Struktur- und Funktionsuntersuchungen des C 4-Dicarboxylat-Sensors DcuS von Escherichia coli

Das Zweikomponentensystem DcuSR reguliert die Expression der Gene der anaeroben Fumaratatmung in E. coli in Abhängigkeit von externen C4-Dicarbonsäuren. Die membranständige Histidinkinase DcuS detektiert den Reiz und leitet ihn über die Membran an den Responseregulaor DcuR weiter, der die Aktivität der Zielgene reguliert. Das Substratspektrum von DcuS wurde näher untersucht und strukturelle Eigenschaften der Substrate sowie ihre Affinität zu DcuS bestimmt. Es wird vermutet, dass Histidinkinasen im aktiven Zustand als Dimere oder höhere Oligomere vorliegen. Der Oligomerisierungszustand von DcuS in der Membran wurde mittels EPR-Spektroskopie untersucht. Es wurden funktionelle Cysteinmutanten von DcuS hergestellt, die nur an bestimmten Positionen der periplasmatischen Domäne Cysteinreste, aber sonst keine weiteren Cysteinreste, enthielten. Die Proteine wurden isoliert, über die Cysteinreste mit Nitroxiden markiert und in Liposomen rekonstituiert. Erste EPR-Messungen zeigten, dass rekonstituiertes DcuS in einem geordneten Zustand in der Membran vorliegt, der diskrete Abstände zwischen den Monomeren aufweist. Die Struktur von rekonstituiertem DcuS in der Membran soll durch Festkörper-NMR aufgeklärt werden. Ein geeignetes C-terminal verkürztes Konstrukt, DcuS-PD/PAS wurde zu diesem Zweck hergestellt. Das Protein ließ sich in hoher Reinheit isolieren und konnte wieder in Liposomen rekonstituiert werden. Vorbereitende NMR-Messungen zeigten, dass eine Strukturaufklärung an diesem Protein möglich ist. Weitere Strukturuntersuchungen werden zur Zeit durchgeführt.

Seismic performance of rooftop cooling towers in buildings

Negli ultimi anni la ricerca ha fatto grandi passi avanti riguardo ai metodi di progetto e realizzazione delle strutture portanti degli edifici, a tal punto da renderle fortemente sicure sotto tutti i punti di vista. La nuova frontiera della ricerca sta quindi virando su aspetti che non erano mai stati in primo piano finora: gli elementi non-strutturali. Considerati fino ad oggi semplicemente carico accessorio, ci si rende sempre più conto della loro capacità di influire sui comportamenti delle strutture e sulla sicurezza di chi le occupa. Da qui nasce l’esigenza di questo grande progetto chiamato BNCs (Building Non-structural Component System), ideato dall’Università della California - San Diego e sponsorizzato dalle maggiori industrie impegnate nel campo delle costruzioni. Questo progetto, a cui ho preso parte, ha effettuato test su tavola vibrante di un edificio di cinque piani in scala reale, completamente arredato ed allestito dei più svariati elementi non-strutturali. Lo scopo della tesi in questione, ovviamente, riguarda l’identificazione strutturale e la verifica della sicurezza di uno di questi elementi non-strutturali: precisamente la torre di raffreddamento posta sul tetto dell’edificio (del peso di circa 3 tonnellate). Partendo da una verifica delle regole e calcoli di progetto, si è passato ad una fase di test sismici ed ispezioni post-test della torre stessa, infine tramite l’analisi dei dati raccolti durante i test e si è arrivati alla stesura di conclusioni.

Der C 4-Dicarboxylat- und Citratsensor DcuS aus Escherichia coli - Signalerkennung und Regulation

