Zielsetzung: Diese Arbeit untersuchte die Beziehung zwischen intrazellulärem Eisengehalt (pgFe/Zelle) und der Fähigkeit der Histochemie und des MRT, in vitro mit Eisenoxidnanopartikel gelabelte Zellen zu detektieren. Methoden: Immortalisierte murine Peritonealmakrophagen wurden mit Very Small Iron Oxide Nanoparticles (VSOP) in aufsteigenden Konzentrationen (n=10) von 0 bis 200 µg/ml für 4 Stunden inkubiert. Die MRT-Messungen wurden an einem 7-Tesla Bruker Biospec durchgeführt. Für jedes Label-Protokoll wurden Objektträgerproben (n=6) mit den Zellen angefertigt und mit der PB-, DAB-PB- und AgAu-DAB-PB-Färbung gefärbt. Es wurde der prozentuale Anteil der sichtbar gefärbten Zellen ermittelt. Über ICP-MS bestimmten wir den intrazellulären Eisengehalt und TEM-Aufnahmen bestätigten den vesikulären Uptake von VSOP. Zusätzlich wurde der Einfluss der Zelldichte auf MR-Detektionsgrenzen an identisch gelabelten Zellen zwischen 2x10^5 und 8x10^6 Zellen/0,5ml zwischen nierigen (0,22 pgFe/Zelle) und hohen (3,81pgFe/Zelle) Eisenbeladungen untersucht. Ergebnisse: Der intrazelluläre Eisengehalt reichte von 0.12 bis 12.25 pgFe/Zelle. Die Histochemie zeigte einen höheren Prozentsatz an eisen-positiven Zellen mit steigendem Eisengehalt. Das Enhancement der Preußisch Blau Färbung(PB) mit Diaminobenzidin (DAB) und einer modifizierten AgAu-DAB Färbung führte zu einer höheren Sensitivität für intrazelluläres Eisen (>50% gefärbte Zellen bei 1,3 pgFe/Zelle versus 1,6 pgFe/Zelle) als die Preußisch Blau Färbung selbst (2,2 pgFe/Zelle). Jedoch zeigten beide Färbungen bei einem Eisengehalt unter 0,7 pgFe/Zelle weniger als 25% eisenpositive Zellen. Die T2 und T2* verkürzenden Effekte von VSOP zeigten eine positive Korrelation zur intrazellulären Eisenbeladung und zur Zelldichte. Selbst bei 0.26 pgFe/Zelle war eine sichtbare Änderung der Relaxationsraten sichtbar. Schlussfolgerung: Diese Arbeit zeigte, dass in MRT-Messungen selbst kleinste Mengen an intrazellulärem VSOP nachgewiesen werden können, welche in der Histochemie noch nicht nachgewiesen werden können. Es wurde ebenso gezeigt, dass positive Korrelationen zwischen der Zelldichte, dem intrazellulären Eisengehalt und der T2/T2*-Relaxationsraten bestehen. / Purpose: This work investigated the relation between intracellular iron content (pgFe/cell) and the capability of histochemistry and MRI to detect in vitro iron-oxide-nanoparticles labeled cells. Methods: Immortalized peritoneal mouse macrophages were incubated with Very Small Iron Oxide Nanoparticles (VSOP) at increasing concentrations (n=10) ranging from 0 to 200 μg/ml for 4 hours. MR relaxometry was performed on a 7 Tesla Bruker Biospec. Histological slides (n=6) were prepared from cells of each labeling-protocol for PB-, DAB-PB- and AgAu-DAB-PB-staining and the percentage of apparently stained cells was recorded. ICP-MS was used to determine intracellular iron content and TEM images confirmed vesicular uptake of VSOPs. Additionally, the impact of cell densitiy on MR detection limits was investigated on 2x10^5 to 8x10^6 identically prepared cells per 0.5 ml with low (0.22 pgFe/cell) and high (3.81 pgFe/cell) iron content. Results: Intracellular iron content after cell labeling ranged form 0.12 to 12.25 pg/cell. Histological slides showed a higher percentage of iron-positive cells with increasing intracellular iron content. The enhancement of Prussian-blue (PB) by diaminobenzidine (DAB) and a modified AgAu-DAB staining lead to a higher sensitivity for intracellular iron (>50% stained cells at 1,3 pgFe/cell versus 1,6 pgFe/cell) than PB staining alone (2,2 pgFe/cell) . Nevertheless at iron contents below 0,7 pgFe/cell both staining methods showed less than 25% iron positive cells. The T2 and T2* shortening effects of VSOP were positively correlated with intracellular iron content and cell density. Even at 0.26 pg/cell a significant change of relaxation rates was observed. Conclusion: We have shown that MRI is able to detect even low amounts of intracellular VSOP that histochemistry might fail to detect. We also showed that there are positive correlations between cell density, intracellular iron content and T2/T2*-values.

