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Ductal adenocarcinomas of the pancreas are the 4th most common cause of cancer death. The 1 and 5 year survival rates for all stages combined are currently 26% and 5% respectively. Median survival is less than 6 months. Despite remarkable progress in the fields of genetics, cancer biology, and advances in surgical techniques as well as chemotherapeutics, our ability to recognize and treat patients with pancreatic cancer remains poor. GPCR signaling modules have been increasingly implicated in the genesis and progression of pancreatic cancers. Aberrant agonist production, receptor expression and dysfunctional signaling resulting from genomic instability in a background of a heterotopic tumor-stromal microenvironment, contribute to the initiation, progression, and eventual metastasis of the disease. Numerous GPCR agonists, including lysophosphatidic acid (LPA), along with their cognate receptors have been implicated in this oncogenic process. LPA, one of the simplest bioactive lipids, has been shown to be a potent stimulant of metastatic behavior in in vitro models. It also acts as a mitogen by inducing proliferation and cell survival pathways in various normal and transformed cell lines. In patients with pancreatic cancer both the receptors and ligand have been found to be overexpressed. It has been noted that pancreatic cancer cell lines expressing higher levels of the LPA receptors present with greater motility. This has led to the hypothesis that LPA contributes to the progression of pancreatic cancer through the promotion of a metastatic phenotype. However, the underlying mechanisms have not been well described. LPA receptors have been shown to couple to the Gi, Gq, or G12 family of heterotrimeric G proteins. Consequently, signals transduced through these receptors have been shown to stimulate Gαi, Gαq, and Gα12/13 dependent pathways. While earlier studies have linked Gαi to LPA induced migration, there is recent evidence to suggest that Gα13 may provide a major signaling mechanism for LPA receptors stimulating migration in diverse cell types including cancer cell lines. Given the ominous nature of pancreatic cancers it is of critical importance to understand the mechanisms that promote more malignant phenotypes and to assess the role of Gα13 in this process. The goal of this thesis therefore is to define the role of Gα13 in LPA-mediated migration of pancreatic cancer cells. To assess the oncogenic potential of LPA and the role of Gα13 in stimulating the migration of pancreatic cancer cells, a panel of pancreatic cancer cell lines was assembled and characterized with regard to their expression of the LPA receptors as well as the Gα subunits of the heterotrimeric G proteins. These cell lines were further studied through a series of proliferation, wound healing, and transwell migration assays to assess the role of LPA in the induction of proliferation and migration in pancreatic cancer cells. The results demonstrated that LPA functions as a mitogen in certain pancreatic cancer cell lines, but is a potent stimulant of cell motility and invasive migration. Interestingly, these studies indicated that this response proceeds through routes that may not involve Gαi, as a potent migratory response was observed in MDAPanc28 cells which lack expression of the Gαi subunit. This was verified through the transwell assays conducted in the presence of PTX demonstrating that migration occurs independently of PTX sensitive mechanism and thus independently of Gαi.. Using a dominant negative mutant strategy, the studies presented in this thesis establishes the role of Gα13 in mediating LPA-LPAR stimulated migration of pancreatic cancer cells. Using pancreatic cancer cell lines that stably express the competitively inhibitory dominant negative mutant of Gα13, the ability of these mutants to inhibit a LPA mediated migratory response was monitored by wound-healing as well as transwell migration assays The results of these studies indicated a substantial attenuation of the migratory response and demonstrated for the first time the critical role of Gα13in LPA induced migration in a pancreatic cancer cell line. / Molecular Biology and Genetics

No / Most inhibitory signals are mediated via γ-aminobutyric acid (GABA) receptors whereas glutamate receptors mediate most excitatory signals (Trends Neurosci 14:515–519, 1991; Annu Rev Neurosci 17:31–108, 1994). Many factors influence the regulation of excitatory and inhibitory synaptic inputs on a given neuron. One important factor is the subtype of neurotransmitter receptor present not only at the correct location to receive the appropriate signals but also their abundance at synapses (Pharmacol Rev 51: 7–61, 1999; Cold Spring Harb Perspect Biol 3, 2011). GABAB receptors are G-protein-coupled receptors and different subunits dimerise to form a functional receptor. GABAB receptor subunits are widely expressed in the brain and by assembling different isoform combinations and accessory proteins they produce variety of physiological and pharmacological profiles in mediating both inhibitory and excitatory neurotransmission. This chapter will describe the understanding of the molecular mechanisms underlying GABAB receptor regulation of glutamate and GABAA receptors and how they modulate excitatory and inhibitory neurotransmission.

