-apoptotic activity by itself. Moreover, Aven co-localizes with the activated Apaf-1/Caspase-9 complex suggesting that it is a component of the apoptosome. Furthermore, the expression of Aven is regulated in mammary glands during the pregnancy cycle. Fte-1/S3a has been already implicated in increased transformation capacity of v-Fos in fibroblasts (Kho and Zarbl 1992; Kho, Wang et al. 1996). This work shows that it has anti-apoptotic activity and can protect against Bak- and Apaf-1-induced apoptosis. It can bind directly to activated Apaf-1 at the linker domain between the WD40 repeats and the CED4-like domain, suggesting that it may protect by sequestering the activated Apaf-1 to some organelles whose nature remains to be determined. Moreover, expression studies on mRNA and protein level showed upregulation of Fte-1/S3a in colon, lung and kidney carcinoma. Hmgb1 (Flohr, Rogalla et al. 2001; Pasheva, Ugrinova et al. 2002; Stros, Ozaki et al. 2002) was identified during a survival screen performed with a NIH 3T3 mouse fibroblast cDNA library in a Bak-expressing yeast S. pombe strain. HMGB1 can protect against Bak-, UV-, FasL- and TRAIL-induced apoptosis. Significant overexpression of HMGB1 was found in breast and colon carcinoma, and elevated mRNA amounts were detected in uterus, colon and stomach carcinoma, suggesting that it may be a tumour marker (Brezniceanu et al., 2003).
Resistive Plate Chambers (RPCs) are gaseous parallel plate avalanche detectors that implement electrodes made from a material with a high volume resistivity between 10 high 7 and 10 high 12 omega cm. Large area RPCs with 2mm single gaps operated in avalanche mode provide above 98% efficiency and a time resolution of around 1 ns up to a flux of several kHz/cm high 2. These Trigger RPCs will, as an example, equip the muon detector system of the ATLAS experiment at CERN on an area of 3650 m high 2 and with 355.000 independent read out channels. Timing RPCs with a gas gap of 0.2 to 0.3mm are widely used in multi gap configurations and provide 99% efficiency and time resolution down to 50 ps. While their performance is comparable to existing scintillator-based Time-Of-Flight (TOF) technology, Timing RPCs feature a significantly, up to an order of magnitude, lower price per channel. They will for example equip the 176 m high 2 TOF barrel of the ALICE experiment at CERN with 160.000 independent read out cells. RPCs were originally operated in streamer mode providing large signals which simplifies readout electronics and gap uniformity requirements. However, high rate applications and detector aging issues made the operation in avalanche mode popular. This was also facilitated by the development of new highly quenching C2F4H2-based gas mixtures with small contents of SF6. While the physics of streamers is difficult to study, the avalanche mode opened the possibility for a detailed simulation of the detector physics processes in RPCs. Even though RPCs were introduced in the early eighties and have been (will be) used in experiments, there are still disagreements about the explanation of several aspects of the RPC performance. The high efficiency of single gap RPCs would require a large ionization density of the used gases, which according to some authors contradicts measurements. Even in the case of a large ionization density the gas gain has to be extremely large, in order to arrive at the observed RPC efficiency. This raises other questions: A very strong space charge effect is required to explain the observed small avalanche charges around 1 pC. Doubts have been raised whether an avalanche can progress under such extreme conditions without developing into a streamer. To overcome these difficulties, other processes, like the emission of an electron from the cathode, were suggested. Moreover, the shape of measured charge spectra of single gap RPCs differs largely from what is expected from the statistics of the primary ionization and the avalanche multiplication. In this thesis we discuss the detector physics processes of RPCs, from the primary ionization and the avalanche statistics to the signal induction and the read out electronics. We present Monte-Carlo simulation procedures that implement the described processes. While the fundament of the described model and some results were already published elsewhere [1], the subject of this thesis is the implementation of the space charge effect. We present analytic formulas for the electrostatic potential of a point charge in the gas gap of an RPC. These formulas were developed in collaboration with the University of Graz [2] and were published in [3, 4]. The simulation model presented in [1] is completed by the dynamic calculation of the space charge field using these formulas. Since the gas parameters like drift velocity and the Townsend and attachment coefficients depend on the electric field, they are calculated dynamically as well. The functional dependence of these parameters on the field is obtained with the simulation programs MAGBOLTZ and IMONTE. For the primary ionization parameters, we use the values that are predicted by the program HEED. While the described procedure only simulates the longitudinal avalanche development towards the anode of the RPC, we also present more dimensional models that allow a careful study of the transverse repulsive and attractive forces of the space charge fields, and of the consequences for the avalanche propagation. We shall show that the efficiencies of single gap Timing RPCs is indeed explained by the high primary ionization density (about 9.5 /cm as predicted by HEED) and a large effective Townsend coefficient (around 113 /mm as predicted by IMONTE). We show that the space charge field reaches the same magnitude as the applied electric field in avalanches at large gas gain. This strong space charge effect effectively suppresses large values for the avalanche charges. The shape of the simulated charge spectra is very similar to the measurements. Also the simulated average charges are close to the experimental results. RPCs are operated in a strong space charge regime over a large range of applied voltage, contrary to wire chambers. We apply only standard detector physics simulations to RPCs. The performance of Timing and Trigger RPCs is well reproduced by our simulations. The results concerning the space charge effect were presented and discussed at the 'RPC 2001' workshop [5] and on the '2002 NSS/MIC' conference [6].
