Thesis (Ph. D.)--University of Washington, 2002. / Vita. Includes bibliographical references (leaves 141-161).

Thesis (Ph. D.)--University of Oregon, 2002. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 159-167). Also available for download via the World Wide Web; free to University of Oregon users.

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

The tumor suppressor protein, p53, is mutated or dysregulated in nearly all human cancers(1). The amino terminal domains are essential for transcriptional activation in stressed cells and play a vital role in cell cycle regulation, apoptosis and senescence. The transactivation (TAD) and proline rich domains in this region are dynamic and intrinsically disordered; lacking stable secondary or tertiary structure. This region contains multiple binding sites; arguably, the most significant of these is for p53's negative regulator, the E3 ligase, MDM2. An important, but less understood interaction involving the single stranded DNA binding protein, RPA70A, is hypothesized to be involved in maintaining genome integrity(2-4). Additionally, the amino terminus contains an important single nucleotide polymorphism that has demonstrated different affinity for MDM2 and is of significant biological importance in the induction of apoptosis (5). Isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR) spectroscopy were employed to investigate how the thermodynamics and the inherent flexibility of the amino terminus of p53 play a role in complex formation with the MDM2 or RPA70 proteins. Understanding the structure, dynamics, and function of p53 is paramount in the fight against cancer.

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In this thesis we study a class of problems that require simultaneously controlling a large number of dynamical systems, with varying system dynamics, using the same control signal. We call such problems ensemble control problems, as the goal is to simultaneously steer the entire ensemble of systems. These problems are motivated by many physical systems and we will be particularly interested in the manipulation of nuclear spins in Nuclear Magnetic Resonance (NMR) experiments. System dispersion arise from imprecise magnets for controls, or from disruptive intermolecular interactions. In all cases, the aim is to attenuate the aspects fo the dynamics that correspond to noise or errors, while perserving the aspects that contain the quantities of interest. In liquid NMR experiments this could correspond to preserving Larmor frequency in the presence of inhomogeneities of the strength of the applied radio frequency (RF) field. In solid state NMR, reducing or eliminating orientation dependent magnetic fields is of key concern, so that a precise spectrum can be observed. We approach the problem from the standpoint of mathematical control theory in which the challenge is to simultaneously steer a continuum of systems between points of interest with the same control signal. At the heart of this problem is finding ways for the nonlinearity of the system to be used to our advantage, so that while all members of the ensemble will be driven with the same controls, their final orientations can be orchestrated to arbitrary precision. This thesis develops the methods necessary for two such ensemble control problems arising in NMR, RF (control) amplitude inhomogeneity and systems with periodic drifts that exhibit dispersions in their amplitude and phase. In both cases, robust controls will rely on the non-commutativity of the system's dynamics enabling the generation of alternative and more robust control elements. / Engineering and Applied Sciences

Sophisticated electromagnetic pulse sequences that control spin dynamics have been developed in Nuclear Magnetic Resonance (NMR) over the last few decades. However, due to more and more demanding criteria, such as unknown parameters, larger bandwidths, higher signal to noise ratio (SNR), less power consumption, etc., new pulse sequences are constantly needed. This thesis presents new pulse sequences for several important applications of NMR. / Engineering and Applied Sciences

Carbon nanotubes (CNTs) exhibit unique and fascinating intrinsic electrical, optical, thermal or mechanical properties that lead to a plethora of potential applications in composite materials, electronics, energy storage, medicine, among others. However, the manipulation of nanotubes is not trivial and there are significant difficulties to overcome before achieving their full potential in applications. Because of their high aspect ratio and strong tube-to-tube van der Waals interactions, nanotubes form bundles and ropes that are difficult to disperse in liquids. In this thesis, the topic of dispersing carbon nanotubes in water was addressed by several experimental methods such as nuclear magnetic resonance (NMR) diffusometry and light/electron microcopy. The main goal was to obtain molecular information on how the dispersants interact with carbon nanotubes. In dispersions of single-walled carbon nanotubes (SWNTs) in water, only a small fraction of the polymeric dispersant (Pluronic F127) was shown to be adsorbed at the CNT surface. Regarding dynamic features, the residence time of F127 on the SWNT surface was measured to be in the order of hundred milliseconds, and the lateral diffusion coefficient of the polymer along the nanotube surface proved to be an order of magnitude slower than that in the solution. The surface coverage of SWNTs by F127 was also investigated and the competitive adsorption of F127 and the protein bovine serum albumin, BSA, was assessed. F127 was found to bind stronger to the CNT surface than BSA does. Low molecular weight dispersants, viz. surfactants, were also investigated. Using carefully controlled conditions for the sonication and centrifugation steps, reproducible sigmoidal dispersibility curves were obtained, that exhibited an interesting variation with molecular properties of the surfactants. Various metrics that quantify the ability of different surfactants to disperse CNTs were obtained. In particular, the concentration of surfactant required to attain maximal dispersibility depends linearly on alkyl chain length, which indicates that the CNT-surfactant association, although hydrophobic in nature, is different from a micellization process. No correlation between dispersibility and the critical micellization concentration, cmc, of the surfactants was found. For gemini surfactants of the n-s-n type with spacer length s and hydrophobic tail length n, the dispersibility of multiwalled carbon nanotubes (MWNTs) also followed sigmoidal curves that were compared to those obtained with single-tailed homologues. The increase in spacer length caused an increase in the dispersion efficiency. The observations indicate a loose type of monolayer adsorption rather than the formation of micelle-like aggregates on the nanotube surface. With the future goal of embedding nanotubes in liquid crystal (LC) phases and thereby creating nanocomposites, the effect of the spacer length on the thermotropic behavior of the gemini 12-s-12 surfactant was investigated. Different mesophases were observed and a non-monotonic effect of the spacer length was found and rationalized within a model of the surfactant packing in the solid state. The relative binding strength of simple surfactants to CNTs was assessed by the amount of F127 they displace from the CNT surface upon addition. Anionic surfactants were found to replace more F127, which was interpreted as a sign of stronger binding to CNT. The data collected for all surfactants showed a good correlation with their critical dispersibility concentration that suggests the existence of a surface coverage threshold for dispersing nanotubes. On the macroscopic scale, the formation of weakly bound CNT aggregates in homogeneous dispersions was found to be induced by vortex-shaking. These aggregates could quickly and easily be re-dispersed by mild sonication. This counterintuitive behavior was related to the type of dispersant used and of the duration of mechanical agitation and was explained as a result of loose coverage by the dispersant. / <p>This Ph.D thesis was completed under the Thesis Co-supervision Agreement between KTH Royal Institute of Technology and the University of Port. QC 20151105</p>

