Die vorliegende Arbeit wurde im Rahmen einer kooperativen Promotion zwischen der TU Dresden und der Hochschule Mittweida angefertigt. In dieser werden neuartige, computerorientierte Ansätze für die Analyse von Membranproteinen vorgestellt. Membranproteine sind von essentieller Bedeutung für eine Vielzahl biologischer Prozesse innerhalb eines Organismus und stellen wichtige Zielmoleküle für eine breite Palette von Pharmazeutika dar. Ihre Sequenzen liefern wertvolle und teilweise noch nicht entschlüsselte Informationen über die dreidimensionale Struktur und funktionale Eigenschaften. Innerhalb der Proteomik und Genomik stellen Analysen an Membranproteinstrukturen einen wichtigen Teil für das Verständnis komplexer biologischer Prozesse dar. Im Zuge von Untersuchungen an Membranproteinen konnte eine Vielzahl kurzer wiederkehrender Muster, sogenannte Motive, in den Sequenzen von Membranproteinen beobachtet werden. Diese Motive unterstützen das Verständnis, wie sich Membranproteine in der Zellmembran falten. Im Fokus dieser Arbeit stehen derartige Sequenzmotive. Innerhalb von drei Projekten bilden ausschließlich sequenzmotivbasierte Ansätze die Grundlage für nähere Untersuchungen an Membranproteinstrukturen. Letztendlich liefern die in dieser Arbeit postulierten Methoden wertvolle Erkenntnisse über die strukturelle und funktionelle Rolle von Sequenzmotiven, auf deren Grundlage dazu beigetragen wird, den komplexen Aufbau von Membranproteinen besser verstehen zu können. Generell wird die Zusammenführung proteomischer und mutagener Informationen intensiviert. Nicht zuletzt wird dazu beigetragen, die in dieser Arbeit zusammengetragenen Ergebnisse, für die Planung von in vitro Experimenten sowie weiterführenden Arbeiten auf dem Gebiet der Membranproteinanalyse, der Wissenschaft zur Verfügung zu stellen. / The present work was written as part of a cooperative doctorate between the TU Dresden and the University of Applied Sciences Mittweida. In the doctoral thesis, novel, computer-oriented approaches for the analysis of membrane proteins are presented. Membrane proteins are essential for many cellular processes and are important targets for a wide range of pharmaceuticals. Their sequences provide valuable and partly not yet decoded information about their three-dimensional structure and functional characteristics. The analysis of membrane proteins is an important part for the understanding of complex biological processes in the context of proteomics and genomics. Research of membrane proteins revealed a large number of short, distinct sequence motifs. The motifs found so far support the understanding of the folded protein in the Membrane environment. In this dissertation, in three different approaches it is shown how the output of sequence motif-based methods can support the understanding of structural and functional properties of membrane proteins. In general, the junction of proteomic and mutagenic information is intensified. Last but not least, the results of this work are made available for the planning of in vitro experiments as well as for further works in the field of membrane Protein analysis.

No description available.

Several chlamydial antigens have been detected in the infected epithelial cell cytosol and on the host cell surface prior to their presumed natural release at the end of the 72-96 h developmental cycle. These extra-inclusion antigens are proposed to influence vital host cell functions, antigen trafficking and presentation and, ultimately, contribute to a prolonged inflammatory response. To begin to dissect the mechanisms for escape of these antigens from the chlamydial inclusion, which are enhanced on exposure to antibiotics, polarized endometrial epithelial cells (HEC-1B) were infected with Chlamydia trachomatis serovar E for 36 h or 48 h. Infected cells were then exposed to chemotactic human polymorphonuclear neutrophils not loaded or pre-loaded in vitro with the antibiotic azithromycin. Viewed by electron microscopy, the azithromycin-mediated killing of chlamydiae involved an increase in chlamydial outer membrane blebbing followed by the appearance of the blebs in larger vesicles (i) everting from but still associated with the inclusion as well as (ii) external to the inclusion. Evidence that the vesicles originated from the chlamydial inclusion membrane was shown by immuno-localization of inclusion membrane proteins A, F, and G on the vesicular membranes. Chlamydial heat shock protein 60 (chsp60) copies 2 and 3, but not copy 1, were released from RB and incorporated into the everted inclusion membrane vesicles and delivered to the infected cell surface. These data represent direct evidence for one mechanism of early antigen delivery, albeit membrane-bound, beyond the confines of the chlamydial inclusion.

