Thesis (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2005. / Not embargoed. Vita. Bibliography: 198-212.

abstract: Proteins and peptides fold into dynamic structures that access a broad functional landscape, however, designing artificial polypeptide systems continues to be a great chal-lenge. Conversely, deoxyribonucleic acid (DNA) engineering is now routinely used to build a wide variety of two dimensional and three dimensional (3D) nanostructures from simple hybridization based rules, and their functional diversity can be significantly ex-panded through site specific incorporation of the appropriate guest molecules. This dis-sertation describes a gentle methodology for using short (8 nucleotide) peptide nucleic acid (PNA) linkers to assemble polypeptides within a 3D DNA nanocage, as a proof of concept for constructing artificial catalytic centers. PNA-polypeptide conjugates were synthesized directly using microwave assisted solid phase synthesis or alternatively PNA linkers were conjugated to biologically expressed proteins using chemical crosslinking. The PNA-polypeptides hybridized to the preassembled DNA nanocage at room tempera-ture or 11 ⁰C and could be assembled in a stepwise fashion. Time resolved fluorescence anisotropy and gel electrophoresis were used to determine that a negatively charged az-urin protein was repelled outside of the negatively charged DNA nanocage, while a posi-tively charged cytochrome c protein was retained inside. Spectroelectrochemistry and an in-gel luminol oxidation assay demonstrated the cytochrome c protein remained active within the DNA nanocage and its redox potential decreased modestly by 10 mV due to the presence of the DNA nanocage. These results demonstrate the benign PNA assembly conditions are ideal for preserving polypeptide structure and function, and will facilitate the polypeptide-based assembly of artificial catalytic centers inside a stable DNA nanocage. A prospective application of assembling multiple cyclic γ-PNA-peptides to mimic the oxygen-evolving complex (OEC) catalytic active site from photosystem II (PSII) is described. In this way, the robust catalytic capacity of PSII could be utilized, without suffering the light-induced damage that occurs by the photoreactions within PSII via triplet state formation, which limits the efficiency of natural photosynthesis. There-fore, this strategy has the potential to revolutionize the process of designing and building robust catalysts by leveraging nature's recipes, and also providing a flexible and con-trolled artificial environment that might even improve them further towards commercial viability. / Dissertation/Thesis / Ph.D. Bioengineering 2014

Selectins are key adhesion molecules responsible for initiating a multistep process that leads a cell out of the blood circulation and into a tissue or organ. The adhesion of cells (expressing ligands) to the endothelium (expressing the selectin i.e.,E-selectin) occurs through spatio-temporally regulated interactions that are mediated by multiple intra- and inter-cellular components. The mechanism of cell adhesion is investigated primarily using ensemble-based experiments, which provides indirect information about how individual molecules work in such a complex system. Recent developments in single-molecule (SM) fluorescence detection allow for the visualization of individual molecules with a good spatio-temporal resolution nanometer spatial resolution and millisecond time resolution). Furthermore, advanced SM fluorescence techniques such as Förster Resonance Energy Transfer (FRET) and super-resolution microscopy provide unique opportunities to obtain information about nanometer-scale conformational dynamics of proteins as well as nano-scale architectures of biological samples. Therefore, the state-of-the-art SM techniques are powerful tools for investigating complex biological system such as the mechanism of cell adhesion. In this project, several constructs of fluorescently labeled E-selectin will be used to study the conformational dynamics of E-selectin binding to its ligand(s) using SM-FRET and combination of SM-FRET and force microscopy. These studies will be beneficial to fully understand the mechanistic details of cell adhesion and migration of cells using the established model system of hematopoietic stem cells (HSCs) adhesion to the selectin expressing endothelial cells (such as the E-selectin expressing endothelial cells in the bone marrow).