Das Zweikomponentensystem DcuSR aus Escherichia coli reguliert in Abhängigkeit von C4-Dicarboxylaten die Expression der Gene der Fumaratatmung. Die Erkennung von C4-Dicarboxylaten erfolgt über die periplasmatische Domäne der Sensorkinase DcuS und führt zur Autophosphorylierung des konservierten Histidinrestes in der Kinasedomäne. Die Phosphatgruppe wird anschließend auf den Responseregulator DcuR übertragen und führt zur Induktion der Zielgene. Dazu gehören der Antiporter DcuB (dcuB), die anaerobe Fumarase B (fumB) und die Fumaratreduktase (frdABCD). DcuS detektiert neben C4-Dicarboxylaten auch Citrat über die periplasmatische Domäne. In dem nah verwandten Sensor CitA wird Citrat spezifisch über die drei Carboxyl- und die Hydroxylgruppe durch die Bindestellen C1, C2, C3 und H erkannt. DcuS benötigt für die Erkennung von C4-Dicarboxylaten und Citrat die gleichen Bindestellen. Die Citratbindung von DcuS ähnelte der von C4-Dicarboxylaten und unterschied sich von der Citraterkennung in CitA. DcuS konnte durch gerichtete Mutagenese der Bindungsstelle in Varianten überführt werden, die spezifisch für C4-Dicarboxylate (DcuSDC) oder Citrat (DcuSCit) waren. DcuSDC und DcuSCit hatten komplementäre Substratspezifitäten und reagierten entweder auf C4-Dicarboxylate oder auf Citrat (und Mesaconat). Citrat wurde vermutlich als C4-Dicarboxylat (mit einem Acetylrest) und somit über die gleichen Bindestellen wie C4-Dicarboxylate erkannt. Die Bindestellen C2 und C3 sind hoch konserviert und essentiell für die Bindung von zwei Carboxylgruppen von Citrat und C4-Dicarboxylaten. Die Stellen C1 und H werden vermutlich für koordinative Zwecke benötigt. Der Fumarat/Succinat-Antiporter DcuB hat neben der Transportaktivität eine regulatorische Aufgabe im DcuSR-System. Die Deletion von DcuB führte zur konstitutiven Expression der dcuB´-´lacZ Reportergenfusion und anderer DcuSR-regulierter Gene in Abwesenheit von C4-Dicarboxylaten. Die Effektor-unabhängige Expression setzte eine intakte periplasmatische Domäne von DcuS voraus und zeigte in Anwesenheit der spezifischen DcuS-Mutanten (DcuSDC, DcuSCit) eine geänderte Antwort. Die lässt vermuten, dass DcuB die regulatorischen Eigenschaften über eine direkte Wechselwirkung mit DcuS ausübt. Um den phosphorylierten Responseregulator DcuR-P in den Ursprungszustand zurückzuführen, muss dieser dephosphoryliert werden. Die bisher unbekannte Dephosphatase kann dabei entweder von dem Responseregulator, der Sensorkinase oder einem weiteren Protein stammen. DcuR verfügt über eine intrinsische Phosphataseaktivität, die durch den Sensor geringfügig stimuliert wurde.

Oligomerisation, localisation and interaction of the sensor histidine kinases DcuS and CitA in Escherichia coli

The two-component system DcuSR of Escherichia coli regulates gene expression of anaerobic fumarate respiration and aerobic C4-dicarboxylate uptake. C4-dicarboxylates and citrate are perceived by the periplasmic domain of the membrane-integral sensor histidine kinase DcuS. The signal is transduced across the membrane by phosphorylation of DcuS and of the response regulator DcuR, resulting in activation of DcuR and transcription of the target genes.rnIn this work, the oligomerisation of full-length DcuS was studied in vivo and in vitro. DcuS was genetically fused to derivatives of the green fluorescent protein (GFP), enabling fluorescence resonance energy transfer (FRET) measurements to detect protein-protein interactions in vivo. FRET measurements were also performed with purified His6-DcuS after labelling with fluorescent dyes and reconstitution into liposomes to study oligomerisation of DcuS in vitro. In vitro and in vivo fluorescence resonance energy transfer showed the presence of oligomeric DcuS in the membrane, which was independent of the presence of effector. Chemical crosslinking experiments allowed clear-cut evaluation of the oligomeric state of DcuS. The results showed that detergent-solubilised His6-DcuS was mainly monomeric and demonstrated the presence of tetrameric DcuS in proteoliposomes and in bacterial membranes.rnThe sensor histidine kinase CitA is part of the two-component system CitAB of E. coli, which is structurally related to DcuSR. CitAB regulates gene expression of citrate fermentation in response to external citrate. The sensor kinases DcuS and CitA were fused with an enhanced variant of the yellow fluorescent protein (YFP) and expressed in E. coli under the control of an arabinose-inducible promoter. The subcellular localisation of DcuS-YFP and CitA-YFP within the cell membrane was studied by means of confocal laser fluorescence microscopy. Both fusion proteins were found to accumulate at the cell poles. The polar accumulation was slightly increased in the presence of the stimulus fumarate or citrate, respectively, but independent of the expression level of the fusion proteins. Cell fractionation demonstrated that polar accumulation was not related to inclusion bodies formation. The degree of polar localisation of DcuS-YFP was similar to that of the well-characterised methyl-accepting chemotaxis proteins (MCPs), but independent of their presence. To enable further investigations on the function of the polar localisation of DcuS under physiological conditions, the sensor kinase was genetically fused to the flavin-based fluorescent protein Bs2 which shows fluorescence under aerobic and anaerobic conditions. The resulting dcuS-bs2 gene fusion was inserted into the chromosome of various E. coli strains.rnFurthermore, a protein-protein interaction between the related sensor histidine kinases DcuS and CitA, regulating common metabolic pathways, was detected via expression studies under anaerobic conditions in the presence of citrate and by in vivo FRET measurements.