In summary, the cooled heavy-ion beams of the ESR storage ring offer excellent experimental conditions for a precise study of the effects of QED in the groundstate of high-Z one- and two-electron ions. This has been demonstrated within the series of experiments conducted at the electron cooler device as well as at the gasjet target. In this work we have used a recently developed experimental approach to obtain the first direct measurement of the two-electron contributions to the ground state binding energy of helium-like uranium. By employing our method, all one-electron contributions to the binding energy such as finite-nuclear size corrections and the one-electron self energy cancel out completely. Note, this is a distinctive feature of this particular kind of QED test and is in contrast to all other tests of bound state QED for high-Z ions such as 1s Lamb shift (in one-electron systems), g-factor of bound electrons, or hyperfine splitting. Compared to former investigations conducted at the superEBIT in Livermore we could already substantially improve the statistical accuracy and extend studies to the higher-Z regime. Moreover, our result has reached a sensitivity on specific two-electron QED contributions. Our value agrees with the theoretical predictions within the experimental uncertainty. Similar to the superEBIT experiment possible sources of systematic errors are essentially eliminated and the final result is limited only by counting statistics. For the case of the 1s Lamb shift in hydrogen-like uranium, the achieved accuracy of +- 4.2 eV is a substantial improvement by a factor of 3 compared to the most precise value up to now [44] (see Fig. 5.6). Our result already provides a test of the first-order QED contributions at the 1.5% level and only a slight improvement is required in order to achieve a sensitivity to QED contributions beyond first-order SE and VP.
The mechanism of peptide transport has been studied on two different ABC transporters of S. cerevisiae. Thereby, the aim of this PhD thesis was to characterise the transporter function on molecular level and shed light on the physiological role of these transporters. The ABC gene YLL048 encodes a novel intracellular transporter translocating peptides from the cytosol to the lumen of the ER. Deletion of the gene resulted in loss of peptide transport activity. The transport activity was fully restored after transformation of the deletion mutant by plasmid-encoded YLL048. Studying the substrate specificity using randomized peptide libraries it was demonstrated that peptides of the size from 6 to 56 amino acids are recognized. So far, no upper limit of the substrate size was obtained. Introduction of D-amino acids in various positions of a nonamer peptide did not impair transport activity. The physiological function of YLL048p is not well understood. The gene product is not essential for cell viability as the deletion mutant did not show any growth phenotype. To examine the possibility that YLL048 encoded protein is part of a quality control of yeast cells involved in the unfolded protein response (UPR), upregulation of YLL048 transcription by heat shock and stress conditions were investigated. We could not observe an influence of stress factors on YLL048 mRNA level. Upregulation of gene expression by the transcription factors Pdr1p and Pdr3p was excluded. The ABC transporter Mdl1p has been identified as peptide transporter of the inner mitochondrial membrane. This protein is required for the export of peptides with the size of 6 to 21 amino acids from the matrix into the intermembrane space. These peptides are generated by m-AAA proteases degrading non-assembled or missfolded membrane proteins. In order to understand the transport mechanism in detail, Mdl1p was expressed in S. cerevisiae and E. coli. Partially enriched protein was reconstituted into liposomes and was active in ATP binding. The association of the NBDs has been described as a central