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第21599号 / 理博第4506号 / 新制||理||1647(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 杉山 弘, 教授 秋山 芳展, 准教授 竹田 一旗 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

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Three-dimensional (3D) optical data storage based on two-photon processes provides highly confined excitation in a recording medium and a mechanism for writing and reading data with less cross talk between multiple memory layers, due to the quadratic dependence of two photon absorption (2PA) on the incident light intensity. The capacity for highly confined excitation and intrinsic 3D resolution affords immense information storage capacity (up to 1012 bits/cm3). Recently, the use of photochromic materials for 3D memory has received intense interest because of several major advantages over current optical systems, including their erasable/rewritable capability, high resolution, and high sensitivity. This work demonstrates a novel two-photon 3D optical storage system based on the modulation of the fluorescence emission of a highly efficient two-photon absorbing fluorescent dye (fluorene derivative) and a photochromic compound (diarylethene). The feasibility of using efficient intermolecular Förster Resonance Energy Transfer (RET) from the non-covalently linked two-photon absorbing fluorescent fluorene derivative to the photochromic diarylethene as a novel read-out method in a two-photon optical data storage system was explored. For the purpose of the development of this novel two-photon 3D optical storage system, linear and two-photon spectroscopic characterization of commercial diarylethenes in solution and in a polymer film and evidence of their cyclization (O→C) and cycloreversion (C→O) reactions induced by two-photon excitation were undertaken. For the development of a readout method, Resonance Energy Transfer (RET) from twophoton absorbing fluorene derivatives to photochromic compounds was investigated under one and two-photon excitation. The Förster's distances and critical acceptor concentrations were determined for non-bound donor-acceptor pairs in homogeneous molecular ensembles. To the best of my knowledge, modulation of the two-photon fluorescence emission of a dye by a photochromic diarylethene has not been reported as a mechanism to read the recorded information in a 3D optical data storage system. This system was demonstrated to be highly stable and suitable for recording data in thick storage media. The proposed RET-based readout method proved to be non-destructive (exhibiting a loss of the initial fluorescence emission less than 20% of the initial emission after 10,000 readout cycles). Potential application of this system in a rewritable-erasable optical data storage system was proved. As part of the strategy for the development of diarylethenes optimized for 3D optical data storage, derivatives containing Ï€-conjugated fluorene molecules were synthesized and characterized. The final part of this reasearch demonstrated the photostability of fluorine derivatives showing strong molecular polarizability and high fluorescence quantum yields. These compounds are quite promising for application in RET-based two-photon 3D optical data storage. Hence, the photostability of these fluorene derivatives is a key parameter to establish, and facilitates their full utility in critical applications.

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The interior of the cell is a densely crowded and complex arena, full of a vast and diverse array of molecules and macromolecules. A fundamental understanding of cellular physiology will depend not only upon a reductionist analysis of the chemistry, structure, and function of individual components and subsystems, but also on a sagacious exegesis of the dynamic and emergent properties that characterize the higher-level system of living cells. Here, we present work on two aspects of the supramolecular organization of the cell: the controlled assembly of the mitotic spindle during cell division and the regulation of cellular metabolism through the formation of multienzyme complexes. During division, the cell undergoes a profound morphological and molecular reorganization that includes the creation of the mitotic spindle, a process that must be highly controlled in order to ensure that accurate segregation of hereditary material. Chapter 2 describes results that implicate the kinase, Zeste-white3/Shaggy (Zw3/Sgg), as having a role in regulating spindle morphology. The congregation of metabolic enzymes into macromolecular complexes is a key feature of cellular physiology. Given the apparent pervasiveness of these assemblies, it seems likely that some of the mechanisms involved in their organization and regulation might be conserved across a range of biosynthetic pathways in diverse organisms. The Winkel laboratory makes use of the flavonoid biosynthetic pathway in Arabidopsis as an experimental model for studying the architecture, dynamics, and functional roles of metabolic complexes. Over the past several years, we have accumulated substantive and compelling evidence indicating that a number of these enzymes directly interact, perhaps as part of a dynamic globular complex involving multiple points of contact between proteins. Chapter 3 describes the functional analysis of a predicted flavonol synthase gene family in Arabidopsis. The first evidence for the interaction of flavonoid enzymes in living cells, using fluorescent lifetime imaging microscopy fluorescent resonance energy transfer analysis (FLIM-FRET), is presented in Chapter 4. / Ph. D.

A novel luminescence resonance energy transfer (LRET) nanocircuit assay involving a donor and two acceptors in tandem was developed to study the dynamic interaction of skeletal muscle contraction proteins. The donor transmits energy relayed to the acceptors distinguishing myosin subfragment-1 (S1) lever arm orientations. The last acceptor allows the detection of S1's bound near or in between troponin complexes on the thin filament. Additionally, calcium related changes between troponin T and myosin were detected. Based on this data, the troponin complex situated every 7 actin monomers, hinders adjacently bound myosins to complete their power stroke; whereas myosins bound in between troponin complexes undergo complete power strokes.