The C-4-Dicarboxylate carriers DcuB and DctA of Escherichia coli: function as cosensors and topology

Das fakultativ anaerobe Enterobakterium Escherichia coli nutzt C4-Dicarboxylate sowohl unter aeroben als auch anaeroben Bedingungen als Kohlenstoff- und Energiequelle. Die Aufnahme der C4-Dicarboxylaten und die Energiekonservierung mittels Fumaratatmung wird durch das Zweikomponentensystem DcuSR reguliert. Die Sensorhistidinkinase DcuS und der nachgeschaltete Responseregulator DcuR aktivieren bei Verfügbarkeit von C4-Dicarboxylaten die Expression der Gene für den Succinat Transporter DctA, den anaeroben Fumarat/Succinat Antiporter DcuB, die Fumarase B sowie die Fumaratreduktase FrdABCD. Die Transportproteine DctA und DcuB wiederum regulieren die Expression der DcuSR-abhängigen Gene negativ. Fehlen von DctA oder DcuB resultiert bereits ohne Effektor in einer maximalen Expression von dctA bzw. dcuB. Durch gerichtete und ungerichtete Mutagenese wurde gezeigt, dass die Transportfunktion des Carriers DcuB unabhängig von seiner regulatorischen Funktion ist. DcuB kann daher als Cosensor des DcuSR Systems angesehen werden.rnUnter Verwendung von Reportergenfusionen von C-terminal verkürzten Konstrukten von DcuB mit der Alkalischen Phosphatase und der β-Galactosidase wurde die Topologie des Multitransmembranproteins DcuB bestimmt. Zusätzlich wurde die Zugänglichkeit bestimmter Aminosäurereste durch chemische Modifikation mit membran-durchlässigen und membran-undurchlässigen Thiolreagenzien untersucht. Die erhaltenen Ergebnisse deuten auf die Existenz eines tief in die Membran reichenden, hydrophilen Kanal hin, welcher zum Periplasma hin geöffnet ist. Mit Hilfe der Topologie-Studien, des Hydropathie-Blots und der Sekundärstruktur-Vorhersage wurde ein Modell des Carriers erstellt. DcuB besitzt kurze, periplasmatisch liegende Proteinenden, die durch 12 Transmembranhelices und zwei große hydrophile Schleifen jeweils zwischen TM VII/VIII und TM XI/XII verbunden sind. Die regulatorisch relevanten Reste K353, T396 und D398 befinden sich innerhalb von TM XI sowie auf der angrenzenden cytoplasmatischen Schleife XI-XII. Unter Berücksichtigung der strukturellen und funktionellen Aspekte wurde ein Regulationsmodell erstellt, welches die gemeinsam durch DcuB und DcuS kontrollierte C4-Dicarboxylat-abhängige Genexpression darstellt. rnDer Effekt von DctA und DcuSR auf die Expression einer dctA´-´lacZ Reportergenfusion und auf die aerobe C4-Dicarboxylat-Aufnahme wurde untersucht. In-vivo FRET-Messungen weisen auf eine direkte Wechselwirkung zwischen dem Carrier DctA und dem Sensor DcuS hin. Dieses Ergebnis stützt die Theorie der Regulation von DcuS durch C4-Dicarboxylate und durch die Cosensoren DctA bzw. DcuB mittels direkter Protein-Protein Interaktion.rn