Οι macro τομείς αποτελούν μία οικογένεια δομών, συντηρημένη εξελικτικά σε πολλά είδη οργανισμών. Ομόλογά τους βρίσκονται σε βακτήρια, αρχαία, ασπόνδυλα, φυτά καθώς και σε θηλαστικά. Η βιολογική τους λειτουργία δεν έχει αποσαφηνιστεί πλήρως αλλά το βασικό βιοχημικό τους χαρακτηριστικό είναι η ύπαρξη μιας θετικά φορτισμένης κοιλότητας η οποία χρησιμεύει ως σημείο πρόσδεσης της διφωσφορικής αδενικής ριβόζης (ADPr). Ο macro τομέας αποτελεί επίσης μέρος των μη δομικών πρωτεϊνών ιών, οι οποίοι φέρουν ως γενετικό υλικό νοηματικό μονόκλωνο RNA. Τέτοιου είδους ιοί είναι και οι άλφα ιοί στους οποίους ανήκει και ο ιός Mayaro. Στην παρούσα εργασία, πραγματοποιείται δομική μελέτη του macro τομέα του ιού Mayaro. Με χρήση της τεχνολογίας του ανασυνδυασμένου DNA, ο πρωτεϊνικός τομέας εκφράστηκε σε μεγάλες ποσότητες και κατέστη δυνατή η μελέτη του με τη χρήση πολυπυρηνικής/πολυδιάστατης φασματοσκοπίας πυρηνικού μαγνητικού συντονισμού. Η NMR δομή του macro τομέα του ιού Mayaro επιλύθηκε σε υψηλή διακριτικότητα (tf=1.03+/-9.7*10e-2, RMSD=0.90+/-0.15 και RMSD=1.44+/-0.14 για τα άτομα της πολυπεπτιδικής αλυσίδας και τα βαρέα άτομα αντίστοιχα) και αποκάλυψε μια αβα σάντουιτς δομή στο κέντρο της οποίας σχηματίζεται μια εκτεταμένη β-πτυχωτή επιφάνεια. Στη συνέχεια πραγματοποιήθηκαν πειράματα αλληλεπίδρασης, τα οποία αποκάλυψαν ότι το ADPr αποτελεί προσδέτη στο macro τομέα του ιού Mayaro. / Macro domains are a family of structures, evolutionarily conserved in many kinds of organisms such as bacteria, archaea, invertebrates, plants and mammals. Their biological function is not fully elucidated but their key biochemical feature seems to be the binding of the Adenosine Diphosphate ribose(ADPr). Macro domain is also found in non-structural proteins of several positive strand RNA viruses like Mayaro virus, a member of the genus of Alphavirus. In the present study, a structural analysis of the macro domain of virus Mayaro is being performed. Using the technology of recombinant DNA, the macro domain was expressed in high yield, making the analysis by multinuclear/multidimensional Nuclear Magnetic Resonance possible. The NMR solution structure of the macro domain od virus Mayaro was determined in high resolution(tf=1.03+/-9.7*10e-2, RMSD=0.90+/-0.15 and RMSD=1.44+/-0.14 for backbone and heavy atoms respectively) and revealed a well folded 3-Layer(aba)Sandwich structure in the center of which, an extended beta sheet is formed. Furthermore, interaction experiments were performed which revealed that the ADPr is a ligand for the macro domain of virus Mayaro.

Polyethylene (PE) is produced in a huge scale globally and has plenty of desirable properties. It is used in coating, packaging, and artificial joint replacements. The growing need for high performance polyethylene led to the development of new catalysts, monomers and polymerizations. The synthesis of polymethylene (equivalent to polyethylene) by living polyhomologation opened the way to well-defined polymethylenes-based polymeric materials with controlled structure, molecular weight and narrow polydispersity. Such model polymers are substantial to study the structure-properties relationships. This research presents a new strategy based on the in situ formation of B-thexyl-silaboracyclic serving as initiating sites for the polyhomologation of dimethylsulfoxonium methylide. Combination with metal-free ring-opening polymerization (ROP) of ɛ-caprolactone (CL) and atom transfer radical polymerization (ATRP) of styrene led to three polymethylene-based 3-miktoarm stars copolymers PCL(PM-OH)2, Br-PCL(PM-OH)2 and PS(PM-OH)2.