Proteins, as pivotal players in biological processes, undergo evolutionary changes due to mutations, whether spontaneous or induced by external factors. These mutations lead to significant genomic differences, contributing to the emergence of new species. From the basic principles of evolution, including variation, selection, fitness, inheritance, and reproduction, to the detailed analysis of specific proteins in different taxonomic groups, this dissertation explores the intricate field of protein evolution. In this thesis the study of bacterial and eukaryotic proteins is covered. It includes the study of enzymes in bacteria, such as CCA-adding enzyme and poly(A) polymerase, providing insights into the evolutionary divergence of these vital proteins. An analysis of existing species protein sequences and the prediction of corresponding ancestral sequences reveals a putative ancestral gammaproteobacterial CCA-adding enzyme, which is functional, thermotolerant and has a high specificity for CCA incorporation and substrate interactions. To address the challenges of suboptimal protein sequence data quality, the develop- ment of the ExceS-A split aligner is presented, which provides an automated solution to search for high quality protein sequences across diverse species groups. It is designed for exon-by-exon comparisons of coding sequences. The computation of exon/intron structure, inherent in spliced alignment procedures, is crucial for distinguishing paralo- gous members within gene families. The simplicity and effectiveness of this blat-based approach offer distinct advantages, especially for genes with extensive introns and applications involving fragmented genome assemblies, outperforming established tools in these scenarios. The application of the tool ExceS-A is then demonstrated in the study of neu- ropeptide Y/RFamide-like receptors in nematodes, shedding light on the evolutionary dynamics within this G protein-coupled receptor (GPCR) family. The Neuropeptide Y/RFamide-like receptors play crucial roles in locomotion, feeding, and reproduction. This extensively studied receptor group in Caenorhabditis elegans, comprising 41 recep- tors, served as a starting point for understanding the family’s expansion in nematodes. 159 nematode genomes revealed a total of 1557 neuropeptide Y/RFamide-like receptor sequences. The high conservation of these receptors across nematoda underscores their significance while highlighting family diversification in nematode evolution, with clade-specific duplications and losses across the phylum and unique patterns observed in the genus Caenorhabditis. Further, the dissertation focuses on the detailed analysis of GPCRs, with a particular interest in the ADRB2 and ADRB1 and Y1R and Y2R receptor, unraveling their conservation patterns and investigating their roles in G protein coupling. The investigation extends to the broader context of GPCR signaling pathways, emphasizing the crucial long-distance signaling and proposing hypotheses regarding amino acid conservation within chordates. Molecular dynamics simulations are used to uncover allosteric mechanisms and networks, providing valuable insights into protein dynamics and interactions. The investigation aimed at determining whether the conservation of amino acids within the chordate group is higher along the transmission pathway of GPCRs compared to the normal shortest path. Contrary to the hypothesis, results for ADRB2 and Y2R receptors, both with ligands and G-proteins, showed no significant difference in conservation rates between weighted and unweighted paths. Analysis revealed that unweighted paths favor hydrophobic interactions, while weighted paths predominantly involve peptide bonds, emphasizing their importance in allosteric signal transmission. Possible reasons for the lack of a significant increase in conservation values include the overall high conservation of amino acids in transmembrane helix 2-6 and the need for more precise information about mutual information in conservation score calculations. Future efforts will explore modified k-shortest path algorithms to identify alternative geometrically related contacts. The dissertation concludes by highlighting the crucial role of bioinformatics in performing complex analyses and processing large datasets. The basics laid here provide a foundation for interdisciplinary collaboration and contribute significant insights into the evolution of proteins. As a comprehensive knowledge framework, this work is able to guide future research efforts and underscores the ongoing importance of uncovering the complex interactions that govern protein evolution in the field of biological research.