Bioinspired fabrication of biosilica-based bone substitution materials

Until today, autogenic bone grafts from various donor regions represent the gold standard in the field of bone reconstruction, providing both osteoinductive and osteoconductive characteristics. However, due to low availability and a disequilibrium between supply and demand, the risk of disease transfer and morbidity, usually associated with autogeneic bone grafts, the development of biomimic materials with structural and chemical properties similar to those of natural bone have been extensively studied. So far,rnonly a few synthetic materials, so far, have met these criteria, displaying properties that allow an optimal bone reconstitution. Biosilica is formed enzymatically under physiological-relevant conditions (temperature and pH) via silicatein (silica protein), an enzyme that was isolated from siliceous sponges, cloned, and prepared in a recombinant way, retaining its catalytic activity. It is biocompatible, has some unique mechanical characteristics, and comprises significant osteoinductive activity.rnTo explore the application of biosilica in the fields of regenerative medicine,rnsilicatein was encapsulated, together with its substrate sodium metasilicate, into poly(D,L-lactide)/polyvinylpyrrolidone(PVP)-based microspheres, using w/o/wrnmethodology with solvent casting and termed Poly(D,L-lactide)-silicatein silicacontaining-microspheres [PLASSM]. Both silicatein encapsulation efficiency (40%) and catalytic activity retention upon polymer encapsulation were enhanced by addition of an essential pre-emulsifying step using PVP. Furthermore, the metabolic stability, cytoxicity as well as the kinetics of silicatein release from the PLASSM were studied under biomimetic conditions, using simulated body fluid. As a solid support for PLASSM, a polyvinylpyrrolidone/starch/Na2HPO4-based matrix (termed plastic-like filler matrix containing silicic acid [PMSA]) was developed and its chemical and physical properties determined. Moreover, due to the non-toxicity and bioinactivity of the PMSA, it is suggested that PMSA acts as osteoconductive material. Both components, PLASSM and PMSA, when added together, form arnbifunctional 2-component implant material, that is (i)non-toxic(biocompatible), (ii)moldable, (iii) self-hardening at a controlled and clinically suitable rate to allows a tight insertion into any bone defect (iv) biodegradable, (v)forms a porous material upon exposure to body biomimetic conditions, and (vi)displays both osteoinductive (silicatein)and osteoconductive (PMSA) properties.rnPreliminary in vivo experiments were carried out with rabbit femurs, by creatingrnartificial bone defects that were subsequently treated with the bifunctional 2-component implant material. After 9 weeks of implantation, both computed tomography (CT) and morphological analyses showed complete resorption of the implanted material, concurrent with complete bone regeneration. The given data can be considered as a significant contribution to the successful introduction of biosilica-based implants into the field of bone substitution surgery.

Funktion der C 4-Dicarboxylat-Transporter DctA und DcuB als Co-Sensoren von DcuS in Escherichia coli