Das Ziel dieser Arbeit war die Entwicklung und die Anfertigung eines 3D Erdfeld-NMR Tomographen, um damit die benötigte Technik der MR eines MR-MPI-Tomographen am Lehrstuhl zu etablieren. Daraufhin wurden alle nötigen Komponenten für ein komplettes 3D Erdfeld-NMR-System entwickelt, gebaut und getestet. Mit diesem Wissen wurde in enger Zusammenarbeit mit der MPI-Arbeitsgruppe am Lehrstuhl ein multimodaler MR-MPI-Tomograph angefertigt und die prinzipielle Machbarkeit der technischen Kombination dieser zwei Modalitäten (MRT/MPI) in einer einzigen Apparatur gezeigt. Auf diesem Entwicklungsweg sind zusätzlich innovative Systemkomponenten entstanden, wie der Bau eines neuen Präpolarisationssystems, mit dem das Präpolarisationsfeld kontrolliert und optimiert abgeschaltet werden kann. Des Weiteren wurde ein neuartiges 3D Gradientensystem entwickelt, das parallel und senkrecht zum Erdmagnetfeld ausgerichtet werden kann, ohne die Bildgebungseigenschaften zu verlieren. Hierfür wurde ein 3D Standard-Gradientensystem mit nur einer weiteren Spule, auf insgesamt vier Gradientenspulen erweitert. Diese wurden entworfen, gefertigt und anhand von Magnetfeldkarten ausgemessen. Anschließend konnten diese Ergebnisse mit der hier präsentierten Theorie und den Simulationsergebnissen übereinstimmend verglichen werden. MPI (Magnetic Particle Imaging) ist eine neue Bildgebungstechnik mit der nur Kontrastmittel detektiert werden können. Das hat den Vorteil der direkten und eindeutigen Detektion von Kontrastmitteln, jedoch fehlt die Hintergrundinformation der Probe. Wissenschaftliche Arbeiten prognostizieren großes Potential, die Hintergrundinformationen der MRT mit den hochauflösenden Kontrastmittelinformationen mittels MPI zu kombinieren. Jedoch war es bis jetzt nicht möglich, diese beiden Techniken in einer einzigen Apparatur zu etablieren. Mit diesem Prototyp konnte erstmalig eine MR-MPI-Messung ohne Probentransfer durchgeführt und die empfindliche Lokalisation von Kontrastmittel mit der Überlagerung der notwendigen Hintergrundinformation der Probe gezeigt werden. Dies ist ein Meilenstein in der Entwicklung der Kombination von MRT und MPI und bringt die Vision eines zukünftigen, klinischen, multimodalen MR-MPI-Tomographen ein großes Stück näher. / Developement of an 3D MRI System for Earth Field MRI and the Kombination with MPI

In the recent years, Dynamic Nuclear Polarization (DNP) has emerged as a very promising technique for enhancing the sensitivity of the magnetic resonance spectroscopy and imaging (MRSI). A number of nuclei, namely 13C, 15N, 29Si, 89Y, and 129Xe, have been successfully polarized and a few of them have been employed in the in-vivo studies for functional imaging and metabolism. Hyperpolarized 13C-labeled compounds have wide applications in the metabolic and perfusion studies and can be used for early stage disease diagnosis, response to treatment, prognosis etc. DNP has been demonstrated in the 31P nucleus in nucleotides triphosphates as an application for the structural analysis and identification techniques. In this work, 31P DNP has been successfully applied, optimized and demonstrated in Dimethyl Methyl Phosphonate (DMMP) for the first time. DMMP is a freely diffusible tracer and hyperpolarized DMMP can potentially be used in the perfusion studies using MR imaging and spectroscopic techniques. The polarization buildup and signal enhancements were optimized for two different radicals, a nitroxyl radical TEMPO and a trityl radical OX063. Microwave frequency sweeps were done for both the radicals to find out the optimum frequencies for maximum polarization, Maximum signal enhancement (¡Ö2300 folds) and maximum percent polarization buildup (2.15%) were achieved by polarizing DMMP with the radical OX063 at the microwave frequency of 94.080 GHz with a glassing matrix containing D2O and glycerol and by using D2O in the dissolution step. DMMP was hyperpolarized at the optimum conditions and injected in a mouse for in-vivo spectroscopy and imaging. The results show that hyperpolarized DMMP is a potential candidate for functional imaging and metabolism.