Le remodelage cardiaque est le processus par lequel la structure ou la fonction cardiaque change en réponse à un déséquilibre pathophysiologique tel qu'une maladie cardiaque, un contexte d'arythmie prolongée ou une modification de l'équilibre hormonal. Le système rénine-angiotensine (SRA) est un système hormonal largement étudié et il est impliqué dans de nombreuses activités associées au remodelage cardiovasculaire. L’existence d'un système circulatoire couplé à un système de tissus locaux est une représentation classique, cependant de nouvelles données suggèrent un SRA indépendant et fonctionnellement actif à l'échelle cellulaire. La compréhension de l'activité intracellulaire du SRA pourrait mener à de nouvelles pistes thérapeutiques qui pourraient prévenir un remodelage cardiovasculaire défavorable. L'objectif de cette thèse était d'élucider le rôle du SRA intracellulaire dans les cellules cardiaques. Récemment, les récepteurs couplés aux protéines G (RCPG), les protéines G et leurs effecteurs ont été détectés sur des membranes intracellulaires, y compris sur la membrane nucléaire, et les concepts de RCPG intracellulaires fonctionnels sont en voie d'être acceptés comme une réalité. Nous avons dès lors fait l'hypothèse que la signalisation du SRA délimitant le noyau était impliquée dans le contrôle de l'expression des gènes cardiaques. Nous avons démontré la présence de récepteurs d'angiotensine de type-1 (AT1R) et de type-2 (AT2R) nucléaires dans les cardiomyocytes ventriculaires adultes et dans une fraction nucléaire purifiée de tissu cardiaque. Des quantités d'Ang II ont été détectées dans du lysat de cardiomyocytes et des microinjections d'Ang-II-FITC ont donné lieu à des liaisons préférentielles aux sites nucléaires. L'analyse transcriptionnelle prouve que la synthèse d'ARN de novo dans des noyaux isolés stimulés à l'Ang-II, et l'expression des ARNm de NF-κB étaient beaucoup plus importants lorsque les noyaux étaient exposés à de l'Ang II par rapport aux cardiomyocytes intacts. La stimulation des AT1R nucléaires a engendré une mobilisation de Ca2+ via les récepteurs de l'inositol trisphosphate (IP3R), et le blocage des IP3R a diminué la réponse transcriptionnelle. Les méthodes disponibles actuellement pour l'étude de la signalisation intracrine sont limitées aux méthodes indirectes. L'un des objectifs de cette thèse était de synthétiser et caractériser des analogues d'Ang-II cellule-perméants afin d’étudier spécifiquement dans les cellules intactes l'activité intracellulaire du SRA. Nous avons synthétisé et caractérisé pharmacologiquement des analogues photosensibles Ang-II encapsulée en incorporant un groupement 4,5-diméthoxy-2-nitrobenzyl (DMNB) photoclivable sur les sites actifs identifiés du peptide. Chacun des trois analogues d'Ang II encapsulée synthétisés et purifiés: [Tyr(DMNB)4]Ang-II, Ang-II-ODMNB et [Tyr(DMNB)4]Ang-II-ODMNB a montré une réduction par un facteur deux ou trois de l'affinité de liaison envers AT1R et AT2R dans les dosages par liaison compétitive et une activité réduite dans la contraction de l'aorte thoracique. La photostimulation de [Tyr(DMNB)4]Ang-II dans des cellules HEK a augmenté la phosphorylation d'ERK1/2 (via AT1R) et la production de cGMP (via AT2R) alors que dans les cardiomyocytes isolés elle générait une augmentation de Ca2+ nucléoplasmique et initiait la synthèse d'ARNr 18S et d'ARNm du NF-κB. Les fibroblastes sont les principaux générateurs de remodelage cardiaque structurel, et les fibroblastes auriculaires sont plus réactifs aux stimuli profibrotiques que les fibroblastes ventriculaires. Nous avons émis l'hypothèse que l’Ang-II intracellulaire et l'activation des AT1R et AT2R nucléaires associés contrôlaient les profils d'expression des gènes des fibroblastes via des systèmes de signalisation distincts et de ce fait jouaient un rôle majeur dans le développement de la fibrose cardiaque. Nous avons remarqué que les fibroblastes auriculaires expriment l’AT1R et l’AT2R nucléaire et l'Ang-II au niveau intracellulaire. L’expression d'AT1R nucléaire a été régulés positivement dans les cas d’insuffisance cardiaque (IC), tandis que l'AT2R nucléaire a été glycosylé post-traductionnellement. La machinerie protéique des protéines G, y compris Gαq/11, Gαi/3, et Gβ, a été observée dans des noyaux isolés de fibroblastes. AT1R et AT2R régulent l'initiation de la transcription du fibroblaste via les