Escherichia coli kann C4-Dicarboxylate sowohl unter aeroben als auch unter anaeroben Bedingungen zur Energiekonservierung nutzen. Die Synthese der beteiligten Transporter und Enzyme wird auf der Transkriptionsebene durch das Zweikomponentensystem DcuSR reguliert. DcuS ist der Sensor für C4-Dicarboxylate. Der Antwortregulator DcuR wird von DcuS aktiviert und induziert die Expression des C4-Dicarboxylat-Transporters DctA unter aeroben Verhältnissen. Anaerob verstärkt DcuSR die Expression des Fumarat/Succinat-Antiporters DcuB, der Fumarase B und der Fumaratreduktase FrdABCD. DctA und DcuB agieren als Co-Sensoren von DcuS und üben einen negativen Effekt auf die Genexpression von dctA bzw. dcuB aus.rnIn dieser Arbeit wurde die Funktion von DctA und DcuB als Co-Sensoren von DcuS untersucht. Sowohl für DcuB als auch für DctA wurde eine direkte Protein-Protein-Interaktion mit DcuS über ein bakterielles Two-Hybrid System nachgewiesen. DcuS bildete ein Transporter-Sensor-Cluster mit DctA und DcuB. C-terminale Verkürzung und die Mutagenese einzelner Aminosäuren der C-terminalen Helix 8b von DctA führten zu einem Verlust der Interaktion mit DcuS. Mit dieser Interaktion gingen sowohl die regulatorische Funktion als auch die Transportfunktion der Punktmutante DctA-L414A verloren. Ein Verlust der Interaktion wurde ebenfalls zwischen einer konstitutiv aktiven DcuS-Mutante und wildtypischem DctA beobachtet. Ebenso zeigte sich eine partielle Reduktion der Interaktion von DcuS mit DctA, wenn DcuS nach der zweiten Transmembranhelix verkürzt wurde. Die Interaktion zwischen DcuS und DctA wurde durch den Effektor Fumarat modifiziert, ging aber nicht komplett verloren.rnDctA konnte in verschiedenen Plasmidsystemen überproduziert werden und bildete Homotrimere. Die Topologie von DctA wurde mit experimentellen und in silico Methoden aufgeklärt. DctA ähnelt der Struktur und Topologie des Aminosäuretransporters Glt aus Pyrococcus horikoshii. DctA besitzt acht Transmembranhelices mit einem cytosolischen N- und C-Terminus sowie zwei Haarnadelschleifen. Die Substratbindung findet höchstwahrscheinlich in den Haarnadelschleifen statt und der Transport erfolgt nach dem „alternating access“ Modell.rnAußerdem wurde die Funktion des Transporters YfcC untersucht. Das Gen yfcC wurde mit Schlüsselgenen des Acetatstoffwechsels co-transkribiert. In yfcC-Deletionsstämmen zeigte sich ein stammspezifischer Defekt bei Wachstum mit Acetat und Transport von Acetat.

Bindeprotein-abhängige DctS-Sensorkinasen aus Bacillus subtilis und Geobacillus kaustophilus

Das Enterobakterium Escherichia coli sowie das Bodenbakterium Bacillus subtilis können C4-Dicarbonsäuren als aerobe Kohlenstoffquelle zur Energiekonservierung nutzen. Die Regulation des C4-Dicarboxylatstoffwechsels erfolgt in E. coli und B. subtilis durch das Zweikomponentensystem DcuSREc bzw. DctSRBs, bestehend aus einer Sensorkinase und einem Responseregulator. Diese kontrollieren die Expression des C4-Dicarboxylat-Transporters DctA. Der Sensor DcuSEc benötigt für seine Funktion im aeroben Stoffwechsel den Transporter DctA als Cosensor. Für das DctSRBs-System gibt es Hinweise aus genetischen Untersuchungen, dass DctSBs das Bindeprotein DctBBs und möglicherweise auch DctABs als Cosensoren für seine Funktion benötigt. In dieser Arbeit sollte ein direkter Nachweis geführt werden, ob DctBBs und DctABs gemeinsam oder nur jeweils eine der Komponenten als Cosensoren für DctSBs fungieren. Sowohl für DctBBs als auch für DctABs wurde eine direkte Protein-Protein-Interaktion mit DctSBs durch zwei in vivo Interaktionsmethoden nachgewiesen. Beide Methoden beruhen auf der Co-Reinigung der Interaktionspartner mittels Affinitätschromatographie und werden je nach Affinitätssäule als mSPINE oder mHPINE (Membrane Strep/His-Protein INteraction Experiment) bezeichnet. Die Interaktion von DctSBs mit DctBBs wurde zusätzlich über ein bakterielles Two-Hybrid System nachgewiesen. Nach Coexpression mit DctSBs interagieren DctABs und DctBBs in mSPINE-Tests gleichzeitig mit der Sensorkinase. DctSBs bildet somit eine sensorische DctS/DctA/DctB-Einheit in B. subtilis und das Bindeprotein DctBBs agiert nur als Cosensor, nicht aber als Transport-Bindeprotein. Eine direkte Interaktion zwischen dem Transporter DctABs und dem Bindeprotein DctBBs besteht nicht. Transportmessungen belegen, dass der DctA-vermittelte Transport von [14C]-Succinat unabhängig ist von DctBBs. Außerdem wurde untersucht, ob Zweikomponentensysteme aus anderen Bakteriengruppen nach einem ähnlichen Schema wie DcuSREc bzw. DctSRBs aufgebaut sind. Das thermophile Bakterium Geobacillus kaustophilus verfügt über ein DctSR-System, welches auf genetischer Ebene mit einem Transporter des DctA-Typs und einem DctB-Bindeprotein geclustert vorliegt. Die Sensorkinase DctSGk wurde in E. coli heterolog exprimiert und gereinigt. Diese zeigt in einer E. coli DcuS-Insertionsmutanten Komplementation der DcuS-Funktion und besitzt dabei Spezifität für die C4-Dicarbonsäuren Malat, Fumarat, L-Tartrat und Succinat sowie für die C6-Tricarbonsäure Citrat. In Liposomen rekonstituiertes DctSGk zeigt Autokinase-Aktivität nach Zugabe von [γ-33P]-ATP. Der KD-Wert für [γ-33P]-ATP der Kinasedomäne von DctSGk liegt bei 43 μM, die Affinität für ATP ist damit etwa 10-fach höher als in DcuSEc.

