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GPCRs and ligand-gated ion channels mediate a great variety of physiological effects within the human brain and periphery. The search for selective ligands at these target sites as pharmacological tools or new drug candidates is of great interest. With increasing knowledge of the great diversity of some receptor families, compounds formerly considered to be selective, turned out to be non-selective with regard to recently identified subtypes, splice variants or additional receptor subunits. This work provides SAR studies by means of radioligand binding experiments at serotonergic h5-HT3A and h5-HT4(b) receptors, histamine hH1 receptors and muscarinic hM1-5 receptors. ...
The heat stress (hs) response is universal to all organisms. As the cell senses increase in temperature, heat stress transcription factors (Hsfs) are activated to upregulate the expression of a number of genes encoding heat stress proteins (Hsp) which act as molecular chaperones to protect cells against heat damages. In higher plants, the phenomenon seems to be unusually complex both at the level of Hsfs and Hsps (e.g., 21 Hsf encoding genes in Arabidopsis and at least 17 in tomato). Upon prolonged hs, another characteristic property of plant cells is the assembly of large cytosolic aggregates called heat stress granules (HSG), which are composed of Hsps, HsfA2, RNA and RNA-binding proteins. The present work was aimed to understand plant hs response using tomato as a model system. To study the function of tomato Hsfs in their native system, we generated transgenic tomato lines altered in expression of HsfA1, HsfA2, and HsfB1. Tomato plants with 10-fold overexpression of HsfA1 (OE plants) were characterised by integration of a single HsfA1 expression cassette, whereas the plants harbouring a tandem inverted repeat (IR) of the cassette showed cosuppression of HsfA1 (CS plants). The lack of HsfA1 expression in CS plants results from posttranscriptional gene silencing connected with the formation of small interfering RNA (siRNA). Under normal growth conditions, major developmental features were similar for wild-type (WT), OE and CS plants. However, in contrast to the former two, CS plants and fruits were extremely sensitive to elevated temperature because hs-induced synthesis of major chaperones and Hsfs was strongly reduced or lacking. Despite the complexity of the plant Hsf family, the function of tomato HsfA1 is unique as master regulator of induced thermotolerance. On the other hand, maintenance of essential chaperones in CS plants during seed development suggests involvement of other Hsfs and/or transcription factor(s). HsfB1 and HsfA2 transgenic tomato plants, unaffected in thermotolerance, further supported the function of HsfA1 as the major factor regulating hs-inducible genes. Hs87 independent phenotypes of plants with altered expression of HsfB1 indicates developmental role of this Hsf. Using transient reporter assays with mesophyll protoplasts from WT tomato, we demonstrated that plasmids encoding Hsfs A1, A2 and A3 were well expressed which could function as activators for reporter gene expression. However, in protoplasts derived from CS plants, plasmids encoding HsfA2 and HsfA3 were normally expressed but even higher amounts of HsfA1 expression plasmids were completely silenced. Therefore, silencing of HsfA1 in CS plants was also reproduced in its mesophyll protoplasts. Lacking thermotolerance in CS protoplasts could be restored after transformation with expression plasmids encoding functionally equivalent HsfA2 or HsfA3 resulting in (i) expression of chaperones, (ii) survival of the cells at otherwise lethal temperature, (iii) thermoprotection of firefly luciferase, and (iv) assembly of heat stress granules (HSGs). The strong silencing caused by an IR in CS plants opened the possibility of a broad use of RNAi for gene knock-down also in the transient system of mesophyll protoplasts. Using this technology, we attempted to dissect essential components of thermotolerance and HSG assembly. We demonstrated the previously reported function of chaperones such as Hsp70 and Hsp101, and could discriminate the in vivo chaperone functions of different isoforms of Hsp20 and Hsp70 proteins. Hsp17-CI, Hsp70 (hs-inducible isoforms), and Hsp101 are absolutely essential chaperones for thermotolerance in plants. Furthermore, the results also show that despite Hsp17-CI and -CII being major components of HSG complexes, they are dispensable for assembly of these complexes. Based on these results, it is proposed that in the transient protoplast system an approach with gene-specific IRs can be used to discriminate functions of closely related isoforms among protein-families and to dissect complex protein networks.