voies de transduction de signal d'IP3R et du NO. La photostimulation de [Tyr(DMNB)4]Ang-II dans une culture de fibroblastes auriculaire déclenche la libération de Ca2+ nucléoplasmique, la prolifération, et la synthèse et sécrétion de collagène qui ne sont pas inhibées par les bloqueurs d'AT1R et/ou AT2R extracellulaires. / Cardiac remodelling is the process by which cardiac structure and/or function change in response to pathophysiological imbalances such as hypertension, cardiac disease, prolonged arrhythmia or altered hormonal balance. The renin-angiotensin system (RAS) is an extensively studied hormonal system involved in numerous processes associated with cardiovascular remodelling. Classically viewed as a circulating and a local tissue system, emerging evidence suggests an independent and functionally active RAS within individual cells. Understanding intracellular RAS actions might lead to new therapeutic avenues that could prevent adverse cardiac remodelling. The purpose of this thesis was to elucidate the role of intracellular RAS in cardiac cells. Recently, G protein-coupled receptors (GPCRs), G proteins, and their downstream effectors have been detected on intracellular membranes, including the nuclear membrane, and the concept of functional intracellular GPCRs is slowly being accepted as a reality. We therefore hypothesized that nuclear-delimited angiotensin II (Ang-II) signalling is involved in controlling cardiac gene expression. We demonstrated the presence of nuclear angiotensin-type 1 (AT1R) and angiotensin-type 2 (AT2R) receptors in adult ventricular cardiomyocytes and in a purified nuclear preparation from cardiac tissue. Ang-II was detected in cardiomyocyte lysate and microinjected Ang-II-FITC preferentially bound to nuclear sites. Transcriptional analysis demonstrated that Ang-II enhanced de novo RNA synthesis in isolated nuclei and NF-κB mRNA expression was much greater when nuclei were exposed to Ang-II. Nuclear AT1R-stimulation produced Ca2+ mobilization via nuclear inositol 1,4,5-trisphosphate receptor (IP3R) Ca2+-channels, and IP3R-blockade attenuated the AT1R-mediated transcriptional responses in isolated nuclei. Current methods available to study intracrine RAS signalling are limited to indirect methodologies because of a lack of selective intracellularly-acting probes. An aim of this thesis was to synthesize and characterize cell-permeant Ang-II analogues to probe intracellular RAS action with spatial and temporal precision. Using solid-phase peptide technology we synthesized and pharmacologically characterized light-sensitive caged Ang-II analogues. This was achieved by incorporating a photocleavable 4,5-dimethoxy-2-nitrobenzyl (DMNB) moiety on sites of Ang-II responsible for receptor recognition and activation. All of the three synthesized and purified caged-Ang-II analogues: [Tyr(DMNB)4]Ang-II, Ang-II-ODMNB and [Tyr(DMNB)4]Ang-II-ODMNB, showed two-to-three orders of magnitude reduced binding affinity towards the AT1R and AT2R in competition binding assays and reduced potency in contraction assays using thoracic aorta. Photolysis of [Tyr(DMNB)4]Ang-II in HEK cells increased ERK1/2 phosphorylation (via AT1R) and cGMP production (via AT2R) whereas in isolated cardiomyocytes it induced an increase in nucleoplasmic Ca2+ and increased the abundance of 18S rRNA and NF-κB mRNA. Fibroblasts are the main drivers of cardiac structural remodelling. Atrial fibroblasts are more responsive to pro-fibrotic stimuli than ventricular fibroblasts. We hypothesized that intracellular Ang-II and associated nuclear AT1R and AT2R activation control fibroblast gene-expression patterns via discrete signalling systems and thereby play a key role in cardiac fibrosis. Atrial fibroblasts were found to express Ang-II, and nuclear AT1R and AT2R. The nuclear localisation of AT1R was increased in fibroblasts isolated from failing hearts whereas nuclear AT2R showed alterations in glycosylation. Heterotrimeric G protein subunits including Gαq/11, Gαi/3, and Gβ were observed in isolated fibroblast nuclei. AT1R and AT2R increased fibroblast transcription initiation via IP3R and NO signal transduction pathways, respectively. Photolysis of [Tyr(DMNB)4]Ang-II in cultured atrial fibroblasts induced an increase in nucleoplasmic Ca2+, proliferation, collagen synthesis and secretion that was not prevented by extracellular AT1R and/or AT2R blockers.