An investigation of the dichioromethane extract of the sponge, Xestospongia testudinaria indicated that the extract was composed of approximately 40% sterols, 30% saturated fatty acids, 10% mono-unsaturated fatty acids and 20% poly-unsaturated acids. The sterol profile was found to vary between two collections of the sponge. In the first collection the major sterol was the C30 compound, xestosterol (4), which had not previously been reported to occur in this species. In the second collection there was a wider distribution of components with cholesterol (2a) being a major constituent and xestosterol being present in a much lower percentage than in the first collection. The poly-unsaturated acid fraction contained an extremely complex mixture. The novel brominated bisacetylenic C18 (47) and brominated C28 (65) acids were found to be the major components. Another six novel brominated acetylenic acids, which were very unstable, were also identified as well as an ester of 4 with 47. The method developed for the separation of the poly-unsaturated acids from the other classes of metabolites and for the isolation of the pure compounds is discussed and their structural elucidation, largely on the basis of NIMR spectroscopy is described. From the hexane extract of Carteriospongia foliascens, two novel bisalkylated norscalarane derivatives (114 and 116) and a bisalkylated scalarane derivative (130) have been isolated. By use of high field NMR and multipulse NMR techniques a complete assignment of the 111 and 13C NMR spectra of 130 has been achieved on 1.5mg of material. This represents the first report of a complete assignment of the 1J4 NMR spectrum of a scalarane derivative. The C-4 stereochemistry of 130 was determined by use of 1H NMR spectroscopic techniques, which gave results in agreement with the previously used 13C NMR method.

The plant homeodomain (PHD) is a protein domain of ~45�100 residues characterised by a Cys4-His-Cys3 zinc-binding motif. When we commenced our study of the PHD in 2000, it was clear that the domain was commonly found in proteins involved in transcription. Sequence alignments indicate that while the cysteines, histidine and a few other key residues are strictly conserved, the rest of the domain varies greatly in terms of both amino acid composition and length. However, no structural information was available on the PHD and little was known about its function. We were therefore interested in determining the structure of a PHD in the hope that this might shed some light on its function and molecular mechanism of action. Our work began with the structure determination of a representative PHD, Mi2b-P2, and this work is presented in Chapter 3. Through comparison of this structure with the two other PHD structures that were determined during the course of our work, it became clear that PHDs adopt a well-defined globular fold with a superimposable core region. In addition, PHDs contain two loop regions (termed L1 and L3) that display increased flexibility and overlay less well between the three PHD structures available. These L1 and L3 regions correspond to variable regions identified earlier in PHD sequence alignments, indicating that L1 and L3 are probably not crucial for the PHD fold, but are instead likely to be responsible for imparting function(s) to the PHD. Indeed, numerous recent functional studies of PHDs from different proteins have since demonstrated their ability in binding a range of other proteins. In order to ascertain whether or not L1 and L3 were in fact dispensable for folding, we made extensive mutations (including both insertions and substitutions) in the loop regions of Mi2b-P2 and showed that the structure was maintained. We then went on to illustrate that a new