step of the ATPase cycle of ABC transporters, but it is still controversial how both motor domains cooperate and coordinate ATP hydrolysis. To address this question, the Mdl1p-NBD was overexpressed in E. coli and purified to homogeneity. The isolated NBD was active in ATP binding and hydrolysis with a turnover of 0.5 ATP per min and a Km value of 0.2 mM. Isolated NBDs did not show cooperativity in ATPase activity. However, the ATPase activity was observed to be non-linearly dependent on protein concentration suggesting the active form of this enzyme is not a monomer. Very importantly, for the first time an ATP-induced dimer was observed after trapping the NBD by ortho-vanadate or BeFx. The nucleotide composition of the trapped intermediate state was determined and two ADP molecules were simultaneously bound per dimer. An ATP-induced dimer of the ATPase inactive mutant (E559Q) was observed already in the absence of ATPase inhibitor. The E599Q dimer contained two ATP molecules in the absence of Mg2+ at 4°C. Prolonged incubation at 30°C in the presence of Mg2+ induced a stable dimer in which one ATP and ADP molecule were trapped at the same time. Based on these experiments, a new cycle for ATPase activity of ABC transporters was proposed. Binding of ATP to two NBD monomers induces dimerization. Both nucleotides are hydrolysed sequentially. During the hydrolysis cycle the nucleotides cannot be released from the dimer. After hydrolysis of two ATP molecules the domains dissociate and start a new cycle.
Die Entwicklung der Renormierungsgruppen-Technik, die in ihrer feldtheoretischen Version auf Ideen von Stückelberg und Petermann und in der Festkörperphysik auf K.G. Wilson zurückgeht, hat wesentliche Einsichten in die Natur physikalischer Systeme geliefert. Insbesondere das Konzept der so genannten Universalitätsklassen erhellt, warum Systeme, die durch scheinbar sehr verschiedene Hamilton-Operatoren beschrieben werden, doch im Wesentlichen die selbe (Niederenergie-)Physik zeigen. Ein weiterer Grund für den Erfolg dieser Methode liegt darin begründet, dass sie in systematischer Weise unendlich viele Feynman-Diagramme aufsummiert und somit über konventionelle Störungstheorie hinaus geht. Dies spielt in der Festkörperphysik vor allem dann eine wichtige Rolle, wenn das vorliegende physikalische System stark korreliert ist. Entsprechend der Vielzahl von Anwendungsmöglichkeiten hat sich in den vergangenen Jahrzehnten eine große Bandbreite verschiedener Formulierungen der Renormierungsgruppen-Technik ergeben. Eine davon ist die sogenannte funktionale Renormierungsgruppe, die auf Wegner und Houghton zurück geht und die auch in der vorliegenden Arbeit benutzt und weiter entwickelt wurde. Wir haben hier insbesondere auf die Einbeziehung der wichtigen Reskalierungsschritte wertgelegt. Als erstes Anwendungsgebiet des neu entwickelten Formalismus wurden stark korrelierte Elektronen in einer Raumdimension ausgewählt und hier insbesondere ein Modell, das als Tomonaga-Luttinger-Modell (TLM) bezeichnet wird. Im TLM wechselwirken Elektronen mit einer strikt linearen Energiedispersion ausschließlich über so genannte Vorwärtsstreu-Prozesse. Aufgrund der Linearisierung der Energiedispersion nahe der Fermipunkte ergibt sich ein Modell, das z.B. mit Hilfe der so genannten Bosonisierungs-Technik exakt gelöst werden kann. Hauptziel der vorliegenden Arbeit ist es, die bekannte Spektralfunktion dieses Modells unter Verwendung des Renormierungsgruppen-Formalismus zu reproduzieren. Gegenüber der bisherigen Implementierung der Renormierungsgruppe, bei der lediglich der Fluss einer endlichen Anzahl von Kopplungskonstanten betrachtet wird, stellt die Berechnung des Flusses ganzer Korrelationsfunktionen eine enorme Erweiterung dar. Der Erfolg dieser Herangehensweise im TLM bestärkt die Hoffnung, dass es in Zukunft auch möglich sein wird, die Spektralfunktionen anderer Modelle mit dieser Methode zu berechnen, bei denen herkömmliche Techniken versagen.