Vascular occlusive diseases are one of the leading mortality causes in westernised countries. Occlusions of one of the major arteries can be overcome without devastating consequences provided a timely induction of compensating collateral arteries occurs. Perhaps the most outstanding feature of collateral vessel growth is the proliferation of smooth muscle cells (SMCs). Understanding the molecular mechanisms and identifying key molecular players of SMC proliferation would contribute significantly to the development of efficient therapies to intervene with all processes involving neointima formation, including collateral growth. mRNA and protein coding for co-transcription factor Egr1 were found to be up-regulated in growing collateral vessels 6, 12 or 24 hours following femoral artery ligation in mice. Since Egr1 is required for SMC proliferation in vitro and in vivo and likely to be implicated in the initiation of collateral artery growth, the key signalling mediators regulating Egr1 expression specifically in proliferating vascular SMCs were investigated. Northern blot and Western blot analysis revealed a strong up-regulation of Egr1 within 2 hours of stimulation with PDGF-AB and FGF-2. These two potent SMC mitogens involved in neointima formation were used to stimulate vascular SMCs not only to delineate the regulators of Egr1 expression but also to identify additional key mediators of SMC proliferation. FGF-2 but not PDGF-AB led to a drastic reduction of desmin amount in proliferating SMCs, correlating closely with the phenotypic modulation of SMCs in vivo. Both growth factors triggered a dramatic increase in DNA-synthesis rate with a concomitant loss of p27 exp Kip1. Stimulation with PDGF-AB and FGF-2 triggered a rapid and transient activation of PDGFRβ and FGFR1 respectively, thus providing the basis for activation of down-stream targets. Analysis of an array of signalling pathways demonstrated a strong activation of the Ras-Raf-MEK-ERK cascade in response to both factors as measured by the level of phosphorylation of prominent members MEK, ERK1/2 and c-Myc. SAPK/JNK and p38, which also belong to the superfamily of MAP kinases, did not become activated following stimulation with either PDGF-AB or FGF-2. The analysis of various PKC isoforms identified PKCδ and PKCθ to be the key mediators of PDGF-AB- and FGF-2-induced mitogenesis in proliferating SMCs. Whereas PDGF-AB potently stimulated PKB/Akt with concomitant GSK3β phosphorylation, FGF-2-induced inactivation of GSK3β was independent of PKB/Akt. Specific inhibition in order to evaluate the contribution of individual pathways to Egr1 expression and vascular SMC proliferation revealed that inhibition of the Raf-MEK-ERK module by UO126 completely abolished DNA-synthesis and Egr1 expression without a compensation by alternative pathways. Surprisingly, inhibition of PI3K led to a switch to the mitogenic RafMEK-ERK signalling cascade which resulted in an augmented Egr1 expression. In conclusion, in porcine vascular SMCs, activation of the Ras-Raf-MEK-ERK signalling module appears to be the main prerequisite for Egr1 expression and DNA synthesis induction in response to PDGF-AB and FGF-2 whereas related kinases SAPK/JNK and p38 play no significant role. Inhibition of the PI3K-Akt cascade represents an alternative way to activate ERK1/2 and induce Egr1 expression. Whereas MEK is the central regulator of mitogenic effects in proliferating vascular SMCs, the PI3K-Akt pathway most likely exerts survival function. Inactivation of MEK by its specific inhibitors identified hyperphosphorylation as ayet unknown mechanism of kinase inhibition.