Folic acid derivatives for PET imaging and therapy addressing folate receptor positive tumors

Folic acid, also known as vitamin B9, is the oxidized form of 5,6,7,8-tetrahydrofolate, which serves as methyl- or methylene donor (C1-building blocks) during DNA synthesis. Under physiological conditions the required amount of 5,6,7,8-tetrahydrofolate for survival of the cell is accomplished through the reduced folate carrier (RFC). In contrast, the supply of 5,6,7,8-tetrahydrofolate is insufficient under pathophysiological conditions of tumors due to an increased proliferation rate. Consequently, many tumor cells exhibit an (over)expression of the folate receptor. This phenomenon has been applied to diagnostics (PET, SPECT, MR) to image FR-positive tumors and on the other hand to treat malignancies related to a FR (over)expression. Based on this concept, a new 18F-labeled folate for PET imaging has been developed and was evaluated in vivo using tumor-bearing mice. The incorporation of oligoethylene spacers into the molecular structure led to a significant enhancement of the pharmacokinetics in comparison to previously developed 18F-folates. The liver uptake could be reduced by one sixth by remaining a tumor uptake of 3%ID/g leading to better contrast ratios. Encouraged by these results, a clickable 18F-labeled serine-based prosthetic group has been synthesized, again with the idea to improve the metabolic and pharmacokinetic profile of hydrophilic radiotracers. Therefore, an alkyne-carrying azido-functionalized serine derivative for coupling to biomolecules was synthesized and a chlorine leaving group for 18F-labeling, which could be accomplished using a microwave-assisted synthesis, a [K⊂2.2.2]+/carbonate system in DMSO. Radiochemical yields of 77±6% could be achieved.rnThe promising results obtained from the FR-targeting concept in the diagnostic field have been transferred to the boron neutron capture therapy. Therefore, a folate derivative was coupled to different boron clusters and cell uptake studies were conducted. The synthesis of the folate-boron clusters was straightforward. At first, a linker molecule based on maleic acid was synthesized, which was coupled to the boron cluster via Michael Addition of a thiol and alkene and subsequently coupled to the targeting moiety using CuAAC. The new conjugates of folate and boron clusters led to a significant increase of boron concentration in the cell of about 5-times compared to currently used and approved boron pharmaceuticals. rnMoreover, azido-folate derivatives were coupled to macromolecular carrier systems (pHPMA), which showed an enhanced and specific accumulation at target sites (up to 2.5-times) during in vivo experiments. A specific blockade could be observed up to 30% indicating an efficient targeting effect. A new kind of nanoparticles consisting of a PDLLA core and p((HPMA)-b-LMA)) as surfactants were developed and successfully radiolabeled via 18F-click chemistry in good RCYs of 8±3%rnThe nanoparticles were obtained via the miniemulsion technique in combination with solvent evaporation. The 18F-labeled nanoparticles were applied to in vivo testing using a mouse model. PET imaging showed a “mixed” biodistribution of low molecular weight as well as high molecular weight systems, indicating a partial loss of the 18F-labeled surfactant.rnIn conclusion, the presented work successfully utilized the FR-targeting concept in both, the diagnostic field (PET imaging) and for therapeutic approaches (BNCT, drug delivery systems). As a result, the high potential of FR-targeting in oncological applications has been shown and was confirmed by small animal PET imaging.rn

Curvature induced nanoscale rafts in lipid membranes

We present a coarse grained model for computer simulations of lipid mixtures, which we use to study generic mechanisms for the formation of nanoscale membrane structures (lipid rafts). We observe that even a two component system can separate into rafts of finite size, and we study these rafts and other membrane structures in detail. We look at the characteristics of our model that enable these phenomena and how they may relate to lipid-cholesterol or lipid-lipid mixtures. We propose an explanation for our findings using elastic theory to describe a possible mechanism of raft stabilization via curvature differences between coexisting lipid phases and we investigate whether this theory can be used to explain the results of our computer simulations.