Enterohemorrhagic E. coli (EHEC) has emerged as an important agent of diarrheal disease in the developed countries. Attachment to host cells, an essential step during intestinal colonization by EHEC, is associated with the formation of a highly organized cytoskeletal structure containing filamentous actin, termed attaching and effacing (A/E) lesion, directly beneath bound bacteria. The outer membrane protein, intimin, is required for the formation of this structure, as is Tir, a bacterial protein that is translocated into the host cell and thought to function as a receptor for intimin. In this thesis, we characterized A/E lesion formation by in vivo and in vitro-grown EHEC, aimed at testing whether bacterial adaptation to the mammalian host included up regulation of A/E lesion formation. Our results showed that actin signaling by EHEC was induced upon bacterial growth in vivo, and this induction was likely due to the up regulation of multiple activities by in vivo-grown EHEC. We also focused on the interaction between intimin and the host cell, an interaction that triggers actin condensation of A/E lesion formation. We evaluated the role of β1 integrins, one of the proposed receptors of intimin, in A/E lesion formation, and demonstrated that β1 integrins are not essential for intimin-mediated cell binding and actin condensation. To better understand intimin function, we mapped the functional domains of intimin, showed that the minimal cell binding domain of intimin correlates with the minimal Tir-binding domain. This minimal Tir-binding domain, when purified and coated on latex beads, was sufficient to trigger actin condensation on preinfected mammalian cells, suggesting that Tir-binding by intimin is critical in the final step of A/E lesion formation. To further demonstrate the significance of the interaction between intimin and Tir in A/E lesion formation, we developed a yeast two-hybrid system to identify intimin mutants diminished in Tir-binding, and then characterized those mutants for the ability to trigger actin condensation, the final step of A/E lesion formation. Finally, as a first step to study the downstream actin signaling pathway after Tir-binding, we mapped the domain of Tir involved in intimin-binding, and showed that the N-terminus and C-terminus of Tir are likely to be localized in the host cell cytoplasm, available to interact with downstream effectors in actin signaling.

The immune system is a complex network of cells and molecules that is a powerful and necessary defense mechanism to protect the host from pathogens. When this system is non-functional or dysregulated, the host is susceptible to takeover or attack against self, both with often lethal sequelae. Over the past century remarkable advances have been made in understanding how the immune system functions and how to manipulate this knowledge for human benefit. One strategy used to understand immune system function is to determine how the activity of immune system cells is modulated by the proteins these cells express on their surface. One rat T cell surface protein which was originally identified with antibodies almost two decades ago is the rat T cell alloantigen, RT6. During the intervening time enormous progress has been made in understanding the function of RT6+ T cells in normal and abnormal immune responses. In addition, during this time the characterization of RT6 genes, proteins, and homologues has occurred. One characterization of RT6 that is enigmatically missing is the function of this molecule. With this information it would be possible to determine how this molecule modulates T cell function. Therefore this project set out to begin to functionally characterize RT6 proteins. Part 1 of this project set out to determine if cell-surface RT6 proteins, like some other T cell surface proteins, could mediate T cell activation. Part 2 of this project was based on the recent observation that RT6 is homologous to NAD-catabolizing enzymes, and it was investigated whether RT6 proteins have ADP-ribosyltransferase activity. In Part 1 of this work it is demonstrated that cell-surface RT6 proteins are capable of delivering activation signals to T cells. Crosslinking cell-surface RT6 with antibodies potentiates the ability of PMA treated T cells to proliferate in response to the T cell growth factors IL-2 and/or IL-4. Crosslinking RT6 on these cells increases the surface expression of IL-2 receptors, suggesting that RT6-mediated signals selectively enhance growth factor receptor expression. This work also investigated the mechanism through which RT6 may deliver its signal. It is demonstrated that RT6 proteins are physically associated with five other proteins, including the src family tyrosine kinases p56lck and p60fyn. This work also suggests a novel mechanism to regulate T cell signaling by accessory molecules, since PKC activation causes qualitative and quantitative changes in the proteins physically associated with RT6. This work indicates that cell-surface RT6 is capable of delivering an accessory T cell activation signal. Therefore, RT6 proteins may be involved in vivo with the activation and proliferation of RT6+ T cells. Previous work in another laboratory has demonstrated that the RT6.2 protein possesses NAD glycohydrolase activity and indicated that RT6 proteins share overall sequence homology with ADP-ribosyltransferases. In Part 2 of this work, RT6 proteins are shown to possess NAD:arginine ADP-ribosyltransferase activity. ADP-ribosylation of proteins is a modification known to affect cell signaling and function. It is further demonstrated in this work that the substrate for RT6, extracellular NAD, inhibits T cell proliferation in a dose- and stimulus-dependent manner. Taken together, these studies suggest that through their enzymatic activities RT6 proteins modulate T cell activity. This work is the first to demonstrate that RT6 has two, possibly separate, functional characteristics. RT6 can therefore be described as a bifunctional T cell surface protein. RT6+ T cells play critical roles in regulating immune system responses in health and disease. Because of these functional studies on RT6 proteins, it can now be investigated how RT6 proteins may modulate T cell responses in different immunological situations. Thus, this work will provide the foundation to determine if and how RT6 proteins modulate immune system function in health and disease.