The objective of this study is the avifauna of the North American Green River Formation. Five new Green River bird species as well as several new specimens of already known species are described. * Galliformes: Gallinuloides wyomingensis EASTMAN 1900 A second specimen of the galliform Gallinuloides wyomingensis could be identified. Gallinuloides wyomingensis resembles closely Paraortygoides MAYR 1999, which is known from Messel and the London Clay. The new specimen exhibits characters such as a cup-like cotyla scapularis of the coracoid that clearly indicate that Gallinuloides is a stem-group representative of galliforms. * Eurypygidae: Eoeurypyga olsoni gen. et sp. nov. Eoeurypyga is the only fossil representative of the Eurypygidae. Eoeurypyga and the modern sunbittern Eurypyga helias share the typical long bill, the caudally situated neck and the elongated vertebrae cervicales. Additional synapomorph characters were found. The new species indicates a North American origin for the Eurypygidae. * Messelornithidae: Messelornis nearctica HESSE 1992 The original description of Messelornis nearctica was based on a single specimen. Ten new specimens, described in this study, reveal additional information. Messelornis nearctica shows the same large intraspecific size range as Messelornis cristata HESSE 1988 from Messel, the type species of the genus. * Apodidae: Wyomingcypselus pohli gen. nov. sp. nov. Wyomingcypselus pohli is the first described fossil apodiform bird for North American. Due to characters of the wing, especially the position of the processus musculi extensor metacarpi radialis, Wyomingcypselus is referrred to the Apodidae. * Trogoniformes: unnamed species The Green River birds include a poorly preserved, but apparently heterodactyl specimen, which also resembles trogons in overall appearance. * Primobucconidae: Primobucco mcgrewi BRODKORB 1970 Originally, Primobucco mcgrewi was only known from a partial skeleton consisting of the right wing. Three new specimens could be referred to the species. Primobucco mcgrewi clearly exhibits an anisodactyl foot, which makes the assignment to the zygodactyl Bucconidae highly doubtful. Instead, Primobucco mcgrewi is referrred to the Coraciiformes s.s. Thus, Primobucconidae are the first New World representatives of stem-group Coraciiformes. * ?Leptosomidae: Plesiocathartes wyomingensis sp. nov. and Plesiocathartes major sp. nov. Plesiocathartes wyomingensis and Plesiocathartes major represent the first North American record for the genus. Both species exhibit the diagnostic characters for the Leptosomidae as listed by MAYR (2002a, b). * Primoscenidae: Eozygodactylus americanus gen. et sp. nov. and unnamed species Eozygodactylus americanus is the first North American member of this taxon. Both Eozygodactylus americanus and the unnamed species show the zygodactyl foot and the large processus intermetacarpalis of the carpometacarpus, which are typical for Primoscendiae. Due to differences mainly of the humerus, it was placed in a new genus. Besides the descriptionof new species, the avifauna of the Green River Formatin was studied and compared with the avifauna of Messel. The formations show a high concordance, more than 60 % of the Green River taxa also occur in Messel. Such a high concordance is also found for mammals. This is due to the existence of two landbridges, the Thule landbridge and the de Geer landbridge, between Europe and North America during the early Eocene.