Mehrfach ungesättigte omega-3 Fettsäuren (n-3 PUFAs), wie Eicosapentaensäure (EPA) und Docosahexaensäure (DHA), schützen vor kardiovaskulären Erkrankungen, wie tödlichen Arrhythmien. In vitro Untersuchungen belegen, dass rekombinante Cytochrom P450 (CYP) Enzyme nicht nur die n-6 PUFA Arachidonsäure (AA), sondern auch die n-3 PUFAs EPA und DHA als alternative Substrate verwenden. Dabei entstehen bioaktive regio- und stereoisomere Epoxy- und Hydroxymetaboliten, CYP-Eicosanoide, die als sekundäre Botenstoffe bei der Regulation von Gefäß-, Nieren- und Herzfunktionen fungieren. Die genauen molekularen Mechanismen dieser Metabolite sind noch weitgehend unerforscht. In der vorliegenden Arbeit wurde zunächst der ernährungsbedingte Einfluss auf das endogene CYP-Eicosanoidprofil im Menschen untersucht. Die Ergebnisse der klinischen Studie zeigten, dass n-3 PUFAs auch in vivo alternative Substrate von CYP-Enzymen darstellen und wenn verfügbar sogar effektiver zu ihren Metaboliten umgesetzt wurden als AA. Als ein wichtiger Metabolit entsteht nach EPA/DHA-Supplementation 17,18-EEQ, welcher womöglich der eigentliche Vermittler der kardioprotektiven Effekte von n-3 PUFAs ist. Unter Verwendung eines etablierten Zellmodells mit spontan schlagenden neonatalen Rattenkardiomyozyten (NRKMs) wurde der anti-arrhythmische Effekte von 17,18-EEQ genauer untersucht. Der negativ chronotrope Effekt von EPA auf NRKMs wurde tatsächlich durch 17,18-EEQ vermittelt, insbesondere dem R,S-Enantiomer. Mittels Strukturfunktionsanalyse wurden synthetische Analoga mit gleicher Wirksamkeit wie dem 7,18-EEQ gefunden, wobei strikte strukturelle Merkmale für die biologische Funktion identifiziert wurden. Die Suche nach einem molekularen Ziel für CYP-Epoxyeicosanoide führte zu einem möglichen Rezeptorkandidaten, der hinsichtlich seiner Ligandenspezifität untersucht wurde. Dieser oder zukünftige andere Rezeptorkandidaten stellen ein mögliches neues zelluläres Ziel zur Behandlung kardialer Arrhythmien dar. / The n-3 polyunsaturated fatty acids (n-3 PUFAs) eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), protect from cardiovascular disease, especially from fetal arrhythmia. Moreover, in vitro studies proved that recombinant cytochrome P450 (CYP) enzymes not only accept the physiologically most important n-6 PUFA arachidonic acid (AA), but also EPA and DHA as alternative substrates, thereby generating regio- and stereospecific biologically active epoxy- and hydroxymetabolites, CYP-eicosanoids. These metabolites serve as second messengers regulating vascular, renal and cardiac function. The precise underlying molecular mechanisms are only partially understood and need further investigation. The first aim of the thesis was to show that the endogenous CYP-eicosanoid profile depends on the availability of the precursor fatty acids. The results of a clinical trial with 20 volunteers, show that n-3 PUFAs serve also in vivo as alternative CYP-dependent substrates and are even preferentially metabolized compared to AA. After EPA/DHA-supplementation 17,18 EEQ was generated as a major metabolite, potentially an important mediator of cardiovascular effects originally attributed to n-3 PUFAs. To test the anti-arrhythmic effect of EPA and 17,18-EEQ, an established cell model with neonatal rat cardiomyocytes (NRKMs) was used. The negative chronotropic effect of EPA was mimicked by 17,18-EEQ, attributed only to the R,S-enantiomer. A structure activity relationship study revealed synthetic analogs, exerting the same biological effect as 17,18-EEQ. Strict structural requirements were found for agonistic function, hinting at a specific interaction with cellular targets, like GPCRs. The search of a molecular target of CYP-eicosanoids led to a putative receptor, which was tested for ligand binding specificity. If the preliminary results on the ligand binding are confirmed in future experiments this receptor might be a novel target for the treatment of cardiac arrhythmia.