function could be imparted to Mi2b-P2 by inserting a five-residue CtBP-binding motif into the L1 region and showed this chimera could fold and bind CtBP. Having established that the PHD could adopt a new binding function, we next sought to use combinatorial methods to introduce other novel functions into the PHD scaffold. Phage display was selected for this purpose, because it is a well-established technique and has been used successfully to engineer zinc-binding domains by other researchers. However, in order to establish this technique in our laboratory, we first chose a control system in which two partner proteins were already known to interact in vitro. We chose the protein complex formed between the transcriptional regulators LMO2 and ldb1 as a test case. We have examined this interaction in detail in our laboratory, and determined its three-dimensional structure. Furthermore, inappropriate formation of this complex is implicated in the onset of T-cell acute lymphoblastic leukemia. We therefore sought to use phage display to engineer ldb1 mimics that could potentially compete against wild-type ldb1 for LMO2, and this work is described in Chapter 4. Using a phage library containing ~3 x 10 7 variants of the LMO2-binding region of ldb1, we isolated mutants that were able to interact with LMO2 with higher affinity and specificity than wild-type ldb1. These ldb1 mutants represent a first step towards finding potential therapeutics for treating LMO-associated diseases. Having established phage display in our laboratory, we went on to search for PHD mutants that could bind selected target proteins. This work is described in Chapter 5. We created three PHD libraries with eight randomized residues in each of L1, L3 or in both loops of the PHD. These PHD libraries were then screened against four target proteins. After four rounds of selection, we were able to isolate a PHD mutant (dubbed L13-FH6) that could bind our test protein Fli-ets. This result demonstrates that a novel function can be imparted to the PHD using combinatorial methods and opens the way for further work in applying the PHD scaffold to other protein design work. In summary, the work detailed in Chapters 3 and 5 demonstrates that the PHD possesses many of the properties that are desirable for a protein scaffold for molecular recognition, including small size, stability, and a well-characterised structure. Moreover, the PHD motif possesses two loops (L1 and L3) of substantial size that can be remodeled for target binding. This may lead to an enhancement of binding affinities and specificities over other small scaffolds that have only one variable loop. In light of the fact that PHDs are mainly found in nuclear proteins, it is reasonable to expect that engineered PHDs could be expressed and function in an intracellular environment, unlike many other scaffolds that can only function in an oxidizing environment. Therefore, our results together with other currently available genomic and functional information indicate PHD is an excellent candidate for a scaffold that could be used to modify cellular processes. Appendices 1 and 2 describe completed bodies of work on unrelated projects that I have carried out during the course of my PhD candidature. The first comprises the invention and application of DNA sequences that contain all N-base sequences in the minimum possible length. This work is presented as a reprint of our recently published paper in Nucleic Acids Research. The second Appendix describes our structural analysis of an antifreeze protein from the shorthorn sculpin, a fish that lives in the Arctic and Antarctic oceans. This work is presented as a manuscript that is currently under review at the Journal of the American Chemical Society.