In contrast to the class A heat stress transcription factors (Hsfs) of plants, a considerable number of Hsfs assigned to classes B and C have no evident function as transcription activators on their own. In the course of my PhD work I showed that tomato HsfB1, a heat stress induced member of class B Hsf family, is a novel type of transcriptional coactivator in plants. Together with class A Hsfs, e.g. tomato HsfA1, it plays an important role in efficient transcrition initiation during heat stress by forming a type of enhanceosome on fragments of Hsp promoter. Characterization of promoter architecture of hsp promoters led to the identification of novel, complex heat stress element (HSE) clusters, which are required for optimal synergistic interactions of HsfA1 and HsfB1. In addition, HsfB1 showed synergistic activation of the expression of a subset of viral and house keeping promoters. CaMV35S promoter, the most widely expressed constitutive promoter turned out to be the the most interesting candidate to study this effect in detail. Because, for most house-keeping promoters tested during this study, the activators responsible for constitutive expression are not known, but in case of CaMV35S promoter they are quite well known (the bZip proteins, TGA1/2). These proteins belong to the acidic activators, similar to class A Hsfs. Actually, on heat stress inducible promoters HsfA1 or other class A Hsfs are the synergistic partners of HsfB1, whereas on house-keeping or viral promoters, HsfB1 shows synergistic transcriptional activation in cooperation with the promoter specific acidic activators, e.g. with TGA proteins on 35S promoter. In agreement with this the binding sites for HsfB1 were identified in both house-keeping and 35S promoter. It has been suggested during this study that HsfB1 acts in the maintenance of transcription of a sub-set of house-keeping and viral genes during heat stress. The coactivator function of HsfB1 depends on a single lysine residue in the GRGK motif in its CTD. Since, this motif is highly conserved among histones as the acetylation motif, especially in histones H2A and H4,. It was suggested that the GRGK motif acts as a recruitment motif, and together with the other acidic activator is responsible for corecruitment of a histone acetyl transferase (HAT). So, the effect of mammalian CBP (a well known HAT) and its plant orthologs (HAC1) was tested on the stimulation of synergistic reporter gene activation obtained with HsfA1 and HsfB1. Both in plant and mammalian cells, CBP/HAC1 further stimulated the HsfA1/B1 synergistic effect. Corecruitment of HAC1 was proven by in vitro pull down assays, where the NTD of HAC1 interacted specifically both with HsfA1 and HsfB1. Formation of a ternary complex between HsfA1, HsfB1 and CBP/HAC1 was shown via coimmunoprecipitation and electrophoretic mobility shift assays (EMSA). In conclusion, the work presented in my thesis presents a new model for transcriptional regulation during an ongoing heat stress.
In an attempt to search for potential candidate molecules involved in the pathogenesis of endometriosis, a novel 2910 bp cDNA encoding a putative 411 amino acid protein, shrew-1 was discovered. By computational analysis it was predicted to be an integral membrane protein with an outside-in transmembrane domain but no homology with any known protein or domain could be identified. Antibodies raised against the putative open-reading frame peptide of shrew-1 labelled a protein of ca. 48 kDa in extracts of shrew-1 mRNA positive tissues and also detected ectopically expressed shrew-1. In the course of my PhD work, I confirmed the prediction that shrew-1 is indeed a transmembrane protein, by expressing epitope-tagged shrew-1 in epithelial cells and analysing the transfected cells by surface biotinylation and immunoblots. Additionally, I could show that shrew-1 is able to target to E-cadherin-mediated adherens junctions and interacts with the E-cadherin-catenin complex in polarised MCF7 and MDCK cells, but not with the N-cadherin-catenin complex in non-polarised epithelial cells. A direct interaction of shrew-1 with beta-catenin could be shown in an in vitro pull-down assay. From this data, it could be assumed that shrew-1 might play a role in the function and/or regulation of the dynamics of E-cadherin-mediated junctional complexes. In the next part of my thesis, I showed that stable overexpression of shrew-1 in normal MDCK cells. causes changes in morphology of the cells and turns them invasive. Furthermore, transcription by ²-catenin was activated in these MDCK cells stably overexpressing shrew-1. It was probably the imbalance of shrew-1 protein at the adherens junctions that led to the misregulation of adherens junctions associated proteins, i.e. E-cadherin and beta-catenin. Caveolin-1 is another integral membrane protein that forms complexes with Ecadherin- beta-catenin complexes and also plays a role in the endocytosis of E-cadherin during junctional disruption. By immunofluorescence and biochemical studies, caveolin-1 was identified as another interacting partner of shrew-1. However, the functional relevance of this interaction is still not clear. In conclusion, it can be said that shrew-1 interacts with the key players of invasion and metastasis, E-cadherin and caveolin-1, suggesting its possible role in these processes and making it an interesting candidate to unravel other unknown mechanisms involved in the complex process of invasion.