Solid-state NMR (ssNMR) has matured into a versatile method to provide structural information, probe protein dynamics and detect small molecule binding and -protein interaction of a variety of biomolecular assemblies including amyloid fibrils, viral particles and membrane proteins. Membrane proteins embedded in liposomes are natural targets for ssNMR as their native states are solids. Magic angle spinning (MAS) ssNMR studies using moderate spinning frequencies provide detailed structural information and probe subtle conformational change. Development of fast magic angle spinning ssNMR enables proton-detection which increases sensitivity and facilitates protein dynamics measurements. In this dissertation, we applied moderate and fast MAS ssNMR to study potassium ion channel and protein dynamics Chapter 1 will introduce concepts and theory of solid-state NMR pulse sequences and experiments. Chapter 2 will discuss the application and perspectives of solid-state NMR to membrane protein systems. In Chapter 3, we test an allostery mechanism for inactivation using a KcsA mutant (H25R/E118A) that exhibits an open pH gate across a broad range of pH values. We present solid-state NMR measurements of this open mutant at neutral pH to probe the affinity for potassium at the selectivity filter. This result strongly supports our assertion that the open pH gate allosterically affects the potassium binding affinity of the selectivity filter. In this mutant the protonation state of a glutamate residue (E120) in the pH sensor is sensitive to potassium binding, suggesting that this mutant also has flexibility in the activation gate and is subject to transmembrane allostery. In Chapter 4, I optimize protein expression, purification and reconstitution into native environment protocols of a bacterial potassium transporter, KtrB. In chapter 5, methods and experimental details of setting up 60 and 40 kHz fast MAS ssNMR are discussed. With fast MAS ssNMR setup, multidimensional NMR experiments with higher sensitivity could be collected on a perdeuterated sample with less sample mass required. In Chapter 6, we employ fast MAS ssNMR to measure bulk and residue site-specific 15N and carbonyl 13C relaxation of microcrystalline ubiquitin. Carbonyl R1ρ relaxation profiles provide additional information on protein backbone dynamics.

No description available.

No description available.

Transmembrane protein 59 (tmem59) is a gene that encodes a protein involved in autophagy and apoptosis in human. A previous study in zebrafish showed that tmem59 mRNA was several folds higher in thrombocytes than those found in red blood cells (RBCs). Therefore, we hypothesized that tmem59 has a role in thrombocytes function. We injected a hybrid of control vivo-morpholino (cVMO) and tmem59 specific antisense standard oligonucleotide (tmem59SO) into adult zebrafish to knockdown tmem59.This piggyback knockdown approach resulted in fish that had more bleeding in gill bleeding assay than the control fish. The thrombocytes fromtmem59 knockdown zebrafish aggregated faster with ADP and collagen agonists. Also, the number of blood cells was reduced after the knockdown of tmem59. We also found the effects of MS-222 anesthesia on hemostasis and found that the bleeding was reduced yielding less blood and the blood cell counts increased probably due to vasoconstriction of the blood vessels. In summary, we found tmem59 is a negative regulator of hemostasis and inferred that anesthesia should be avoided in hemostasis studies.

Mutations in the gene encoding the nuclear lamina protein lamin A/C (LMNA) and the associated integral inner nuclear membrane protein emerin (EMD) give rise to similar disease phenotypes and are both classified as Emery-Dreifuss muscular dystrophy (EDMD). However, the connection between the function of these nuclear envelope proteins and disease phenotype remains elusive. Given the consistent manifestation of dilated cardiomyopathy in EDMD, my investigation focused on deciphering the roles of these nuclear envelope proteins in the heart. To better understand their functions, I generated a set of isogenic human induced pluripotent stem cell (iPSC) lines with either LMNA mutation causing lamin A/C haploinsufficiency or EMD mutation causing emerin deficiency. I differentiated these iPSCs into cardiomyocytes (iPSC-CMs) and obtained their RNA transcript and protein expression profiles. I found that both mutant lines exhibited significant overlap in transcriptome and proteome changes. Analyzing alterations at both RNA and protein levels shed light on the potential functional roles of lamin A/C and emerin in cardiomyocytes and pathogenic mechanisms. To better understand the cardiac defects caused by loss of lamin A/C. I generated mice lines with tissue-specific and temporally regulated knockout of Lmna in the heart. The mutant mice experienced lethality due to heart failure, regardless of whether Lmna was knocked out at the embryonic or mature adult heart. This demonstrates that lamin A/C has a vital role in the normal function of cardiomyocytes.