Rhodopsin ist als Sehpigment der Photorezeptorzellen einer der am aktivsten untersuchten GPCRs. Es besteht aus dem Apoprotein Opsin und dem inversen Agonisten 11-cis-Retinal. Der inaktivierende Ligand ist in der sieben Transmembran- Helix (TM)-Struktur des Rezeptors kovalent gebunden und muss durch Licht cis/trans-isomerisiert werden, um den Rezeptor zu aktivieren. Der aktivierte Rezep-tor katalysiert den Nukleotidaustausch im G-Protein und zerfällt innerhalb von Minuten in Opsin und all-trans-Retinal. Das visuelle Pigment wird dann durch erneute Beladung des Opsins mit 11-cis-Retinal wieder hergestellt. In der vorliegenden Arbeit wird die erfolgreiche Kristallisation des nativen Opsins aus der Stäbchenzelle der Rinderretina und die Bestimmung der Proteinstruktur bei 2.9 Å Auf-lösung dargestellt. Im Vergleich zur bekannten Struktur des inaktiven Rhodopsins zeigt Opsin deutliche Strukturänderungen in den konservierten E(D)RY und NPxxY(x)5,6F Regionen und in TM5-TM7. Auf der intrazellulären Seite ist TM6 ca. 6-7 Å nach außen gekippt, während die TM5 Helix verlängert und näher zu TM6 verschoben ist. Durch die strukturellen Änderungen, von denen einige einem aktiven GPCR Zustand zugeschrieben werden können, wird die leere Retinalbindungstasche reorganisiert, um zwei Öffnungen für Aus- und Eintritt von Retinal bereitzustellen. Die Struktur von Opsin liefert neue Erkenntnisse zur Bindung von hydrophoben Liganden an GPCRs, zur GPCR-Aktivierung und zur Signalübertragung auf das G-Protein. / Rhodopsin as the visual pigment in photoreceptor cells is one of the most actively studied GPCRs. It consists of the apoprotein opsin and the inverse agonist, 11-cis-retinal. The inactivating ligand is bound in the seven-transmembrane helix (TM) bundle and cis/trans-isomerized by light to activate the receptor. The active receptor state is capable of catalyzing nucleotide exchange in the G protein and decays within minutes into opsin and all-trans-retinal. The visual pigment is then restored by reloading opsin with new 11-cis-retinal. In the present work, the successful crystallization of native opsin from bovine retinal rod cells and determination of the protein structure to 2.9 Å resolution is presented. Compared with the known structure of inactive rhodopsin, opsin displays prominent structural changes in the conserved E(D)RY and NPxxY(x)5,6F regions and TM5-TM7. At the cytoplasmic side, TM6 is tilted outwards by 6-7 Å, whereas the helix structure of TM5 is more elongated and close to TM6. These structural changes, of which some are attributed to an active GPCR state, reorganize the empty retinal binding pocket to disclose two openings for exit and entry of retinal. The opsin structure thus sheds new light on binding of hydrophobic ligands to GPCRs, GPCR activation and signal transfer to the G protein.