Remodeling of extracellular matrix (ECM) is an important physiologic feature of normal growth and development. In addition to this critical function in physiology many diseases have been associated with an imbalance of ECM synthesis and degradation. In the kidney, dysregulation of ECM turnover can lead to interstitial fibrosis, and glomerulosclerosis. The major physiologic regulators of ECM degradation in the glomerulus are the large family of zinc-dependent proteases, collectively refered to matrix metalloproteinases (MMPs). The tight regulation of most of these proteases is accomplished by different mechanisms, including the regulation of MMP gene expression, the processing and conversion of the inactive zymogen by other proteases such as serine proteases and finally the inhibition of active MMPs by endogenous inhibitors of MMPs, denoted as tissue inhibitors of metalloproteinases (TIMPs). Namely, the MMP-9 has been shown to be critically involved in the dysregulation of ECM turnover associated with severe pathologic conditions such as rheumatoid arthritis or fibrosis of lung, skin and kidney. In the present work I searched for a possible modulation of MMP-9 expression and/or activity in glomerular mesangial cells which are thought as key players of many inflammatory and non-inflammatory glomerular diseases. I found that various structurally different PPARalpha agonists such as WY-14,643, LY-171883 and fibrates potently suppress the cytokine-induced MMP-9 expression in renal MC. Furthermore, I demonstrate that the inhibition of MMP-9 expression by PPARalpha agonists was paralleled by a strong increase of cytokine-induced iNOS expression and subsequent NO formation, suggesting that PPARalpha-dependent effects on MMP-9 expression level primarily result from alterations in NO production which in turn reduces the MMP-9 mRNA half-life. Searching for the detailed mechanism of NO-dependent effects on MMP-9 mRNA stability, I found that NO either given from exogenous sources or endogenously produced increases the MMP-9 mRNA degradation by decreasing the expression of the mRNA stabilizing factor HuR. Furthermore, I demonstrate a reduction in the RNA-binding capacity of HuR containing complexes to MMP-9 ARE motifs in cells treated with NO. Since the reduction of HuR expression can be mimicked by the cGMP analog 8-Bromo-cGMP, I suggest that NO reduces in a cGMP-dependent manner the expression of HuR. Finally, I elucidated the modulatory effect of extracellular nucleotides, mainly ATP, on cytokine-triggered MMP-9 expression. Interestingly, I found that in contrast to NO, gamma-S-ATP the stable analog of ATP potently amplifies the IL-beta mediated MMP-9 expression. The increase in mRNA stability was paralleled by an increase in the nuclear-cytosolic shuttling of the mRNA stabilizing factor HuR. Furthermore, I demonstrate an increase in the RNA-binding capacity of HuR containing complexes to the 3'-UTR of MMP-9 by ATP. In summary, the data presented here may help to find new targets (posttranscriptional regulation) that could be used to manipulate or modulate the expression of not only MMP-9 but also other genes regulated on the level of mRNA stability.