Annexins as intracellular calcium sensors

The annexins are a multigene family of Ca(2+)- and charged phospholipid-binding proteins. Although they have been ascribed with diverse functions, there is no consensus about the role played by this family as a whole. We have mapped the Ca(2+)-induced translocations of four members of the annexin family and of two truncated annexins in live cells, and demonstrated that these proteins interact with the plasma membrane as well as with internal membrane systems in a highly coordinated manner. Annexin 2 was the most Ca(2+) sensitive of the studied proteins, followed by annexins 6, 4 and 1. The calcium sensitivity of annexin 2 increased further following co-expression with S100A10. Upon elevation of [Ca(2+)](i), annexins 2 and 6 translocated to the plasma membrane, whereas annexins 4 and 1 also became associated with intracellular membranes and the nuclear envelope. The NH(2)-terminus had a modulatory effect on plasma membrane binding: its truncation increased the Ca(2+) sensitivity of annexin 1, and decreased that of annexin 2. Given the fact that several annexins are present within any one cell, it is likely that they form a sophisticated [Ca(2+)] sensing system, with a regulatory influence on other signaling pathways.

Controlling electronic and magnetic properties of ultra narrow multilayered nanowires

Interest in the study of magnetic/non-magnetic multilayered structures took a giant leap since Grünberg and his group established that the interlayer exchange coupling (IEC) is a function of the non-magnetic spacer width. This interest was further fuelled by the discovery of the phenomenal Giant Magnetoresistance (GMR) effect. In fact, in 2007 Albert Fert and Peter Grünberg were awarded the Nobel Prize in Physics for their contribution to the discovery of GMR. GMR is the key property that is being used in the read-head of the present day computer hard drive as it requires a high sensitivity in the detection of magnetic field. The recent increase in demand for device miniaturization encouraged researchers to look for GMR in nanoscale multilayered structures. In this context, one dimensional(1-D) multilayerd nanowire structure has shown tremendous promise as a viable candidate for ultra sensitive read head sensors. In fact, the phenomenal giant magnetoresistance(GMR) effect, which is the novel feature of the currently used multilayered thin film, has already been observed in multilayered nanowire systems at ambient temperature. Geometrical confinement of the supper lattice along the 2-dimensions (2-D) to construct the 1-D multilayered nanowire prohibits the minimization of magnetic interaction- offering a rich variety of magnetic properties in nanowire that can be exploited for novel functionality. In addition, introduction of non-magnetic spacer between the magnetic layers presents additional advantage in controlling magnetic properties via tuning the interlayer magnetic interaction. Despite of a large volume of theoretical works devoted towards the understanding of GMR and IEC in super lattice structures, limited theoretical calculations are reported in 1-D multilayered systems. Thus to gauge their potential application in new generation magneto-electronic devices, in this thesis, I have discussed the usage of first principles density functional theory (DFT) in predicting the equilibrium structure, stability as well as electronic and magnetic properties of one dimensional multilayered nanowires. Particularly, I have focused on the electronic and magnetic properties of Fe/Pt multilayered nanowire structures and the role of non-magnetic Pt spacer in modulating the magnetic properties of the wire. It is found that the average magnetic moment per atom in the nanowire increases monotonically with an ~1/(N(Fe)) dependance, where N(Fe) is the number of iron layers in the nanowire. A simple model based upon the interfacial structure is given to explain the 1/(N(Fe)) trend in magnetic moment obtained from the first principle calculations. A new mechanism, based upon spin flip with in the layer and multistep electron transfer between the layers, is proposed to elucidate the enhancement of magnetic moment of Iron atom at the Platinum interface. The calculated IEC in the Fe/Pt multilayered nanowire is found to switch sign as the width of the non-magnetic spacer varies. The competition among short and long range direct exchange and the super exchange has been found to play a key role for the non-monotonous sign in IEC depending upon the width of the Platinum spacer layer. The calculated magnetoresistance from Julliere's model also exhibit similar switching behavior as that of IEC. The universality of the behavior of exchange coupling has also been looked into by introducing different non-magnetic spacers like Palladium, Copper, Silver, and Gold in between magnetic Iron layers. The nature of hybridization between Fe and other non-magnetic spacer is found to dictate the inter layer magnetic interaction. For example, in Fe/Pd nanowire the d-p hybridization in two spacer layer case favors anti-ferromagnetic (AFM) configuration over ferromagnetic (FM) configuration. However, the hybridization between half-filled Fe(d) and filled Cu(p) state in Fe/Cu nanowire favors FM coupling in the 2-spacer system.