<p>Isotropic bicelles are disc-shaped aggregates of lipids and detergents, and are suitable model systems for high-resolution NMR studies of membrane-interacting peptides. In this thesis the structures for the two peptides motilin and transportan were determined by homonuclear ¹H methods in the presence of bicelles, and the structure of the bovine prion protein peptide (bPrPp) was solved in the presence of DHPC micelles. All of these peptides were found to be largely a-helical when bound to the model membranes. In subsequent experiments both motilin and transportan were shown to reside on the surface of the bicelles, whereas bPrPp is more likely to have a transmembrane configuration. </p><p>NMR translational diffusion experiments revealed that the isotropic bicelles studied here are very large objects compared to what is regularly indicated by high-resolution NMR spectroscopy. Furthermore, these studies showed that all three peptides examined interact strongly with bicelles. Investigation of the NMR-relaxation of labeled sites in the peptides motilin and penetratin demonstrated that the overall rotational correlation times for these peptides do not reflect the bicellar size. Such decoupling of NMR relaxation from the dependence of overall size is also seen for the dynamics of the lipid molecules in the bicelles. It is therefore concluded that the overall size is not the sole determinant of the linewidths in NMR spectra, but that extensive motions within the bicelles also exert significant effects. </p><p>Another interesting observation is that the membrane-bound structures of the peptides motilin, transportan, penetratin and bPrPp are very similar, even though these peptides have very different biological functions. In contrast, considerably more variation is observed in the membrane-positioning and molecular dynamics of these peptides. Since the bicelles have been found to induce differences in membrane positioning and molecular dynamics compared to micelles, these model membranes are likely to be important in order to enhance our understanding of the biological function of membrane interacting peptides.</p>

Aminoglycoside antibiotics are losing their bactericidal efficacy due to the spread of enzymes that catalyze a covalent modification to them. A common property of many of these aminoglycoside modifying enzymes (AGMEs) is the capacity to modify multiple diverse aminoglycosides thus conferring resistance to these drugs among several pathogenic bacterial species. To gain a better understanding of the protein-antibiotic interactions responsible for resistance and the promiscuous nature of AGMEs, a variety of biophysical techniques including nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC), steady state kinetics, intrinsic tryptophan fluorescence, and computational modeling are employed in this work. Results and discussion presented herein are divided into two parts. In Part I, a detailed thermodynamic and kinetic characterization of the association between the aminoglycoside acetyltransferase-(3)-IIIb (AAC) and several antibiotics and/or coenzyme(s) provides insight into the global properties of the protein. AAC is shown to have a broad substrate range where antibiotic interaction occurs with a favorable enthalpy and unfavorable entropy. When coenzyme A (the non-catalytic form of the acetyl donor, acetyl coenzyme A) is present, enthalpy becomes more favored, entropy more disfavored, and antibiotic affinity significantly increases. AAC shows preference for antibiotics with amine groups at the 2′ and 6′ positions and to those possessing four or more pseudo-saccharide rings. These and other data lay the foundation for understanding AAC and lead into the next discussion wherein the source of promiscuity of AGMEs is explored in Part II. The aminoglycoside phosphotransferase-(3′)-IIIa (APH), a representative from the phosphotransferase family of AGMEs, has been well characterized previously. However, none of the data presented to date provides rationale for its promiscuity. In this work, NMR derived hydrogen-deuterium exchange experiments reveal that APH maneuvers its entire structure to accommodate diverse antibiotics. Furthermore, presence of an antibiotic creates a more stable APH conformation while coenzyme induces an antibiotic dependent increase in the flexibility of APH. For comparison, a computationally derived homology model of AAC predicts that its promiscuous nature may be due to a large flexible loop. Taken together, APH and AAC, two structurally and functionally diverse proteins, utilize different aspects of structural flexibility to facilitate a broad substrate repertoire that is key to bacterial survival.

Isotropic bicelles are disc-shaped aggregates of lipids and detergents, and are suitable model systems for high-resolution NMR studies of membrane-interacting peptides. In this thesis the structures for the two peptides motilin and transportan were determined by homonuclear 1H methods in the presence of bicelles, and the structure of the bovine prion protein peptide (bPrPp) was solved in the presence of DHPC micelles. All of these peptides were found to be largely a-helical when bound to the model membranes. In subsequent experiments both motilin and transportan were shown to reside on the surface of the bicelles, whereas bPrPp is more likely to have a transmembrane configuration. NMR translational diffusion experiments revealed that the isotropic bicelles studied here are very large objects compared to what is regularly indicated by high-resolution NMR spectroscopy. Furthermore, these studies showed that all three peptides examined interact strongly with bicelles. Investigation of the NMR-relaxation of labeled sites in the peptides motilin and penetratin demonstrated that the overall rotational correlation times for these peptides do not reflect the bicellar size. Such decoupling of NMR relaxation from the dependence of overall size is also seen for the dynamics of the lipid molecules in the bicelles. It is therefore concluded that the overall size is not the sole determinant of the linewidths in NMR spectra, but that extensive motions within the bicelles also exert significant effects. Another interesting observation is that the membrane-bound structures of the peptides motilin, transportan, penetratin and bPrPp are very similar, even though these peptides have very different biological functions. In contrast, considerably more variation is observed in the membrane-positioning and molecular dynamics of these peptides. Since the bicelles have been found to induce differences in membrane positioning and molecular dynamics compared to micelles, these model membranes are likely to be important in order to enhance our understanding of the biological function of membrane interacting peptides.