In this thesis the anti-proton to proton ratio in 197Au + 197Au collisions, measured at mid-rapidity, at a center of mass energy of psNN = 200GeV is reported. The value was measured to be ¹p/p = 0.81+-0.002stat +- 0.05syst: in the 5% most central collisions. The ratio shows no dependence on rapidity in the range jyj < 0:5. Furthermore, a dependence on transverse momentum within 0:4< p? < 1:0 GeV/c is not observed. At higher p?, a slight drop in the ratio is observed. In the present analysis, the highest momentum considered is p? = 4:5 GeV/c yielding ¹p=p = 0:645§0:005stat: §0:10syst:. However, the systematic error is higher in this momentum range. A slight centrality dependence was observed, where a decrease from ¹p=p = 0:83§0:002stat:§0:05syst: for most peripheral collisions (less than 80% central) to ¹p=p = 0:78§0:002stat:§0:05syst: for the 5% most central collisions was measured. An estimate of the feed-down contributions fromthe decay of heavier strange baryons results in ¹p=p = 0:77 § 0:05syst:. The measured ratio indicates a » 12:5 times higher value compared to the highest SPS energy of psNN = 17:3 and an \almost net-baryon free" region, at mid- rapidity. The asymmetry of protons and anti-protons may be explained by the contribution ofvalence quarks in a nucleus break-up picture. In such a scenario, the absolute value of the ratio and the fact that the ratio does not depend on rapidity (at mid-rapidity) is well reproduced. Fragmentation of quarks and anti- quarks into protons and anti-protons is assumed. An estimate of the ratio, when feed-down correction is taken into consideration, agrees well with the prediction of a statistical model analysis at a temperature of T = 177 § 7 MeV and a baryon chemical potential of ¹B = 29 § 8 MeV. The temperature achieved is only slightly higher when compared to the top SPS energy, while the baryochemical potential is factor »10 lower. As in the case of the SPS results, these parameters are close to the phase boundary of Figure 1.6. The measurement of the ratio at high transverse momentum was of special in- terest in this analysis, since at RHIC energies, the cross section for hadrons at high transverse momentum is increased with respect to SPS energies. The weak dependence of the ratio on the transverse momentum is well described by the non- perturbative quenched and baryon junction scenario (i.e. Soft+Quench model), where baryon creation is enhanced by baryon junctions. In comparison the ratio does not decrease within the considered momentum range as predicted by pQCD.
Der Produktion von Interleukin-8 (IL-8), Hämoxygenase-1 (HO-1), und dem vaskulären endothelialen Wachstumsfaktor (VEGF) wird zunehmend größere Bedeutung im Rahmen der Regulation der Immunantwort bei Entzündung, Infektion und Tumorwachstum zugemessen. Ziel dieser Arbeit war die Untersuchung der Regulation dieser Botenstoffe in vitro durch Verwendung der humanen Dickdarmkarzinomzellinie DLD-1. Die Substanz Pyrrolidinedithiocarbamate (PDTC) verstärkt nicht nur die durch Tumornekrosefaktor-a (TNF-a) vermittelte Ausschüttung von IL-8, sondern induziert auch als alleiniger Stimulus die IL-8-Sekretion. Mutationsanalysen des IL-8-Promotors und "Electrophoretic Mobility Shift" Untersuchungen (EMSA) zeigten, daß die Aktivierung des Transkriptionsfaktors AP-1 (Aktivator Protein-1) und die Bindungsaktivität von konstitutiv aktiviertem NF-KB in DLD-1 Zellen für die PDTC induzierte IL-8 Expression zwingend erforderlich waren. Weiterhin war PDTC in der Lage in DLD-1 Zellen neben IL-8 auch die Expression von HO-1 und VEGF zu verstärken. Die Induktion von IL-8 durch PDTC war nicht nur auf DLD-1 Zellen beschränkt, sondern wurde auch in Caco-2 Zellen (ebenfalls Dickdarmkrebszellen) und in humanen mononukleären Blutzellen beobachtet. Die Verwendung von PDTC wird seit kurzem als Kombinationspräparat für Zytostatia zur Behandlung von verschiedenen bösartigen Tumoren, unter ihnen auch Darmkrebs, vorgeschlagen. Aus unseren Versuchen läßt sich ableiten, daß die Induktion von IL-8, HO-1 und VEGF die therapeutische Anwendung dieser Substanz nachteilig beeinflussen könnte. Dies ergibt sich daraus, daß alle drei genannten Faktoren durch proangiogene Wirkungen