MULTIPLE POSTTRANSCRIPTIONAL REGULATORY FEATURES CONTROL EXPRESSION OF ETHANOLAMINE UTILIZATION GENES IN ENTEROCOCCUS FAECALIS

Enterococcus faecalis is a Gram-positive bacterium that lives as a commensal organism in the mammalian gastrointestinal tract, but can behave as an opportunistic pathogen. Our lab discovered that mutation of the eutK gene attenuates virulence of E. faecalis in the C. elegans model host. eutK is part of the ethanolamine metabolic pathway which was previously unknown in E. faecalis. I discovered the presence of two unique posttranscriptional regulatory features that control expression of eut locus genes. The first feature I found is an AdoCBL riboswitch, a cis-acting RNA regulatory element that acts as a positive regulator of gene expression. The second feature I discovered is a unique two-component system, EutVW. The EutV response regulator contains an ANTAR family domain, which binds RNA to trigger transcriptional antitermination. I determined that induction of expression of several genes in the eut locus is dependent on ethanolamine, AdoCBL and the two-component system. AdoCBL and ethanolamine are both required for induction of eut locus gene expression. Additionally, I discovered eutG is regulated by a unique mechanism of antitermination. Both the AdoCBL riboswitch and EutV response regulator control the expression of the downstream gene eutG. EutV potentially acts through a novel antitermination mechanism in which a dimer of EutV binds to a pair of mRNA stem loops forming an antitermination complex. My data show a unique mechanism by which two environmental signals are integrated by two different posttranscriptional regulators to regulate a single locus.

Crystal structures of progressive Ca2+ binding states of the Ca2+ sensor Ca2+ binding domain 1 (CBD1) from the CALX Na+/Ca2+ exchanger reveal incremental conformational transitions.

Na(+)/Ca(2+) exchangers (NCX) constitute a major Ca(2+) export system that facilitates the re-establishment of cytosolic Ca(2+) levels in many tissues. Ca(2+) interactions at its Ca(2+) binding domains (CBD1 and CBD2) are essential for the allosteric regulation of Na(+)/Ca(2+) exchange activity. The structure of the Ca(2+)-bound form of CBD1, the primary Ca(2+) sensor from canine NCX1, but not the Ca(2+)-free form, has been reported, although the molecular mechanism of Ca(2+) regulation remains unclear. Here, we report crystal structures for three distinct Ca(2+) binding states of CBD1 from CALX, a Na(+)/Ca(2+) exchanger found in Drosophila sensory neurons. The fully Ca(2+)-bound CALX-CBD1 structure shows that four Ca(2+) atoms bind at identical Ca(2+) binding sites as those found in NCX1 and that the partial Ca(2+) occupancy and apoform structures exhibit progressive conformational transitions, indicating incremental regulation of CALX exchange by successive Ca(2+) binding at CBD1. The structures also predict that the primary Ca(2+) pair plays the main role in triggering functional conformational changes. Confirming this prediction, mutagenesis of Glu(455), which coordinates the primary Ca(2+) pair, produces dramatic reductions of the regulatory Ca(2+) affinity for exchange current, whereas mutagenesis of Glu(520), which coordinates the secondary Ca(2+) pair, has much smaller effects. Furthermore, our structures indicate that Ca(2+) binding only enhances the stability of the Ca(2+) binding site of CBD1 near the hinge region while the overall structure of CBD1 remains largely unaffected, implying that the Ca(2+) regulatory function of CBD1, and possibly that for the entire NCX family, is mediated through domain interactions between CBD1 and the adjacent CBD2 at this hinge.