The Amyloid beta peptide (Ab) is related to Alzheimer’s disease and is suggested to be the molecular pathogenic species of the disease, probably through the neurotoxic effect of Ab oligomers. Here the results from biophysical studies of Ab and fragments thereof, are presented. Pulsed field gradient NMR diffusion experiments show that Ab exists mainly as an unfolded monomer. In addition, the hydrodynamic radius of Ab suggests that Ab has residual secondary structure propensities. CD experiments reveal that Ab has a high propensity to adopt a polyproline type II (PII) helix at low temperature. NMR diffusion measurements as well as the 3JHNH values show that increasing the temperature from 4 C induces a structure transition from PII propensity to a beta strand propensity around 15 C and to a random coil conformation at higher temperature. The small hydrodynamic radius at low temperature may be explained by the presence of a population of a hairpin conformation as was suggested by MD simulations. 15N relaxation and secondary chemical shifts suggest that Ab consists of 6 structural regions, two regions with high PII propensity are separated by a highly mobile region located in the N-terminal part of the peptide. In the C-terminal part two regions with a propensity to adopt b-strand are located, separated by a mobile region. The structural propensities of soluble monomeric Ab agree well with the structure of the peptide in fibril aggregates as well as in SDS micelles. Ab binds zinc specifically and with high affinity. This interaction was studied using heteronuclear correlation experiments. The metal ligands were determined to be three histidines, 6,13 and 14 and the N-terminus. The Ab peptide also binds b-cyclodextrin and the combined use of NMR diffusion experiments and induced chemical shifts show that Ab has at least two binding sites for b-cyclodextrin, and the dissociation constants of these binding sites were determined.

Understanding structure and folding of a protein is the key to understanding its biological function and potential role in diseases. Despite the importance of protein folding, a molecular level understanding of this process is still lacking. Solution-state nuclear magnetic resonance (NMR) is a powerful technique to investigate protein structure, dynamics, and folding mechanisms, since it provides residue-specific information. One of the major contributions that govern protein structure appears to be the interaction with the solvent. The importance of these interactions is particularly apparent in membrane proteins, which exist in an amphiphilic environment. Here, individual peptide fragments taken from the disulfide bond forming protein B (DsbB) were investigated in various solvents. The alpha-helical structures that were obtained, suggest that DsbB follows the two-stage model for folding. However, side chains of polar residues showed different conformations compared to the X-ray structure of fulllength protein, implying that polar side-chains may re-orient upon helix packing in order to form the necessary tertiary interactions that stabilize the global fold of DsbB. Model peptides in general represent attractive systems for the investigation of non-covalent interactions important for protein folding, including those with the solvent. NMR structures of the water soluble peptide, BBA5, were obtained in the presence an organic co-solvent, methanol. These structures indicate that the addition of methanol stabilizes an alpha-helix segment, but disrupts a hydrophobic cluster forming a beta-hairpin. Since dynamic effects reduce the ability for experimental observation of individual, bound solvent molecules, results were compared with molecular dynamics simulations. This comparison indicates that the observed effects of NMR structures are due to preferred binding of methanol and reduction of peptide-water hydrogen bonding. NMR structures, such as those determined here, represent a distribution of conformations under equilibrium. The dynamic process of protein unfolding can nevertheless be accessed through denaturation. A method was developed to probe thermal denaturation by measuring the temperature dependence of NOE intensity. Applied to a model peptide, trpzip4, it was confirmed that the beta-hairpin structure of this peptide is stabilized by the hydrophobic cluster formed by tryptophan residues. Together, the peptides investigated here illustrate the important roles that solvent-peptide interactions and side chain-side chain hydrophobic interactions play in forming stable secondary and tertiary structures.