das Tumorwachstum fördern. Die Expression der induzierbaren Stickoxidsynthase und die Produktion von Stickoxid (NO) korreliert mit der Angiogenese bei verschiedenen Krebserkrankungen darunter Melanome, Tumore im Hals- und Kopfbereich und Darmkrebs. Da tumorbegünstigende Funktionen von NO mit vermehrter Angiogenese in Verbindung gebracht werden, wurden die Effekte von NO hinsichtlich der Produktion von ausgesuchten Chemokinen, die an der Steuerung des Tumorwachstums beteiligt sind, untersucht. Zu diesen Chemokinen gehören das proangiogene IL-8 sowie das tumorsuppressiv durch Interferon induzierbare Protein-10 (IP-10) und das Monokin induziert durch Interferon-y (MIG). Diese Chemokine werden, nach Stimulation mit IL- 1ß und lnterferon-? (IFN-?) von DLD-1 Zellen, ausgeschüttet. Unter diesen Bedingungen wird die IL-8 Freisetzung alleine durch IL-1ß vermittelt, aber nicht durch INFy. Im Gegensatz zu IL-8 hängt die Sekretion von IP-10 und MIG von der Aktivierung durch IFNy ab. Die Effekte von NO wurden analysiert indem DLD-1 Zellen mit dem NO-Donor DETA-NO inkubiert wurden. DETA-NO besitzt eine Halbwertzeit von 16,5h und simuliert damit die Effekte der endogenen NO-Synthase. Synthese und Freisetzung von IL-8 wurden durch die Behandlung mit NO stark gesteigert. Außerdem wurde in Zellen die dem NO-Donor ausgesetzt wurden die basale Sekretion des VEGF signifikant verstärkt. Dies steht im Gegensatz zur IL-Iß/IFNy-induzierten Produktion von IP-10 und MIG, beide wurden durch Koinkubation mit NO unterdrückt. Ebenso wurde die Regulation der IFNy abhängigen induzierbaren Stickoxidsynthase in DLD-1 Zellen von NO unterdrückt. Die vorliegenden Daten ergänzen vorherige Studien, in denen NO mit Tumorangiogenese und verstärkten Tumorwachstum in Verbindung gebracht wird. Die NO vermittelte Induktion von IL-8 und VEGF, ebenso wie die Verminderung der IP-10 and MIG Expression, könnte zu diesem Phänomen beitragen. Unsere Studien stützen die Hypothese, daß spezifische lnhibitoren der iNOS therapeutischen Nutzen bei humanen Neoplasien haben könnten.
Cytochrome c oxidase is the terminal enzyme in the respiratory chain of mitochondria and aerobic bacteria. This enzyme ultimately couples electron transfer from cytochrome c to an oxygen molecule with proton translocation across the inner mitochondrial and bacterial membrane. This reaction requires complicated chemical processes to occur at the catalytic site of the enzyme in coordination with proton translocation, the exact mechanism of which is not known at present. The mechanisms underlying oxygen activation, electron transfer and coupling of electron transfer to proton translocation are the main questions in the field of bioenergetics. The major goal of this work was to investigate the coupling of electron transfer and proton translocation in cytochrome c oxidase from Paracoccus denitrificans. Different theoretical approaches have been used to investigate the coupling of electron and proton transfer. This thesis presents an internal water prediction scheme in the enzyme and a molecular dynamics study of cytochrome c oxidase from Paracoccus denitrificans in the fully oxidized state, embedded in a fully hydrated dimyristoylphosphatidylcholine lipid bilayer membrane. Two parallel molecular dynamics simulations with different levels of protein hydration, 1.125 ns each in length, were carried out under conditions of constant temperature and pressure using three-dimensional periodic boundary conditions and full electrostatics to investigate the distribution and dynamics of water molecules and their corresponding hydrogen-bonded networks inside cytochrome c oxidase. The average number of solvent sites in the proton conducting K- and D- pathways was determined. The highly fluctuating hydrogen-bonded networks, combined with the significant diffusion of individual water molecules provide a basis for the transfer of protons in cytochrome c oxidase, therefore leading to a better understanding of the mechanism of proton pumping. The importance of the hydrogen bonding network and the possible coupling of local structural changes to larger scale changes in the cytochrome c oxidase during the catalytic cycle have been shown.